Query 022926
Match_columns 290
No_of_seqs 340 out of 1604
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:09:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802 Transcription factor O 100.0 1.1E-43 2.3E-48 337.4 8.1 151 6-168 204-354 (398)
2 KOG1168 Transcription factor A 99.9 4.4E-24 9.6E-29 195.8 3.9 152 7-169 216-370 (385)
3 KOG0489 Transcription factor z 99.7 1.8E-18 3.8E-23 160.1 5.2 67 101-172 157-223 (261)
4 KOG0484 Transcription factor P 99.7 2.5E-18 5.3E-23 136.9 4.8 69 99-172 13-81 (125)
5 PF00157 Pou: Pou domain - N-t 99.7 2.4E-18 5.2E-23 130.1 0.4 71 5-75 4-74 (75)
6 KOG2251 Homeobox transcription 99.7 6.9E-17 1.5E-21 144.0 9.6 68 98-170 32-99 (228)
7 KOG0488 Transcription factor B 99.7 3.1E-17 6.7E-22 155.0 5.5 66 99-169 168-233 (309)
8 KOG0842 Transcription factor t 99.7 9.2E-17 2E-21 150.6 7.1 69 99-172 149-217 (307)
9 KOG4577 Transcription factor L 99.7 7.1E-17 1.5E-21 148.6 6.1 114 51-171 109-230 (383)
10 KOG0843 Transcription factor E 99.7 1.2E-16 2.5E-21 138.5 6.5 64 102-170 101-164 (197)
11 KOG0850 Transcription factor D 99.6 3.6E-16 7.8E-21 140.1 7.0 67 98-169 117-183 (245)
12 KOG0487 Transcription factor A 99.6 1.7E-16 3.6E-21 148.9 4.7 65 101-170 233-297 (308)
13 KOG0492 Transcription factor M 99.6 4E-16 8.7E-21 137.9 5.5 66 99-169 140-205 (246)
14 KOG0485 Transcription factor N 99.6 4.6E-16 1E-20 138.3 3.4 66 100-170 101-166 (268)
15 PF00046 Homeobox: Homeobox do 99.6 8E-16 1.7E-20 109.9 3.8 57 104-165 1-57 (57)
16 KOG0494 Transcription factor C 99.6 1.5E-15 3.1E-20 138.2 4.0 67 102-173 140-206 (332)
17 TIGR01565 homeo_ZF_HD homeobox 99.5 4.6E-14 1E-18 102.3 5.7 52 104-160 2-57 (58)
18 KOG0844 Transcription factor E 99.5 1.3E-14 2.8E-19 134.6 2.9 65 100-169 178-242 (408)
19 KOG0848 Transcription factor C 99.5 1.4E-14 2.9E-19 132.4 2.3 61 105-170 201-261 (317)
20 smart00389 HOX Homeodomain. DN 99.4 7.3E-14 1.6E-18 98.8 3.7 55 105-164 2-56 (56)
21 cd00086 homeodomain Homeodomai 99.4 1.2E-13 2.6E-18 98.4 4.2 57 105-166 2-58 (59)
22 KOG0486 Transcription factor P 99.4 8.7E-14 1.9E-18 129.6 4.3 68 99-171 108-175 (351)
23 KOG0847 Transcription factor, 99.4 8.8E-14 1.9E-18 124.0 3.7 69 101-174 165-233 (288)
24 KOG0493 Transcription factor E 99.4 1.6E-13 3.5E-18 125.0 3.4 60 103-167 246-305 (342)
25 KOG0491 Transcription factor B 99.4 1.8E-13 3.9E-18 117.3 1.3 66 102-172 99-164 (194)
26 KOG0483 Transcription factor H 99.3 3.6E-13 7.8E-18 119.8 2.5 61 104-169 51-111 (198)
27 COG5576 Homeodomain-containing 99.3 1.6E-12 3.4E-17 111.9 5.5 63 102-169 50-112 (156)
28 KOG0490 Transcription factor, 99.2 1.8E-11 3.8E-16 109.4 6.0 104 56-168 17-120 (235)
29 smart00352 POU Found in Pit-Oc 99.2 9.8E-12 2.1E-16 94.2 2.8 71 5-75 4-74 (75)
30 KOG0849 Transcription factor P 99.0 2E-09 4.4E-14 103.8 8.5 66 99-169 172-237 (354)
31 KOG0775 Transcription factor S 98.7 5.8E-08 1.3E-12 89.6 8.1 48 112-164 185-232 (304)
32 KOG0774 Transcription factor P 98.6 1.1E-06 2.5E-11 80.7 12.9 61 103-167 188-250 (334)
33 PF05920 Homeobox_KN: Homeobox 98.2 5.3E-07 1.2E-11 60.7 0.6 33 126-162 8-40 (40)
34 KOG2252 CCAAT displacement pro 98.1 3.7E-06 8E-11 84.1 6.5 58 101-163 418-475 (558)
35 KOG0490 Transcription factor, 98.0 7.8E-06 1.7E-10 73.0 5.3 65 99-168 149-213 (235)
36 KOG1146 Homeobox protein [Gene 97.6 9.3E-05 2E-09 80.5 5.7 63 102-169 902-964 (1406)
37 PF11569 Homez: Homeodomain le 95.4 0.0053 1.1E-07 44.3 0.5 42 115-161 10-51 (56)
38 KOG3623 Homeobox transcription 95.3 0.049 1.1E-06 57.0 7.4 52 115-171 568-619 (1007)
39 KOG0773 Transcription factor M 94.9 0.023 5E-07 54.4 3.4 62 103-168 239-302 (342)
40 PF08880 QLQ: QLQ; InterPro: 89.4 0.48 1E-05 31.3 3.1 22 42-63 2-23 (37)
41 PF04218 CENP-B_N: CENP-B N-te 84.9 0.85 1.8E-05 32.2 2.5 47 104-160 1-47 (53)
42 PF04967 HTH_10: HTH DNA bindi 63.1 7 0.00015 27.8 2.4 38 110-153 1-41 (53)
43 KOG3623 Homeobox transcription 57.6 43 0.00093 36.0 7.8 127 21-169 559-687 (1007)
44 PF04545 Sigma70_r4: Sigma-70, 52.9 14 0.00031 24.9 2.5 45 109-163 4-48 (50)
45 cd06171 Sigma70_r4 Sigma70, re 51.1 9.2 0.0002 24.8 1.3 44 109-162 10-53 (55)
46 PF01527 HTH_Tnp_1: Transposas 48.6 12 0.00026 27.2 1.7 44 105-157 2-45 (76)
47 PF08281 Sigma70_r4_2: Sigma-7 47.1 13 0.00029 25.3 1.7 42 110-161 11-52 (54)
48 COG3413 Predicted DNA binding 45.1 18 0.00038 32.3 2.5 38 109-152 155-195 (215)
49 KOG3755 SATB1 matrix attachmen 43.5 5.8 0.00013 41.2 -0.9 49 119-168 708-759 (769)
