Query tr|B0R5N9|B0R5N9_HALS3 Bacteriorhodopsin OS=Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) GN=bop PE=4 SV=1 Match_columns 262 No_of_seqs 139 out of 808 Neff 8.00461 Searched_HMMs 38292 Date Thu Sep 8 14:11:13 2016 Command hhsearch -realign -mact 0 -cpu 1 -E 0.001 -i B0R5N0.hhblits.a3m -d /scratch0/NOT_BACKED_UP/dbuchan/hhblitsdb/pdb70 -o B0R5N0.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1m0k_A BR, bacteriorhodopsin; 100.0 2.9E-54 7.5E-59 378.3 29.7 262 1-262 1-262 (262) 2 3wqj_A AR 2, archaerhodopsin-2 100.0 5.9E-48 1.5E-52 337.6 31.2 258 4-261 1-259 (259) 3 4qi1_A Bacteriorhodopsin-I; pr 100.0 1.9E-46 5E-51 328.6 31.2 256 1-262 1-257 (262) 4 4l35_A Cruxrhodopsin-3, COP-3, 100.0 2E-45 5.2E-50 320.4 30.4 244 5-259 1-250 (250) 5 3ddl_A Xanthorhodopsin; carote 100.0 1.7E-45 4.4E-50 324.7 26.0 255 1-262 1-273 (273) 6 3qap_A Sensory rhodopsin-2; ph 100.0 1.8E-44 4.7E-49 312.4 31.2 236 19-260 1-239 (239) 7 4fbz_A Deltarhodopsin; transme 100.0 2.3E-44 5.9E-49 312.1 30.4 240 15-254 1-241 (241) 8 1xio_A Anabaena sensory rhodop 100.0 1.4E-42 3.7E-47 304.1 31.2 239 19-262 1-245 (261) 9 3am6_A Rhodopsin-2, AR2; seven 100.0 1.2E-42 3.1E-47 299.2 27.1 229 14-247 1-229 (229) 10 2jaf_A Halorhodopsin, HR; chro 100.0 3.3E-42 8.6E-47 303.5 29.1 258 1-262 2-273 (274) 11 3wt9_A Rhodopsin I; membrane p 100.0 1.3E-41 3.4E-46 295.3 26.0 239 1-248 4-244 (244) 12 4hyj_A Rhodopsin; seven-helica 100.0 7.1E-42 1.8E-46 299.3 22.5 249 8-262 1-258 (258) 13 4xtl_A Sodium pumping rhodopsi 100.0 4E-41 1E-45 298.8 26.3 254 1-261 9-288 (288) 14 5b2n_A Chloride pumping rhodop 100.0 3.6E-41 9.4E-46 297.9 22.1 254 1-262 10-275 (279) 15 3ug9_A Archaeal-type opsin 1, 100.0 3.4E-41 9E-46 303.1 22.3 255 1-262 27-329 (333) 16 4knf_A BPR, blue-light absorbi 100.0 1.9E-40 5E-45 290.5 19.8 245 1-257 10-261 (261) 17 4jq6_A Proteorhodopsin; retiny 100.0 1.4E-39 3.7E-44 281.1 23.4 229 12-251 1-235 (235) 18 5azd_A Bacteriorhodopsin; memb 100.0 2E-39 5.1E-44 285.3 24.7 253 2-262 1-266 (268) 19 5b0w_A Halorhodopsin; seven tr 100.0 7E-46 1.8E-50 329.3 -49.3 257 1-262 1-291 (291) No 1 >1m0k_A BR, bacteriorhodopsin; ION pump, membrane protein, retinal protein, lipids, photore haloarchaea, 7-transmembrane, serpentine; HET: RET LI1 SQU; 1.43A {Halobacterium salinarum} SCOP: f.13.1.1 PDB: 1m0l_A* 1m0m_A* 2zfe_A* 2zzl_A* 4hwl_A* 4hyx_A* 3vhz_A* 3vi0_A* 4fpd_A* 1p8h_A* 1o0a_A* 1py6_A* 1r2n_A* 1ucq_A* 1vjm_A* 2ntu_A* 2ntw_A* 4ov0_A* 4xxj_A* 3har_A* 3utv_A* 1c8r_A* 2wjk_A* 2wjl_A* 2i21_A* 1p8i_A* 1p8u_A* 3han_A* 1mgy_A* 1jv7_A* ... Probab=100.00 E-value=2.9e-54 Score=378.30 Aligned_cols=262 Identities=100% Similarity=1.530 Sum_probs=204.3 Template_Neff=7.500 Q ss_pred CcccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT 80 (262) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~ 80 (262) |+|.||+++|+.++++++++++..|+|+++++|++++++|+..+++++++++|.+++++++++.+|+++|+.|++|+++. T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~i~f~~~~~~~~~~~~R~~~~l~~~i~~iA~~aY~~ma~g~g~~ 80 (262) T 1m0k_A 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT 80 (262) T ss_dssp -----------------CCSTTHHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCE T ss_pred CCcccCCcCCCCchhheeCCccHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHhcCCee Confidence 89999999999999999999999999999999999999999998865446789999999999999999999999999887 Q ss_pred eecCCCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 81 MVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLY 160 (262) Q Consensus 81 ~~~~~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~ 160 (262) .+..+.++|++++.||+||++|+|++++.+++++|.+++.+...++.+++|++||++|++.++...||.|+++|+++|+. T Consensus 81 ~~~~g~~~~~v~~~RYvdW~iTtPlll~~L~llag~~~~~i~~lv~~~~~mi~~G~~ga~~~~~~~kw~~~~~s~~~~~~ 160 (262) T 1m0k_A 81 MVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLY 160 (262) T ss_dssp EEEETTEEEEECTHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHH T ss_pred eeecCCCcceeehHHhhCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhccCccchhHHHHHHHHHHHH Confidence 66433345788999999999999999999999999998888888999999999999999987546899999999999999 Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHH Q tr|B0R5N9|B0R5 161 ILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR 240 (262) Q Consensus 161 v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~ 240 (262) ++|+++++.+++++++++++++.|++++.+++++|.+||++|.++++|.+.++++.|+++|+++|+++|++|+++++... T Consensus 161 v~~~l~~~~~~~a~~~~~~~~~~y~~l~~~~~v~W~~YPivw~l~~~g~~~is~~~e~i~y~ilDv~~Kv~fg~~ll~~~ 240 (262) T 1m0k_A 161 ILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR 240 (262) T ss_dssp HHHHHHHCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHSG T ss_pred HHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHh Confidence 99999988888777777778899999999999999999999999767777899999999999999999999999999999 Q ss_pred HhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 241 AIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~ 262 (262) ++.++++.++|++++||++||| T Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~ 262 (262) T 1m0k_A 241 AIFGEAEAPEPSAGDGAAATSD 262 (262) T ss_dssp GGCC------------------ T ss_pred hhhccccCCCCCCCCCCcccCC Confidence 9999999999999999999998 No 2 >3wqj_A AR 2, archaerhodopsin-2; trans-membrane helices, light-driven proton pump, transpor; HET: RET 22B L2P L3P L4P SQL; 1.80A {Halobacterium} PDB: 2ei4_A* 1vgo_A* 2z55_A* 1uaz_A* Probab=100.00 E-value=5.9e-48 Score=337.61 Aligned_cols=258 Identities=55% Similarity=0.949 Sum_probs=207.2 Template_Neff=7.300 Q ss_pred cCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeec Q tr|B0R5N9|B0R5 4 LLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVP 83 (262) Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~ 83 (262) .=|..-....+....++....|+|+++++|++++++|+..+++.+++++|.+++++++++++|+++|+.|++|+|+..+. T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~w~~~~~~~m~~~~~~f~~~~~~~~~~~~R~~~~l~~~i~~ia~~~Y~~ma~g~G~~~v~ 80 (259) T 3wqj_A 1 MDPIALQAGFDLLNDGRPETLWLGIGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVE 80 (259) T ss_dssp ------CCSCCTTSSSCTTHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSTTCEEEE T ss_pred CCcccccchhhhhcCCCcccHHHHHHHHHHHHHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCceeee Confidence 00221223344556677888999999999999999999988765346789999999999999999999999999876543 Q ss_pred CC-CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 84 FG-GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYIL 162 (262) Q Consensus 84 ~~-~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~ 162 (262) .+ ++.|++++.||+||++|||++++.+++++|.+++.+...++.|++|++||++|++++++..||.|+++|+++|+.++ T Consensus 81 ~~~g~~~~v~~~RYvdW~~TtPlll~~L~lla~~~~~~i~~~v~~~~~mi~~G~~ga~~~~~~~~~~w~~~~~~~f~~v~ 160 (259) T 3wqj_A 81 LASGTVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIGALSKTPLARYTWWLFSTIAFLFVL 160 (259) T ss_dssp CTTSCEEEECTHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHH T ss_pred cCCCCcceeehHHhhCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHH Confidence 21 23478889999999999999999999999999887778899999999999999998754578999999999999999 Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHh Q tr|B0R5N9|B0R5 163 YVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAI 242 (262) Q Consensus 163 ~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~ 242 (262) |.++++.++.+++++++.++.|+.++.+++++|.+||++|+++++|.|.++++.|+++|+++|+++|++|+++++...++ T Consensus 161 ~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~ 240 (259) T 3wqj_A 161 YYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVGTEGAGVVGLGIETLAFMVLDVTAKVGFGFVLLRSRAI 240 (259) T ss_dssp HHHHTHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHTCTTC T ss_pred HHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCcCChhHHHHHHHHHHHHHHHHHHHHHHHHhhh Confidence 99999999888777777889999999999999999999999986777889999999999999999999999999999999 Q ss_pred hcCCCCCCcCcCCCccccC Q tr|B0R5N9|B0R5 243 FGEAEAPEPSAGDGAAATS 261 (262) Q Consensus 243 ~~~~~~~~~~~~~~~~~~~ 261 (262) .