Query psy10196
Match_columns 354
No_of_seqs 244 out of 1628
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 20:16:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.8 1.1E-18 2.4E-23 170.5 8.0 67 67-133 168-234 (309)
2 KOG0489|consensus 99.8 2.2E-19 4.7E-24 171.5 2.4 67 69-135 157-223 (261)
3 KOG0494|consensus 99.7 1.8E-18 3.8E-23 163.8 7.3 105 70-178 140-249 (332)
4 KOG0842|consensus 99.7 1.7E-17 3.7E-22 161.4 11.0 72 66-137 148-219 (307)
5 KOG0484|consensus 99.7 7.2E-19 1.6E-23 146.8 0.7 65 66-130 12-76 (125)
6 KOG0487|consensus 99.7 1E-17 2.2E-22 163.0 3.7 66 66-131 230-295 (308)
7 KOG0850|consensus 99.7 2.5E-17 5.4E-22 153.7 5.8 66 66-131 117-182 (245)
8 KOG0844|consensus 99.7 2.1E-16 4.5E-21 152.6 9.8 94 67-160 177-270 (408)
9 KOG0485|consensus 99.7 7.3E-17 1.6E-21 149.7 6.2 69 67-135 100-168 (268)
10 KOG0843|consensus 99.7 3.8E-17 8.2E-22 147.8 3.7 64 69-132 100-163 (197)
11 KOG2251|consensus 99.6 5.1E-16 1.1E-20 144.3 8.2 68 66-133 32-99 (228)
12 KOG0492|consensus 99.6 1.1E-15 2.3E-20 141.2 4.2 65 67-131 140-204 (246)
13 KOG0493|consensus 99.6 1.9E-15 4E-20 143.6 5.7 69 72-140 247-315 (342)
14 KOG0848|consensus 99.5 1.2E-15 2.7E-20 145.1 0.6 66 68-133 196-261 (317)
15 PF00046 Homeobox: Homeobox do 99.5 3.3E-15 7.2E-20 110.2 2.7 57 72-128 1-57 (57)
16 KOG0491|consensus 99.5 3.4E-15 7.3E-20 133.7 1.6 67 70-136 99-165 (194)
17 KOG0486|consensus 99.5 1.7E-14 3.7E-19 139.9 5.9 63 69-131 110-172 (351)
18 TIGR01565 homeo_ZF_HD homeobox 99.5 3.4E-14 7.3E-19 107.7 5.2 53 71-123 1-57 (58)
19 KOG3802|consensus 99.4 2.5E-14 5.5E-19 142.5 1.5 124 1-131 231-354 (398)
20 smart00389 HOX Homeodomain. DN 99.4 2.6E-13 5.6E-18 99.1 4.2 56 72-127 1-56 (56)
21 cd00086 homeodomain Homeodomai 99.4 5E-13 1.1E-17 98.0 4.0 57 73-129 2-58 (59)
22 KOG0483|consensus 99.3 6.6E-13 1.4E-17 122.8 2.9 55 77-131 56-110 (198)
23 KOG4577|consensus 99.3 7.6E-13 1.6E-17 127.4 3.3 66 70-135 166-231 (383)
24 COG5576 Homeodomain-containing 99.3 1.6E-12 3.4E-17 116.3 4.7 63 70-132 50-112 (156)
25 KOG0490|consensus 99.3 1.5E-12 3.3E-17 119.2 2.9 64 68-131 57-120 (235)
26 KOG0847|consensus 99.2 3E-12 6.4E-17 119.5 1.7 63 69-131 165-227 (288)
27 KOG0849|consensus 99.1 8.7E-11 1.9E-15 117.1 4.3 68 65-132 170-237 (354)
28 KOG0490|consensus 98.6 2.5E-08 5.5E-13 91.3 4.5 122 10-131 86-213 (235)
29 KOG1168|consensus 98.5 4.9E-08 1.1E-12 94.7 1.7 62 70-131 308-369 (385)
30 KOG0774|consensus 98.2 1.5E-06 3.3E-11 83.4 5.5 67 71-137 188-257 (334)
31 KOG0775|consensus 98.2 5E-06 1.1E-10 80.3 7.3 52 80-131 185-236 (304)
32 KOG1146|consensus 97.8 5E-05 1.1E-09 85.6 7.8 65 67-131 899-963 (1406)
33 PF05920 Homeobox_KN: Homeobox 97.8 6E-06 1.3E-10 58.2 0.2 34 92-125 7-40 (40)
34 KOG2252|consensus 97.7 3.9E-05 8.5E-10 80.0 4.9 58 69-126 418-475 (558)
35 PF11569 Homez: Homeodomain le 94.5 0.018 3.9E-07 43.7 1.3 42 83-124 10-51 (56)
36 KOG0773|consensus 94.3 0.041 9E-07 54.4 3.7 59 71-129 239-300 (342)
37 KOG3623|consensus 89.5 0.23 5.1E-06 54.3 2.6 46 83-128 568-613 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 88.1 0.56 1.2E-05 34.7 3.1 47 72-123 1-47 (53)
39 KOG1146|consensus 63.7 6.1 0.00013 46.2 3.3 66 69-134 442-507 (1406)
