Query 028506
Match_columns 208
No_of_seqs 254 out of 1489
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:34:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028506.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028506hhsearch_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 4.8E-34 1E-38 254.2 5.6 141 7-156 214-354 (398)
2 KOG0488 Transcription factor B 99.7 2.3E-18 4.9E-23 152.3 5.8 79 84-167 165-243 (309)
3 KOG1168 Transcription factor A 99.7 4.1E-19 8.9E-24 153.0 -0.6 144 7-158 225-371 (385)
4 KOG0489 Transcription factor z 99.7 6E-18 1.3E-22 146.6 5.7 68 89-161 157-224 (261)
5 KOG0484 Transcription factor P 99.7 3.4E-18 7.4E-23 127.3 3.1 65 89-158 15-79 (125)
6 KOG2251 Homeobox transcription 99.7 3E-17 6.5E-22 136.8 8.6 68 86-158 32-99 (228)
7 KOG0842 Transcription factor t 99.7 2.2E-17 4.7E-22 144.8 7.6 66 88-158 150-215 (307)
8 KOG4577 Transcription factor L 99.7 5.2E-18 1.1E-22 146.1 2.5 118 35-158 103-229 (383)
9 KOG0850 Transcription factor D 99.7 4.5E-17 9.7E-22 136.5 6.1 69 85-158 116-184 (245)
10 KOG0843 Transcription factor E 99.7 6.3E-17 1.4E-21 131.1 6.0 64 90-158 101-164 (197)
11 KOG0487 Transcription factor A 99.6 1.4E-16 3E-21 139.8 5.9 65 89-158 233-297 (308)
12 KOG0485 Transcription factor N 99.6 1.6E-16 3.4E-21 132.3 4.7 68 88-160 101-168 (268)
13 KOG0492 Transcription factor M 99.6 1.6E-16 3.5E-21 131.3 4.1 68 87-159 140-207 (246)
14 PF00046 Homeobox: Homeobox do 99.6 3.1E-16 6.8E-21 105.1 3.9 57 92-153 1-57 (57)
15 KOG0494 Transcription factor C 99.6 1.8E-15 3.8E-20 128.9 5.3 63 91-158 141-203 (332)
16 KOG0848 Transcription factor C 99.5 3.8E-15 8.2E-20 127.3 1.8 61 93-158 201-261 (317)
17 TIGR01565 homeo_ZF_HD homeobox 99.5 4E-14 8.7E-19 95.9 5.5 53 91-148 1-57 (58)
18 smart00389 HOX Homeodomain. DN 99.5 3.6E-14 7.9E-19 94.3 3.9 55 93-152 2-56 (56)
19 KOG0491 Transcription factor B 99.5 2.2E-14 4.7E-19 115.0 2.8 68 90-162 99-166 (194)
20 cd00086 homeodomain Homeodomai 99.5 5.3E-14 1.2E-18 94.1 4.3 57 93-154 2-58 (59)
21 KOG0844 Transcription factor E 99.4 3E-14 6.4E-19 123.9 2.7 64 89-157 179-242 (408)
22 KOG0493 Transcription factor E 99.4 1.1E-13 2.3E-18 118.2 5.3 62 91-157 246-307 (342)
23 COG5576 Homeodomain-containing 99.4 3.5E-13 7.6E-18 108.5 5.3 65 90-159 50-114 (156)
24 KOG0486 Transcription factor P 99.4 1.6E-13 3.4E-18 119.7 3.3 67 88-159 109-175 (351)
25 KOG0483 Transcription factor H 99.3 5.4E-13 1.2E-17 111.0 3.0 63 91-158 50-112 (198)
26 KOG0847 Transcription factor, 99.3 5.4E-12 1.2E-16 105.5 5.2 67 89-160 165-231 (288)
27 KOG0490 Transcription factor, 99.2 1.3E-11 2.8E-16 103.5 5.6 103 48-156 18-120 (235)
28 KOG0849 Transcription factor P 99.0 7.6E-10 1.7E-14 99.9 7.9 65 88-157 173-237 (354)
29 PF00157 Pou: Pou domain - N-t 98.8 1.9E-10 4.1E-15 81.5 -2.3 59 8-66 16-74 (75)
30 KOG0775 Transcription factor S 98.8 9E-09 2E-13 88.7 7.4 54 97-155 182-235 (304)
31 KOG0774 Transcription factor P 98.5 4.1E-07 8.8E-12 78.2 8.2 62 91-157 188-252 (334)
32 PF05920 Homeobox_KN: Homeobox 98.2 5.8E-07 1.3E-11 56.5 0.6 34 112-150 7-40 (40)
33 KOG0490 Transcription factor, 98.0 6.4E-06 1.4E-10 69.0 3.9 63 89-156 151-213 (235)
34 KOG2252 CCAAT displacement pro 97.9 8.8E-06 1.9E-10 76.3 3.7 57 90-151 419-475 (558)
35 smart00352 POU Found in Pit-Oc 97.9 3.4E-06 7.4E-11 59.8 0.1 59 8-66 16-74 (75)
36 KOG1146 Homeobox protein [Gene 97.6 7.4E-05 1.6E-09 76.1 4.4 64 90-158 902-965 (1406)
37 PF11569 Homez: Homeodomain le 95.9 0.0028 6.1E-08 42.5 0.7 42 103-149 10-51 (56)
38 KOG0773 Transcription factor M 95.0 0.022 4.7E-07 51.0 3.5 61 91-156 239-302 (342)
39 KOG3623 Homeobox transcription 94.0 0.056 1.2E-06 53.0 3.9 49 103-156 568-616 (1007)
40 PF08880 QLQ: QLQ; InterPro: 91.1 0.3 6.6E-06 30.0 3.0 22 33-54 2-23 (37)
41 PF04218 CENP-B_N: CENP-B N-te 85.4 1.3 2.8E-05 29.1 3.4 46 92-147 1-46 (53)
42 PF04967 HTH_10: HTH DNA bindi 69.8 6.4 0.00014 26.0 3.1 38 98-141 1-41 (53)
43 PF01527 HTH_Tnp_1: Transposas 61.2 7.1 0.00015 26.5 2.2 42 93-144 2-44 (76)
44 cd06171 Sigma70_r4 Sigma70, re 53.2 9.9 0.00021 23.0 1.6 41 98-148 11-51 (55)
45 COG3413 Predicted DNA binding 50.5 17 0.00037 30.2 3.1 39 97-141 155-196 (215)
46 PF04545 Sigma70_r4: Sigma-70, 47.0 16 0.00036 22.9 2.0 39 97-145 4-42 (50)
