Rd0003

Pastash edited this page Jun 21, 2011 · 9 revisions

Prophage

Location

sequence            start    end      direction
TY-2482_chromosome  1058696  1009406  -1
scaffold00001       1618391  1665842  -1

Prophage integrated into yecE.

List of genes

  unigene description pubmed size sequence position
—> E1RYP9 Putative uncharacterized protein 21075930 1216 TY-2482_chromosome[1057926:1059141]
—> B7MPT9 Phage integrase 19165319 1320 TY-2482_chromosome[1056622:1057941]
—> B6I1E3 Putative phage excisionase 18931093 234 TY-2482_chromosome[1056342:1056575]
—> B2TYH9 Hypothetical bacteriophage protein 240 TY-2482_chromosome[1055941:1056180]
—> B3WUG8 Upf89.5 756 TY-2482_chromosome[1055098:1055853]
—> C8TPV2 Putative uncharacterized protein 19815525 552 TY-2482_chromosome[1054547:1055098]
—> E7UPB9 Phage EaA protein 546 TY-2482_chromosome[1054036:1054581]
—> C8U7N3 Putative uncharacterized protein 19815525 237 TY-2482_chromosome[1053800:1054036]
—> C8U7N2 Putative uncharacterized protein 19815525 201 TY-2482_chromosome[1053604:1053804]
—> P76515 Uncharacterized protein yfdS 9278503;16738553 360 TY-2482_chromosome[1053245:1053604]
—> C8TW07 Putative uncharacterized protein 19815525 534 TY-2482_chromosome[1052718:1053251]
—> B7NVE7 Putative uncharacterized protein yfdR 19165319 515 TY-2482_chromosome[1052706:1053220]
—> P76513 Uncharacterized protein yfdQ 9278503;16738553 822 TY-2482_chromosome[1051766:1052587]
—> C8TW05 Putative uncharacterized protein 19815525 591 TY-2482_chromosome[1051107:1051697]
<— B7LJJ4 Putative uncharacterized protein 19165319 453 TY-2482_chromosome[1051074:1051526:r]
<— Q1R2C0 Putative uncharacterized protein 16585510 330 TY-2482_chromosome[1050735:1051064:r]
—> D7YL88 Conserved domain protein 252 TY-2482_chromosome[1050715:1050966]
—> C8UKW2 Putative repressor protein CI 19815525 690 TY-2482_chromosome[1049943:1050632]
<— C8UKW3 Putative antirepressor protein Cro 19815525 258 TY-2482_chromosome[1049588:1049845:r]
<— D6HVI9 YmfL protein 588 TY-2482_chromosome[1049038:1049625:r]
<— B3WIT4 Putative antirepressor 1191 TY-2482_chromosome[1047848:1049038:r]
<— C8TW00 Putative uncharacterized protein 19815525 222 TY-2482_chromosome[1047627:1047848:r]
<— B7MND7 Replication protein from phage origin 19165319 855 TY-2482_chromosome[1046812:1047666:r]
<— C8U2N0 Putative uncharacterized protein 19815525 486 TY-2482_chromosome[1046321:1046806:r]
<— C8U2N1 Putative DNA methylase 19815525 651 TY-2482_chromosome[1045668:1046318:r]
<— E9YXI8 Phage N-6-adenine-methyltransferase 396 TY-2482_chromosome[1045403:1045798:r]
<— C8TVZ6 Putative uncharacterized protein 19815525 324 TY-2482_chromosome[1045345:1045668:r]
<— D3QMI2 Crossover junction endodeoxyribonuclease rusA (EC 3.1.22.4) 20090843 393 TY-2482_chromosome[1044953:1045345:r]
<— D3QMI3 KilA-N domain family 20090843 813 TY-2482_chromosome[1043975:1044787:r]
<— E8HWB8 Putative uncharacterized protein (Fragment) 411 TY-2482_chromosome[1043560:1043970:r]
<— C8TVZ3 Putative uncharacterized protein 19815525 987 TY-2482_chromosome[1042978:1043964:r]
—> Q8KTV8 Putative uncharacterized protein 12117937 342 TY-2482_chromosome[1042918:1043259]
<— B3HVA5 Antitermination protein Q 339 TY-2482_chromosome[1042619:1042957:r]
—> B3IDN1 Putative uncharacterized protein 546 TY-2482_chromosome[1042055:1042600]
—> B3HVA3 Putative uncharacterized protein 924 TY-2482_chromosome[1041142:1042065]
<— B7NVG6 Putative uncharacterized protein 19165319 234 TY-2482_chromosome[1040677:1040910:r]
<— C6USM2 Putative DNA adenine methyltransferase encoded by prophage CP-933O 19564389 1056 TY-2482_chromosome[1039467:1040522:r]
<— ref|NC_010473|:2875549-2875624|Ile tRNA| [gene=ileY] [locus_tag=ECDH10B_2820] 76 TY-2482_chromosome[1039348:1039423:r]
<— B7MV04 Putative uncharacterized protein 19165319 291 TY-2482_chromosome[1038847:1039137:r]
<— B7MPX6 Putative uncharacterized protein 19165319 1881 TY-2482_chromosome[1036831:1038711:r]