40 PF02178 AT_hook: AT hook moti 52.6 5.8 0.00013 21.8 0.4 10 293-302 2-11 (13)
41 KOG3623|consensus 48.5 18 0.0004 40.2 3.7 99 14-129 586-684 (1007)
42 smart00384 AT_hook DNA binding 46.8 11 0.00023 24.6 1.0 13 293-305 2-14 (26)
43 PF04967 HTH_10: HTH DNA bindi 40.4 29 0.00063 26.0 2.6 38 78-115 1-40 (53)
44 PF01527 HTH_Tnp_1: Transposas 33.8 35 0.00076 25.7 2.3 44 73-121 2-46 (76)
45 cd06171 Sigma70_r4 Sigma70, re 32.5 35 0.00077 22.7 2.0 42 78-124 11-52 (55)
46 PF08281 Sigma70_r4_2: Sigma-7 31.5 33 0.00072 24.4 1.7 42 78-124 11-52 (54)
47 PF04545 Sigma70_r4: Sigma-70, 30.8 30 0.00065 24.4 1.4 40 77-121 4-43 (50)
48 cd00569 HTH_Hin_like Helix-tur 30.3 75 0.0016 18.7 3.1 36 78-118 6-41 (42)
49 TIGR03879 near_KaiC_dom probab 24.3 20 0.00044 28.6 -0.5 35 87-121 21-55 (73)
50 PF10668 Phage_terminase: Phag 23.0 29 0.00064 26.7 0.1 20 100-119 24-43 (60)
51 KOG0843|consensus 22.8 33 0.00071 32.2 0.4 37 6-43 125-161 (197)
52 PRK03975 tfx putative transcri 22.7 55 0.0012 29.2 1.8 49 76-130 5-53 (141)
53 PRK12526 RNA polymerase sigma 20.1 66 0.0014 29.2 1.9 35 97-131 168-202 (206)
No 1
>KOG0488|consensus
Probab=99.76 E-value=1.1e-18 Score=170.52 Aligned_cols=67 Identities=34% Similarity=0.393 Sum_probs=63.8
Q ss_pred ccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccC
Q psy10196 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATF 133 (354)
Q Consensus 67 ~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~ 133 (354)
..||+|+.||.||..||.+||+.|++++|++..+|++||+.|||+..|||+||||||+|||++....
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 4588899999999999999999999999999999999999999999999999999999999998763
No 2
>KOG0489|consensus
Probab=99.75 E-value=2.2e-19 Score=171.52 Aligned_cols=67 Identities=30% Similarity=0.368 Sum_probs=62.5
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCC
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGP 135 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~ 135 (354)
.+.||.||.||..||.+||+.|..|+|+++..|.+||..|.|+|+|||||||||||||||.......
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 4578999999999999999999999999999999999999999999999999999999988765544
No 3
>KOG0494|consensus
Probab=99.75 E-value=1.8e-18 Score=163.81 Aligned_cols=105 Identities=34% Similarity=0.443 Sum_probs=85.3
Q ss_pred CCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCCCCCcccchhcccc
Q psy10196 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEAESTSQHFLFLLS 149 (354)
Q Consensus 70 K~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~~~~~s~~~~~~~~ 149 (354)
|+|+-||.||..|+.+||++|+..+||++..|+.||.++.|+|.+|||||||||+||+|....++.. ..++.+.++
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s----T~maeygly 215 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS----TIMAEYGLY 215 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc----hhhhhhccc
Confidence 3444499999999999999999999999999999999999999999999999999999988877763 345567778
Q ss_pred ccccCCCCCCCCCCCCC-----CCCCCCCCCChh
Q psy10196 150 SRILDRFLPPPGVEPGS-----LDCQASVFTAPA 178 (354)
Q Consensus 150 ~~~l~~~~Ppp~~~pps-----~sc~~s~f~a~~ 178 (354)
+.++.+.+|.|.....+ .+|.+|.|....