47 PF08281 Sigma70_r4_2: Sigma-7 45.9 8.8 0.00019 24.4 0.6 39 98-146 11-49 (54)
48 cd00569 HTH_Hin_like Helix-tur 43.4 48 0.001 17.5 3.5 37 98-144 6-42 (42)
49 PF10668 Phage_terminase: Phag 39.8 13 0.00027 25.3 0.6 19 122-144 25-43 (60)
50 PRK09652 RNA polymerase sigma 35.2 33 0.00072 26.6 2.4 47 97-153 128-174 (182)
51 PF06056 Terminase_5: Putative 33.6 21 0.00045 23.8 0.9 20 122-145 16-35 (58)
52 PRK09646 RNA polymerase sigma 33.4 43 0.00093 26.9 2.9 48 97-154 142-189 (194)
53 PRK09413 IS2 repressor TnpA; R 33.2 59 0.0013 24.5 3.4 41 95-145 10-51 (121)
54 PRK09642 RNA polymerase sigma 31.0 48 0.001 25.5 2.7 47 98-154 107-153 (160)
55 PF00196 GerE: Bacterial regul 30.6 40 0.00087 21.7 1.9 43 97-150 3-45 (58)
56 PRK03975 tfx putative transcri 30.5 59 0.0013 25.8 3.1 49 96-155 5-53 (141)
57 KOG1146 Homeobox protein [Gene 30.5 70 0.0015 34.1 4.4 61 90-155 704-764 (1406)
58 TIGR02937 sigma70-ECF RNA poly 30.2 43 0.00094 24.5 2.3 46 97-152 110-155 (158)
59 PRK06759 RNA polymerase factor 29.5 46 0.001 25.3 2.4 44 97-150 106-149 (154)
60 PRK12526 RNA polymerase sigma 29.2 53 0.0012 26.8 2.8 31 121-155 171-201 (206)
61 KOG3623 Homeobox transcription 29.2 1E+02 0.0022 31.2 5.0 61 93-158 628-688 (1007)
62 PRK12541 RNA polymerase sigma 28.7 45 0.00097 25.7 2.2 46 97-152 112-157 (161)
63 PRK09480 slmA division inhibit 28.6 54 0.0012 25.8 2.7 38 105-148 18-55 (194)
64 PRK09644 RNA polymerase sigma 28.6 54 0.0012 25.4 2.7 50 97-156 108-157 (165)
65 KOG3755 SATB1 matrix attachmen 28.0 19 0.00042 35.2 -0.1 20 136-155 739-758 (769)
66 PRK12512 RNA polymerase sigma 27.8 69 0.0015 25.3 3.2 50 97-156 131-180 (184)
67 PRK12516 RNA polymerase sigma 27.5 63 0.0014 26.0 2.9 49 98-156 117-165 (187)
68 TIGR02948 SigW_bacill RNA poly 26.9 55 0.0012 25.7 2.4 46 98-153 137-182 (187)
69 PF13384 HTH_23: Homeodomain-l 26.4 27 0.00058 21.7 0.4 21 122-146 20-40 (50)
70 PRK11924 RNA polymerase sigma 26.2 58 0.0013 25.1 2.4 28 122-153 144-171 (179)
71 PRK12519 RNA polymerase sigma 26.0 47 0.001 26.5 1.9 30 120-153 158-187 (194)
72 TIGR02985 Sig70_bacteroi1 RNA 26.0 67 0.0015 24.2 2.7 43 98-150 114-156 (161)
73 cd02413 40S_S3_KH K homology R 25.8 63 0.0014 23.0 2.3 26 120-145 50-75 (81)
74 TIGR02999 Sig-70_X6 RNA polyme 25.8 62 0.0013 25.4 2.5 46 98-153 135-180 (183)
75 PRK12533 RNA polymerase sigma 25.5 66 0.0014 26.8 2.8 49 98-156 135-183 (216)
76 cd04761 HTH_MerR-SF Helix-Turn 25.3 29 0.00063 21.1 0.4 22 122-147 3-24 (49)
77 PRK05602 RNA polymerase sigma 25.2 71 0.0015 25.3 2.8 31 122-156 147-177 (186)
78 PRK09639 RNA polymerase sigma 24.2 67 0.0014 24.7 2.4 47 97-154 112-158 (166)
79 PRK12514 RNA polymerase sigma 23.4 94 0.002 24.4 3.2 28 122-153 148-175 (179)
80 PRK00118 putative DNA-binding 23.1 83 0.0018 23.6 2.6 46 98-153 18-63 (104)
81 TIGR02959 SigZ RNA polymerase 23.1 75 0.0016 25.0 2.5 49 97-155 100-148 (170)
82 PF13936 HTH_38: Helix-turn-he 23.1 25 0.00054 21.8 -0.2 39 96-144 3-41 (44)
83 PF13518 HTH_28: Helix-turn-he 23.1 37 0.00079 21.0 0.6 21 122-146 15-35 (52)
84 PRK09047 RNA polymerase factor 22.7 84 0.0018 24.0 2.7 47 97-153 106-152 (161)
85 TIGR02983 SigE-fam_strep RNA p 22.4 85 0.0018 24.1 2.7 45 99-153 112-156 (162)
86 PRK09637 RNA polymerase sigma 22.3 77 0.0017 25.3 2.5 49 98-156 107-155 (181)
87 TIGR02989 Sig-70_gvs1 RNA poly 22.1 77 0.0017 24.1 2.4 39 97-145 111-149 (159)
88 PRK12515 RNA polymerase sigma 22.0 85 0.0018 24.9 2.7 48 97-154 131-178 (189)
89 TIGR02952 Sig70_famx2 RNA poly 21.4 86 0.0019 24.1 2.6 39 97-145 122-160 (170)
90 PF02796 HTH_7: Helix-turn-hel 21.0 56 0.0012 20.2 1.1 38 97-144 5-42 (45)
91 smart00421 HTH_LUXR helix_turn 20.6 1.1E+02 0.0024 18.4 2.5 38 97-145 3-40 (58)
92 PRK12546 RNA polymerase sigma 20.3 83 0.0018 25.4 2.3 31 122-156 132-162 (188)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=4.8e-34 Score=254.21 Aligned_cols=141 Identities=19% Similarity=0.222 Sum_probs=123.9
Q ss_pred CCCcCchhhhhhhcccCCcccCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcccccccCCCCCCCCCCCccCC
Q 028506 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG 86 (208)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~y~~ic~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~ 86 (208)
.|+|++++.+|+|+|||+|+|.+||+|||+++|||||++.++|++||+..++|.|||.+.+.... ..+....+.. .