++++.++|++++||++.. T Consensus 241 ~~~~~~~~~~~~~~~~~~~ 259 (259) T 3wqj_A 241 LGETEAPEPSAGADASAAD 259 (259) T ss_dssp ------------------- T ss_pred hccccCCCCCCCCCCccCC Confidence 9999999999999999752 No 3 >4qi1_A Bacteriorhodopsin-I; proton pump, membrane, membrane protein; HET: RET MPG; 1.85A {Haloquadratum walsbyi} PDB: 4qid_A* 4wav_A* Probab=100.00 E-value=1.9e-46 Score=328.56 Aligned_cols=256 Identities=53% Similarity=0.866 Sum_probs=202.6 Template_Neff=7.300 Q ss_pred CcccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT 80 (262) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~ 80 (262) |-|.- +.-+. -.++.+..++|+++++|++++++|.+.+++++++++|++++++++++++|+++|+.|++|+|+. T Consensus 1 ~~~~~--~~~~~----~~~~~~~~~l~v~~~~m~~~~l~f~~~~~~~~~~~~R~~~~l~~~i~~iA~~~Y~~ma~g~g~~ 74 (262) T 4qi1_A 1 MAQLA--LQMSS----LGVEGEGIWLALGTIGMLLGMLYFIADGLDVQDPRQKEFYVITILIPAIAAASYLSMFFGFGLT 74 (262) T ss_dssp ----------------CCSSSTHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEE T ss_pred CcHHH--HHHhh----hhhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchhhHHHHHHHHHHHHHHHHHHHHhCCCce Confidence 00000 00011 1233677889999999999999999997533347788999999999999999999999999886 Q ss_pred eecCC-CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 81 MVPFG-GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAML 159 (262) Q Consensus 81 ~~~~~-~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~ 159 (262) .+..+ ++.|++++.||+||++|||++++.+++++|.+.+.+...++.|++|++||++|++.+++..||.|+++|+++|+ T Consensus 75 ~v~~~~~~~r~v~~~RYvdW~lTtPlll~~L~llag~~~~~i~~~v~~~~~MIv~G~~ga~~~~~~~kw~~~~~g~~~f~ 154 (262) T 4qi1_A 75 EVSLANGRVVDVYWARYADWLFTTPLLLLDIGLLAGASQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMV 154 (262) T ss_dssp EEECTTSCEEEEETHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_pred eeecCCCCeeeecHHHHhCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHH Confidence 54321 24578889999999999999999999999999888788899999999999999997754579999999999999 Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHH Q tr|B0R5N9|B0R5 160 YILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRS 239 (262) Q Consensus 160 ~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~ 239 (262) .++|.++++.++.+++++++.++.++.++.+++++|.+||++|.++++|.+.++++.|+++|+++|+++|++|+++++.. T Consensus 155 ~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~G~~~is~~~e~i~y~ilDv~~K~~fg~~ll~~ 234 (262) T 4qi1_A 155 FLLYYLVAVFGEAVSDADEDTRSTFNALRNIILVTWAIYPVAWLVGTEGLALTGLYGETLLFMVLDLVAKVGFGFILLRS 234 (262) T ss_dssp HHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHHHHHHHHHHHHHTC T ss_pred HHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHH Confidence 99999999998887777778899999999999999999999999997877788899999999999999999999999999 Q ss_pred HHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 240 RAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) .++.++++.++|++++||+.-.. T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~ 257 (262) T 4qi1_A 235 RAIMGGGSEPTPSAQETAADLEH 257 (262) T ss_dssp GGGC------------------- T ss_pred hHHhccccCCCCCCCCCccchhh Confidence 99999999999999999875321 No 4 >4l35_A Cruxrhodopsin-3, COP-3, CR-3; protein-bacterioruberin complex, seven transmembrane alpha H light-driven proton pump, membrane; HET: RET 22B; 2.10A {Haloarcula vallismortis} PDB: 4jr8_A* 4pxk_A* Probab=100.00 E-value=2e-45 Score=320.39 Aligned_cols=244 Identities=52% Similarity=0.908 Sum_probs=209.1 Template_Neff=7.800 Q ss_pred CCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecC Q tr|B0R5N9|B0R5 5 LPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPF 84 (262) Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~ 84 (262) .| .+..+..++|+++++|.+++++|+..+++++++++|.+|+++++++.+|+++|+.|++|+++..++. T Consensus 1 ~~-----------~~~~~~~~~w~~~~~~~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~va~~~Y~~ma~g~g~~~~~~ 69 (250) T 4l35_A 1 MP-----------APEGEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATILITAIAFVNYLAMALGFGLTIVEI 69 (250) T ss_dssp CC-----------CCCSSHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEEE T ss_pred CC-----------cchhhhHHHHHHHHHHHHHHHHHHHHHccCCCCccchhHHHHHHHHHHHHHHHHHHHhCCCcceeec Confidence 00 1225677888999999999999998876544466778888999999999999999999998766543 Q ss_pred CCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcc------hhHHHHHHHHHHHH Q tr|B0R5N9|B0R5 85 GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVY------SYRFVWWAISTAAM 158 (262) Q Consensus 85 ~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~------~~~~~~~~~s~~~~ 158 (262) ++++|++++.||+||++|+|++++.+++++|.+++.+...++.|++|++||++|++.+++ ..||.|+++|+++| T Consensus 70 ~~~~~~~~~~RYi~W~iTtPlll~~L~~lag~~~~~i~~~v~~~~~mi~~G~~~a~~~~~~~~~~~~~~w~~~~~~~~~f 149 (250) T 4l35_A 70 AGEQRPIYWARYSDWLFTTPLLLYDLGLLAGADRNTISSLVSLDVLMIGTGLVATLSAGSGVLSAGAERLVWWGISTAFL 149 (250) T ss_dssp TTEEEEEETHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSCHHHHHHHHHHHHHHHH T ss_pred CCCCceecHHHHHhHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhHHHHHHHHHHH Confidence 235588899999999999999999999999999888888899999999999999986542 47899999999999 Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHH Q tr|B0R5N9|B0R5 159 LYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLR 238 (262) Q Consensus 159 ~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~ 238 (262) +.++|.++++.++.++++++++++.+++++.+.+++|.+||++|.++++|.|.++++.|+++|+++|+++|++|++++++ T Consensus 150 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~ 229 (250) T 4l35_A 150 LVLLYFLFSSLSGRVADLPSDTRSTFKTLRNLVTVVWLVYPVWWLVGTEGIGLVGIGIETAGFMVIDLVAKVGFGIILLR 229 (250) T ss_dssp HHHHHHHHHTTHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHHHHHHHHHHHHTS T ss_pred HHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHhcccccCccCchHHHHHHHHHHHHHHHHHHHHHHH Confidence 99999999888877666677788999999999999999999999998777778899999999999999999999999999 Q ss_pred HHHhhcCCCCCCcCcCCCccc Q tr|B0R5N9|B0R5 239 SRAIFGEAEAPEPSAGDGAAA 259 (262) Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~ 259 (262) .+++.++++++.|++++|.+. T Consensus 230 ~~~~~~~~~~~~~~~~~~~~~ 250 (250) T 4l35_A 230 SHGVLDGAAETTGAGATATAD 250 (250) T ss_dssp CHHHHHGGGSCSCCC------ T ss_pred HhHhcccccCCCCCCCCCCCC Confidence 999999999888777776531 No 5 >3ddl_A Xanthorhodopsin; carotenoid, ION pump, light-harvesting, antenna, retinal, transport protein; HET: SXN UNL RET PX4 PCW; 1.90A {Salinibacter ruber} Probab=100.00 E-value=1.7e-45 Score=324.68 Aligned_cols=255 Identities=23% Similarity=0.325 Sum_probs=207.8 Template_Neff=7.700 Q ss_pred CcccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT 80 (262) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~ 80 (262) ||+|||++++++.+.+ + .++|+++++|++++++|...++++ ++++|.+++++++++++|+++|+.|++|+++. T Consensus 1 ~~~~~~~~~~~~~~~~----~--~~~w~~~~~m~~~~i~f~~~~~~~-~~~~R~~~~l~~~i~~va~i~Y~~ma~g~g~~ 73 (273) T 3ddl_A 1 MLQELPTLTPGQYSLV----F--NMFSFTVATMTASFVFFVLARNNV-APKYRISMMVSALVVFIAGYHYFRITSSWEAA 73 (273) T ss_dssp ---CCCCBCHHHHHHH----H--HHHHHHHHHHHHHHHHHHHGGGGS-CGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCccccCCCccchhHH----H--HHHHHHHHHHHHHHHHHHHHhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHHcccch Confidence 8999999999987777 4 666699999999999999887775 47889999999999999999999999999874 Q ss_pred eecCC-----CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHH----HHHHHHHHHHHHHHHHHHHcCc---chhHH Q tr|B0R5N9|B0R5 81 MVPFG-----GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTI----LALVGADGIMIGTGLVGALTKV---YSYRF 148 (262) Q Consensus 81 ~~~~~-----~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~----~~~v~~~~~miv~G~~g~~~~~---~~~~~ 148 (262) ....+ +++++..+.||+||++|||++++.+++++|.+++.+ ...++.|++|++||++|+++.+ ...