50 PF00424 REV: REV protein (ant 42.5 25 0.00054 27.9 2.7 38 115-171 14-51 (91)
51 KOG1146 Homeobox protein [Gene 39.8 11 0.00023 42.6 0.3 65 103-172 444-508 (1406)
52 cd00569 HTH_Hin_like Helix-tur 38.0 50 0.0011 18.7 3.1 37 110-156 6-42 (42)
53 PF11336 DUF3138: Protein of u 34.9 2.7E+02 0.0058 28.4 9.0 83 33-124 12-94 (514)
54 PRK09646 RNA polymerase sigma 34.4 39 0.00084 29.1 2.9 47 110-166 143-189 (194)
55 PRK09652 RNA polymerase sigma 33.2 38 0.00082 28.1 2.6 48 109-166 128-175 (182)
56 PRK03975 tfx putative transcri 33.1 43 0.00094 28.5 2.9 51 107-168 4-54 (141)
57 PF10668 Phage_terminase: Phag 32.8 15 0.00033 26.8 0.1 26 134-165 25-50 (60)
58 PRK06759 RNA polymerase factor 32.1 32 0.00069 28.1 2.0 46 109-164 106-151 (154)
59 TIGR02937 sigma70-ECF RNA poly 30.2 42 0.00092 26.3 2.3 47 109-165 110-156 (158)
60 PF00196 GerE: Bacterial regul 29.3 34 0.00073 23.8 1.4 44 109-163 3-46 (58)
61 PRK12526 RNA polymerase sigma 27.7 52 0.0011 28.8 2.6 31 133-167 171-201 (206)
62 PRK11924 RNA polymerase sigma 26.2 57 0.0012 26.9 2.5 30 133-166 143-172 (179)
63 PRK12519 RNA polymerase sigma 26.0 46 0.00099 28.5 2.0 30 132-165 158-187 (194)
64 PRK09642 RNA polymerase sigma 25.8 69 0.0015 26.4 2.9 48 110-167 107-154 (160)
65 PRK04217 hypothetical protein; 25.5 66 0.0014 26.2 2.6 50 108-167 41-90 (110)
66 PRK09413 IS2 repressor TnpA; R 24.9 76 0.0017 25.7 3.0 40 107-156 10-50 (121)
67 PRK12512 RNA polymerase sigma 24.6 71 0.0015 27.0 2.9 48 110-167 132-179 (184)
68 PRK12514 RNA polymerase sigma 24.0 74 0.0016 26.8 2.9 28 134-165 148-175 (179)
69 PF12720 DUF3807: Protein of u 24.0 50 0.0011 29.1 1.8 14 41-54 48-61 (172)
70 PRK12515 RNA polymerase sigma 24.0 73 0.0016 27.2 2.8 50 109-168 131-180 (189)
71 PF13936 HTH_38: Helix-turn-he 23.9 30 0.00066 23.1 0.3 39 108-156 3-41 (44)
72 TIGR02985 Sig70_bacteroi1 RNA 23.6 78 0.0017 25.5 2.8 44 111-164 115-158 (161)
73 TIGR02948 SigW_bacill RNA poly 23.4 63 0.0014 27.2 2.3 31 132-166 153-183 (187)
74 TIGR02999 Sig-70_X6 RNA polyme 23.3 72 0.0016 26.8 2.6 46 110-165 135-180 (183)
75 PRK00118 putative DNA-binding 23.0 76 0.0016 25.6 2.5 47 110-166 18-64 (104)
76 PRK12533 RNA polymerase sigma 22.8 95 0.0021 27.7 3.4 30 134-167 153-182 (216)
77 PRK09644 RNA polymerase sigma 22.3 82 0.0018 26.1 2.8 49 110-168 109-157 (165)
78 PRK09648 RNA polymerase sigma 22.2 75 0.0016 27.0 2.6 47 109-165 139-185 (189)
79 TIGR02983 SigE-fam_strep RNA p 21.8 84 0.0018 25.8 2.7 47 111-167 112-158 (162)
80 PRK12541 RNA polymerase sigma 21.5 71 0.0015 26.4 2.2 46 110-165 113-158 (161)
81 PF06056 Terminase_5: Putative 21.3 35 0.00075 24.5 0.2 26 134-165 16-41 (58)
82 PRK09639 RNA polymerase sigma 20.9 84 0.0018 25.9 2.5 47 110-167 113-159 (166)
83 TIGR02959 SigZ RNA polymerase 20.3 91 0.002 26.2 2.7 50 109-168 100-149 (170)
84 PRK12540 RNA polymerase sigma 20.3 1.3E+02 0.0027 25.8 3.6 32 133-168 129-160 (182)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=1.1e-43 Score=337.37 Aligned_cols=151 Identities=20% Similarity=0.233 Sum_probs=132.5
Q ss_pred HHHHHHHHHhhhhhhhhccCCcCCCCCccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCC
Q 022926 6 IREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRL 85 (290)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~~~~~~sg~~~ 85 (290)
..||||||||+||||||||||||+|||+|||+|||+|||||+||||+++..+|+|||++++.+.|||..++.....++
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~-- 281 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGS-- 281 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCC--
Confidence 368999999999999999999999999999999999999999999999999999999999999999998877531111
Q ss_pred CCcccCCCCcCCCCCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 86 GNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 86 ~~~~~~p~~~s~~~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
.+.+.... ...++|++||+|+...+..||+.|.. |++|+..+|..||.+| +|.+.+|+|||||||.|.||
T Consensus 282 ---~~~~e~i~--a~~RkRKKRTSie~~vr~aLE~~F~~-npKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 282 ---PNSIEKIG--AQSRKRKKRTSIEVNVRGALEKHFLK-NPKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred ---CCCHHHhh--ccccccccccceeHHHHHHHHHHHHh-CCCCCHHHHHHHHHHh----ccccceEEEEeecccccccc
Confidence 11211111 12256788999999999999999999 6999999999999999 99999999999999999999
Q ss_pred Hhh
Q 022926 166 KQL 168 (290)
Q Consensus 166 ~~~ 168 (290)
...