T Consensus 214 ~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~-~~~~~~~e~i---~ 289 (398)
T KOG3802|consen 214 TFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRES-TGSPNSIEKI---G 289 (398)
T ss_pred HHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccc-cCCCCCHHHh---h
Confidence 58999999999999999999999999999999999999999999999999999999999886411 1111111111 2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 87 ~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
...++|++||.|....+..||+.|.+|+ .|+.++|..||..| +|...+|+|||||||.|+||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 2237888999999999999999999998 99999999999999 99999999999999999999876
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=2.3e-18 Score=152.28 Aligned_cols=79 Identities=23% Similarity=0.286 Sum_probs=69.2
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCCCCCC
Q 028506 84 ASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPNNA 163 (208)
Q Consensus 84 ~~~~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~~~~~ 163 (208)
....++|+|+.||.||..||..||+.|++.+ |.+..+|.+||..| ||+..||++||||||+||||+.....+...
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~~~~~ 239 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGGELLY 239 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhhcccc
Confidence 3455678889999999999999999999997 99999999999999 999999999999999999999888655443
Q ss_pred CCcc
Q 028506 164 ESEA 167 (208)
Q Consensus 164 ~s~~ 167 (208)
....
T Consensus 240 ~~~~ 243 (309)
T KOG0488|consen 240 QAGN 243 (309)
T ss_pred cccc
Confidence 3333
No 3
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.72 E-value=4.1e-19 Score=152.97 Aligned_cols=144 Identities=17% Similarity=0.209 Sum_probs=118.6
Q ss_pred CCCcCchhhhhhhcccCCcccCc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcccccccCCCCCCCCCCCc
Q 028506 7 NFQQGGEMERQFQQDGGDTSNGL---CVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFV 83 (208)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~---~~~~~t~~q~~~lr~qi~~y~~ic~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~ 83 (208)
-|+|++++.+-+|+|||.|+.-| .+..+++.+||+|+..-++--+|--..+.++.||.....-...-...+....+.
T Consensus 225 rFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~ 304 (385)
T KOG1168|consen 225 RFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELL 304 (385)
T ss_pred HHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhcc
Confidence 48999999999999999998877 788999999999999999989999999999999998754211111111111111
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 84 ASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 84 ~~~~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
.+ ..++|+||.+.......||.+|...+ .|+.+.|..||++| +|-..+|+|||||.|+|.||.....
T Consensus 305 -~~--~ekKRKRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 305 -PG--GEKKRKRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred -Cc--cccccccccccCcccccHHHHhccCC-CCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhhh
Confidence 11 14778899999999999999999998 89999999999999 9999999999999999999965543
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.72 E-value=6e-18 Score=146.57 Aligned_cols=68 Identities=25% Similarity=0.352 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCCCC
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 161 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~~~ 161 (208)
...||.||.||..|+.+||+.|+.|. |.++..|.+||..| .|+|+||||||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45789999999999999999999996 99999999999999 9999999999999999999988776544
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.71 E-value=3.4e-18 Score=127.26 Aligned_cols=65 Identities=32% Similarity=0.532 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
++.||-||+|+..||..||+.|... |||++..|++||.+| .|++..|+|||||||+|.+|+.+..
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 4677889999999999999999999 599999999999999 9999999999999999999987654
No 6
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.71 E-value=3e-17 Score=136.82 Aligned_cols=68 Identities=29% Similarity=0.500 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 86 ~~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
.++++.||.||+|+..|+.+||..|.+.. ||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 56778999999999999999999999997 99999999999999 9999999999999999999998875
No 7
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.70 E-value=2.2e-17 Score=144.79 Aligned_cols=66 Identities=26% Similarity=0.377 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 88 ~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
..++||.|..|+..|..+||+.|.+. +|++.+||++||..| .|+++||||||||||-|.||++...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhh
Confidence 44677889999999999999999999 599999999999999 9999999999999999999998775
No 8
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.70 E-value=5.2e-18 Score=146.12 Aligned_cols=118 Identities=23% Similarity=0.306 Sum_probs=101.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcccccccCCCCCCCCCCCccCC---------CCCCCCCCCCCCCHHHHHH
Q 028506 35 TDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG---------SQKLTARQRWTPTPAQLQI 105 (208)
Q Consensus 35 t~~q~~~lr~qi~~y~~ic~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~---------~~~~~rr~Rt~~s~~ql~~ 105 (208)
-.+|+ .-++|..+|+..|.+++.+.+.|++.++|.-|..+.+.|.-..... +....+|+||++++.||+.
T Consensus 103 pPtqV-VRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLET 181 (383)
T KOG4577|consen 103 PPTQV-VRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLET 181 (383)
T ss_pred ChHHH-HHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHH
Confidence 34443 3488999999999999999999999999988888877766543222 3345789999999999999
Q ss_pred HHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 106 LEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 106 Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
|...|...+ .|.+.-|+.|+... ||..++|+|||||||+|+||.++..