+| T Consensus 74 ~~~~~~~~~~~~~~~~~~~RYv~W~~TtPlll~~L~ll~g~~~~~~~~~~~~~i~~~~~mi~~G~~g~~~~~~~~~~~~~ 153 (273) T 3ddl_A 74 YALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRG 153 (273) T ss_dssp EEECSSSEEECSCCCCCHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCCCTTSHHH T ss_pred hcccccccCCCCceeeccHHhccHHHHHHHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHhcccccccchhH Confidence 43211 112344569999999999999999999999987644 5678899999999999999764 25789 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcC---C--CCCCC-hHHHHHHHH Q tr|B0R5N9|B0R5 149 VWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSE---G--AGIVP-LNIETLLFM 222 (262) Q Consensus 149 ~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~---g--~~~i~-~~~e~i~y~ 222 (262) .|+.+|+++|+.++|.++++.++.+++++++.++.|++++.+++++|.+||++|.+++. | .+.++ ++.|+++|+ T Consensus 154 ~w~~~s~~~f~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~l~~v~W~~YPivw~l~~~~~~g~~~~~is~~~~e~i~y~ 233 (273) T 3ddl_A 154 LWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYT 233 (273) T ss_dssp HHHHHHHHHHHHHHHHHHHSCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTC------CTTCHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHHHHHHHHccCcccccccccccccHHHHHHHH Confidence 99999999999999999999998877777788999999999999999999999999843 2 23455 799999999 Q ss_pred HHHHHhHHHHHHHHHHHHHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 223 VLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 223 ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) ++|+++|++|+++++...++.++.++++|+++..++..|. T Consensus 234 ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 273 (273) T 3ddl_A 234 IADVLAKAGYGVLIYNIAKAKSEEEGFNVSEMVEPATASA 273 (273) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTCC------------ T ss_pred HHHHHHHHHHHHHHHHHHHhhhcccccchHHhhcccccCC Confidence 9999999999999999999999999999998876554431 No 6 >3qap_A Sensory rhodopsin-2; phototaxis, nphtrii, membrane, transport protein; HET: RET BOG LFA L2P; 1.90A {Natronomonas pharaonis} PDB: 1gue_A* 1gu8_A* 1h68_A* 3qdc_A* 4gyc_A* 2f93_A* 2f95_A* 2ksy_A* 1h2s_A* 1jgj_A* Probab=100.00 E-value=1.8e-44 Score=312.43 Aligned_cols=236 Identities=28% Similarity=0.491 Sum_probs=198.4 Template_Neff=7.900 Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCCCCcccHHHHHH Q tr|B0R5N9|B0R5 19 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYAD 98 (262) Q Consensus 19 ~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~~~~RYv~ 98 (262) +..+..++|+++++|.+++++|.+..+++ ++++|+++++.++++.+++++|+.|++|+++..+ ++|++++.||+| T Consensus 1 ~~~~~~~~~~~~~~m~~~~~~f~~~~~~~-~~~~r~~~~~~~~i~~ia~~~Y~~ma~g~g~~~~----~~~~~~~~RYi~ 75 (239) T 3qap_A 1 MVGLTTLFWLGAIGMLVGTLAFAWAGRDA-GSGERRYYVTLVGISGIAAVAYVVMALGVGWVPV----AERTVFAPRYID 75 (239) T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHTTC-CTTTHHHHHHHHHHHHHHHHHHHHHHTTCCEEEE----TTEEEEHHHHHH T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHhcC-CCchhhhHHHHHHHHHHHHHHHHHHHcCCCEEec----CCceEehhHHhh Confidence 12566788999999999999999988764 4778999999999999999999999999887654 458889999999 Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCH Q tr|B0R5N9|B0R5 99 WLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRP 178 (262) Q Consensus 99 W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~ 178 (262) |++|||++++.+++++|.+++.+...++.+.+|+++|++|++.++ ..||.|+++|+++|+.++|+++++.+++++++++ T Consensus 76 W~lTtPlll~~l~~la~~~~~~i~~~i~~~~~mi~~G~~~~~~~~-~~kw~~~~~~~~~~~~v~~~l~~~~~~~a~~~~~ 154 (239) T 3qap_A 76 WILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-IERYALFGMGAVAFLGLVYYLVGPMTESASQRSS 154 (239) T ss_dssp HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSCH T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhccc-cHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhcCc Confidence 999999999999999999988777778899999999999998764 5799999999999999999999999988877777 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCC---cCcCC Q tr|B0R5N9|B0R5 179 EVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPE---PSAGD 255 (262) Q Consensus 179 ~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~---~~~~~ 255 (262) ++++.+++++.+++++|.+||++|.++++|.+.++++.|.++|+++|+++|++|++++++..++.++++.++ +++++ T Consensus 155 ~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~is~~~~~~~~~ilDv~~K~~f~~~ll~~~~~~~~~~~~~~~~~~~~~ 234 (239) T 3qap_A 155 GIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGESLAGVDTDA 234 (239) T ss_dssp HHHHHHHHHHHHHHHHHTHHHHHHHHSTTTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------------- T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcccccCccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcccccCCCCC Confidence 889999999999999999999999999777677889999999999999999999999999999988888776 66788 Q ss_pred Ccccc Q tr|B0R5N9|B0R5 256 GAAAT 260 (262) Q Consensus 256 ~~~~~ 260 (262) ||.+. T Consensus 235 ~~~~~ 239 (239) T 3qap_A 235 PAVAD 239 (239) T ss_dssp ----- T ss_pred CcccC Confidence 88752 No 7 >4fbz_A Deltarhodopsin; transmembrane helices, light-driven proton pump, cell MEMB membrane protein; HET: RET 22B SQL L2P BNG; 2.70A {Haloterrigena thermotolerans} Probab=100.00 E-value=2.3e-44 Score=312.14 Aligned_cols=240 Identities=53% Similarity=0.907 Sum_probs=208.0 Template_Neff=7.900 Q ss_pred hhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCCCCcccHH Q tr|B0R5N9|B0R5 15 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWA 94 (262) Q Consensus 15 ~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~~~~ 94 (262) +.+.+..+..++|+++++|++++++|...+++++++++|.+++++++++.+|+++|+.|++|+|++....+.++|++++. T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~r~~~~l~~~i~~ia~~~Y~~ma~g~g~~~~~~~~~~r~v~~~ 80 (241) T 4fbz_A 1 MAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITTFITTIAAAMYFAMATGFGVTEVVVGDEALTIYWA 80 (241) T ss_dssp CCCCCCTTHHHHHHHHHHHHHHHHHHHHHTTTCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTTTCEEEECSSCEEEECTH T ss_pred CCCCcccchHHHHHHHHHHHHHHHHHHHHhccCCCCceehHHHHHHHHHHHHHHHHHHHHhCCCceEEecCCCCceehHH Confidence 00123467788999999999999999998876544678999999999999999999999999998765433356889999 Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 95 RYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAE 174 (262) Q Consensus 95 RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~ 174 (262) ||+||++|+|++++.+++++|.+++.+...++.|++|+++|++|++.+++..||.|+++|+++|+.++|+++++.++.++ T Consensus 81 RYv~W~~TtPlll~~l~~l~~~~~~~~~~~v~~~~~mi~~g~~g~~~~~~~~kw~~~~~s~~~~~~v~~~l~~~~~~~a~ 160 (241) T 4fbz_A 81 RYADWLFTTPLLLLDLGLLAGANRNTIATLIGLDVFMIGTGMIAAFAATPGTRIAWWGISTGALLALLYVLVGTLSKDAR 160 (241) T ss_dssp HHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHT T ss_pred HHhHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHH Confidence 99999999999999999999999888888899999999999999998754579999999999999999999999998887 Q ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCC-CCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCCcCc Q tr|B0R5N9|B0R5 175 SMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGA-GIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA 253 (262) Q Consensus 175 ~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~-~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~ 253 (262) +++++.++.|+.++.+++++|.+||++|.++++|. +.++++.|+++|+++|+++|++|++++++..++.+++++++-.. T Consensus 161 ~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~G~~~i~~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~ 240 (241) T 4fbz_A 161 GQSPEVASLFGRLRNLVIVLWLLYPVVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVVLLRSRSVLRRVVTPTAAP 240 (241) T ss_dssp TSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGSSCCSCHHHHHHHHHHHHHHHHHHHHHHHSSCHHHHGGGCCSCC-- T ss_pred hcChhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCccCchHHHHHHHHHHHHHHHHHHHHHHHHhHHhccccCCCCCC Confidence 77778899999999999999999999999997764 45667999999999999999999999999998888777654211 Q ss_pred C Q tr|B0R5N9|B0R5 254 G 254 (262) Q Consensus 254 ~ 254 (262) . T Consensus 241 ~ 241 (241) T 4fbz_A 241 T 241 (241) T ss_dssp - T ss_pred C Confidence 0 No 8 >1xio_A Anabaena sensory rhodopsin; signaling protein, photoreceptor; HET: RET PEE; 2.00A {Nostoc SP} SCOP: f.13.1.1 PDB: 2m3g_A* 4tl3_A* Probab=100.00 E-value=1.4e-42 Score=304.14 Aligned_cols=239 Identities=26% Similarity=0.418 Sum_probs=192.1 Template_Neff=7.700 Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCCCCcccHHHHHH Q tr|B0R5N9|B0R5 19 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYAD 98 (262) Q Consensus 19 ~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~~~~RYv~ 98 (262) +..