T Consensus 352 ~~~ 354 (398)
T KOG3802|consen 352 ITP 354 (398)
T ss_pred CCC
Confidence 776
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.89 E-value=4.4e-24 Score=195.83 Aligned_cols=152 Identities=16% Similarity=0.162 Sum_probs=124.8
Q ss_pred HHHHHHHHhhhhhhhhccCCcCCCCCccCccc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCC
Q 022926 7 REAAQQETQTQNQNQNQRGGENDNNNVVNGVM---YVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGG 83 (290)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~---~~~~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~~~~~~sg~ 83 (290)
-.|||-||.-|||||||||+||+|||-|+--| .+.-+||.+||||+-+..+--+|.-+++.++.||..+......-.
T Consensus 216 PReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~ 295 (385)
T KOG1168|consen 216 PRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKD 295 (385)
T ss_pred HHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhc
Confidence 45899999999999999999999999665443 678899999999999999999999999999999988765432111
Q ss_pred CCCCcccCCCCcCCCCCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHH
Q 022926 84 RLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (290)
Q Consensus 84 ~~~~~~~~p~~~s~~~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~ 163 (290)
..+ +-.....++. +||+||.+-....+.||.+|.. .+.|+.+.|..||++| +|.+.+|+|||||.|+|.
T Consensus 296 ~~p----d~~~l~~~~e--kKRKRTSIAAPEKRsLEayFav-QPRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQ 364 (385)
T KOG1168|consen 296 TKP----DINELLPGGE--KKRKRTSIAAPEKRSLEAYFAV-QPRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQ 364 (385)
T ss_pred cCC----chhhccCccc--cccccccccCcccccHHHHhcc-CCCCchhHHHHHHHhh----hhhhceEEEEeeccHHHH
Confidence 111 0001111133 4778999999999999999999 5999999999999999 999999999999999999
Q ss_pred HHHhhh
Q 022926 164 KRKQLV 169 (290)
Q Consensus 164 Kr~~~~ 169 (290)
||....
T Consensus 365 KRm~~S 370 (385)
T KOG1168|consen 365 KRMKRS 370 (385)
T ss_pred HHhhhh
Confidence 996553
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=1.8e-18 Score=160.06 Aligned_cols=67 Identities=33% Similarity=0.384 Sum_probs=62.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcc
Q 022926 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (290)
Q Consensus 101 k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (290)
...||.||.||..||.+||+.|.. |+|.++..|.|||..| .|+|+||||||||||+||||..+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf-N~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF-NKYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc-ccccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhccccc
Confidence 457899999999999999999999 7999999999999999 999999999999999999998886554
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.73 E-value=2.5e-18 Score=136.93 Aligned_cols=69 Identities=32% Similarity=0.494 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcc
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (290)
..++.||-||+||..||..||+.|.. ++||++-.|++||.++ .|++..|+|||||||+|.||+.+....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~E-THYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAE-THYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHh-hcCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34567889999999999999999999 7999999999999999 999999999999999999998876544
No 5
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=99.69 E-value=2.4e-18 Score=130.14 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=65.9
Q ss_pred hHHHHHHHHHhhhhhhhhccCCcCCCCCccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 022926 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (290)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~ 75 (290)
...+||++||+.||||||+|||||+|||.++|.+||++||+++|+||+++..+++++|+.++.+.+||...
T Consensus 4 ~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 4 PDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 35689999999999999999999999999999999999999999999999999999999999999998754
No 6
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.69 E-value=6.9e-17 Score=143.97 Aligned_cols=68 Identities=35% Similarity=0.574 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhh
Q 022926 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (290)
Q Consensus 98 ~~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~ 170 (290)
.++++.||.||+|+..||.+||.+|.+ ++||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~k-TqYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAK-TQYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHh-hcCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 378889999999999999999999999 8999999999999999 9999999999999999999988864
No 7
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.68 E-value=3.1e-17 Score=155.00 Aligned_cols=66 Identities=29% Similarity=0.352 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
..|++|+.||.||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||....
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHh
Confidence 557888999999999999999999994 999999999999999 999999999999999999998876
No 8
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=9.2e-17 Score=150.55 Aligned_cols=69 Identities=29% Similarity=0.388 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcc
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (290)
+..++||+|..|+..|+.+||+.|.+ .+|++.+||++||..| .|+++||||||||||.|.||+++....
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrq-QRYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQ-QRYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHh-hhccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhh
Confidence 45567778999999999999999999 6999999999999999 999999999999999999998886544
No 9
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.66 E-value=7.1e-17 Score=148.56 Aligned_cols=114 Identities=23% Similarity=0.316 Sum_probs=95.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCCcCC--------CCCCCCCCCCCCCCHHHHHHHHHHH
Q 022926 51 LRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSG--------GGHKISARQRWTPTPVQLQILESIF 122 (290)
Q Consensus 51 lr~qi~~~~~ic~~~~~~~k~ls~~~~~~~sg~~~~~~~~~p~~~s~--------~~~k~~rR~Rt~ft~~Ql~~LE~~F 122 (290)
-++|..+|+..|.+++...+.|...+.+. .+..+.+.|....... .+....||+||++|..||+.|+.+|
T Consensus 109 RkAqd~VYHl~CF~C~iC~R~L~TGdEFY--LmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY 186 (383)
T KOG4577|consen 109 RKAQDFVYHLHCFACFICKRQLATGDEFY--LMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY 186 (383)
T ss_pred HHhhcceeehhhhhhHhhhcccccCCeeE--EeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence 48899999999999999999999888876 4444555554332111 1445678999999999999999999
Q ss_pred hhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhc
Q 022926 123 DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (290)
Q Consensus 123 ~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~ 171 (290)
..+ +.|.+.-|++|+..+ ||..++|+|||||||+|+||.++...
T Consensus 187 n~S-pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 187 NTS-PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred cCC-CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcc
Confidence 995 999999999999999 99999999999999999999887543
No 10
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.66 E-value=1.2e-16 Score=138.54 Aligned_cols=64 Identities=38% Similarity=0.447 Sum_probs=60.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhh
Q 022926 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (290)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~ 170 (290)
+.||.||.|+.+||..||.+|+. ++|....+|+.||..| +|++.||+|||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~-~~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG-NQYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc-CCeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 67889999999999999999999 6999999999999999 9999999999999999999988764
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=3.6e-16 Score=140.07 Aligned_cols=67 Identities=31% Similarity=0.405 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 98 ~~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
++.||.|++||.++.-||..|.+.|++ ++|+.-+||.+||..| ||+.+||+|||||||.|.||..+.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQk-TQYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQ-TQYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhh-cchhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 467888899999999999999999999 6999999999999999 999999999999999999998883
No 12
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.63 E-value=1.7e-16 Score=148.85 Aligned_cols=65 Identities=29% Similarity=0.327 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhh
Q 022926 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (290)
Q Consensus 101 k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~ 170 (290)
+..|++|..+|+.|+.+||+.|-. |.|.+++.|.+|++.| +|+++||+|||||||+|.||..++.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf-N~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF-NMYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH-HHHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhh
Confidence 567889999999999999999999 7999999999999999 9999999999999999999988643
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.62 E-value=4e-16 Score=137.87 Aligned_cols=66 Identities=38% Similarity=0.445 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
+++..|++||.||..||..||+.|.. .+|.++.+|.+++..| .|+++||+|||||||+|.||.+..
