Query 027250
Match_columns 226
No_of_seqs 296 out of 1507
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:08:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027250.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027250hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802 Transcription factor O 100.0 1.3E-33 2.9E-38 255.0 4.5 141 7-156 214-354 (398)
2 KOG0488 Transcription factor B 99.7 1.1E-18 2.4E-23 156.7 6.2 73 83-160 164-236 (309)
3 KOG0489 Transcription factor z 99.7 7.7E-19 1.7E-23 154.5 4.4 69 88-161 156-224 (261)
4 KOG0484 Transcription factor P 99.7 1E-18 2.2E-23 131.8 3.6 66 88-158 14-79 (125)
5 KOG0850 Transcription factor D 99.7 1.5E-17 3.2E-22 141.3 6.1 69 85-158 116-184 (245)
6 KOG1168 Transcription factor A 99.7 1.9E-18 4.1E-23 151.0 -0.5 144 7-158 225-371 (385)
7 KOG0842 Transcription factor t 99.7 1.4E-17 3.1E-22 148.1 4.8 67 88-159 150-216 (307)
8 KOG2251 Homeobox transcription 99.7 3.3E-17 7.1E-22 138.5 6.5 68 86-158 32-99 (228)
9 KOG0843 Transcription factor E 99.7 3E-17 6.5E-22 134.9 5.8 64 90-158 101-164 (197)
10 KOG4577 Transcription factor L 99.7 2E-17 4.2E-22 144.6 3.5 112 43-159 110-230 (383)
11 KOG0487 Transcription factor A 99.7 7.9E-17 1.7E-21 143.4 5.8 66 87-157 231-296 (308)
12 KOG0485 Transcription factor N 99.6 1.2E-16 2.7E-21 134.7 5.1 68 87-159 100-167 (268)
13 KOG0492 Transcription factor M 99.6 1.3E-16 2.8E-21 133.8 4.2 67 87-158 140-206 (246)
14 PF00046 Homeobox: Homeobox do 99.6 3.5E-16 7.6E-21 106.4 5.0 57 92-153 1-57 (57)
15 KOG0494 Transcription factor C 99.6 6E-16 1.3E-20 133.5 5.7 65 89-158 138-203 (332)
16 KOG0848 Transcription factor C 99.5 1.7E-15 3.6E-20 131.3 2.2 61 93-158 201-261 (317)
17 KOG0491 Transcription factor B 99.5 4.7E-15 1E-19 120.4 2.7 67 90-161 99-165 (194)
18 TIGR01565 homeo_ZF_HD homeobox 99.5 3.9E-14 8.5E-19 97.3 5.3 53 91-148 1-57 (58)
19 smart00389 HOX Homeodomain. DN 99.5 4E-14 8.6E-19 95.5 4.7 55 93-152 2-56 (56)
20 cd00086 homeodomain Homeodomai 99.5 5.8E-14 1.3E-18 95.4 5.3 57 93-154 2-58 (59)
21 KOG0847 Transcription factor, 99.5 7.9E-14 1.7E-18 118.0 5.8 116 89-222 165-280 (288)
22 KOG0493 Transcription factor E 99.4 9.6E-14 2.1E-18 120.1 5.7 62 91-157 246-307 (342)
23 KOG0844 Transcription factor E 99.4 4.9E-14 1.1E-18 124.2 3.1 65 89-158 179-243 (408)
24 COG5576 Homeodomain-containing 99.4 2.2E-13 4.8E-18 111.2 5.8 65 91-160 51-115 (156)
25 KOG0486 Transcription factor P 99.4 1.2E-13 2.6E-18 122.1 4.3 66 89-159 110-175 (351)