+..++|+++++|++++++|++.+++. ++++|.++.++++++++|+++|+.|++|+++... +++++++.||+| T Consensus 1 ~~~~~~~~w~~~~~m~~~~l~f~~~~~~~-~~~~r~~~~~~~~i~~iaa~~Y~~ma~~~g~~~~----~~~~v~~~RYi~ 75 (261) T 1xio_A 1 MNLESLLHWIYVAGMTIGALHFWSLSRNP-RGVPQYEYLVAMFIPIWSGLAYMAMAIDQGKVEA----AGQIAHYARYID 75 (261) T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHTSC-TTCCHHHHHHHHHHHHHHHHHHHHHHHC-------------CTTHHHHHH T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHhcCC-CcceehhhHHHHHHHHHHHHHHHHHHhcCCcccC----CCceecHHHHhH Confidence 12566788899999999999999998765 4667777878778999999999999999987653 346779999999 Q ss_pred HHHHHHHHHHHHHHHcCC----CHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 99 WLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAE 174 (262) Q Consensus 99 W~lTtPlll~~L~ll~g~----~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~ 174 (262) |++|||++++.+++++|. +++.+...++.|++|++||++|++.+++..||.|+++|+++|+.++|+++++.++.++ T Consensus 76 W~iTtPlll~~l~~la~~~~~~~~~~i~~~v~~~~~miv~G~~ga~~~~~~~kw~~~~i~~~~f~~v~~~l~~~~~~~a~ 155 (261) T 1xio_A 76 WMVTTPLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSGLIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTR 155 (261) T ss_dssp HHHHHHHHHHHHHHHHTTTSCCCHHHHHHHHHHHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHT T ss_pred HHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHHHHHhcCccHHHHhHHHHHHHHHHHHHHHHHHHHHHHH Confidence 999999999999999998 5656677889999999999999998754459999999999999999999999988877 Q ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCCcCcC Q tr|B0R5N9|B0R5 175 SMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAG 254 (262) Q Consensus 175 ~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~~ 254 (262) +++++.++.++.++.+++++|.+||++|.++++|.+.++++.|+++|+++|+++|++|++++++..++.++++.+..++. T Consensus 156 ~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~~~i~y~i~Dv~~K~~fg~~ll~~~~~~~~~~~~~~~~~ 235 (261) T 1xio_A 156 TQSSELANLYDKLVTYFTVLWIGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLNDSRQTTGDRF 235 (261) T ss_dssp TSCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC--------- T ss_pred hcChHHHHHHHHHHHHHHHHHHHHHHHHHHccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHH Confidence 77777899999999999999999999999997776778999999999999999999999999999999887666553333 Q ss_pred CCccccC--C Q tr|B0R5N9|B0R5 255 DGAAATS--D 262 (262) Q Consensus 255 ~~~~~~~--~ 262 (262) ....+.- + T Consensus 236 ~e~~~~~~~~ 245 (261) T 1xio_A 236 AENTLQFVEN 245 (261) T ss_dssp ---------- T ss_pred HHHHHHHHhh Confidence 2111100 0 No 9 >3am6_A Rhodopsin-2, AR2; seven trans-membrane, transport protein; HET: RET CLR; 3.20A {Acetabularia acetabulum} Probab=100.00 E-value=1.2e-42 Score=299.21 Aligned_cols=229 Identities=28% Similarity=0.423 Sum_probs=198.0 Template_Neff=7.900 Q ss_pred hhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCCCCcccH Q tr|B0R5N9|B0R5 14 QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW 93 (262) Q Consensus 14 ~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~~~ 93 (262) -..+.+..+..++|+++++|.+++++|...++++ ++++|.+++++.+++.+++++|+.|++|++....+ ++|++++ T Consensus 1 ~~~~~t~~g~~~~w~~~~~~~~~~i~f~~~~~~~-~~~~R~~~~~~~~i~~vaa~~Y~~ma~~~g~~~~~---~~r~~~~ 76 (229) T 3am6_A 1 MADVETETGMIAQWIVFAIMAAAAIAFGVAVHFR-PSELKSAYYINIAICTIAATAYYAMAVNYQDLTMN---GERQVVY 76 (229) T ss_dssp CCBCCCHHHHHHHHHHHHHHHHHHHHHHHHGGGC-C--CHHHHHHHHHHHHHHHHHHHHHHHTTTSCCBS---SSBBCCT T ss_pred CCccccCCccHHHHHHHHHHHHHHHHHHHHHccC-CcccchHHHHHHHHHHHHHHHHHHHHhCCCccccC---CCceeeh Confidence 0112344677888899999999999999988775 47889999999999999999999999998765432 4689999 Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 94 ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA 173 (262) Q Consensus 94 ~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a 173 (262) .||+||++|+|++++.+++++|.+++.+...++.|++|++||++|+...++..||.|+++|+++|+.+++.++++.++++ T Consensus 77 ~RYv~W~~TtPlll~~l~~l~~~~~~~~~~~~~~~~~mi~~G~~g~~~~~~~~~w~~~~~s~~~f~~v~~~l~~~~~~~a 156 (229) T 3am6_A 77 ARYIDWVLTTPLLLLDLIVMTKMGGVMISWVIGADIFMIVFGILGAFEDEHKFKWVYFIAGCVMQAVLTYGMYNATWKDD 156 (229) T ss_dssp HHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCC T ss_pred HHHhhHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhcCccHHHHHHHHHHHHHHHHHHHHHHHHHHHH Confidence 99999999999999999999999988888889999999999999999764468999999999999999999998888766 Q ss_pred HhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCC Q tr|B0R5N9|B0R5 174 ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAE 247 (262) Q Consensus 174 ~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~ 247 (262) ++++++.++.+++++.+++++|.+||++|.++ +|.+.++++.|+++|+++|+++|++|+.++++..++.+++- T Consensus 157 ~~~~~~~~~~~~~l~~~~~~~W~~YPi~w~l~-~g~~~i~~~~~~i~~~ilDv~~K~~fg~~ll~~~~~~~~~~ 229 (229) T 3am6_A 157 LKKSPEYHSSYVSLLVFLSILWVFYPVVWAFG-SGSGVLSVDNEAILMGILDVLAKPLFGMGCLIAHETIFKKM 229 (229) T ss_dssp --CCHHHHHHHHHHHHHHHHHHTHHHHHHHHT-TTTSSSCHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTC- T ss_pred HhcChHHHHHHHHHHHHHHHHHHHHHHHHHHc-cccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC Confidence 66666678899999999999999999999998 56678899999999999999999999999999888877641 No 10 >2jaf_A Halorhodopsin, HR; chromophore, chloride pump, ION transport, membrane, chloride, receptor, ION pump, transport, sensory transduction; HET: BOG PLM RET; 1.7A {Halobacterium salinarium} PDB: 2jag_A* 5ahy_A* 5ahz_A* 1e12_A* Probab=100.00 E-value=3.3e-42 Score=303.47 Aligned_cols=258 Identities=32% Similarity=0.511 Sum_probs=198.8 Template_Neff=7.200 Q ss_pred CcccCCcccC------CCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 1 MLELLPTAVE------GVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSML 74 (262) Q Consensus 1 ~~~~~~~~~~------~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma 74 (262) -...+|..+| +.++....+..+..++|+++++|++++++|+...++.+++++|.+|+++++++++++++|+.|+ T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lw~~~~~m~~~~lvf~~~~~~~~~~~~R~~~~l~~~i~~iaavaY~~Ma 81 (274) T 2jaf_A 2 SITSVPGVVDAGVLGAQSAAAVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLL 81 (274) T ss_dssp --------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCTTHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred CccCCCCCCCCCCCChhhheeeeeccchhHHHHHHHHHHHHHHHHHHHHHhccCCcccchHHHHHHHHHHHHHHHHHHHH Confidence 0123444443 3344444455678889999999999999999988764357889999999999999999999999 Q ss_pred hcCCceeec--CC----CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCc-chhH Q tr|B0R5N9|B0R5 75 LGYGLTMVP--FG----GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKV-YSYR 147 (262) Q Consensus 75 ~g~g~~~~~--~~----~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~-~~~~ 147 (262) +|+|+..+. .+ .+++..++.||+||++|+|++++.+++++|.+++.+..+++.|++|++||++|++.++ ...| T Consensus 82 ~~~g~~~v~~~~~~~~~~~~~~~~~~RYidW~lTtPlll~~l~llag~~~~~i~~li~~~~~mIv~Gl~g~~~~~~~~~k 161 (274) T 2jaf_A 82 SGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFR 161 (274) T ss_dssp HTTTCEEEECCTTSTTTTSEEEECHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHCCSCHHHH T ss_pred hcCCcceeeeecccccCCCCceeeHHHHhHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcc Confidence 987654432 11 0123448999999999999999999999999988888899999999999999999764 2379 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCh-HHHHHHHHHHHH Q tr|B0R5N9|B0R5 148 FVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPL-NIETLLFMVLDV 226 (262) Q Consensus 148 ~~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~-~~e~i~y~ilDv 226 (262) |.