T Consensus 182 LK~AYn~Sp-KPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 182 LKQAYNTSP-KPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred HHHHhcCCC-chhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhc
Confidence 999999998 99999999888887 9999999999999999999988875
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.68 E-value=4.5e-17 Score=136.48 Aligned_cols=69 Identities=26% Similarity=0.405 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 85 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 85 ~~~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
.++.+|.|+.||.++.-||..|.+.|++++ |+-.+||.+||..| ||+.+||+|||||||.|.||..+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhcC
Confidence 355667888999999999999999999997 99999999999999 9999999999999999999999854
No 10
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=6.3e-17 Score=131.15 Aligned_cols=64 Identities=36% Similarity=0.463 Sum_probs=61.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
+.+|.||.|+.+||..||.+|+.+. |....+|+.||..| +|++.||+|||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7889999999999999999999996 99999999999999 9999999999999999999988774
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.65 E-value=1.4e-16 Score=139.76 Aligned_cols=65 Identities=26% Similarity=0.296 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
++.|++|..+|..|+.+||+.|..|. |.+++.|.+|++.| +|+++||+|||||||+|.||..++.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhh
Confidence 56888999999999999999999998 99999999999999 9999999999999999999988644
No 12
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.64 E-value=1.6e-16 Score=132.29 Aligned_cols=68 Identities=28% Similarity=0.362 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCCC
Q 028506 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (208)
Q Consensus 88 ~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~~ 160 (208)
..++|+.||+|+..|+..||..|+.. +|.+..+|..||+.| .|+|.||+|||||||.||||+-....+
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 44788899999999999999999999 599999999999999 999999999999999999998766543
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.63 E-value=1.6e-16 Score=131.33 Aligned_cols=68 Identities=32% Similarity=0.427 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCC
Q 028506 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (208)
Q Consensus 87 ~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~ 159 (208)
+++..|+.||.||..||..||+-|...+ |.++.+|.+++..| .|++.||+|||||||+|.||.+..+.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHHH
Confidence 4556778899999999999999999997 99999999999999 99999999999999999999887654
No 14
>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=99.62 E-value=3.1e-16 Score=105.10 Aligned_cols=57 Identities=39% Similarity=0.640 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 92 rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
|++|+.|+..|+.+|+.+|..++ ||+..++..||..| ||+..+|++||+|||++.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-cccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 57899999999999999999997 99999999999999 99999999999999999986
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=1.8e-15 Score=128.89 Aligned_cols=63 Identities=25% Similarity=0.378 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
+|+-||.||..|+..||+.|... |||+...|+.||.++ .|.+.+|+|||||||+||||..+.-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhc
Confidence 33449999999999999999999 599999999999999 9999999999999999999988774
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.51 E-value=3.8e-15 Score=127.30 Aligned_cols=61 Identities=28% Similarity=0.361 Sum_probs=57.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 93 r~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
+-|.++|..|+.+||+.|.-+ ||.++..+.+||..| ||+|+||+|||||||+|+||..+..
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 558899999999999999999 599999999999999 9999999999999999999887665
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=4e-14 Score=95.91 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=50.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCC----CCHhHHHHHHHHHHHhCCCCccccccccccch
Q 028506 91 TARQRWTPTPAQLQILEHVYDECKGT----PRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~~~~~~----Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR 148 (208)
++|.||.||+.|+..||..|+.+. | |+..+|.+||..| ||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 378999999999999999999996 9 9999999999999 999999999999965
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=3.6e-14 Score=94.32 Aligned_cols=55 Identities=40% Similarity=0.655 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHH
Q 028506 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (208)
Q Consensus 93 r~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~K 152 (208)
+.|+.|+..++.+|+..|..++ ||+..++..||..| ||+..+|++||+|||.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999997 99999999999999 9999999999999998754
No 19
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.46 E-value=2.2e-14 Score=114.96 Aligned_cols=68 Identities=31% Similarity=0.451 Sum_probs=62.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCCCCC
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPNN 162 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~~~~ 162 (208)
++++.|++|+..|+..||+.|+... |.+.++|.+||..| +|++.||+.||||||+|.||.++...+.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n 166 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQPKN 166 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 4667799999999999999999994 99999999999999 99999999999999999999988776443
No 20
>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=99.46 E-value=5.3e-14 Score=94.14 Aligned_cols=57 Identities=40% Similarity=0.678 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhh
Q 028506 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (208)
Q Consensus 93 r~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~ 154 (208)
+.|..++..++.+|+.+|..++ ||+..++..||..| ||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 5678999999999999999997 99999999999999 999999999999999998763
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.45 E-value=3e-14 Score=123.87 Aligned_cols=64 Identities=28% Similarity=0.380 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcC
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~ 157 (208)
..-||-||.||.+|+..||+.|-+-+ |.+++.|.+||..| +|+|..|+|||||||+|+||++..
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 35678999999999999999999997 99999999999999 999999999999999999998765
No 22
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.44 E-value=1.1e-13 Score=118.20 Aligned_cols=62 Identities=32% Similarity=0.504 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcC
Q 028506 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~ 157 (208)
-+|.||.|+.+||..|+..|..+ ||.+...|.+||.+| +|.+.||+|||||+|+|-||-...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhccCC
Confidence 35789999999999999999999 699999999999999 999999999999999999986544
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.39 E-value=3.5e-13 Score=108.49 Aligned_cols=65 Identities=31% Similarity=0.448 Sum_probs=58.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCC
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~ 159 (208)
..+++|+..+..|+.+|++.|+.++ ||+...|..|+..| +|+++.|+|||||||++.|+......
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccch
Confidence 3555666779999999999999997 99999999999999 99999999999999999999877654
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.39 E-value=1.6e-13 Score=119.74 Aligned_cols=67 Identities=27% Similarity=0.399 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCC
Q 028506 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (208)
Q Consensus 88 ~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~ 159 (208)
..|+||.||.|+..||..||..|.++ |||+...|++||.-. +|++.+|+|||.|||+||+|+.+...
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 34788999999999999999999999 699999999999999 99999999999999999999877654
No 25
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.33 E-value=5.4e-13 Score=111.02 Aligned_cols=63 Identities=30% Similarity=0.447 Sum_probs=57.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
..+++..|+.+|+..||..|+... |....++..||+.| ||.++||.|||||||||||.++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 344556789999999999999996 99999999999999 9999999999999999999988774
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.26 E-value=5.4e-12 Score=105.51 Aligned_cols=67 Identities=27% Similarity=0.408 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCCCC
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~~~ 160 (208)
.+++..|.+|+..|+..||..|+..+ |+-.++|.+||..| |+++.+|+|||||||.||||+...+..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhh-cccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchh
Confidence 45667899999999999999999997 99999999999999 999999999999999999999877653
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.22 E-value=1.3e-11 Score=103.54 Aligned_cols=103 Identities=19% Similarity=0.204 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHhhHhhhcccccccCCCCCCCCCCCccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHH
Q 028506 48 VYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA 127 (208)
Q Consensus 48 ~y~~ic~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~ 127 (208)
.++.-|-.+..+...+......... .|...+..........+.|+.|+.|+..|+.+||+.|+.. |||+...++.||.