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfre-kqYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFRE-KQYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhH-hhhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHH
Confidence 67778889999999999999999999 5999999999999999 999999999999999999998764
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.59 E-value=4.6e-16 Score=138.32 Aligned_cols=66 Identities=30% Similarity=0.376 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhh
Q 022926 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (290)
Q Consensus 100 ~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~ 170 (290)
..++|+.||+|+..|+..||..|+. .+|.+..+|..||.+| .|+|+||+|||||||.||||+-...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~-krYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL-KRYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH-HhhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 3456788999999999999999999 6999999999999999 9999999999999999999987643
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=99.59 E-value=8e-16 Score=109.86 Aligned_cols=57 Identities=42% Similarity=0.663 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
||+|+.||.+|+.+||.+|.. ++||+..+++.||..| ||+..+|++||+|||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE-NPYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH-SSSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH-hccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 578999999999999999999 7999999999999999 99999999999999999986
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.56 E-value=1.5e-15 Score=138.19 Aligned_cols=67 Identities=24% Similarity=0.314 Sum_probs=60.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhccc
Q 022926 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSA 173 (290)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~~ 173 (290)
++|+-||.||..|+..||+.|+.. +||+...|+.||.++ .|.|.+|+|||||||+||||..+.....
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 444459999999999999999995 999999999999999 9999999999999999999999876443
No 17
>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=4.6e-14 Score=102.27 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCC----CCHHHHHHHHHHHhhcCCCCccceeeccchhh
Q 022926 104 ARQRWTPTPVQLQILESIFDQGTGT----PSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (290)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~y----Ps~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRR 160 (290)
||.||.||.+|+..||..|+. ++| |+..+|.+||..| ||++++|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~-~~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK-LGWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH-cCCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 789999999999999999999 799 9999999999999 999999999999975
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.48 E-value=1.3e-14 Score=134.57 Aligned_cols=65 Identities=32% Similarity=0.434 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 100 ~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
...-||.||.||.+|+..||+.|-+. -|-+++.|.+||..| +|.|..|+|||||||+|+||++..
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 33568899999999999999999995 599999999999999 999999999999999999998754
No 19
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.47 E-value=1.4e-14 Score=132.40 Aligned_cols=61 Identities=30% Similarity=0.378 Sum_probs=56.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhh
Q 022926 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (290)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~ 170 (290)
+.|.++|..|+.+||+.|.. .+|.++.++.+||..| +|+||||+|||||||+|+||..+..
T Consensus 201 KYRvVYTDhQRLELEKEfh~-SryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHT-SRYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhcc-ccceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 45889999999999999999 5999999999999999 9999999999999999999987754
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=7.3e-14 Score=98.85 Aligned_cols=55 Identities=44% Similarity=0.644 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHH
Q 022926 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (290)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~K 164 (290)
+.|+.|+..|+.+||..|.. ++||+..++..||..| ||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK-NPYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 56788999999999999999 6999999999999999 9999999999999998864
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=99.43 E-value=1.2e-13 Score=98.35 Aligned_cols=57 Identities=44% Similarity=0.653 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
+.|+.|+..|+.+||.+|.. ++||+..++..||..| ||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK-NPYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 46789999999999999999 7999999999999999 999999999999999998863
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=8.7e-14 Score=129.58 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhc
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~ 171 (290)
+.++.||.||.|+..||..||..|.+ |+||+...|++||.-. +|++.+|+|||.|||+||||+.+-..
T Consensus 108 ki~KqrrQrthFtSqqlqele~tF~r-NrypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 108 KISKQRRQRTHFTSQQLQELEATFQR-NRYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHhh-ccCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 45588999999999999999999999 8999999999999999 99999999999999999999887655
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.42 E-value=8.8e-14 Score=124.05 Aligned_cols=69 Identities=29% Similarity=0.373 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcccc
Q 022926 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSAN 174 (290)
Q Consensus 101 k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~~~ 174 (290)
.+++..|.+|+-.|+..||+.|+. ++|+-.++|.+||..| |+++.+|+|||||||.||||+........
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq-tkylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ-TKYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh-hhcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 355667999999999999999999 7999999999999999 99999999999999999999887654433
No 24
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.39 E-value=1.6e-13 Score=125.03 Aligned_cols=60 Identities=33% Similarity=0.501 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 103 SARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
-||+||.||.+||..|+..|.. |+|.+...|.+||.+| +|.+.||+|||||+|+|-||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e-nRYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE-NRYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh-hhhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhcc
Confidence 3578999999999999999999 7999999999999999 9999999999999999988844
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.35 E-value=1.8e-13 Score=117.30 Aligned_cols=66 Identities=32% Similarity=0.408 Sum_probs=61.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcc
Q 022926 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (290)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (290)
++++.||+|+..|+..||+.|+. .+|.+-++|.+||..| +|+++||+.||||||+|.||.++...+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~-QrYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER-QRYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhh-hhhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 45667999999999999999999 5999999999999999 999999999999999999998886554
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.34 E-value=3.6e-13 Score=119.82 Aligned_cols=61 Identities=34% Similarity=0.480 Sum_probs=55.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
.+++.+|+.+|+..||+.|+. +.|....++..||..| ||.++||.|||||||||||.++..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~-~~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFES-EKKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhcc-ccccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhh
Confidence 345567899999999999999 6899999999999999 999999999999999999998754
No 27
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.32 E-value=1.6e-12 Score=111.94 Aligned_cols=63 Identities=30% Similarity=0.428 Sum_probs=57.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
..+++|+.-+..|+.+|++.|+. ++||+...|..|+..| +|+++.|++||||||++.|+....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i-~p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI-NPYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc-CCCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhccc
Confidence 34566677799999999999999 6999999999999999 999999999999999999987664
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.21 E-value=1.8e-11 Score=109.45 Aligned_cols=104 Identities=24% Similarity=0.293 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCCcCCCCCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHH
Q 022926 56 AVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIK 135 (290)
Q Consensus 56 ~~~~~ic~~~~~~~k~ls~~~~~~~sg~~~~~~~~~p~~~s~~~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~ 135 (290)
..+..-|-.+......+...... ....|..+|....... ...+.||.|+.|+..|+.+||++|+. ++||+...|+
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~g~~~~~~d~~~~-~~~~~rr~rt~~~~~ql~~ler~f~~-~h~Pd~~~r~ 91 (235)
T KOG0490|consen 17 RYWHASCLKCAECDNPLGVGDTC---FSKDGSIYCKRDYQRE-FKFSKRCARCKFTISQLDELERAFEK-VHLPCFACRE 91 (235)
T ss_pred HHHHHHHHhhhhhcchhccCCCc---ccCCCcccccccchhh-hhccccccCCCCCcCHHHHHHHhhcC-CCcCccchHH
Confidence 34444455555555444411111 1124445554433321 24567889999999999999999999 6999999999
Q ss_pred HHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 136 EITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 136 ~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
.||..+ ++++..|+|||||||+||+++.+
T Consensus 92 ~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 92 CLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred HHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 999999 99999999999999999999875
No 29
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.19 E-value=9.8e-12 Score=94.17 Aligned_cols=71 Identities=11% Similarity=0.126 Sum_probs=67.3
Q ss_pred hHHHHHHHHHhhhhhhhhccCCcCCCCCccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 022926 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (290)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~ 75 (290)
....|+|.|+..|+++|+++|+||.+++-++|++||..+|+.+|++|+....+++++|+..+.+.+|+...