|+++|+++|+.++|+++++.++.+++ +++++.|++++.+.+++|.+||++|+++++|.+.+++ +.|+++|+++|+ T Consensus 162 w~~f~is~~~f~~v~~~l~~~~~~~a~~--~~~~~~y~~l~~~~~v~W~~YPivw~l~~~G~~~i~~~~~e~i~y~ilDv 239 (274) T 2jaf_A 162 WAFYAISCAFFVVVLSALVTDWAASASS--AGTAEIFDTLRVLVVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDV 239 (274) T ss_dssp HHHHHHHHHHHHHHHHHHHTHHHHHHHH--HTCHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCCHHHHHHHHHHHHH T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHccc--ccHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcCcchHHHHHHHHHHH Confidence 9999999999999999999888766543 3578899999999999999999999999777767764 569999999999 Q ss_pred HhHHHHHHHHHHHHHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 227 SAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 227 ~~K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) ++|++|++++++.+++.++....+ -++-++-.+| T Consensus 240 ~~K~~fg~~ll~~~~~~~~~~~~~--~~~~~~~~~~ 273 (274) T 2jaf_A 240 FAKYVFAFILLRWVANNERTVAVA--GQTLGTMSSD 273 (274) T ss_dssp HHTHHHHHHHHHHHHHTHHHHHTC------------ T ss_pred HHHHHHHHHHHHHHhhcccccCcC--CeecccCCCC Confidence 999999999999999887555433 1111111111 No 11 >3wt9_A Rhodopsin I; membrane protein, retinal, water cluster, green algae, photo cell-free synthesis, microbial-type rhodopsin; HET: RET OLC; 1.48A {Acetabularia acetabulum} PDB: 3wt8_A* 3wta_A* 5awz_A* 5ax0_A* 5ax1_A* Probab=100.00 E-value=1.3e-41 Score=295.31 Aligned_cols=239 Identities=25% Similarity=0.377 Sum_probs=201.1 Template_Neff=7.700 Q ss_pred CcccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT 80 (262) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~ 80 (262) =-..+| ..+.+.+ ..+..++|+++++|.+++++++..++++ ++++|.+++++.+++.+++++|+.|++|+++. T Consensus 4 ~~~~~~----~~~~~~t--~~g~~~~w~~~~~~~~~~l~f~~~~~~~-~~~~R~~~~l~~~i~~ia~i~Y~~ma~~~g~~ 76 (244) T 3wt9_A 4 GSSGMS----NPNPFQT--TLGTDAQWVVFAVMALAAIVFSIAVQFR-PLPLRLTYYVNIAICTIAATAYYAMAVNGGDN 76 (244) T ss_dssp -----C----CCSCSCC--HHHHHHHHHHHHHHHHHHHHHHHHHTTS-CGGGHHHHHHHHHHHHHHHHHHHHHHHHGGGC T ss_pred CCCCCC----CCCcccc--ccccHHHHHHHHHHHHHHHHHHHHHhcC-CcccchHHHHHHHHHHHHHHHHHHHHhCCCCc Confidence 000011 1222332 2456677799999999999999998765 47889999999999999999999999998875 Q ss_pred eecCC--CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHH Q tr|B0R5N9|B0R5 81 MVPFG--GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAM 158 (262) Q Consensus 81 ~~~~~--~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~ 158 (262) ....+ .++|++++.||+||++|||++++.+++++|.+++.+...++.|++|+++|++|++.++ ..||.|+++|+++| T Consensus 77 ~~~~~~~~~~r~v~~~RYv~W~~TtPlll~~l~~l~~~~~~~i~~~v~~~~~mi~~g~~g~~~~~-~~kw~~~~~g~~~~ 155 (244) T 3wt9_A 77 KPTAGTGADERQVIYARYIDWVFTTPLLLLDLVLLTNMPATMIAWIMGADIAMIAFGIIGAFTVG-SYKWFYFVVGCIML 155 (244) T ss_dssp CCEESCGGGCEECCCHHHHHHHHHHHHHHHHHHTTBCCCHHHHHHHHHHHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHH T ss_pred CcccccCCCceeeehHHHhhHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcCc-chHHHHHHHHHHHH Confidence 54211 2568999999999999999999999999999988878889999999999999999874 67999999999999 Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHH Q tr|B0R5N9|B0R5 159 LYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLR 238 (262) Q Consensus 159 ~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~ 238 (262) +.++|.++.+.++++++++++.++.+++++.+.+++|.+||++|.+++ +.++++++.|+++|+++|+++|++|+++++. T Consensus 156 ~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~~~W~~YPi~w~l~~-g~~ii~~~~e~i~y~ilDv~~K~~f~~~ll~ 234 (244) T 3wt9_A 156 AVLAWGMINPIFKEELQKHKEYTGAYTTLLIYLIVLWVIYPIVWGLGA-GGHIIGVDVEIIAMGILDLLAKPLYAIGVLI 234 (244) T ss_dssp HHHHHHHHHHHHCGGGBSCTTTHHHHHHHHHHHHHHHHHHHHHHHHTT-TTCCSCHHHHHHHHHHHHHHHTHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHcc-ccccCCchHHHHHHHHHHHHHHHHHHHHHHH Confidence 999999998888777777777899999999999999999999999985 4467889999999999999999999999999 Q ss_pred HHHhhcCCCC Q tr|B0R5N9|B0R5 239 SRAIFGEAEA 248 (262) Q Consensus 239 ~~~~~~~~~~ 248 (262) ..++.+.... T Consensus 235 ~~~~~~~~~~ 244 (244) T 3wt9_A 235 TVEVVYGKLG 244 (244) T ss_dssp HHHHHHHHHC T ss_pred HHHHhcCCCC Confidence 8877665321 No 12 >4hyj_A Rhodopsin; seven-helical transmembrane protein, proton pump, membrane, transport; HET: RET LFA; 2.30A {Exiguobacterium sibiricum} Probab=100.00 E-value=7.1e-42 Score=299.31 Aligned_cols=249 Identities=25% Similarity=0.340 Sum_probs=195.9 Template_Neff=7.800 Q ss_pred ccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCC Q tr|B0R5N9|B0R5 8 AVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGE 87 (262) Q Consensus 8 ~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~ 87 (262) .+|.+ .....+..++|+++++|++++++|+..++++ ++++|.+++++++++++|+++|+.|++|+++.....+ + T Consensus 1 ~~~~~----~~~~~~~~~~w~~~~~~~~~~l~f~~~~~~~-~~~~R~~~~l~~~i~~va~iaY~~ma~g~g~~~~~~~-~ 74 (258) T 4hyj_A 1 MEEVN----LLVLATQYMFWVGFVGMAAGTLYFLVERNSL-APEYRSTATVAALVTFVAAIHYYFMKDAVGTSGLLSE-I 74 (258) T ss_dssp --CCC----HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGS-CTTTHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCGGG-C T ss_pred CCccc----hhHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CcchhHHHHHHHHHHHHHHHHHHHHHHcCCccccccc-c Confidence 01111 1222567888999999999999999998875 5788999999999999999999999999988765322 3 Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHHHHHHHHHcCc-----chhHHHHHHHHHHHH Q tr|B0R5N9|B0R5 88 QNPIYWARYADWLFTTPLLLLDLALLVDADQ----GTILALVGADGIMIGTGLVGALTKV-----YSYRFVWWAISTAAM 158 (262) Q Consensus 88 ~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~----~~~~~~v~~~~~miv~G~~g~~~~~-----~~~~~~~~~~s~~~~ 158 (262) ++++++.||+||++|+|++++.+++++|.+. +.+...++.|++|++||++|++..+ ...||.|+++|+++| T Consensus 75 ~~~~~~~RYv~W~iTtPlll~~l~ll~g~~~~~~~~~~~~li~~~~~mi~~G~~ga~~~~~~~~~~~~~w~~~~~s~~~~ 154 (258) T 4hyj_A 75 DGFPTEIRYIDWLVTTPLLLVKFPLLLGLKGRLGRPLLTKLVIADVIMIVGGYIGESSINIAGGFTQLGLWSYLIGCFAW 154 (258) T ss_dssp CSCHHHHHHHHHHHHHHHHHTHHHHHHC---CCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH T ss_pred CCCCchhHhhCHHhhHHHHHHHHHHHHcccccccHhHHHHHHHHHHHHHHHHHHHHHhcccccccchHHHHHHHHHHHHH Confidence 4678899999999999999999999999986 4556788999999999999999742 357899999999999 Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHH Q tr|B0R5N9|B0R5 159 LYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLR 238 (262) Q Consensus 159 ~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~ 238 (262) +.+++.++++.++.++++++++++.|+.++.+++++|.+||++|.++++|.+..++..+++.|+++|+++|++|++++++ T Consensus 155 ~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~g~~~~~~~~~~y~ilDv~~K~~fg~~ll~ 234 (258) T 4hyj_A 155 IYIIYLLFTNVTKAAENKPAPIRDALLKMRLFILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFF 234 (258) T ss_dssp HHHHHHHTTHHHHHHTTSCHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCcccHHHHHHHHHHHHHHHHHHHHHHHH Confidence 99999999999888877777889999999999999999999999999655444445667778999999999999999999 Q ss_pred HHHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 239 SRAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) ..++.+++++++-++-+.-..... T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~ 258 (258) T 4hyj_A 235 AVKTMSSLSSSKGKTLTSHHHHHH 258 (258) T ss_dssp HHHHTCC----------------- T ss_pred HHHhhhcccCCCCCccccccccCC Confidence 999988887765433221100000 No 13 >4xtl_A Sodium pumping rhodopsin; ION pump, membrane protein; HET: LYR LFA; 1.45A {Dokdonia eikasta} PDB: 4xtn_A* 4xto_A* 3x3b_A* 3x3c_A* Probab=100.00 E-value=4e-41 Score=298.81 Aligned_cols=254 Identities=21% Similarity=0.272 Sum_probs=200.3 Template_Neff=7.500 Q ss_pred CcccCC----cccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhc Q tr|B0R5N9|B0R5 1 MLELLP----TAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLG 76 (262) Q Consensus 1 ~~~~~~----~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g 76 (262) =.|.+= .+|+++ ...+..++|+++++|++++++|+..++++ ++++|.+++++++++++++++|+.