26 KOG0483 Transcription factor H 99.4 1.5E-13 3.2E-18 116.1 3.2 62 94-160 53-114 (198)
27 KOG0490 Transcription factor, 99.3 2.2E-12 4.7E-17 110.0 5.7 104 47-156 17-120 (235)
28 KOG0849 Transcription factor P 99.0 2.9E-10 6.2E-15 104.2 5.0 66 87-157 172-237 (354)
29 PF00157 Pou: Pou domain - N-t 98.8 2.5E-10 5.5E-15 82.0 -2.6 59 8-66 16-74 (75)
30 KOG0775 Transcription factor S 98.8 3.2E-08 6.9E-13 86.6 8.3 56 93-153 169-233 (304)
31 KOG0774 Transcription factor P 98.6 6.5E-07 1.4E-11 78.1 10.8 102 33-157 146-252 (334)
32 PF05920 Homeobox_KN: Homeobox 98.2 9.8E-07 2.1E-11 56.2 1.9 33 114-150 8-40 (40)
33 KOG0490 Transcription factor, 98.0 5.5E-06 1.2E-10 70.5 4.4 64 88-156 150-213 (235)
34 smart00352 POU Found in Pit-Oc 97.9 2E-06 4.3E-11 61.9 0.0 59 8-66 16-74 (75)
35 KOG2252 CCAAT displacement pro 97.8 1.8E-05 3.9E-10 75.3 4.5 57 90-151 419-475 (558)
36 KOG1146 Homeobox protein [Gene 97.2 0.00031 6.7E-09 72.8 4.4 62 90-156 902-963 (1406)
37 PF11569 Homez: Homeodomain le 96.2 0.0024 5.1E-08 43.5 1.3 42 103-149 10-51 (56)
38 KOG0773 Transcription factor M 94.7 0.031 6.8E-07 50.8 3.7 59 91-153 239-299 (342)
39 KOG3623 Homeobox transcription 93.9 0.079 1.7E-06 52.7 4.7 50 103-157 568-617 (1007)
40 PF04218 CENP-B_N: CENP-B N-te 89.1 0.71 1.5E-05 30.8 3.8 47 92-148 1-47 (53)
41 PF08880 QLQ: QLQ; InterPro: 88.6 0.58 1.3E-05 29.2 2.9 22 33-54 2-23 (37)
42 PF04967 HTH_10: HTH DNA bindi 65.5 7.8 0.00017 26.0 2.9 39 98-141 1-41 (53)
43 PF04545 Sigma70_r4: Sigma-70, 63.1 13 0.00028 23.7 3.6 44 97-150 4-47 (50)
44 cd06171 Sigma70_r4 Sigma70, re 61.0 8.9 0.00019 23.6 2.5 43 98-150 11-53 (55)
45 PF01527 HTH_Tnp_1: Transposas 57.1 8.8 0.00019 26.5 2.1 44 93-146 2-46 (76)
46 PF08281 Sigma70_r4_2: Sigma-7 51.8 18 0.00038 23.3 2.8 41 98-148 11-51 (54)
47 cd00569 HTH_Hin_like Helix-tur 50.0 31 0.00067 18.6 3.4 37 98-144 6-42 (42)
48 COG3413 Predicted DNA binding 48.0 25 0.00054 29.7 3.8 50 97-152 155-205 (215)
49 KOG3755 SATB1 matrix attachmen 46.0 15 0.00033 36.4 2.3 50 107-157 708-760 (769)
50 PRK03975 tfx putative transcri 39.9 41 0.00088 27.1 3.6 50 96-156 5-54 (141)
51 PF10668 Phage_terminase: Phag 38.6 15 0.00032 25.3 0.8 19 122-144 25-43 (60)
52 PRK06759 RNA polymerase factor 37.2 38 0.00083 26.2 3.1 46 97-152 106-151 (154)
53 PRK09646 RNA polymerase sigma 37.0 45 0.00099 27.2 3.6 47 98-154 143-189 (194)
54 PF13936 HTH_38: Helix-turn-he 36.7 21 0.00045 22.6 1.2 40 96-145 3-42 (44)
55 PRK09652 RNA polymerase sigma 36.4 50 0.0011 26.0 3.7 48 97-154 128-175 (182)
56 PRK09413 IS2 repressor TnpA; R 33.9 63 0.0014 24.8 3.8 41 95-145 10-51 (121)