<— D3H2S6 Putative phage lysis protein 20098708 291 TY-2482_chromosome[1036465:1036755:r]
<— E6AD14 Putative uncharacterized protein (Fragment) 396 TY-2482_chromosome[1036122:1036517:r]
<— B7LES2 Putative uncharacterized protein 19165319 804 TY-2482_chromosome[1035654:1036457:r]
—> B7LES3 Putative uncharacterized protein 19165319 312 TY-2482_chromosome[1035327:1035638]
<— B7LES4 Lysozyme (EC 3.2.1.17) 19165319 531 TY-2482_chromosome[1034668:1035198:r]
<— E8HUW1 Lysozyme (EC 3.2.1.17) 418 TY-2482_chromosome[1034583:1035000:r]
—> D7X133 Conserved domain protein 213 TY-2482_chromosome[1034507:1034719]
<— D6IMM0 Predicted protein 213 TY-2482_chromosome[1034329:1034541:r]
<— B7MPY1 Putative uncharacterized protein 19165319 219 TY-2482_chromosome[1034183:1034401:r]
<— B7N3K3 Endopeptidase (Lysis protein) from bacteriophage origin (EC 3.4.-.-) 19165319 471 TY-2482_chromosome[1033713:1034183:r]
—> E7HI62 Putative uncharacterized protein 262 TY-2482_chromosome[1032621:1032882]
<— A1AAK5 Prophage Qin DNA packaging protein NU1-like protein 17293413 786 TY-2482_chromosome[1031961:1032746:r]
<— B7L465 Terminase large subunit (Gp2) 19165319 1968 TY-2482_chromosome[1030061:1032028:r]
<— C8TKW0 Head-tail joining protein 19815525 204 TY-2482_chromosome[1029871:1030074:r]
<— C8TUI5 Putative portal protein 19815525 1590 TY-2482_chromosome[1028282:1029871:r]
<— B7L468 Head-tail preconnector protein GP5 19165319 1503 TY-2482_chromosome[1026787:1028289:r]
<— D3H3D9 Phage head decoration protein 20098708 345 TY-2482_chromosome[1026403:1026747:r]
<— D8BRM0 Phage major capsid protein E (Fragment) 453 TY-2482_chromosome[1025902:1026354:r]
<— B7L470 Major head protein (Head protein gp7) 19165319 1026 TY-2482_chromosome[1025317:1026342:r]
<— B7L471 Putative uncharacterized protein 19165319 429 TY-2482_chromosome[1024882:1025310:r]
<— B7L472 Tail attachment protein (Minor capsid protein FII) 19165319 351 TY-2482_chromosome[1024536:1024886:r]
<— D3H3E3 Phage minor tail protein 20098708 573 TY-2482_chromosome[1023946:1024518:r]
<— C8U3B0 Putative minor tail protein 19815525 393 TY-2482_chromosome[1023554:1023946:r]
<— B2TZ73 Major tail protein V 750 TY-2482_chromosome[1022794:1023543:r]
—> A1AAL5 Putative uncharacterized protein 17293413 1335 TY-2482_chromosome[1022113:1023447]
<— C8UCF4 Putative minor tail protein 19815525 411 TY-2482_chromosome[1021918:1022328:r]
<— C8UEI9 Putative tail length tape measure protein 19815525 2610 TY-2482_chromosome[1019325:1021934:r]
<— B7LBD1 Minor tail protein M 19165319 327 TY-2482_chromosome[1018999:1019325:r]
—> Q1RCC4 Putative uncharacterized protein 16585510 804 TY-2482_chromosome[1018292:1019095]
—> D8A602 Putative uncharacterized protein (Fragment) 402 TY-2482_chromosome[1018088:1018489]
<— B7LEU3 Putative tail fiber component K of prophage 19165319 783 TY-2482_chromosome[1017553:1018335:r]
<— D3GSI6 Phage tail assembly protein 20098708 669 TY-2482_chromosome[1016984:1017652:r]
<— D7ZF50 Conserved domain protein (Fragment) 438 TY-2482_chromosome[1016537:1016974:r]
<— Q7ARG4 Phage lambda-related host specificity protein J (Putative phage tail protein) 11586360;15368893 2727 TY-2482_chromosome[1014239:1016965:r]
<— B7L8N6 Host specificity protein J 19165319 3393 TY-2482_chromosome[1013528:1016920:r]
<— E8J0W2 Putative uncharacterized protein (Fragment) 458 TY-2482_chromosome[1013463:1013920:r]
<— D3H3F5 Putative prophage-encoded outer membrane protein 20098708 597 TY-2482_chromosome[1012861:1013457:r]
<— B5YU13 Tail fiber protein 1140 TY-2482_chromosome[1011603:1012742:r]
<— B7LEU7 Putative tail fiber protein (Modular protein) 19165319 1536 TY-2482_chromosome[1011171:1012706:r]
<— B7LEU8 Putative uncharacterized protein 19165319 693 TY-2482_chromosome[1010554:1011246:r]
—> C6V226 Putative uncharacterized protein 19564389 246 TY-2482_chromosome[1009764:1010009]