|++| T Consensus 9 ~~~~~~~~~~~~~~~~------~~~~~~~lw~~~~~~~~~~l~f~~~~~~~-~~~~R~~~~l~~~i~~iaa~~Y~~ma~g 81 (288) T 4xtl_A 9 NFENFIGATEGFSEIA------YQFTSHILTLGYAVMLAGLLYFILTIKNV-DKKFQMSNILSAVVMVSAFLLLYAQAQN 81 (288) T ss_dssp CHHHHHHHHTCBCHHH------HHHHHHHHHHHHHHHHHHHHHHHHTGGGS-CGGGHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred cHHHHhcccccCCCCc------cchHHHHHHHHHHHHHHHHHHHHHHHccC-CcchhHHHHHHHHHHHHHHHHHHHHHhc Confidence 000010 112221 22567788899999999999999998875 4788999999999999999999999999 Q ss_pred CCceeecC---------CCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHH----HHHHHHHHHHHHHHHHHHHcCc Q tr|B0R5N9|B0R5 77 YGLTMVPF---------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTI----LALVGADGIMIGTGLVGALTKV 143 (262) Q Consensus 77 ~g~~~~~~---------~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~----~~~v~~~~~miv~G~~g~~~~~ 143 (262) +++..... +.++|++++.||+||++|+|++++.+++++|.+++.+ ..+++.|++|++||++|++..+ T Consensus 82 ~g~~~~~~~~~~~~~~~~~~~r~~~~~RYvdW~iTtPlll~~L~ll~g~~~~~~~~~~~~lv~~~~~mi~~Gl~g~~~~~ 161 (288) T 4xtl_A 82 WTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVVSLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEV 161 (288) T ss_dssp HHHHEEEETTTTEEEECTTSCCCCTHHHHHHHHHHHHHHHHHGGGTSCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHTTT T ss_pred cchhhccccccccccccCCCCceechHHhhCHHhhHHHHHHHHHHHHCcchhhhHHHHHHHHHHHHHHHHHHHHHHhccc Confidence 98765431 1134788999999999999999999999999987765 5788999999999999999764 Q ss_pred --chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCc----CCCCCC--ChH Q tr|B0R5N9|B0R5 144 --YSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGS----EGAGIV--PLN 215 (262) Q Consensus 144 --~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~----~g~~~i--~~~ 215 (262) ...||.|+++|+++|+.++|.++++.++.+++++++.++.|++++.+++++|.+||++|++++ +|.+++ +++ T Consensus 162 ~~~~~kw~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPivw~ls~~~~~eG~~i~~~s~~ 241 (288) T 4xtl_A 162 SNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKILSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVM 241 (288) T ss_dssp TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTCTTSTTSSHHHHH T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCCcH Confidence 257999999999999999999999998877766677889999999999999999999999963 444443 489 Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCC-cCcCCCccccC Q tr|B0R5N9|B0R5 216 IETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPE-PSAGDGAAATS 261 (262) Q Consensus 216 ~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~-~~~~~~~~~~~ 261 (262) .|+++|+++|+++|++|++++++..++.++++++. ++.-+.-.... T Consensus 242 ~e~i~y~ilDvi~K~~fg~lll~~~~~~~~~~~~~~~~~~~~~~~~~ 288 (288) T 4xtl_A 242 ARQLVYTIADVSSXVIYGVLLGNLAITLSKNKELVEANSLEHHHHHH 288 (288) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CC--------------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhcccCC Confidence 99999999999999999999999999888777654 22111000000 No 14 >5b2n_A Chloride pumping rhodopsin; retinal, cell-free synthesis, light-driven chloride pump, ME protein, transport protein; HET: RET D12 D10; 1.58A {Nonlabens marinus s1-08} Probab=100.00 E-value=3.6e-41 Score=297.90 Aligned_cols=254 Identities=23% Similarity=0.246 Sum_probs=204.8 Template_Neff=7.600 Q ss_pred CcccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHH---HHHHHhcC Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTM---YLSMLLGY 77 (262) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~---Y~~ma~g~ 77 (262) =.|.+=.+++++++ ....++|+++++|++++++|+..++++ ++++|.+++++++++.+|+++ |+.|++|. T Consensus 10 ~~~~~~~~~~~~~~------~~~~~~w~~~~~m~~~~i~f~~~~~~~-~~~~R~~~~l~~~i~~va~~~Y~~y~~m~~g~ 82 (279) T 5b2n_A 10 NIESLFDYSAGQFE------FIDHLLTMGVGVHFAALIFFLVVSQFV-APKYRIATALSCIVMVSAGLILNSQAVMWTDA 82 (279) T ss_dssp CGGGGCCBCHHHHH------HHHHHHHHHHHHHHHHHHHHHHHGGGS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred chHHHhcCCccccc------hHHHHHHHHHHHHHHHHHHHHHHhccC-CCcchHHHHHHHHHHHHHHHHHHHHHHHhhcc Confidence 01112223333222 557788899999999999999998875 478899999999999999999 88888765 Q ss_pred CceeecCC---CCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHH----HHHHHHHHHHHHHHHHHHHcCcc--hhHH Q tr|B0R5N9|B0R5 78 GLTMVPFG---GEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTI----LALVGADGIMIGTGLVGALTKVY--SYRF 148 (262) Q Consensus 78 g~~~~~~~---~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~----~~~v~~~~~miv~G~~g~~~~~~--~~~~ 148 (262) +...+++ +++|++++.||+||++|||++++.+++++|.+.+.+ ...++.|++|++||++|++.++. ..|| T Consensus 83 -~~~~~~~~~~~~~r~~~~~RYvdW~iTtPlll~~l~ll~g~~~~~~~~~~~~li~~~~~miv~G~~g~~~~~~~~~~~~ 161 (279) T 5b2n_A 83 -YAYVDGSYQLQDLTFSNGYRYVNWMATIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIITGYVGQLYEVDDIAQLM 161 (279) T ss_dssp -EEEETTEEEECCTTCCTHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCHHHHH T ss_pred -ceecccccccCCCCccchHHHhCHHHHHHHHHHHHHHHHCCchhhhHHHHHHHHHHHHHHHHHHHHHHhhcccccchhh Confidence 2221111 246889999999999999999999999999987653 56889999999999999997753 5789 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHh Q tr|B0R5N9|B0R5 149 VWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSA 228 (262) Q Consensus 149 ~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~ 228 (262) .|+.+|+++|+.++|.++.+.++.+++++++.++.+++++.+++++|.+||++|++++.+++.++++.|+++|+++|+++ T Consensus 162 ~w~~~s~~~f~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~ 241 (279) T 5b2n_A 162 IWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMMFAWTLYPIAYLVPAFMNNADGVVLRQLLFTIADISS 241 (279) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHGGGCCTTHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCSHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCchHHHHHHHHHHHHH Confidence 99999999999999999888877666555667889999999999999999999999966555788999999999999999 Q ss_pred HHHHHHHHHHHHHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 229 KVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 229 K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) |++|++++++..++.++++.++|+......-.+| T Consensus 242 K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 275 (279) T 5b2n_A 242 KVIYGLMITYIAIQQSAAAGYVPAQQALGRIGMD 275 (279) T ss_dssp HHHHHHHHHHHHHHHHHHTTCHHHHHHHHC---- T ss_pred HHHHHHHHHHHHHhcccccccCccceecCCcCcC Confidence 9999999999999999998877665433222222 No 15 >3ug9_A Archaeal-type opsin 1, archaeal-type opsin 2; microbialrhodopsin, seven-transmembrane, light-gated cation membrane protein; HET: RET OLA; 2.30A {Chlamydomonas reinhardtii} PDB: 4yzi_A* Probab=100.00 E-value=3.4e-41 Score=303.07 Aligned_cols=255 Identities=19% Similarity=0.274 Sum_probs=197.8 Template_Neff=6.300 Q ss_pred Cc-------------ccCCcc-cCCCchhhhcCChHH------HHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHH Q tr|B0R5N9|B0R5 1 ML-------------ELLPTA-VEGVSQAQITGRPEW------IWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITT 60 (262) Q Consensus 1 ~~-------------~~~~~~-~~~~~~~~~~~~~~~------~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~ 60 (262) |+ -.+|+- .-..+.+.+++++.+ .++|+++++|++++++|+..++++ ++++|.+|++++ T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Gs~w~~~~~~~~lW~~fai~~~~~l~f~~~s~~~-~~~~R~~~~~~~ 105 (333) T 3ug9_A 27 MLFQTSYTLENNGSVICIPNNGQCFCLAWLKSNGTNAEKLAANILQWITFALSALCLMFYGYQTWKS-TCGWEEIYVATI 105 (333) T ss_dssp CSSBCCCEEETTTTEEECCCSSCCBCHHHHSCCCCHHHHHHHHHHHHHHHHHHHHHHHHC---------CCHHHHHHHHH T ss_pred cccceeeEEecCCceEEecCccchhhhhHHhcCCCchhhhhhhHHHHHHHHHHHHHHHHHHHHHhcC-CCCceEeeehHH Confidence 00 012210 001122444444443 448899999999999999998875 478899999999 Q ss_pred -HHHHHHHHHHHHHHhcCCceeecCCCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHH---HHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 61 -LVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG---TILALVGADGIMIGTGL 136 (262) Q Consensus 61 -~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~---~~~~~v~~~~~miv~G~ 136 (262) +++++ ++|+.|++|.++...+ ++|++++.||+||++|+|++++.+++++|.+.. .+..+++.