57 PF00196 GerE: Bacterial regul 32.8 69 0.0015 20.9 3.4 44 97-151 3-46 (58)
58 PRK12526 RNA polymerase sigma 32.1 60 0.0013 26.9 3.6 31 121-155 171-201 (206)
59 PRK09480 slmA division inhibit 31.8 40 0.00088 27.0 2.5 36 108-149 21-56 (194)
60 PRK12512 RNA polymerase sigma 31.4 73 0.0016 25.5 4.0 50 98-157 132-181 (184)
61 TIGR02937 sigma70-ECF RNA poly 31.4 63 0.0014 24.0 3.4 46 98-153 111-156 (158)
62 PRK09642 RNA polymerase sigma 31.4 73 0.0016 24.8 3.9 48 98-155 107-154 (160)
63 PRK12516 RNA polymerase sigma 29.6 91 0.002 25.4 4.3 50 98-157 117-166 (187)
64 PRK04217 hypothetical protein; 29.2 78 0.0017 24.4 3.5 51 96-156 41-91 (110)
65 PRK12519 RNA polymerase sigma 29.2 54 0.0012 26.6 2.9 30 121-154 159-188 (194)
66 PF06056 Terminase_5: Putative 29.1 29 0.00064 23.5 1.0 20 122-145 16-35 (58)
67 PRK00118 putative DNA-binding 29.0 78 0.0017 24.1 3.5 46 98-153 18-63 (104)
68 PRK09644 RNA polymerase sigma 28.9 76 0.0017 25.0 3.6 49 98-156 109-157 (165)
69 COG4367 Uncharacterized protei 28.6 62 0.0013 24.2 2.7 39 98-141 3-41 (97)
70 PF02796 HTH_7: Helix-turn-hel 28.0 40 0.00087 21.2 1.5 38 97-144 5-42 (45)
71 PRK12514 RNA polymerase sigma 27.8 91 0.002 24.8 3.9 28 122-153 148-175 (179)
72 PRK12541 RNA polymerase sigma 27.7 74 0.0016 24.9 3.3 46 98-153 113-158 (161)
73 TIGR02948 SigW_bacill RNA poly 27.6 72 0.0016 25.5 3.3 30 121-154 154-183 (187)
74 PRK11924 RNA polymerase sigma 27.5 74 0.0016 24.9 3.3 29 122-154 144-172 (179)
75 KOG1146 Homeobox protein [Gene 27.4 54 0.0012 35.5 3.0 61 90-155 704-764 (1406)
76 TIGR02999 Sig-70_X6 RNA polyme 26.9 80 0.0017 25.2 3.5 46 98-153 135-180 (183)
77 PF13518 HTH_28: Helix-turn-he 26.7 37 0.0008 21.3 1.2 23 122-148 15-37 (52)
78 cd04761 HTH_MerR-SF Helix-Turn 26.3 35 0.00075 21.1 1.0 22 122-147 3-24 (49)
79 TIGR02985 Sig70_bacteroi1 RNA 25.8 1.1E+02 0.0023 23.4 3.9 45 98-152 114-158 (161)
80 PF13384 HTH_23: Homeodomain-l 25.8 35 0.00076 21.4 0.9 22 121-146 19-40 (50)
81 TIGR02989 Sig-70_gvs1 RNA poly 25.6 84 0.0018 24.3 3.3 44 97-150 111-154 (159)
82 TIGR02959 SigZ RNA polymerase 25.4 87 0.0019 25.0 3.4 50 97-156 100-149 (170)
83 PRK09648 RNA polymerase sigma 24.9 91 0.002 25.1 3.4 46 98-153 140-185 (189)
84 PRK09639 RNA polymerase sigma 24.5 1E+02 0.0023 24.0 3.6 47 98-155 113-159 (166)
85 PRK12515 RNA polymerase sigma 24.5 96 0.0021 25.0 3.5 48 98-155 132-179 (189)
86 smart00421 HTH_LUXR helix_turn 24.3 1.7E+02 0.0037 17.9 4.0 39 97-146 3-41 (58)