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 44678999999999999999999999999999999999999999999999999999999999999998753
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.95 E-value=2e-09 Score=103.80 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
..++.+|.||+|+..|+..||+.|+. ++||+...|++||.++ ++++..|+|||+|||+|++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~r-t~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQR-TPYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcC-CCCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 44566778999999999999999999 6899999999999999 999999999999999999998853
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.68 E-value=5.8e-08 Score=89.55 Aligned_cols=48 Identities=29% Similarity=0.497 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHH
Q 022926 112 PVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (290)
Q Consensus 112 ~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~K 164 (290)
..-+..|..+|.. ++||+..++.+||+.+ ||+..||-+||+|||+|+|
T Consensus 185 ekSR~~LrewY~~-~~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 185 EKSRSLLREWYLQ-NPYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HhhHHHHHHHHhc-CCCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhh
Confidence 3445689999999 6999999999999999 9999999999999999998
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.56 E-value=1.1e-06 Score=80.70 Aligned_cols=61 Identities=28% Similarity=0.461 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--CCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 103 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~--~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
.||+|..|+..-.++|..+|.. +|+||+.+.+++||+++ +++..||-+||.|+|-+.||.-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhh
Confidence 4678889999999999999976 67999999999999999 9999999999999999999854
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=98.16 E-value=5.3e-07 Score=60.66 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhH
Q 022926 126 TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (290)
Q Consensus 126 n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK 162 (290)
++||+..++.+||..+ ||+..||..||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 6999999999999999 99999999999999975
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.15 E-value=3.7e-06 Score=84.15 Aligned_cols=58 Identities=29% Similarity=0.462 Sum_probs=54.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHH
Q 022926 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (290)
Q Consensus 101 k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~ 163 (290)
-..|++|.+||..|+..|..+|+. +++|+.+..+.|+.+| +|..+.|.+||-|.|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke-~~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKE-NKRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhc-CCCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 346778999999999999999999 7999999999999999 999999999999999885
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.01 E-value=7.8e-06 Score=72.97 Aligned_cols=65 Identities=34% Similarity=0.519 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
...+.++.|+.+...|+..|+..|.. +.+|+...+..|+..+ +++++.|++||+|+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRA-TPKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccC-CCCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 33467788999999999999999999 6999999999999999 99999999999999999998665
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.57 E-value=9.3e-05 Score=80.47 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
.+|+.|+.++..||.+|..+|.. ..||...+.+.|-..+ ++..++|.|||||-|+|.|+....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~-q~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEA-QRTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhh-ccCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhc
Confidence 46778999999999999999999 5999999999999999 999999999999999999997773
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.37 E-value=0.0053 Score=44.25 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=30.4
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhh
Q 022926 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (290)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRa 161 (290)
+.-|+.+|.. .+++...+...|..+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~-h~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLK-HKQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHH-T----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHH-cCCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 3459999999 7999999999999999 9999999999976543
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.34 E-value=0.049 Score=56.98 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=46.9
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhc
Q 022926 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (290)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~ 171 (290)
+..|..+|.. |..|+..+...||.+. ||....|++||++++++..+..+...
T Consensus 568 ~sllkayyal-n~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL-NGLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCcc
Confidence 6788999999 7999999999999999 99999999999999999888776543
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.88 E-value=0.023 Score=54.40 Aligned_cols=62 Identities=23% Similarity=0.305 Sum_probs=49.5
Q ss_pred CCCCCCCCCHHHHHHHHHH-Hhh-CCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 103 SARQRWTPTPVQLQILESI-FDQ-GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~-F~~-~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
..|++..+......+|+.+ |+. ..+||+..++..||.++ ||+..||.+||-|.|.|..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCCchH
Confidence 4455668888889999877 332 23799999999999999 99999999999999988655433
No 40
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=89.44 E-value=0.48 Score=31.34 Aligned_cols=22 Identities=36% Similarity=0.501 Sum_probs=20.3
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 022926 42 VMTDEQLETLRKQIAVYATICE 63 (290)
Q Consensus 42 ~~t~~q~~~lr~qi~~~~~ic~ 63 (290)
.||.+|+..||+||.+|+.+..
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5899999999999999998875
No 41
>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=84.88 E-value=0.85 Score=32.17 Aligned_cols=47 Identities=19% Similarity=0.271 Sum_probs=34.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhh
Q 022926 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (290)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRR 160 (290)
||+|..+|-++...+-..++.. . ....||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 4678899998888887888873 2 356899999 999999999998753
No 42
>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=63.09 E-value=7 Score=27.77 Aligned_cols=38 Identities=29% Similarity=0.390 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCC---HHHHHHHHHHHhhcCCCCcccee
Q 022926 110 PTPVQLQILESIFDQGTGTPS---KQKIKEITVELSQHGQISETNVY 153 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs---~~~r~~LA~~L~~~~~Ls~~qV~ 153 (290)
+|+.|+.+|..+|+. .|-+ .....+||+.| |++...|.