+++|+++|+ T Consensus 106 ~~i~~i--iaY~~Masg~G~~~~~---~gr~v~~~RYidWllTtPLLLl~L~llag~~~~~~~~i~~li~ad~~mIv~Gl 180 (333) T 3ug9_A 106 EMIKFI--IEYFHEFDEPAVIYSS---NGNKTVWLRYAEWLLTCPVILIHLSNLTGLANDYNKRTMGLLVSDIGTIVWGT 180 (333) T ss_dssp HHHHHH--HHHHHTTSTTTSEECT---TSCEECHHHHHHHHHHHHHHHHHHTTTTSCCCCCCHHHHHHHHHHHHHHHHHH T ss_pred HHHHHH--HHHHHHHhcCCceecc---CCceecHHHHhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHH Confidence 88887 9999999999887653 468999999999999999999999999999874 45677889999999999 Q ss_pred HHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChH Q tr|B0R5N9|B0R5 137 VGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAES-MRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLN 215 (262) Q Consensus 137 ~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~~-~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~ 215 (262) +|++..+ ..||.|+++|+++|+.++|.++.+.++++++ ++++.++.|+.++.+++++|.+||++|+++++|.+.++++ T Consensus 181 ~gal~~~-~~kw~~f~~g~~~~l~vl~~l~~~~~~~a~~~~~~~~~~~y~~L~~~~~v~W~lYPIvW~Ls~eG~~~Is~~ 259 (333) T 3ug9_A 181 TAALSKG-YVRVIFFLMGLCYGIYTFFNAAKVYIEAYHTVPKGRCRQVVTGMAWLFFVSWGMFPILFILGPEGFGVLSVY 259 (333) T ss_dssp HHHHSCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTCSSCHH T ss_pred HHHHhcc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHHHHhHhhHHHHHHHHHhhcccccCChH Confidence 9999875 6899999999999999999999888887766 4567889999999999999999999999997887889999 Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCCcCcCCCcc---------------------ccC--C Q tr|B0R5N9|B0R5 216 IETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAA---------------------ATS--D 262 (262) Q Consensus 216 ~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~---------------------~~~--~ 262 (262) .|+++|+++|+++|++|++++++..++.++....+-+-+.|.. ..+ | T Consensus 260 ~e~i~y~IlDllsK~~Fg~lll~~~~~i~~~~~~~g~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~ 329 (333) T 3ug9_A 260 GSTVGHTIIDLMSKNCWGLLGHYLRVLIHEHILIHGDIRKTTKLNIGGTEIEVETLVEDEAEAGAVSSED 329 (333) T ss_dssp HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHCCEEEEEEC------CEEEEEESCC---------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhccCcCCCcceeecCEEEEEEeeeccccccchhcccc Confidence 9999999999999999999999999988876633322222211 000 0 No 16 >4knf_A BPR, blue-light absorbing proteorhodopsin; membrane, proton transport, ION transport, proton pump, RETI schiff base; HET: RET; 2.60A {Gamma proteobacterium} PDB: 4kly_A* 2l6x_A* Probab=100.00 E-value=1.9e-40 Score=290.50 Aligned_cols=245 Identities=23% Similarity=0.300 Sum_probs=191.8 Template_Neff=7.400 Q ss_pred CcccCCcccCCC-chhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCc Q tr|B0R5N9|B0R5 1 MLELLPTAVEGV-SQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL 79 (262) Q Consensus 1 ~~~~~~~~~~~~-~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~ 79 (262) ---.+|+..|.. +.+. +..+..++|+++++|++++++|+..++++ ++++|.+++++++++++|+++|+.|++++ T Consensus 10 ~~~~~~~~~~~~~~~~~--~~~g~~~~w~~~~~m~~~~l~f~~~~~~~-~~~~R~~~~l~~~i~~ia~iaY~~ma~~~-- 84 (261) T 4knf_A 10 SAIALPSFAAAGGDLDI--SDTVGVSFWLVTAGMLAATVFFFVERDQV-SAKWKTSLTVSGLITGIAFWHYLYMRGVW-- 84 (261) T ss_dssp ------------CCCCT--TCHHHHHHHHHHHHHHHHHHHHHHGGGGS-CTTTHHHHHHHHHHHHHHHHHHHHHHHHH-- T ss_pred chhccCCCCCCCCCccc--cchhhHHHHHHHHHHHHHHHHHHHHHccC-CcchhHHHHHHHHHHHHHHHHHHHHHhcc-- Confidence 001245444432 2233 33677788899999999999999998875 57889999999999999999999999832 Q ss_pred eeecCCCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHH Q tr|B0R5N9|B0R5 80 TMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQG----TILALVGADGIMIGTGLVGALTKVYSYRFVWWAIST 155 (262) Q Consensus 80 ~~~~~~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~----~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~ 155 (262) .. .++..++.||+||++|||++++.+++++|.+.+ ....+++.|++|++||++|++.. ..||.|+++|+ T Consensus 85 ~~-----~~~~~~~~RYvdW~lTtPlll~~L~lla~~~~~~~~~~~~~li~~d~~Mi~~G~~g~~~~--~~kw~~~~is~ 157 (261) T 4knf_A 85 ID-----TGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGL--APVLPAFIIGM 157 (261) T ss_dssp HH-----HCCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHHHHHHHHHHHHHTS--SCHHHHHHHHH T ss_pred cc-----CCCccchHHHhhHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHhhh--hhHHHHHHHHH Confidence 21 124456789999999999999999999999764 22356689999999999999976 37999999999 Q ss_pred HHHHHHHHHHH-HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcC-CCCCCChHHHHHHHHHHHHHhHHHHH Q tr|B0R5N9|B0R5 156 AAMLYILYVLF-FGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSE-GAGIVPLNIETLLFMVLDVSAKVGFG 233 (262) Q Consensus 156 ~~~~~v~~~l~-~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~-g~~~i~~~~e~i~y~ilDv~~K~~fg 233 (262) ++|+.++|.++ ...++.+++++++.++.++.++.+++++|.+||++|.++++ +.+.++++.|+++|+++|+++|++|+ T Consensus 158 ~~f~~v~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPivw~l~~~~~~~~i~~~~e~i~y~ilDv~~Kv~fg 237 (261) T 4knf_A 158 AGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGEGVYASNLNLIYNLADFVNKILFG 237 (261) T ss_dssp HHHHHHHHHHHTSGGGSCCCCSCHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSSCC-CCCHHHHHHHHHHHHHHHTHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCcCChhHHHHHHHHHHHHHHHHHH Confidence 99999999999 57676665566678899999999999999999999999854 44578899999999999999999999 Q ss_pred HHHHHHHHhhcCCCCCCcCcCCCc Q tr|B0R5N9|B0R5 234 LILLRSRAIFGEAEAPEPSAGDGA 257 (262) Q Consensus 234 ~~ll~~~~~~~~~~~~~~~~~~~~ 257 (262) ++++...++.++++.+++.....- T Consensus 238 ~~ll~~~~~~~~~~~~~~~~~~~~ 261 (261) T 4knf_A 238 LIIWNVAVKESSNAKLLEHHHHHH 261 (261) T ss_dssp HHHHHHHHHHHHHHTC-------- T ss_pred HHHHHHHHHhhcccCcccccccCC Confidence 999999999888877654321100 No 17 >4jq6_A Proteorhodopsin; retinylidene protein, ION transport, proton transport; HET: RET LI1; 2.31A {Uncultured bacterium} PDB: 5abb_Z Probab=100.00 E-value=1.4e-39 Score=281.10 Aligned_cols=229 Identities=24% Similarity=0.387 Sum_probs=176.5 Template_Neff=8.100 Q ss_pred CchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeecCCCCCCcc Q tr|B0R5N9|B0R5 12 VSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPI 91 (262) Q Consensus 12 ~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~~~~~~~~~~~ 91 (262) -......+..+..++|+++++|.+++++++..++++ ++++|.+|+++++++.+|+++|+.|++++. . +++.. T Consensus 1 ~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~-~~~~R~~~~l~~~i~~ia~~~Y~~ma~~~~--~-----~g~~~ 72 (235) T 4jq6_A 1 MGEILAVDDYVGISFWLAAAIMLASTVFFFVERSDV-PVKWKTSLTVAGLVTGVAFWHYLYMRGVWI--Y-----AGETP 72 (235) T ss_dssp --------CHHHHHHHHHHHHHHHHHHHHHHHTTTS-CGGGHHHHHHHHHHHHHHHHHHHHHHHHHH--H-----HCSCC T ss_pred CCceeecchHHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHHHHHHHHHHHHHHHHHHHHhcc--c-----CCCcc Confidence 000111233677888899999999999999998875 578899999999999999999999998632 1 12455 Q ss_pred cHHHHHHHHHHHHHHHHHHHHHcCC----CHHHHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 92 YWARYADWLFTTPLLLLDLALLVDA----DQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFF 167 (262) Q Consensus 92 ~~~RYv~W~lTtPlll~~L~ll~g~----~~~~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~~s~~~~~~v~~~l~~ 167 (262) ++.||+||++|||++++.++++++. +++.+..+++.|++|++||++|+..++ .+|.|+++|+++|+.++|+++. T Consensus 73 ~~~RYv~W~~TtPlll~~l~~l~~~~~~~~~~~~~~lv~~~~~miv~G~~g~~~~~--~~w~~~~~g~~~~~~v~~~l~~ 150 (235) T 4jq6_A 73 TVFRYIDWLITVPLQIIEFYLIIAAVTAISSAVFWKLLIASLVMLIGGFIGEAGLG--DVVVWWIVGMIAWLYIIYEIFL 150 (235) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC--------CHHHHHHHHHHHHHHHHHHHHTSS--CHHHHHHHHHHHHHHHHHHHHC T ss_pred chHHHhhHHHhHHHHHHHHHHHHHHhcCCcHhHHHHHHHHHHHHHHHHHHHHcccc--cchHHHHHHHHHHHHHHHHHHH Confidence 7899999999999999999999944 445556678999999999999999764 4799999999999999999997 Q ss_pred HHHHH-HHhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcC Q tr|B0R5N9|B0R5 168 GFTSK-AESMR-PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245 (262) Q Consensus 168 ~~~~~-a~~~~-~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~ 245 (262) +.+++ +++++ ++.++.