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~ 95 (235)
T KOG0490|consen 18 YWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLAL 95 (235)
T ss_pred HHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhh
Confidence 3444555555555544422222222 4444444433322234678899999999999999999999 5999999999999
Q ss_pred HHHHhCCCCccccccccccchhhHHhhhc
Q 028506 128 ELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 128 ~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
.+ ++++..|+|||||||+|++++..
T Consensus 96 ~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 96 LL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 99 99999999999999999998874
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.02 E-value=7.6e-10 Score=99.89 Aligned_cols=65 Identities=31% Similarity=0.499 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcC
Q 028506 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (208)
Q Consensus 88 ~~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~ 157 (208)
.++.+|.|++|+..|+..||+.|+.++ ||+...|+.||.++ ++++..|+|||+|||++++|....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 446778899999999999999999997 99999999999999 999999999999999999998843
No 29
>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=98.84 E-value=1.9e-10 Score=81.53 Aligned_cols=59 Identities=15% Similarity=0.120 Sum_probs=54.0
Q ss_pred CCcCchhhhhhhcccCCcccCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcc
Q 028506 8 FQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (208)
Q Consensus 8 ~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~y~~ic~~~~~~~~~~~~~ 66 (208)
|++.++..++.|+|||.++|.+||.+||++.||+|+++..+++++|+..|.+.+|+.+.
T Consensus 16 fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 16 FKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 67788999999999999999999999999999999999999999999999999999763
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.83 E-value=9e-09 Score=88.73 Aligned_cols=54 Identities=22% Similarity=0.372 Sum_probs=47.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~ 155 (208)
.|...-+..|..+|..++ ||+..++.+||+.+ ||+..||-+||+|||+|+|-..
T Consensus 182 CFKekSR~~LrewY~~~~-YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNP-YPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred ehhHhhHHHHHHHHhcCC-CCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhhcc
Confidence 355566789999999997 99999999999999 9999999999999999998433
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.52 E-value=4.1e-07 Score=78.23 Aligned_cols=62 Identities=23% Similarity=0.435 Sum_probs=55.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcC
Q 028506 91 TARQRWTPTPAQLQILEHVYD---ECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~---~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~ 157 (208)
.||+|..|+..-..+|..+|. .++ ||+.+..++||+++ +|+..||-+||.|+|-+.||....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nP-YPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNP-YPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhh
Confidence 677888999999999999995 456 99999999999999 999999999999999999886543
No 32
>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=98.15 E-value=5.8e-07 Score=56.46 Aligned_cols=34 Identities=26% Similarity=0.558 Sum_probs=28.1
Q ss_pred hcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhh
Q 028506 112 ECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (208)
Q Consensus 112 ~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k 150 (208)
.+| ||+.+++..||... ||+..||..||-|.|.|
T Consensus 7 ~nP-YPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNP-YPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp TSG-S--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCC-CCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 356 99999999999999 99999999999998864
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.98 E-value=6.4e-06 Score=68.97 Aligned_cols=63 Identities=35% Similarity=0.555 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 89 ~~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
.+.++.|+.+...++..|+..|..++ +|+...+..|+..+ |+++..|++||+|+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 46778899999999999999999997 99999999999999 99999999999999999998765
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.90 E-value=8.8e-06 Score=76.28 Aligned_cols=57 Identities=26% Similarity=0.426 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhH
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~ 151 (208)
..++.|.+|+..|+..|..+|+.++ +|+.+..+.|+.+| +|....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 4677899999999999999999998 99999999999999 999999999999988775
No 35
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=97.85 E-value=3.4e-06 Score=59.84 Aligned_cols=59 Identities=14% Similarity=0.076 Sum_probs=54.3
Q ss_pred CCcCchhhhhhhcccCCcccCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcc
Q 028506 8 FQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (208)
Q Consensus 8 ~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~y~~ic~~~~~~~~~~~~~ 66 (208)
+.+.+...+..|+++|.++|.+||..+|+.+|++|+....+++++|+..|.+.+|+...
T Consensus 16 lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 16 FKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred HHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 44566778899999999999999999999999999999999999999999999999764
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.56 E-value=7.4e-05 Score=76.08 Aligned_cols=64 Identities=23% Similarity=0.352 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
.+|+.|+.++..||.+|...|... +||...+++.|...+ +++.++|+|||||-|+|.|+.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhcc
Confidence 367789999999999999999999 599999999999999 9999999999999999999987755
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.93 E-value=0.0028 Score=42.55 Aligned_cols=42 Identities=24% Similarity=0.473 Sum_probs=30.1
Q ss_pred HHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchh
Q 028506 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (208)
Q Consensus 103 l~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~ 149 (208)
+..|+++|.... .+...+...|..+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 456999999996 99999999999888 9999999999975543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.02 E-value=0.022 Score=51.01 Aligned_cols=61 Identities=23% Similarity=0.265 Sum_probs=48.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---cCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 91 TARQRWTPTPAQLQILEHVYDE---CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 91 ~rr~Rt~~s~~ql~~Le~~F~~---~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
..|.+..+......+|+.+... .+ ||+..+...||.++ ||+..+|.+||-|.|.|..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~P-YPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHP-YPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCC-CCcchhccccchhc----CCCcccCCchhhhcccccCCchH
Confidence 3455567888888888877433 35 99999888888888 99999999999999988766444
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.02 E-value=0.056 Score=52.97 Aligned_cols=49 Identities=14% Similarity=0.333 Sum_probs=44.9
Q ss_pred HHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 103 l~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
+..|..+|..|. .|+..+...||.++ ||+...|+.||+++++......+
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhcc
Confidence 778999999997 99999999999999 99999999999999999876553
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=91.07 E-value=0.3 Score=29.99 Aligned_cols=22 Identities=32% Similarity=0.468 Sum_probs=19.9
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 028506 33 VMTDEQMELLRKQIAVYAMICE 54 (208)
Q Consensus 33 ~~t~~q~~~lr~qi~~y~~ic~ 54 (208)
.||.+|+..||+||..|..+..