T Consensus 216 Gamvrhslplp~ti~ksa~~~p~s~aPwllGm~k 249 (332)
T KOG0494|consen 216 GAMVRHSLPLPDTILKSAEDGPNSVAPWLLGMHK 249 (332)
T ss_pred chhhcccCCchhhhhhCcccCccccCchhccccc
Confidence 88888888777553321 456666555543
No 4
>KOG0842|consensus
Probab=99.73 E-value=1.7e-17 Score=161.39 Aligned_cols=72 Identities=28% Similarity=0.343 Sum_probs=64.9
Q ss_pred CccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCCC
Q psy10196 66 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEA 137 (354)
Q Consensus 66 ~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~~ 137 (354)
...+++||.|..||..|+.+||+.|..++|++..+|+.||..|+|+++||||||||||.|.||+........
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 346678888999999999999999999999999999999999999999999999999999998876555433
No 5
>KOG0484|consensus
Probab=99.72 E-value=7.2e-19 Score=146.81 Aligned_cols=65 Identities=48% Similarity=0.737 Sum_probs=61.3
Q ss_pred CccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccccc
Q psy10196 66 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAI 130 (354)
Q Consensus 66 ~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~ 130 (354)
..++|+||-||.||..||.+||+.|...+||++..|++||.++.|+|.+|||||||||+|.+|+.
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 34788999999999999999999999999999999999999999999999999999999987764
No 6
>KOG0487|consensus
Probab=99.69 E-value=1e-17 Score=163.05 Aligned_cols=66 Identities=24% Similarity=0.265 Sum_probs=61.9
Q ss_pred CccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 66 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 66 ~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
...++.||+|..+|+.|+.+||+.|..|.|++...|.+|++.|+|+++||||||||||||.||...
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 345778889999999999999999999999999999999999999999999999999999998774
No 7
>KOG0850|consensus
Probab=99.68 E-value=2.5e-17 Score=153.72 Aligned_cols=66 Identities=26% Similarity=0.357 Sum_probs=62.6
Q ss_pred CccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 66 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 66 ~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
...||.|+.||.|+..||..|.+.|++++|+...+|.+||+.|||+..||||||||||.|.||...
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 457888899999999999999999999999999999999999999999999999999999888776
No 8
>KOG0844|consensus
Probab=99.67 E-value=2.1e-16 Score=152.65 Aligned_cols=94 Identities=23% Similarity=0.323 Sum_probs=79.8
Q ss_pred ccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCCCCCcccchhc
Q psy10196 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEAESTSQHFLF 146 (354)
Q Consensus 67 ~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~~~~~s~~~~~ 146 (354)
.....||.||.||.+||..||+.|-+..|.++..|.+||..|||+|..|||||||||||.|+|...+.--....+..+.+
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhpaDPafyty 256 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHPADPAFYTY 256 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCCCChHHHHH
Confidence 34568999999999999999999999999999999999999999999999999999999999987666555566677777
Q ss_pred cccccccCCCCCCC
Q psy10196 147 LLSSRILDRFLPPP 160 (354)
Q Consensus 147 ~~~~~~l~~~~Ppp 160 (354)
+++-.+-...+|.|
T Consensus 257 mm~hAAatgglPYP 270 (408)
T KOG0844|consen 257 MMNHAAATGGLPYP 270 (408)
T ss_pred HHHHHHhcCCCCCC
Confidence 77655555555444
No 9
>KOG0485|consensus
Probab=99.66 E-value=7.3e-17 Score=149.72 Aligned_cols=69 Identities=23% Similarity=0.267 Sum_probs=63.5
Q ss_pred ccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCC
Q psy10196 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGP 135 (354)
Q Consensus 67 ~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~ 135 (354)
...++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|.||||||||||.|||++....-.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 345778899999999999999999999999999999999999999999999999999999999765433
No 10
>KOG0843|consensus
Probab=99.66 E-value=3.8e-17 Score=147.80 Aligned_cols=64 Identities=30% Similarity=0.316 Sum_probs=60.6
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccccccc
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIAT 132 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~ 132 (354)
.+.||.||.||.+||..||.+|+.++|....+|++||+.|+|++.||||||||||.|.||....
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 4889999999999999999999999999999999999999999999999999999998877654
No 11
>KOG2251|consensus
Probab=99.63 E-value=5.1e-16 Score=144.26 Aligned_cols=68 Identities=46% Similarity=0.604 Sum_probs=63.8
Q ss_pred CccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccC
Q psy10196 66 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATF 133 (354)
Q Consensus 66 ~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~ 133 (354)
...+|.||.||.||..|+.+||..|.+.+||++..|++||.+|+|.+.+|||||.|||+|+|++....