T Consensus 1 LT~~Q~e~L~~A~~~--GYfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL--GYFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc--CCCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 478899999999987 3544 44557899999 99987653
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=57.63 E-value=43 Score=35.98 Aligned_cols=127 Identities=16% Similarity=0.230 Sum_probs=76.2
Q ss_pred hhccCCcCCCCCccCcccccc--cCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCCcCCC
Q 022926 21 QNQRGGENDNNNVVNGVMYVK--VMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGG 98 (290)
Q Consensus 21 ~~~~g~~~~~~~~~~~~~~~~--~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~~~~~~sg~~~~~~~~~p~~~s~~ 98 (290)
+|.-+|++...-| -..|.. -.+.+++..+..|+.+-....+.|++-.+.-. .+... .|.++++
T Consensus 559 ~~~k~~~~p~sll--kayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e----~sv~r--------sps~psg- 623 (1007)
T KOG3623|consen 559 RCSKQFNHPTSLL--KAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE----MSVER--------SPSQPSG- 623 (1007)
T ss_pred ccccccCCcHHHH--HHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh----hhhcc--------CccCCCC-
Confidence 5666666662211 112221 24688888999999888888888887554311 11000 0111111
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhh
Q 022926 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (290)
Q Consensus 99 ~~k~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~ 169 (290)
. .+-+-|+.+..++-..|..+|+. +-.++..+-..++.+| ...+.+|.|||++|+..-+.....
T Consensus 624 ~--~p~kv~sp~k~~dq~ql~~a~el-q~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 624 E--RPVKVRSPIKEEDQQQLKQAYEL-QASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred C--CCccccCCCCccchhhhHhhhhc-ccCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCccc
Confidence 1 12233455666666677777777 3556665555667778 888999999999999886665443
No 44
>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=52.89 E-value=14 Score=24.92 Aligned_cols=45 Identities=18% Similarity=0.281 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~ 163 (290)
.+++.+..+|...|... ++ ..+||..| |++...|+.+...-..|-
T Consensus 4 ~L~~~er~vi~~~y~~~--~t----~~eIa~~l----g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--LT----LEEIAERL----GISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST---S----HHHHHHHH----TSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--CC----HHHHHHHH----CCcHHHHHHHHHHHHHHh
Confidence 46788899999998552 22 45899999 999999987765444443
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=51.09 E-value=9.2 Score=24.81 Aligned_cols=44 Identities=18% Similarity=0.220 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK 162 (290)
.+++.+..+++..|... + ...++|..+ |++...|+.|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 35677778887777542 2 245789999 99999999888654433
No 46
>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=48.60 E-value=12 Score=27.17 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=26.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccc
Q 022926 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (290)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQ 157 (290)
+.|..|++++...+-..+... ...+.++|..+ ||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~-----g~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES-----GESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH-----HCHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC-----CCceEeeeccc----ccccccccHHHH
Confidence 456788998776665555331 24567899999 999999888863
No 47
>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=47.10 E-value=13 Score=25.30 Aligned_cols=42 Identities=29% Similarity=0.240 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhh
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRa 161 (290)
+++.+..++.-.|... ....+||..+ |+++..|++|...-|.
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHHh
Confidence 4566677777666552 3345899999 9999999999874443
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=45.13 E-value=18 Score=32.31 Aligned_cols=38 Identities=26% Similarity=0.397 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHH---HHHHHHHHhhcCCCCccce
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQK---IKEITVELSQHGQISETNV 152 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~---r~~LA~~L~~~~~Ls~~qV 152 (290)
.+|..|+.+|..+|.. .|-+.+. ..+||+.| |++...+
T Consensus 155 ~LTdrQ~~vL~~A~~~--GYFd~PR~~~l~dLA~~l----GISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKM--GYFDYPRRVSLKDLAKEL----GISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHc--CCCCCCccCCHHHHHHHh----CCCHHHH
Confidence 6899999999999997 4655554 47899999 9998764
No 49
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=43.48 E-value=5.8 Score=41.23 Aligned_cols=49 Identities=24% Similarity=0.262 Sum_probs=32.9
Q ss_pred HHHHhhCCCCCCHHHHHHHHHHHhh---cCCCCccceeeccchhhhHHHHHhh
Q 022926 119 ESIFDQGTGTPSKQKIKEITVELSQ---HGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 119 E~~F~~~n~yPs~~~r~~LA~~L~~---~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
+.+|.. +..++...+.+..+.+-. .-......|+.||.|||.++|+.+.
T Consensus 708 ~~w~~k-~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 708 HHWKLK-TRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhheec-ccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 445666 577887777666555400 0023457899999999999998654
No 50
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=42.49 E-value=25 Score=27.87 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=21.2
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhc
Q 022926 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (290)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~ 171 (290)
+.+..-.|+. |+||...- -+..= .|||.+|++.+.+..
T Consensus 14 vRiIk~Lyqs-nPyP~~~G---Tr~aR---------------RnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 14 VRIIKILYQS-NPYPSPEG---TRQAR---------------RNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHHT-S-S--S-S----HHHH---------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcc-ccCCCCCC---ccccc---------------cchhhhHHHHHHHHH
Confidence 3455566877 79998531 11111 589999999887653
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=39.77 E-value=11 Score=42.62 Aligned_cols=65 Identities=11% Similarity=0.009 Sum_probs=55.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhhhhcc
Q 022926 103 SARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (290)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (290)
.+-.|+.++.-|+..|-..|+. ..||.-.+...++..| ++..+.+-.||++++.++.....+...
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt-~~cpkc~~~yk~a~~L----~vhmRskhp~~~~~~c~~gq~~~~~ar 508 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKT-LKCPKCNWHYKLAQTL----GVHMRSKHPESQSAYCKAGQNHPRLAR 508 (1406)
T ss_pred hhhhhhcccccceeeeeccccc-ccCCccchhhhhHHHh----hhcccccccccchhHhHhccccccccc
Confidence 3445788888899999999988 6999999999999999 999999999999988888776555444
No 52
>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=38.05 E-value=50 Score=18.73 Aligned_cols=37 Identities=24% Similarity=0.508 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeecc
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWF 156 (290)
++..+...+...|.. .+ ...++|..+ +++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~--~~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA--GE----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHhC
Confidence 566666666666754 33 344788899 99998888773
No 53
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=34.93 E-value=2.7e+02 Score=28.37 Aligned_cols=83 Identities=14% Similarity=0.143 Sum_probs=50.9
Q ss_pred ccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCCcCCCCCCCCCCCCCCCCH
Q 022926 33 VVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTP 112 (290)
Q Consensus 33 ~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~~~~~~k~ls~~~~~~~sg~~~~~~~~~p~~~s~~~~k~~rR~Rt~ft~ 112 (290)
++++++..-.-+..+|+.|.+|+.... ++.-+|.+.|.++..-+..+...+.....+...+. ...++.+|+
T Consensus 12 ~al~~~a~a~a~a~~i~~L~~ql~aLq---~~v~eL~~~laa~~~aa~~gA~~~~~~~a~~~aP~------~~a~~~~T~ 82 (514)
T PF11336_consen 12 GALPGAAMAAATADQIKALQAQLQALQ---DQVNELRAKLAAKPAAAPGGAAIGPAATAAAAAPS------SDAQAGLTN 82 (514)
T ss_pred hhccccccccCCHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCCCCCccccccccccccccCCC------cccccccCh
Confidence 355666667778889999998887654 45556777776665544333333333222222111 125789999
Q ss_pred HHHHHHHHHHhh
Q 022926 113 VQLQILESIFDQ 124 (290)
Q Consensus 113 ~Ql~~LE~~F~~ 124 (290)
+++..+...+..