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5899999999999999988765
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=85.41 E-value=1.3 Score=29.09 Aligned_cols=46 Identities=20% Similarity=0.256 Sum_probs=32.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccc
Q 028506 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 147 (208)
Q Consensus 92 rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNR 147 (208)
+|+|..+|-.+...+-..++.+. ....||..+ |++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~------s~~~ia~~f----gv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE------SKRDIAREF----GVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHH----T--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC------CHHHHHHHh----CCCHHHHHHHHHhH
Confidence 46788999988766666676653 356899999 99999999999874
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=69.78 E-value=6.4 Score=25.99 Aligned_cols=38 Identities=32% Similarity=0.481 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCC---CCHhHHHHHHHHHHHhCCCCccccc
Q 028506 98 PTPAQLQILEHVYDECKGT---PRKQKIQDMTAELAKHGQISETNVY 141 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~---Ps~~~r~~LA~~L~~~~gls~~~V~ 141 (208)
+|+.|+.+|...|+.+ | |-.....+||..| |++...|-
T Consensus 1 LT~~Q~e~L~~A~~~G--Yfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELG--YFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcC--CCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 4788999999999886 4 4445568899999 99987654
No 43
>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=61.23 E-value=7.1 Score=26.51 Aligned_cols=42 Identities=24% Similarity=0.440 Sum_probs=26.2
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHhHHHHHHHHHHHhCCCCcccccccc
Q 028506 93 RQRWTPTPAQLQILEHVY-DECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (208)
Q Consensus 93 r~Rt~~s~~ql~~Le~~F-~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWF 144 (208)
++|..|++++...+-..+ ..+ ..+..+|..+ ||+...+..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~----gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY----GISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH----TS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc----ccccccccHHH
Confidence 456788998866555554 333 3567899999 99999999995
No 44
>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=53.18 E-value=9.9 Score=22.98 Aligned_cols=41 Identities=12% Similarity=0.163 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccch
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR 148 (208)
+++.+..++...|..+ + ....+|..+ |++...|+.|...-+
T Consensus 11 l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHH
Confidence 5667777777776443 2 244788899 999999999875433
No 45
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.49 E-value=17 Score=30.20 Aligned_cols=39 Identities=26% Similarity=0.348 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCC---HhHHHHHHHHHHHhCCCCccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPR---KQKIQDMTAELAKHGQISETNVY 141 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps---~~~r~~LA~~L~~~~gls~~~V~ 141 (208)
.+|+.|+.+|..+|..+ |.+ .....+||+.| |+++..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~G--YFd~PR~~~l~dLA~~l----GISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG--YFDYPRRVSLKDLAKEL----GISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcC--CCCCCccCCHHHHHHHh----CCCHHHHH
Confidence 79999999999999986 544 44557789999 99987543
No 46
>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=46.97 E-value=16 Score=22.87 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
.+++.+..+|...|-.+ + ...+||..| |++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~--~----t~~eIa~~l----g~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--L----TLEEIAERL----GISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--C----CHHHHHHHH----CCcHHHHHHHHH
Confidence 46788889999988444 2 245899999 999999887654
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=45.90 E-value=8.8 Score=24.39 Aligned_cols=39 Identities=21% Similarity=0.182 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCcccccccccc
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQN 146 (208)
+++.+..++...|-.+ ....+||..+ |+++..|+.|...
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHH
Confidence 4566666776666554 2345888999 9999999999863
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=43.36 E-value=48 Score=17.48 Aligned_cols=37 Identities=16% Similarity=0.423 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCcccccccc
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWF 144 (208)
++......+...|... + ....+|..+ |++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~--~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG--E----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHhC
Confidence 4555555565566533 3 345788888 99988888773
No 49
>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=39.75 E-value=13 Score=25.31 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhCCCCcccccccc
Q 028506 122 IQDMTAELAKHGQISETNVYNWF 144 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWF 144 (208)
-..||..| |+++.+|+.|=
T Consensus 25 lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHh
Confidence 45789999 99999999993
No 50
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.17 E-value=33 Score=26.59 Aligned_cols=47 Identities=9% Similarity=-0.009 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
.+++.+..+|...|-.+ ++ ..+||..| |++...|+.|...-+.+.++
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS----YEEIAEIM----GCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 45666666666655433 22 34889999 99999999988754444444
No 51
>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=33.60 E-value=21 Score=23.84 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhCCCCccccccccc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
..+||..| |++...|+.|-+
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH
Confidence 44899999 999999999953
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.42 E-value=43 Score=26.93 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~ 154 (208)
.+++.+..+|...|-.+ ....+||+.| |++...|+++...-|.+.|+.
T Consensus 142 ~L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHH
Confidence 34555555665544332 2345889999 999999999886555554443
No 53
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=33.20 E-value=59 Score=24.53 Aligned_cols=41 Identities=10% Similarity=0.317 Sum_probs=26.8
Q ss_pred CCCCCHHHH-HHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccc
Q 028506 95 RWTPTPAQL-QILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 95 Rt~~s~~ql-~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
|..|+.+.. .++..++..+ ++ ...+|..+ ||+...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--~s----v~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--MT----VSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--CC----HHHHHHHH----CcCHHHHHHHHH
Confidence 344677654 3444444433 33 34789999 999999999953
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.00 E-value=48 Score=25.50 Aligned_cols=47 Identities=15% Similarity=0.107 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhh
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~ 154 (208)
+++.+..++...|-.+ + ...+||..| |+++..|++....-|.+-|+.
T Consensus 107 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEE--K----SYQEIALQE----KIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555544433 2 234888999 999999999886555555543
No 55
>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=30.57 E-value=40 Score=21.74 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k 150 (208)
.+|+.++.+|.-...-. ...+||..| ++++..|+....+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHH
Confidence 47888888887655332 245899999 99999999887655444
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=30.54 E-value=59 Score=25.76 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhh
Q 028506 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 96 t~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~ 155 (208)
..+++.|..+|.. +..+ +. ..+||..| |++...|..|-...+.+.++..
T Consensus 5 ~~Lt~rqreVL~l-r~~G--lT----q~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--LT----QQEIADIL----GTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 5678999999987 4333 22 34899999 9999999999987666655543
No 57
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=30.46 E-value=70 Score=34.14 Aligned_cols=61 Identities=21% Similarity=0.317 Sum_probs=53.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhh
Q 028506 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 90 ~~rr~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~ 155 (208)
+.++.|...-+.++.+|-++|-.+. -|+..-+.-|.... ..+.+.+.+||.|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 4566788888899999999999998 89998888888877 7889999999999999988877
No 58
>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=30.24 E-value=43 Score=24.54 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHH
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~K 152 (208)
.+++.+..++...|-.+ + ...+||..+ |+++..|+.+...-+.|-|
T Consensus 110 ~L~~~~~~ii~~~~~~g--~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG--L----SYKEIAEIL----GISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 34566666665554332 2 344889999 9999999998765444433
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.49 E-value=46 Score=25.31 Aligned_cols=44 Identities=7% Similarity=0.062 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k 150 (208)
.+++.+..++...|-.+ ....+||..| |++...|+.+...-+.+
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEK 149 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHH
Confidence 34555666665555443 2356889999 99999999987543333
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=29.21 E-value=53 Score=26.78 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhCCCCccccccccccchhhHHhhh
Q 028506 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 121 ~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~ 155 (208)
...+||..| |+++..|+++...-+.+.++..