+++++.+..++|.+||++|.++++| +.++++.|+++|+++|+++|++|++++++..++.++ T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g-~~i~~~~e~i~y~ilDv~~K~~f~~~ll~~~~~~~~ 229 (235) T 4jq6_A 151 GETAKANAGSGNAASQQAFNTIKWIVTVGWAIYPIGYAWGYFG-DGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDKE 229 (235) T ss_dssp ------------------CCTHHHHHHHHHHHHHHHHHHHHSS-SSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred HHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHcccc-ccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc Confidence 66643 33333 4578899999999999999999999999766 467899999999999999999999999999999888 Q ss_pred CCCCCc Q tr|B0R5N9|B0R5 246 AEAPEP 251 (262) Q Consensus 246 ~~~~~~ 251 (262) ++..|. T Consensus 230 ~~~~~~ 235 (235) T 4jq6_A 230 TSTSHA 235 (235) T ss_dssp CC---- T ss_pred cccCCC Confidence 776431 No 18 >5azd_A Bacteriorhodopsin; membrane protein, retinal, ION pump, thermal stability, TRAN protein; HET: LYR; 2.80A {Thermus thermophilus jl-18} Probab=100.00 E-value=2e-39 Score=285.25 Aligned_cols=253 Identities=25% Similarity=0.354 Sum_probs=192.2 Template_Neff=7.600 Q ss_pred cccCCcccCCCchhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCCcee Q tr|B0R5N9|B0R5 2 LELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTM 81 (262) Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i~Y~~ma~g~g~~~ 81 (262) .+.||+..++....+ ....|+++++|++++++|+..+++. ++++|.+++++++++++|+++|+.|++|++... T Consensus 1 ~~~~~~~g~~~~w~v------~~~~~~~~~~m~~~~v~f~~~~~~~-~~~~R~~~~l~~~i~~iaaiaY~~ma~g~~~~~ 73 (268) T 5azd_A 1 MRMLPELSFGEYWLV------FNMLSLTIAGMLAAFVFFLLARSYV-APRYHIALYLSALIVFIAGYHYLRIFESWVGAY 73 (268) T ss_dssp --CCCCBCHHHHHHH------HHHHHHHHHHHHHHHHHHHHGGGTS-CGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHE T ss_pred CccccccCCchHHHH------HHHHHHHHHHHHHHHHHHHHHhccC-CcchhHHHHHHHHHHHHHHHHHHHHHhCCCCce Confidence 122343333333333 3345577888888888888886654 467899999999999999999999999765432 Q ss_pred ecCC---CCCCccc--HHHHHHHHHHHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHHHHHHHHcCcchhHHHHHH Q tr|B0R5N9|B0R5 82 VPFG---GEQNPIY--WARYADWLFTTPLLLLDLALLVDADQG----TILALVGADGIMIGTGLVGALTKVYSYRFVWWA 152 (262) Q Consensus 82 ~~~~---~~~~~~~--~~RYv~W~lTtPlll~~L~ll~g~~~~----~~~~~v~~~~~miv~G~~g~~~~~~~~~~~~~~ 152 (262) .... .++++.+ +.||+||++|||++++.+++++|.+.. .+...++.|++|++||++|++..++..+|.|+. T Consensus 74 ~~~~~~~~~~~~~~~~~~RYvdW~lTtPlll~~l~ll~~~~~~~~~~~~~~lv~~~~~Miv~G~~ga~~~~~~~~~~w~~ 153 (268) T 5azd_A 74 QLQDGVYVPTGKPFNDFYRYADWLLTVPLLLLELILVLGLTAARTWNLSIKLVVASVLMLALGYVGEVNTEPGPRTLWGA 153 (268) T ss_dssp EEETTEEEECSCCCCSHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHH T ss_pred eccccccCCCCcccchHHHHhcHHHHHHHHHHHHHHHHCcchhhhHhHHHHHHHHHHHHHHHHHHHHhccCcchhhHHHH Confidence 2100 0223344 999999999999999999999998743 346788999999999999999875456899999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh--cCHHHHHHHHHHHHHHHHHHHHHHHHHHHCc--CCCCCCChHHHHHHHHHHHHHh Q tr|B0R5N9|B0R5 153 ISTAAMLYILYVLFFGFTSKAES--MRPEVASTFKVLRNVTVVLWSAYPVVWLIGS--EGAGIVPLNIETLLFMVLDVSA 228 (262) Q Consensus 153 ~s~~~~~~v~~~l~~~~~~~a~~--~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~--~g~~~i~~~~e~i~y~ilDv~~ 228 (262) +|+++|+.++|.++++.++.+++ ++++.++.++.++.+++++|.+||++|++++ ||+ .++++.|+++|+++|+++ T Consensus 154 ~~~~~f~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~W~~YPi~w~l~~~~egg-~i~~~~e~i~y~ilDvi~ 232 (268) T 5azd_A 154 LSSIPFFYILYVLWVELGQAIREAKFGPRVLELLGATRLVLLMSWGFYPIAYALGTWLPGG-AAQEVAIQIGYSLADLIA 232 (268) T ss_dssp HHHHHHHHHHHHHHTHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCC-HHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc-cccchHHHHHHHHHHHHH Confidence 99999999999999888876654 4556788999999999999999999999996 344 678999999999999999 Q ss_pred HHHHHHHHHHHHHhhcCCCCCCcCcCCCccccCC Q tr|B0R5N9|B0R5 229 KVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD 262 (262) Q Consensus 229 K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 262 (262) |++|+++++...++.+++++....+.+.-+.... T Consensus 233 K~~fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 266 (268) T 5azd_A 233 XPIYGLLVFAIARAKSLEEGFGVEAKAALEHHHH 266 (268) T ss_dssp THHHHHHHHHHHHHHHHHTTC------------- T ss_pred HHHHHHHHHHHHHhcccccccchHHHHHHhhccc Confidence 9999999999999988887765333221110000 No 19 >5b0w_A Halorhodopsin; seven trans-membrane helices, retinylidene protein, light-DR chloride ION pump microbial rhodopsin; HET: RET 22B L3P BNG; 1.70A {Natronomonas pharaonis dsm 2160} PDB: 3a7k_A* 3abw_A* 3qbi_A* 3qbk_A* 3qbl_A* 3vvk_A* 4qry_A* 3qbg_A* 5etz_A* Probab=100.00 E-value=7e-46 Score=329.35 Aligned_cols=257 Identities=30% Similarity=0.533 Sum_probs=203.7 Template_Neff=7.100 Q ss_pred CcccCCcccCCCc------------hhhhcCChHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 1 MLELLPTAVEGVS------------QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFT 68 (262) Q Consensus 1 ~~~~~~~~~~~~~------------~~~~~~~~~~~~~w~~~~~~~~~~i~f~~~~~~~~~~~~r~~~~l~~~i~~ia~i 68 (262) |.|++||++|+.. +...+...+..++|+++++|.+++++|+..+++++++++|.+++++++++.++++ T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~lwv~f~~~~~~~~vf~~~s~~~~~~~~R~~~~l~~~i~~iaa~ 80 (291) T 5b0w_A 1 MTETLPPVTESAVALQAEVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIA 80 (291) T ss_dssp -----------------CEEEEEEEEEEEESTEEEEEEEEEHHHHEEHHHHHHHHEEEEEBEEHHHHHEEEEEHHHHHEE T ss_pred CCCcCCCchHHHHHHHHHHHHHHHHHHHccCchhhHHHHHHHHHHHHHHHHHHHHHhcCCCCceeehHHHHHHHHHHHHH Confidence 8999999998642 1233444577889999999999999999998876446889999999999999999 Q ss_pred HHHHHHhcCCceeecC----------------CCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH Q tr|B0R5N9|B0R5 69 MYLSMLLGYGLTMVPF----------------GGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMI 132 (262) Q Consensus 69 ~Y~~ma~g~g~~~~~~----------------~~~~~~~~~~RYv~W~lTtPlll~~L~ll~g~~~~~~~~~v~~~~~mi 132 (262) +|+.|++|+|+..... .+++|++++.||+||++|+|++++.+++++|.+++.+...++.+++|+ T Consensus 81 aY~~Ma~g~g~~~i~~~~~~~~~~~~~~~~~~~~~~r~v~~~RYvdW~lTtPlll~~L~llag~~~~~i~~~v~~~~~mI 160 (291) T 5b0w_A 81 SYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMC 160 (291) T ss_dssp EEHHHHEEEEEEEEEBCEEEEEEEEEEEEEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHEEEEHHHHHEEHHHHHHHH T ss_pred HHHHHHhCCCCccceeccccccccccccccccCCCcceecHHHHhhHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH Confidence 9999999976433210 014588999999999999999999999999999887778899999999 Q ss_pred HHHHHHHHcCcc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCCC Q tr|B0R5N9|B0R5 133 GTGLVGALTKVY-SYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGI 211 (262) Q Consensus 133 v~G~~g~~~~~~-~~~~~~~~~s~~~~~~v~~~l~~~~~~~a~~~~~~~~~~~~~l~~~~~v~W~~YPi~w~l~~~g~~~ 211 (262) +||++|++..+. ..||.|+++|+++|+.++|.++++.++++++++ .++.|++++.+++++|.+||++|+++++|.+. T Consensus 161 v~Gl~ga~~~~~~~~kw~~~~is~~~f~~v~y~l~~~~~~~a~~~~--~~~~y~~L~~~~~v~W~~YPivw~l~~~G~~~ 238 (291) T 5b0w_A 161 VTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAG--TADIFSTLKLLTVVMWLGYPIVWALGVEGVAV 238 (291) T ss_dssp HHHHHHHEEEEEEEEEEEEEEEHHHHHHHHEHHHHEEEEEEEEEEE--EEEEEEEEHHHHEEEEEESHHHHHHEEEEEEE T ss_pred HHHHHHHHccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC Confidence 999999997753 379999999999999999999998887665543 67889999999999999999999999788778 Q ss_pred CChHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCC-----cCcCCCccccCC Q tr|B0R5N9|B0R5 212 VPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPE-----PSAGDGAAATSD 262 (262) Q Consensus 212 i~~~~e~i~y~ilDv~~K~~fg~~ll~~~~~~~~~~~~~-----~~~~~~~~~~~~ 262 (262) ++++.|+++|+++|+++|++|++++++.+++.++...++ +.+++||+ | T Consensus 239 i~~~~e~i~y~ilDv~~Kv~Fg~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 291 (291) T 5b0w_A 239 LPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGSILDVPSASGAPAD---D 291 (291) T ss_dssp SCEEEEEEEEEEEEEEEEEEEEHHHHEEEEEEEEEEEECC---------------- T ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCccccCCCCCCCCCCC---C Confidence 889999999999999999999999999999988777664 44566665 2