T Consensus 83 d~~~~~~qqiAn 94 (514)
T PF11336_consen 83 DDATEMRQQIAN 94 (514)
T ss_pred HHHHHHHHHHHh
Confidence 999777666554
No 54
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=34.35 E-value=39 Score=29.15 Aligned_cols=47 Identities=13% Similarity=0.093 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
+++.+..+|.-.|-. ....++||+.| |++...|+++...-|.+-|+.
T Consensus 143 L~~~~r~vl~l~~~~------~~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAYYG------GLTYREVAERL----AVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHh----CCChHhHHHHHHHHHHHHHHH
Confidence 455555566554433 13345889999 999999999987656555554
No 55
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.20 E-value=38 Score=28.12 Aligned_cols=48 Identities=13% Similarity=-0.008 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
.+++.+..+|.-.|-. .++ ..+||..| |++...|+.|...-+.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~--~~s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIE--GLS----YEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHc--CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3556666666655543 222 34889999 999999999988555555543
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.12 E-value=43 Score=28.50 Aligned_cols=51 Identities=22% Similarity=0.180 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 107 RWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 107 Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
...+++.|+.+|... .. .+. ..+||..| |++...|..|-...+.+.|+...
T Consensus 4 ~~~Lt~rqreVL~lr-~~--GlT----q~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ER--GLT----QQEIADIL----GTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHH-Hc--CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999874 33 222 34899999 99999999999987777666543
No 57
>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=32.77 E-value=15 Score=26.85 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=19.6
Q ss_pred HHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 134 r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
-.+||.+| |+++.+|+.|=. +-+|..
T Consensus 25 lkdIA~~L----gvs~~tIr~WK~--~dkW~~ 50 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWKS--RDKWDE 50 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHhh--hcchhh
Confidence 35899999 999999999853 334443
No 58
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.08 E-value=32 Score=28.09 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~K 164 (290)
.+++.+..++...|-.+ ....+||..| |++...|++|...-|.+-|
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 34555566665554442 2356899999 9999999999875554444
No 59
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=30.18 E-value=42 Score=26.31 Aligned_cols=47 Identities=21% Similarity=0.211 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
.+++.+..++...|-. .+ ...+||..+ |+++..|+.|...-+.|-|+
T Consensus 110 ~L~~~~~~ii~~~~~~--g~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE--GL----SYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 3456666666555433 22 344889999 99999999888765555443
No 60
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=29.28 E-value=34 Score=23.81 Aligned_cols=44 Identities=27% Similarity=0.244 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~ 163 (290)
.||+.++.+|.-+..- +. ..+||..| ++++..|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G---~~----~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---MS----NKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTT---S-----HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc---CC----cchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 5788889988777643 22 34899999 999999998887666554
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=27.72 E-value=52 Score=28.79 Aligned_cols=31 Identities=13% Similarity=0.137 Sum_probs=23.5
Q ss_pred HHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 133 ~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
..++||..| |+++..|+++...-|.+.++..
T Consensus 171 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 345889999 9999999988876666655543
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=26.20 E-value=57 Score=26.92 Aligned_cols=30 Identities=17% Similarity=0.158 Sum_probs=23.7
Q ss_pred HHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 133 ~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
...+||..| |++...|+.|..--|.+.|+.
T Consensus 143 ~~~eIA~~l----gis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEIL----GVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 345889999 999999999998666666554
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=46 Score=28.47 Aligned_cols=30 Identities=17% Similarity=0.071 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 132 QKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 132 ~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
....+||..| |++...|++|+..-|.+.|+
T Consensus 158 ~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRL----GIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4456899999 99999999999766665554
No 64
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.81 E-value=69 Score=26.37 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
+++.+..++.-.|... ...++||..| |+++..|+++...-|.+-|+..
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE------KSYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3444555555444431 2234889999 9999999999876666655543
No 65
>PRK04217 hypothetical protein; Provisional
Probab=25.47 E-value=66 Score=26.23 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
..++.+++.++...|... + ...+||+.| +++...|+..+..-+.+.+..-
T Consensus 41 ~~Lt~eereai~l~~~eG--l----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG--L----TQEEAGKRM----GVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 457888888888777652 2 345899999 9999999999876666655543
No 66
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=24.94 E-value=76 Score=25.68 Aligned_cols=40 Identities=15% Similarity=0.372 Sum_probs=27.0
Q ss_pred CCCCCHHHHH-HHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeecc
Q 022926 107 RWTPTPVQLQ-ILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (290)
Q Consensus 107 Rt~ft~~Ql~-~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWF 156 (290)
|..|+.++.. ++..++.. .++ ..+||..+ |++...|..|.
T Consensus 10 rr~ys~EfK~~aV~~~~~~--g~s----v~evA~e~----gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP--GMT----VSLVARQH----GVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC--CCC----HHHHHHHH----CcCHHHHHHHH
Confidence 3456776644 44444543 333 34889999 99999999995
No 67
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.58 E-value=71 Score=27.02 Aligned_cols=48 Identities=27% Similarity=0.217 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
+++.+..+|.-.|-. .....+||..| |++...|++++..-|.+.|+..