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 35788999999999999999999999999999999999999999999999999999999998877643
No 12
>KOG0492|consensus
Probab=99.57 E-value=1.1e-15 Score=141.18 Aligned_cols=65 Identities=29% Similarity=0.397 Sum_probs=59.8
Q ss_pred ccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 67 ~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
..+-.|+.||.||.+||..||+.|+..+|+++.+|.+++..|.|++.||||||||||+|.||-..
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 34557788999999999999999999999999999999999999999999999999999877543
No 13
>KOG0493|consensus
Probab=99.57 E-value=1.9e-15 Score=143.56 Aligned_cols=69 Identities=25% Similarity=0.322 Sum_probs=62.8
Q ss_pred CCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCCCCCc
Q psy10196 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEAEST 140 (354)
Q Consensus 72 RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~~~~~ 140 (354)
||.||.||.+||..|+..|+.|+|++...|.+||.+|+|.|.||||||||+|+|.||........+...
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~l 315 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHL 315 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhh
Confidence 478999999999999999999999999999999999999999999999999999999887665544433
No 14
>KOG0848|consensus
Probab=99.53 E-value=1.2e-15 Score=145.06 Aligned_cols=66 Identities=23% Similarity=0.269 Sum_probs=59.5
Q ss_pred cCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccC
Q psy10196 68 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATF 133 (354)
Q Consensus 68 ~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~ 133 (354)
-|.+-+.|.+||..|..+||++|..++|.++..+.+||..|+|+||||||||||||+|.+|...+.
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 344557799999999999999999999999999999999999999999999999999987765544
No 15
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.53 E-value=3.3e-15 Score=110.19 Aligned_cols=57 Identities=35% Similarity=0.416 Sum_probs=54.6
Q ss_pred CCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccc
Q psy10196 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGV 128 (354)
Q Consensus 72 RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk 128 (354)
||.|+.||.+|+..|+..|..++||+..+++.||..|||+..+|++||||||.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999999999999999999999999999999999999999999999874
No 16
>KOG0491|consensus
Probab=99.51 E-value=3.4e-15 Score=133.66 Aligned_cols=67 Identities=28% Similarity=0.392 Sum_probs=62.3
Q ss_pred CCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCC
Q psy10196 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPE 136 (354)
Q Consensus 70 K~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~ 136 (354)
++|+.||+|+..|+..||+.|+.++|++..+|.+||..|+|++.|||.||||||||.||+.....+.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 4567899999999999999999999999999999999999999999999999999999988766653
No 17
>KOG0486|consensus
Probab=99.50 E-value=1.7e-14 Score=139.86 Aligned_cols=63 Identities=40% Similarity=0.548 Sum_probs=60.1
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
+|+||.||.||.+||++||..|++++||++..|+++|..++|+|.+|+|||.|||+||+|...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 489999999999999999999999999999999999999999999999999999999988654
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.49 E-value=3.4e-14 Score=107.65 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=50.9
Q ss_pred CCCCCCccCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHcCCCCcccccccchhh
Q psy10196 71 HRRNRTTFTTYQLHELERAFEKSHY----PDVYSREELAMKVNLPEVRVQFTALAAA 123 (354)
Q Consensus 71 ~RR~RT~fT~~Ql~~LE~~F~~~~y----Ps~~~R~~LA~~LgLse~qVqVWFQNRR 123 (354)
+||.||.||.+|+..||..|..+.| |+..+|++||..|||++++|||||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999964
No 19
>KOG3802|consensus
Probab=99.43 E-value=2.5e-14 Score=142.47 Aligned_cols=124 Identities=14% Similarity=0.026 Sum_probs=91.4
Q ss_pred CCcccccccCCchhhhhhhhcCCCCCchhhhcccCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCccCCCCCCCCccCH
Q psy10196 1 MDIGLILMSQLSQRASIAENSGNSSSDEQAVSDLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTT 80 (354)
Q Consensus 1 ~~~~~~~~S~~Ssr~~lae~~g~~ss~eq~~s~~k~~~s~~~~s~se~~~~~~s~g~s~s~~~~~~~~kK~RR~RT~fT~ 80 (354)
++||.++.+.+|++.....+.-..+++.++....-..++-.+....+.+...++... - ....|+||+||.|..