This list was extracted from Era7_EHEC_BGI_V4_Annotation.txt using rod2html.py. Sequence positions are formatted as Emboss Universal Sequence Addresses.

Using Pfam batch analysis of domains in a given set of protein sequences (http://pfam.sanger.ac.uk/search/batch#tabview=tab1) I analyzed the hypotheticals from the list above. Unfortunately, I'm leaving tomorrow and still many chores on my way, so raw data with not much edition and no links. Sorry, guys...

<seq id> <alignment start>  <alignment end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length>  <bit score> <E-value>   <significance> <clan> 
                         
E1RYP9     21    233 PF01904.12  DUF72             Family  11   211     230    165.2   1.5e-48   1 No_clan
   294    410 PF01124.12  MAPEG             Family   2   123     123     91.1   3.1e-26   1 No_clan
B3WUG8    235    250 PF04448.6   DUF551            Family   1    16      69     20.8   0.00039   0 No_clan
P76515     50    117 PF04448.6   DUF551            Family   3    69      69     18.9    0.0015   0 No_clan
B7NVE7     67    126 PF03387.8   Herpes_UL46       Family  49   111     444     12.8      0.02   0 No_clan
P76513      1    273 PF10065.3   DUF2303           Family   1   276     276    312.6   1.3e-93   1 No_clan
B7LJJ4     22     89 PF05614.5   DUF782            Family  15    81     104     11.2      0.26   0 No_clan
D6HVI9     43    156 PF06892.5   Phage_CP76        Family  25   136     162     11.5      0.11   0 No_clan
   130    170 PF11480.2   ImmE5             Family  40    80      83      9.4       0.7   0 No_clan
B3WIT4    117    212 PF10554.3   Phage_ASH         Family   1   107     108     87.8   4.5e-25   1 No_clan
   221    309 PF09669.4   Phage_pRha        Family   1    92      92    100.8   3.1e-29   1 No_clan
   335    359 PF10548.3   P22_AR_C          Domain  28    52      74     13.3     0.044   0 No_clan
C8U2N0     10     56 PF12802.1   MarR_2            Family  13    60      61     11.3      0.16   0 CL0123
    98    149 PF06069.5   PerC              Family   5    56      90     35.4   6.7e-09   1 No_clan
C8TVZ6      1     65 PF01726.10  LexA_DNA_bind     Domain   1    65      65     68.7   1.9e-19   1 CL0123
C8TVZ3    129    326 PF06147.5   DUF968            Family   2   200     200    261.2   5.5e-78   1 No_clan
   268    308 PF07102.6   DUF1364           Family  32    74      94     12.8     0.066   0 No_clan
B3HVA3    258    301 PF08343.4   RNR_N             Family  29    72      82      9.7      0.59   0 No_clan
B7NVG6     14     61 PF12802.1   MarR_2            Family   2    50      61     12.9     0.053   0 CL0123
B7MPX6     11     63 PF08410.4   DUF1737           Family   1    53      54     67.7   4.3e-19   1 No_clan
   170    283 PF03629.12  DUF303            Family   2   114     115     29.7   3.4e-07   1 No_clan
D3H2S6     30     97 PF04971.6   Lysis_S           Family   1    68      68    157.4   4.3e-47   1 No_clan
E6AD14     21    132 PF07041.5   DUF1327           Family   1   112     113    213.9   2.5e-64   1 No_clan
B7LES2      1    112 PF07041.5   DUF1327           Family   1   112     113    202.9   6.6e-61   1 No_clan
D6IMM0      1     63 PF06749.6   DUF1218           Family   4    60      97     13.9     0.044   0 No_clan
E8J0W2     14     91 PF12421.2   DUF3672           Family  60   135     136     41.2   1.3e-10   1 No_clan
C6V226     15     81 PF06183.7   DinI              Family   1    65      65     98.0   1.8e-28   1 No_clan
    22     75 PF08923.4   MAPKK1_Int        Domain   2    53     119     12.3     0.079   0 CL0431