T Consensus 132 L~~~~r~v~~l~~~~------g~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 132 LPPRQRDVVQSISVE------GASIKETAAKL----SMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHh
Confidence 344444444444333 23345889999 9999999999987777666544
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.98 E-value=74 Score=26.76 Aligned_cols=28 Identities=11% Similarity=0.324 Sum_probs=22.4
Q ss_pred HHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 134 r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
.++||..| |+++..|+++...-|.+.|+
T Consensus 148 ~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 148 YKELAERH----DVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HHHHHHHH----CCChHHHHHHHHHHHHHHHH
Confidence 55889999 99999999998765555554
No 69
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=23.97 E-value=50 Score=29.07 Aligned_cols=14 Identities=43% Similarity=0.769 Sum_probs=12.2
Q ss_pred ccCCHHHHHHHHHH
Q 022926 41 KVMTDEQLETLRKQ 54 (290)
Q Consensus 41 ~~~t~~q~~~lr~q 54 (290)
+.|||+||+.||.-
T Consensus 48 RTLTDEQI~IFRHS 61 (172)
T PF12720_consen 48 RTLTDEQIEIFRHS 61 (172)
T ss_pred ccccHHHHHHHHHH
Confidence 68999999999853
No 70
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.96 E-value=73 Score=27.17 Aligned_cols=50 Identities=14% Similarity=0.248 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
.+++.+..+|+-.|-. .....+||..| |+++..|++-...-|.+.|+...
T Consensus 131 ~L~~~~r~vl~l~~~~------~~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYYH------EKSVEEVGEIV----GIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHHc------CCCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555544433 12345888999 99999999988766766666544
No 71
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.88 E-value=30 Score=23.11 Aligned_cols=39 Identities=28% Similarity=0.361 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeecc
Q 022926 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (290)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWF 156 (290)
..+|.++...++..+... .-..+||..| |.+...|..|-
T Consensus 3 ~~Lt~~eR~~I~~l~~~G------~s~~~IA~~l----g~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG------MSIREIAKRL----GRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC------CCHHHHHHHH----CcCcHHHHHHH
Confidence 457888889999888662 2234799999 99988876654
No 72
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=23.57 E-value=78 Score=25.51 Aligned_cols=44 Identities=23% Similarity=0.107 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHH
Q 022926 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (290)
Q Consensus 111 t~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~K 164 (290)
++.+..+|.-.|-. .+ ...+||..| |+++..|+++...-|.|.|
T Consensus 115 ~~~~r~il~l~~~~--~~----~~~eIA~~l----gis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 115 PEQCRKIFILSRFE--GK----SYKEIAEEL----GISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 44455555544433 22 344789999 9999999888765554444
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.44 E-value=63 Score=27.19 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 132 QKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 132 ~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
...++||..| |+++..|+++...-|.+-|..
T Consensus 153 ~s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3445889999 999999999997666655543
No 74
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=23.31 E-value=72 Score=26.84 Aligned_cols=46 Identities=26% Similarity=0.240 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
+++.+..++.-.|..+ ...++||..| |+++..|++....-|.+-|+
T Consensus 135 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG------LTVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4555555555555442 2345889999 99999999998766655554
No 75
>PRK00118 putative DNA-binding protein; Validated
Probab=23.00 E-value=76 Score=25.61 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHH
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~ 166 (290)
+++.|..++...|... + ...+||..+ |++...|+.|....|.+.|..
T Consensus 18 L~ekqRevl~L~y~eg--~----S~~EIAe~l----GIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--Y----SLGEIAEEF----NVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4566777776666552 2 234899999 999999999997666665543
No 76
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.79 E-value=95 Score=27.69 Aligned_cols=30 Identities=17% Similarity=0.161 Sum_probs=23.5
Q ss_pred HHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 134 r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
.++||..| |+++..|+++-..-|.+.++..
T Consensus 153 ~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 153 YREIAAIA----DVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45889999 9999999998876666655544
No 77
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.31 E-value=82 Score=26.14 Aligned_cols=49 Identities=12% Similarity=-0.010 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
+++.+..++.-.|-. ....++||..| |+++..|++|...-|.+-|+.-.
T Consensus 109 L~~~~r~v~~l~~~~------g~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVH------ELTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHh------cCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 345555555543333 12345889999 99999999999766666555443
No 78
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.17 E-value=75 Score=27.02 Aligned_cols=47 Identities=17% Similarity=-0.041 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
.+++.+..++...|-. ....++||..| |++...|+++...-|.+-|+
T Consensus 139 ~L~~~~r~i~~l~~~~------g~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVV------GLSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHc------CCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3445555555554433 23355889999 99999999988654544443
No 79
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=21.76 E-value=84 Score=25.83 Aligned_cols=47 Identities=15% Similarity=0.085 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 111 t~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
++.+..+|.-.|-. . ...++||..| |++...|+++-..-|.+-|+..
T Consensus 112 ~~~~r~i~~l~~~~--g----~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 112 PARQRAVVVLRYYE--D----LSEAQVAEAL----GISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHhhhHHHh--c----CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHh
Confidence 44555555544433 2 2344889999 9999999998876666655543
No 80
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.49 E-value=71 Score=26.35 Aligned_cols=46 Identities=20% Similarity=0.023 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
+++.|..+|.-.|-.. + ...+||..| |++...|+++...-|.+-|+
T Consensus 113 L~~~~r~v~~l~~~~~--~----s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG--F----SYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 4555555665555441 2 344889999 99999999888755555443
No 81
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=21.32 E-value=35 Score=24.51 Aligned_cols=26 Identities=38% Similarity=0.676 Sum_probs=20.5
Q ss_pred HHHHHHHHhhcCCCCccceeeccchhhhHHHH
Q 022926 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (290)
Q Consensus 134 r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr 165 (290)
..+||..| |++.+.|+.|-+ |.+|..
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH--hhCccc
Confidence 34899999 999999999975 555544
No 82
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.90 E-value=84 Score=25.89 Aligned_cols=47 Identities=23% Similarity=0.227 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHh
Q 022926 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (290)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~ 167 (290)
+++.+..+|.-.| .. + ..++||..| |++...|+++...-|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~g--~----s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG--Y----SYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666 42 2 345899999 9999999999876666655543
No 83
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.30 E-value=91 Score=26.23 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
.+++.+..+|.-.|-.. + ..++||..| |+++..|+++-..-|.+.++...
T Consensus 100 ~L~~~~r~v~~l~~~~g--~----s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--L----SQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666655442 2 345889999 99999999988766665555443
No 84
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.26 E-value=1.3e+02 Score=25.83 Aligned_cols=32 Identities=3% Similarity=-0.013 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhcCCCCccceeeccchhhhHHHHHhh
Q 022926 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (290)
Q Consensus 133 ~r~~LA~~L~~~~~Ls~~qV~vWFQNRRaK~Kr~~~ 168 (290)
..++||..| |+++..|++....-|.+-|+...
T Consensus 129 s~~EIA~~L----gis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAIC----GCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 345889999 99999999988755555554433
Done!