T Consensus 231 lALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~---i----~a~~RkRKKRTSie~ 303 (398)
T KOG3802|consen 231 LALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEK---I----GAQSRKRKKRTSIEV 303 (398)
T ss_pred HHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHH---h----hccccccccccceeH
Confidence 367899999999999999988888888876443222222111111011111111100 0 011268888999999
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 81 YQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 81 ~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
.....||+.|.+|+.|+..+...||.+|+|...+|+|||+|||.|.||-..
T Consensus 304 ~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 304 NVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 999999999999999999999999999999999999999999999988665
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.39 E-value=2.6e-13 Score=99.10 Aligned_cols=56 Identities=43% Similarity=0.562 Sum_probs=52.5
Q ss_pred CCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccc
Q psy10196 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVG 127 (354)
Q Consensus 72 RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~K 127 (354)
++.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|||.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999998754
No 21
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.36 E-value=5e-13 Score=98.05 Aligned_cols=57 Identities=40% Similarity=0.534 Sum_probs=53.6
Q ss_pred CCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccc
Q psy10196 73 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVA 129 (354)
Q Consensus 73 R~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~ 129 (354)
+.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567889999999999999999999999999999999999999999999999987653
No 22
>KOG0483|consensus
Probab=99.32 E-value=6.6e-13 Score=122.75 Aligned_cols=55 Identities=20% Similarity=0.170 Sum_probs=52.2
Q ss_pred ccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 77 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 77 ~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
+||.+|+..||..|+.+.++....+..||..|||.++||.|||||||+|||.+..
T Consensus 56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 4899999999999999999999999999999999999999999999999987643
No 23
>KOG4577|consensus
Probab=99.31 E-value=7.6e-13 Score=127.41 Aligned_cols=66 Identities=27% Similarity=0.249 Sum_probs=60.7
Q ss_pred CCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCC
Q psy10196 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGP 135 (354)
Q Consensus 70 K~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~ 135 (354)
..||.||+||..||+.|+.+|+..+.|.+..|++|+.++||..++|||||||||+|.|+-....|.
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 468899999999999999999999999999999999999999999999999999998776655544
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.31 E-value=1.6e-12 Score=116.28 Aligned_cols=63 Identities=27% Similarity=0.310 Sum_probs=56.4
Q ss_pred CCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccccccc
Q psy10196 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIAT 132 (354)
Q Consensus 70 K~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~ 132 (354)
..+++|++.|..|+.+|+..|..++||+...|.+|+..++|+++-|||||||||++.|+....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345556667999999999999999999999999999999999999999999999988776554
No 25
>KOG0490|consensus
Probab=99.28 E-value=1.5e-12 Score=119.16 Aligned_cols=64 Identities=39% Similarity=0.359 Sum_probs=60.9
Q ss_pred cCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 68 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 68 ~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
..++||.||.|+..|+.+||++|+..+||+...|+.||..+++++..|+|||||||+||+++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 5678999999999999999999999999999999999999999999999999999999987763
No 26
>KOG0847|consensus
Probab=99.22 E-value=3e-12 Score=119.48 Aligned_cols=63 Identities=29% Similarity=0.364 Sum_probs=58.2
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
.+++-.|.+|+..|++.||..|+..+|+-..+|.+||..+|+++.||+|||||||.||+|+..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 445566889999999999999999999999999999999999999999999999999988754
No 27
>KOG0849|consensus
Probab=99.07 E-value=8.7e-11 Score=117.11 Aligned_cols=68 Identities=35% Similarity=0.473 Sum_probs=63.3
Q ss_pred CCccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccccccc
Q psy10196 65 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIAT 132 (354)
Q Consensus 65 ~~~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~ 132 (354)
....++.||.||.|+..|+..||..|+.++||++..|++||.+++|++.+|+|||+|||+|++|+...
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 34577888899999999999999999999999999999999999999999999999999999988753
No 28
>KOG0490|consensus
Probab=98.64 E-value=2.5e-08 Score=91.30 Aligned_cols=122 Identities=25% Similarity=0.183 Sum_probs=91.1
Q ss_pred CCchhhhhhhhcCCCCCchhhhcccCCCCCCCCCC----CccCCCCCCCC--CCCCCCCCCCCccCCCCCCCCccCHHHH
Q psy10196 10 QLSQRASIAENSGNSSSDEQAVSDLRRKPSDTVDS----DLEIDDDKCSR--GGSLSPSLSPVDKKKHRRNRTTFTTYQL 83 (354)
Q Consensus 10 ~~Ssr~~lae~~g~~ss~eq~~s~~k~~~s~~~~s----~se~~~~~~s~--g~s~s~~~~~~~~kK~RR~RT~fT~~Ql 83 (354)
++..++.++.-+...+..+++||++.+........ ........... ..............+.++.|+.++..|+
T Consensus 86 d~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (235)
T KOG0490|consen 86 CFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTTFTENQL 165 (235)
T ss_pred ccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCCccccCCCccccccchh
Confidence 45667888999999999999999999887654321 10100000000 0011111223445678889999999999
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 84 HELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 84 ~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
..|+..|....+|+...++.|+..+|+++..|+|||||+|++.++...