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 345888899 9999999998865555555443
No 61
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=29.21 E-value=1e+02 Score=31.20 Aligned_cols=61 Identities=16% Similarity=0.172 Sum_probs=44.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhcCC
Q 028506 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (208)
Q Consensus 93 r~Rt~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~~~ 158 (208)
+-|+.....+-..|...++.+. .++..+-..++..| ...+.+|.|||++|+...+......
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~-s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~l 688 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQA-SPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLFL 688 (1007)
T ss_pred cccCCCCccchhhhHhhhhccc-CccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCcccc
Confidence 3445566666667788888775 66666666666667 6788889999999999887765553
No 62
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.72 E-value=45 Score=25.75 Aligned_cols=46 Identities=11% Similarity=-0.037 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHH
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~K 152 (208)
.+++.+..+|.-.|-.+ ++ ..+||..| |++...|+++...-|.+-+
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s----~~eIA~~l----gis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FS----YKEIAEMT----GLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 35555666665554443 22 34888999 9999999988764444443
No 63
>PRK09480 slmA division inhibitor protein; Provisional
Probab=28.61 E-value=54 Score=25.75 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=29.2
Q ss_pred HHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccch
Q 028506 105 ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (208)
Q Consensus 105 ~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR 148 (208)
.....|...+ . ....+..||+.. |++...++.+|.|+-
T Consensus 18 aa~~l~~~~~-G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 18 ALAQMLESPP-G-ERITTAKLAARV----GVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHhcC-C-CccCHHHHHHHh----CCCHhHHHHHCCCHH
Confidence 3334455443 5 677888999998 999999999999975
No 64
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.58 E-value=54 Score=25.42 Aligned_cols=50 Identities=14% Similarity=0.034 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
.+++.+..++...|-.+ ....+||..| |+++..|+++...-|.+-|+.-.
T Consensus 108 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE------LTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hCCHHHHHHHHhHHHhc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 34455555554433332 2245888899 99999999998765655555433
No 65
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=27.96 E-value=19 Score=35.16 Aligned_cols=20 Identities=40% Similarity=0.629 Sum_probs=0.0
Q ss_pred CccccccccccchhhHHhhh
Q 028506 136 SETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 136 s~~~V~vWFQNRR~k~Kr~~ 155 (208)
+...|+.||.|||.++|+.+
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhcchHHHHHHHHHHHhhhh
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.76 E-value=69 Score=25.26 Aligned_cols=50 Identities=26% Similarity=0.262 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
.+++.+..++...|-.+ ....+||..| |++...|+..+..-|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG------ASIKETAAKL----SMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhh
Confidence 34455555555544333 2345888999 99999999988766666655443
No 67
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.51 E-value=63 Score=26.00 Aligned_cols=49 Identities=10% Similarity=-0.001 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
+++.+..++.-.|-.+ + ...+||..| |+++..|++....-|.+-++...
T Consensus 117 Lp~~~r~i~~L~~~~g--~----s~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASG--F----AYEEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444555554443332 2 234888999 99999999987765655555443
No 68
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.94 E-value=55 Score=25.71 Aligned_cols=46 Identities=15% Similarity=0.243 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
+++.+..++...|-.+ ....+||..| |++...|++....-|.+-+.
T Consensus 137 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYMED------LSLKEISEIL----DLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4444444554433222 2345888999 99999999988655555444
No 69
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=26.45 E-value=27 Score=21.66 Aligned_cols=21 Identities=29% Similarity=0.801 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhCCCCcccccccccc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQN 146 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQN 146 (208)
..++|+.| |++...|..|.+.
T Consensus 20 ~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 20 IREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHHHH----TS-HHHHHHHHT-
T ss_pred HHHHHHHH----CcCHHHHHHHHHH
Confidence 45889999 9999999999753
No 70
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=26.17 E-value=58 Score=25.08 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
..+||..| |++...|+.|...-|.+.|+
T Consensus 144 ~~eIA~~l----gis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 144 YREIAEIL----GVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999998755555544
No 71
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.04 E-value=47 Score=26.50 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 120 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 120 ~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
....+||..| |++...|++++..-|.+.++
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 3456888999 99999999998755555554
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=26.03 E-value=67 Score=24.19 Aligned_cols=43 Identities=16% Similarity=0.047 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhh
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k 150 (208)
+++.+..+|...|-.+ + ...+||..| |+++..|+.+...-|.+
T Consensus 114 L~~~~r~il~l~~~~~--~----~~~eIA~~l----gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG--K----SYKEIAEEL----GISVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHH
Confidence 3455555555544332 2 344788899 99999999876543333
No 73
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.78 E-value=63 Score=22.95 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHhCCCCccccccccc
Q 028506 120 QKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 120 ~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
..+..|...|.+..+|.+.+|.||+.
T Consensus 50 ~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 50 RRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 34556666666666999999999985
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=25.77 E-value=62 Score=25.42 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
+++.+..++...|-.+ + ...+||..| |+++..|++....-|.+-++
T Consensus 135 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG--L----TVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 5566666666555443 2 245888899 99999999987655544443
No 75
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=25.54 E-value=66 Score=26.78 Aligned_cols=49 Identities=14% Similarity=0.057 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
+++.+..+|...|-.+ ++ ..+||..| |+++..|++....-|.+.++...
T Consensus 135 Lp~~~R~v~~L~y~eg--~s----~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 135 LPVEYREVLVLRELED--MS----YREIAAIA----DVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred CCHHHHhHhhhHHhcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHc
Confidence 3444555555444332 22 44888999 99999999987655555555443
No 76
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.28 E-value=29 Score=21.14 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=17.5
Q ss_pred HHHHHHHHHHhCCCCccccccccccc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQNR 147 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQNR 147 (208)
..++|+.+ |++...|+.|.++-
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHCC
Confidence 35778888 99999999996543
No 77
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.20 E-value=71 Score=25.29 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
..+||..| |++...|+.....-|.+-|+...
