IR1_IR2_AA_helix3_indicated_covary.stk

# STOCKHOLM 1.0
#=GF ID IR1_pure_aligned
#=GF AU hmmsearch (HMMER 3.3.2)

                                           IR1				IR2		helix3
Operon_4595/238-270         AAAAA.CTTGCAATTGGTCGC.AATTGCGACCAT  GATT-CGGGATTGGCTCGGATCAA  PRTWQRWEKG
Operon_321/238-270          AAACA.CTTGCAATCGGTCGC.AATCGCGACCAT  GGTT-CGGGAGTGGCTCGAATCGA  PRTWQRWEKG
Operon_4795/238-270         AAACA.CTTGCAATCGGTCGC.AAATGCGACCAT  GGTT-CGGCAAGGGGTCGAGCCTA  PRTWQRWEKG
Operon_2310/238-270         AAAAA.CTTGCAAATGGTCGC.GATTGCGACCAT  GGTT-CGGCAATGGGTCGAACCAA  PRTWQRWEKG
Operon_379/238-269          -AACT.CTTGCATTTGGTCGC.GATTGCGACCAT  GGTT-CGGGGATGGCTCGAATCAA  TRTWQRWEKG
Operon_4635/240-271         -ATAA.CTTGCTTTTGTTCGC.GATTGCGAACAT  GCTTaCGCAA-TAGTGCGAAGCAA  NRTWQYWESG
Operon_67/243-273           -ATCT.CTTGC-ACTGTTCGC.AATTGCGAACTA  GATT-CGAGATTGGCTCGAATCAC  PRSWQYWESG
Operon_872/238-268          -AACA.CTTGCAAATGGTCGC.AACTGCGACCGT  GGTT-CGGGATTGGCTCGAATCGA  PRTWQRWEKG
Operon_4686/238-270         AAAGG.CTTGCTATTGGTCGC.ATTTACGACCAT  GGTT-CGGCACAGGGTCGAACCAG  PRTWQRWESG
Operon_3769/240-271         -AACA.CTTGCAATCGGTCGC.GAATCCGACCAT  GGTT-CGGAACTGGTTCGAATCAA  PRTWQRWEKG
Operon_365/242-271          -ATGC.CTTGC--TTGTTCGC.GATTGCGAACAT  GGTT-CGAGA-TGGCTCGAATCGC  ARSWQYWESG
Operon_4225/245-273         ----C.CTTGCTTTTGTTCGC.AAGTGCGAACAT  GATT-CGCGATTGGCGCGAATCGA  QRSVQYWEAG
Operon_2550/243-272         -ATAG.CTTGC--ATGTTCGC.AATCGCGAACAT  GATT-CGCGATTGGCGCGAGCCA-  RRTVEYWEAG
Operon_4680/241-271         -AACGcCTTGACATTGTTCGC.AAAAGCGAACA-  GATT-CGCGATTGGCGCGAATCGA  RRSVEYWEAG
Operon_3309/237-267         -ATTC.CTTGC-ATTGTTCGT.AATCGCGAACTA  GGGTuCGAGATCGGCTCGACCCGG  PRSWQYWEAG
Operon_3450/224-251         ----C.CTTGA-CTTGTTCGT.GATTGCGAACTA  GGCTaCGAAA-TCGTTCGAGTCGA  VRSWQYWETG
Operon_2244/241-264         -----.-TTGA-CTTGGTCGC.AAATGCGACCT-  GATT-CGGAACTGGTTCGAATCGA  VRTWQRWEQG
Operon_1810/322-344         -----.--TGG-CATGGTCGC.AATTGCGACCT-  GATT-CGGAACTGGTTCGAATCAA  VRTWQRWEQG
Operon_763/249-269          -----.----A-CATGGTCGC.GATCGCGACCT-  GGTT-CGGGA-TGGCTCGAACCAA  TRSWQRWEDG
^=covarying positions       dddddddddddddddd^ddddddddddddd^ddd  rrrrrrr^rrrrrrrrrrrrrrrr  AAAAA^AAAA
d=DNA (IR1)		   1----.----.----.----.----.----.-33  1----.----.----.----.-23  1----.---9
r=RNA (IR2)                                                                                ^  ^
A=AA (helix3)		                                                                  |  |
			                                                                R30  Q33