T Consensus 166 ~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 166 EVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred HhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999876554
No 29
>KOG1168|consensus
Probab=98.47 E-value=4.9e-08 Score=94.66 Aligned_cols=62 Identities=18% Similarity=0.141 Sum_probs=57.6
Q ss_pred CCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 70 K~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
.+||+||.+-.-.-..||..|..++.|+......+|.+|+|...+|+|||+|.|.|.||...
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 36788999999999999999999999999999999999999999999999999999988443
No 30
>KOG0774|consensus
Probab=98.23 E-value=1.5e-06 Score=83.42 Aligned_cols=67 Identities=25% Similarity=0.279 Sum_probs=60.1
Q ss_pred CCCCCCccCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCCCCC
Q psy10196 71 HRRNRTTFTTYQLHELERAFEK---SHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEA 137 (354)
Q Consensus 71 ~RR~RT~fT~~Ql~~LE~~F~~---~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~~~~ 137 (354)
.||+|..|++.-..+|...|.. ++||+...+++||++.|++..||-.||.|+|.+.||........+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~ 257 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEA 257 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhh
Confidence 4677788999999999999965 889999999999999999999999999999999999887665544
No 31
>KOG0775|consensus
Probab=98.15 E-value=5e-06 Score=80.32 Aligned_cols=52 Identities=21% Similarity=0.121 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 80 TYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 80 ~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
..-...|...|..++||+..++.+||+.+||+..||-.||.|||.|.|-...
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 3345689999999999999999999999999999999999999999874443
No 32
>KOG1146|consensus
Probab=97.78 E-value=5e-05 Score=85.58 Aligned_cols=65 Identities=23% Similarity=0.220 Sum_probs=59.6
Q ss_pred ccCCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 67 ~~kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
+.-.+|++||.++..||..|...|....|+...+.+.|...+++..++|+|||||.|.|.++...
T Consensus 899 ~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 899 DGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34457788999999999999999999999999999999999999999999999999999877655
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.76 E-value=6e-06 Score=58.21 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=28.8
Q ss_pred hcCCCCHHHHHHHHHHcCCCCcccccccchhhhc
Q psy10196 92 KSHYPDVYSREELAMKVNLPEVRVQFTALAAALR 125 (354)
Q Consensus 92 ~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK 125 (354)
.++||+..++.+||..+||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999998864
No 34
>KOG2252|consensus
Probab=97.69 E-value=3.9e-05 Score=80.02 Aligned_cols=58 Identities=22% Similarity=0.269 Sum_probs=53.8
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcc
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRV 126 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~ 126 (354)
-..||.|.+||..|...|...|+.+++|+....+.|+.+|||..+.|..||-|.|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3466779999999999999999999999999999999999999999999999987764
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.46 E-value=0.018 Score=43.69 Aligned_cols=42 Identities=17% Similarity=0.053 Sum_probs=31.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhh
Q psy10196 83 LHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAAL 124 (354)
Q Consensus 83 l~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRa 124 (354)
++.|+..|...+++....-..|..+.+|+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999966543
No 36
>KOG0773|consensus
Probab=94.26 E-value=0.041 Score=54.35 Aligned_cols=59 Identities=20% Similarity=0.173 Sum_probs=46.5
Q ss_pred CCCCCCccCHHHHHHHHHH-HH--hcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccc
Q psy10196 71 HRRNRTTFTTYQLHELERA-FE--KSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVA 129 (354)
Q Consensus 71 ~RR~RT~fT~~Ql~~LE~~-F~--~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~ 129 (354)
+.|.+..|......+|+.- |+ ..+||+..++..||.++||+..||..||-|.|-|..+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 3444556788878877744 33 25799999999999999999999999999999876543
No 37
>KOG3623|consensus
Probab=89.49 E-value=0.23 Score=54.29 Aligned_cols=46 Identities=15% Similarity=0.041 Sum_probs=42.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccc
Q psy10196 83 LHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGV 128 (354)
Q Consensus 83 l~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk 128 (354)
+..|+..|..|..|...+-..+|...||+.+.|++||++++++...