T Consensus 147 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVM----DISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788899 99999999987655555555433
No 78
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.16 E-value=67 Score=24.73 Aligned_cols=47 Identities=13% Similarity=0.200 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~ 154 (208)
.+++.+..+|...| .+ ++ ..+||..| |++...|+.+...-|.+.|+.
T Consensus 112 ~L~~~~r~il~l~~-~g--~s----~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--YS----YKEIAEAL----GIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-cC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35666666776666 43 33 44889999 999999999886555555543
No 79
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.36 E-value=94 Score=24.36 Aligned_cols=28 Identities=7% Similarity=0.388 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
.++||..| |+++..|+++...-|.+.|+
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 99999999987655555444
No 80
>PRK00118 putative DNA-binding protein; Validated
Probab=23.13 E-value=83 Score=23.60 Aligned_cols=46 Identities=20% Similarity=0.285 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
+++.+..++...|..+ + ...+||..+ |++...|+.|...-|.+.+.
T Consensus 18 L~ekqRevl~L~y~eg--~----S~~EIAe~l----GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--Y----SLGEIAEEF----NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 3566666776665554 2 244789999 99999999998755555443
No 81
>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=23.12 E-value=75 Score=24.95 Aligned_cols=49 Identities=16% Similarity=0.099 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~ 155 (208)
.+++.+..+|...|-.+ + ...+||..| |+++..|+++-..-|.+.++..
T Consensus 100 ~L~~~~r~v~~l~~~~g--~----s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--L----SQQEIAEKL----GLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45666666666655443 2 345889999 9999999998765555555443
No 82
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.10 E-value=25 Score=21.81 Aligned_cols=39 Identities=18% Similarity=0.231 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCcccccccc
Q 028506 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (208)
Q Consensus 96 t~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWF 144 (208)
..+|..+...++..+..+. ...+||..| |.+...|..+.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~------s~~~IA~~l----g~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM------SIREIAKRL----GRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC------CHHHHHHHH----CcCcHHHHHHH
Confidence 4567888888888876552 244799999 99988887654
No 83
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.10 E-value=37 Score=20.98 Aligned_cols=21 Identities=29% Similarity=0.817 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCCCcccccccccc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQN 146 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQN 146 (208)
..++|..+ ||+...|..|.+.
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHH
Confidence 34788898 9999999999754
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.71 E-value=84 Score=23.96 Aligned_cols=47 Identities=17% Similarity=0.109 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
.+++.+..++.-.|-.+ ++ ..+||..| |++...|++....-|.+.|+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s----~~EIA~~l----gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MD----VAETAAAM----GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 34555555555544443 22 45889999 99999999876544444443
No 85
>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=22.40 E-value=85 Score=24.06 Aligned_cols=45 Identities=22% Similarity=0.186 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHh
Q 028506 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (208)
Q Consensus 99 s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr 153 (208)
++.+..+|...|-.+ + ...+||..| |++...|+++-..-|.+-++
T Consensus 112 ~~~~r~i~~l~~~~g--~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 112 PARQRAVVVLRYYED--L----SEAQVAEAL----GISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHhhhHHHhc--C----CHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 455555555554332 2 234888899 99999999987655555444
No 86
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.28 E-value=77 Score=25.28 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 98 ~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
+++.+..+|...|-.+ ....+||..| |++...|+..+..-|.+.++...
T Consensus 107 L~~~~r~i~~l~~~~g------~~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 107 LPEKYAEALRLTELEG------LSQKEIAEKL----GLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444555554443332 2345888999 99999999988755555554433
No 87
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=22.12 E-value=77 Score=24.12 Aligned_cols=39 Identities=15% Similarity=0.240 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
.+++.+..++...|-.+ ....+||..| |++...|+++..
T Consensus 111 ~L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHH
Confidence 45566666666544332 2345889999 999999998754
No 88
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.01 E-value=85 Score=24.94 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccccchhhHHhh
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~ 154 (208)
.+++.+..+|...|-.+ ....+||..| |++...|++-...-|.+.++.
T Consensus 131 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 34455555555444332 2345788899 999999999776555555554
No 89
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.40 E-value=86 Score=24.09 Aligned_cols=39 Identities=18% Similarity=0.144 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
.+++.+..+|...|-.+ ....+||..| |+++..|++...
T Consensus 122 ~L~~~~r~vl~l~~~~g------~s~~eIA~~l----~is~~tv~~~l~ 160 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN------LPIAEVARIL----GKTEGAVKILQF 160 (170)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHH
Confidence 34455555555543332 2345888999 999999988653
No 90
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.00 E-value=56 Score=20.20 Aligned_cols=38 Identities=18% Similarity=0.485 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCcccccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWF 144 (208)
.++..+...+...+... + .+.+||+.+ |++...|+-++
T Consensus 5 ~~~~~~~~~i~~l~~~G--~----si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG--M----SIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC--C----CHHHHHHHH----CcCHHHHHHHH
Confidence 35555566666666654 2 356888998 99998887665
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=20.56 E-value=1.1e+02 Score=18.45 Aligned_cols=38 Identities=24% Similarity=0.326 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHHhCCCCccccccccc
Q 028506 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (208)
Q Consensus 97 ~~s~~ql~~Le~~F~~~~~~Ps~~~r~~LA~~L~~~~gls~~~V~vWFQ 145 (208)
.+++.+..++...+ .+ + ...+||..+ |++...|+.|..
T Consensus 3 ~l~~~e~~i~~~~~-~g--~----s~~eia~~l----~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLA-EG--L----TNKEIAERL----GISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHH
Confidence 35677777775532 22 2 235888999 999999998865
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.28 E-value=83 Score=25.37 Aligned_cols=31 Identities=16% Similarity=0.129 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhCCCCccccccccccchhhHHhhhc
Q 028506 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (208)
Q Consensus 122 r~~LA~~L~~~~gls~~~V~vWFQNRR~k~Kr~~~ 156 (208)
..+||..| |++...|+++...-|.+-|+...
T Consensus 132 ~~EIA~~L----giS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 132 YEEAAEMC----GVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHh
Confidence 45888999 99999999998766666555443
Done!