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 7788999999999999999999999999999999999999987644
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=88.11 E-value=0.56 Score=34.68 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=35.6
Q ss_pred CCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhh
Q psy10196 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAA 123 (354)
Q Consensus 72 RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRR 123 (354)
||+|..+|-++-..+-..++... ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899999888888887776 577899999999999999998853
No 39
>KOG1146|consensus
Probab=63.74 E-value=6.1 Score=46.16 Aligned_cols=66 Identities=12% Similarity=0.018 Sum_probs=55.3
Q ss_pred CCCCCCCCccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhccccccccCC
Q psy10196 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFG 134 (354)
Q Consensus 69 kK~RR~RT~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~~~~ 134 (354)
...+-.|++++.-|+..|...|....||.-.++..++..|++..+.+..|||+++.++.+.....+
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~a 507 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLA 507 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccccc
Confidence 334456788899999999999999999999999999999999999999999998877766544333
No 40
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=52.58 E-value=5.8 Score=21.83 Aligned_cols=10 Identities=70% Similarity=1.125 Sum_probs=3.6
Q ss_pred hhcCCCCCCC
Q psy10196 293 RKRGRPPKKH 302 (354)
Q Consensus 293 ~~~~~~~~~~ 302 (354)
|+||||+|..
T Consensus 2 r~RGRP~k~~ 11 (13)
T PF02178_consen 2 RKRGRPRKNA 11 (13)
T ss_dssp --SS--TT--
T ss_pred CcCCCCcccc
Confidence 6899998864
No 41
>KOG3623|consensus
Probab=48.51 E-value=18 Score=40.25 Aligned_cols=99 Identities=12% Similarity=0.059 Sum_probs=64.7
Q ss_pred hhhhhhhcCCCCCchhhhcccCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCccCCCCCCCCccCHHHHHHHHHHHHhc
Q psy10196 14 RASIAENSGNSSSDEQAVSDLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKS 93 (354)
Q Consensus 14 r~~lae~~g~~ss~eq~~s~~k~~~s~~~~s~se~~~~~~s~g~s~s~~~~~~~~kK~RR~RT~fT~~Ql~~LE~~F~~~ 93 (354)
-..+++..|.+---.+.||...+...-+..... . . .....+-+.|+.+..++-..|..++..+
T Consensus 586 lskia~qvglp~~vvk~wfE~~~a~e~sv~rsp----s---------~----psg~~p~kv~sp~k~~dq~ql~~a~elq 648 (1007)
T KOG3623|consen 586 LSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSP----S---------Q----PSGERPVKVRSPIKEEDQQQLKQAYELQ 648 (1007)
T ss_pred HHHHHHHhcccHHHHHHHHHhhhhhhhhhccCc----c---------C----CCCCCCccccCCCCccchhhhHhhhhcc
Confidence 345677778887778889987766543331000 0 0 0111233445666667777788888877
Q ss_pred CCCCHHHHHHHHHHcCCCCcccccccchhhhccccc
Q psy10196 94 HYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVA 129 (354)
Q Consensus 94 ~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~ 129 (354)
.-++..+--..+.+|...+.+|.|||++|+..-+.-
T Consensus 649 ~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 649 ASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred cCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 777666655666668888899999999999876554
No 42
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=46.78 E-value=11 Score=24.62 Aligned_cols=13 Identities=54% Similarity=0.808 Sum_probs=9.9
Q ss_pred hhcCCCCCCCCCC
Q psy10196 293 RKRGRPPKKHPPE 305 (354)
Q Consensus 293 ~~~~~~~~~~~~~ 305 (354)
|+||||+|.....
T Consensus 2 RkRGRPrK~~~~~ 14 (26)
T smart00384 2 RKRGRPRKAPKDX 14 (26)
T ss_pred CCCCCCCCCCCcc
Confidence 6899999876543
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=40.38 E-value=29 Score=25.96 Aligned_cols=38 Identities=29% Similarity=0.381 Sum_probs=30.8
Q ss_pred cCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHcCCCCccc
Q psy10196 78 FTTYQLHELERAFEKSHY--PDVYSREELAMKVNLPEVRV 115 (354)
Q Consensus 78 fT~~Ql~~LE~~F~~~~y--Ps~~~R~~LA~~LgLse~qV 115 (354)
+|..|...|..++...-| |-...-.+||..||++..-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578999999999987654 65667789999999997653
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=33.76 E-value=35 Score=25.71 Aligned_cols=44 Identities=16% Similarity=0.124 Sum_probs=28.4
Q ss_pred CCCCccCHHHHHHHHHHH-HhcCCCCHHHHHHHHHHcCCCCcccccccch
Q psy10196 73 RNRTTFTTYQLHELERAF-EKSHYPDVYSREELAMKVNLPEVRVQFTALA 121 (354)
Q Consensus 73 R~RT~fT~~Ql~~LE~~F-~~~~yPs~~~R~~LA~~LgLse~qVqVWFQN 121 (354)
+.|..||.++...+-..+ ... ....++|..+||+..++..|-.-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHH
Confidence 345678998887776655 332 46778999999999999988643
No 45
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=32.55 E-value=35 Score=22.74 Aligned_cols=42 Identities=17% Similarity=0.084 Sum_probs=29.9
Q ss_pred cCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhh
Q psy10196 78 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAAL 124 (354)
Q Consensus 78 fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRa 124 (354)
++..+...+...|.. ...-.++|..+|++...|..|....+.
T Consensus 11 l~~~~~~~~~~~~~~-----~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGE-----GLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666666665532 235678899999999999998865443
No 46
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=31.49 E-value=33 Score=24.36 Aligned_cols=42 Identities=17% Similarity=0.031 Sum_probs=25.9
Q ss_pred cCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhh
Q psy10196 78 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAAL 124 (354)
Q Consensus 78 fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRa 124 (354)
++..+...+...| .....-.++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3444555554433 33456789999999999999999865443
No 47
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=30.79 E-value=30 Score=24.41 Aligned_cols=40 Identities=10% Similarity=0.134 Sum_probs=29.6
Q ss_pred ccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccch
Q psy10196 77 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALA 121 (354)
Q Consensus 77 ~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQN 121 (354)
.++..+...|...|... ..-.++|..+|++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHH
Confidence 36788888898888332 35678999999999998877543
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=30.31 E-value=75 Score=18.65 Aligned_cols=36 Identities=19% Similarity=0.206 Sum_probs=24.8
Q ss_pred cCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccc
Q psy10196 78 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFT 118 (354)
Q Consensus 78 fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVW 118 (354)
++..+...+...|... + ...++|..+|++...|..|
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 5666666666666532 2 4567899999988877766
No 49
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=24.35 E-value=20 Score=28.60 Aligned_cols=35 Identities=17% Similarity=0.037 Sum_probs=28.1
Q ss_pred HHHHHhcCCCCHHHHHHHHHHcCCCCcccccccch
Q psy10196 87 ERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALA 121 (354)
Q Consensus 87 E~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQN 121 (354)
+..|...+|.......++|..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45566666666667889999999999999999854
No 50
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=23.00 E-value=29 Score=26.71 Aligned_cols=20 Identities=15% Similarity=0.209 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCCCccccccc
Q psy10196 100 SREELAMKVNLPEVRVQFTA 119 (354)
Q Consensus 100 ~R~~LA~~LgLse~qVqVWF 119 (354)
.-.+||.+||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999994
No 51
>KOG0843|consensus
Probab=22.78 E-value=33 Score=32.22 Aligned_cols=37 Identities=14% Similarity=0.121 Sum_probs=31.6
Q ss_pred ccccCCchhhhhhhhcCCCCCchhhhcccCCCCCCCCC
Q psy10196 6 ILMSQLSQRASIAENSGNSSSDEQAVSDLRRKPSDTVD 43 (354)
Q Consensus 6 ~~~S~~Ssr~~lae~~g~~ss~eq~~s~~k~~~s~~~~ 43 (354)
.||. +++|..|+...+.++.+..+||+++|.+.....
T Consensus 125 ~Yvv-g~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 125 QYVV-GAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred Ceee-chHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 3454 899999999999999999999999998876553
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=22.67 E-value=55 Score=29.20 Aligned_cols=49 Identities=16% Similarity=0.101 Sum_probs=37.2
Q ss_pred CccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCCCcccccccchhhhcccccc
Q psy10196 76 TTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQFTALAAALRVGVAI 130 (354)
Q Consensus 76 T~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~ 130 (354)
..+|..|...|...+ .. ....++|..||++...|+.|-++.+.|-++..
T Consensus 5 ~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468899999987732 22 35678999999999999999987666655443
No 53
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=20.14 E-value=66 Score=29.18 Aligned_cols=35 Identities=26% Similarity=0.292 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHcCCCCcccccccchhhhccccccc
Q psy10196 97 DVYSREELAMKVNLPEVRVQFTALAAALRVGVAIA 131 (354)
Q Consensus 97 s~~~R~~LA~~LgLse~qVqVWFQNRRaK~Kk~~~ 131 (354)
....-.++|..+|+++..|+++...-|.+-++.+.
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 33467789999999999999888766665555443
Done!