87 PRK05602 RNA polymerase sigma 24.1 1.1E+02 0.0023 24.7 3.7 31 122-156 147-177 (186)
88 TIGR03879 near_KaiC_dom probab 23.0 28 0.0006 24.9 0.0 23 120-146 33-55 (73)
89 TIGR02983 SigE-fam_strep RNA p 22.8 1.4E+02 0.003 23.2 4.1 46 99-154 112-157 (162)
90 PRK09047 RNA polymerase factor 22.4 1.3E+02 0.0029 23.2 3.9 47 98-154 107-153 (161)
91 TIGR02952 Sig70_famx2 RNA poly 22.2 1.3E+02 0.0028 23.5 3.8 43 98-150 123-165 (170)
92 smart00027 EH Eps15 homology d 22.0 1.4E+02 0.003 21.5 3.6 46 96-145 2-51 (96)
93 PF05777 Acp26Ab: Drosophila a 21.9 1E+02 0.0022 22.6 2.7 30 18-47 51-88 (90)
94 PRK12537 RNA polymerase sigma 21.7 1.3E+02 0.0028 24.1 3.8 27 122-152 152-178 (182)
95 PRK09637 RNA polymerase sigma 21.6 1.1E+02 0.0024 24.8 3.3 49 98-156 107-155 (181)
96 PRK12530 RNA polymerase sigma 21.3 1.2E+02 0.0025 24.7 3.4 28 122-153 153-180 (189)
97 PRK06930 positive control sigm 21.0 1.2E+02 0.0026 24.8 3.4 50 97-156 114-163 (170)
98 PF13443 HTH_26: Cro/C1-type H 20.8 49 0.0011 21.7 0.9 25 121-149 12-36 (63)
99 PRK12546 RNA polymerase sigma 20.6 1.6E+02 0.0035 24.1 4.1 32 122-157 132-163 (188)
100 PRK07037 extracytoplasmic-func 20.4 1.4E+02 0.0029 23.3 3.5 46 98-153 110-155 (163)
101 TIGR02954 Sig70_famx3 RNA poly 20.4 1.4E+02 0.0031 23.4 3.7 46 98-153 120-165 (169)
102 PRK12539 RNA polymerase sigma 20.3 1.5E+02 0.0033 23.8 3.9 47 98-154 132-178 (184)
103 PRK12547 RNA polymerase sigma 20.2 1.3E+02 0.0028 23.7 3.4 46 98-153 113-158 (164)
104 TIGR02939 RpoE_Sigma70 RNA pol 20.1 1E+02 0.0022 24.7 2.8 30 121-154 156-185 (190)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.98 E-value=1.3e-33 Score=255.05 Aligned_cols=141 Identities=18% Similarity=0.195 Sum_probs=123.7
Q ss_pred CCcccchhhhhhhccCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccCCCCCCCCCCcccCC
Q 027250 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG 86 (226)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~ 86 (226)
.|+|++++.+++|+|||+|+|++||+||||++||||+++.++|++||+..+++.|||.+++..... .+..+.+.+.
T Consensus 214 ~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~-~~~~~~e~i~--- 289 (398)
T KOG3802|consen 214 TFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESREST-GSPNSIEKIG--- 289 (398)
T ss_pred HHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhccccc-CCCCCHHHhh---
Confidence 589999999999999999999999999999999999999999999999999999999999863111 1122222222
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 87 ~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
...++|++||.+....+..||+.|.+| +.|+..+|..||.+| +|+..+|+|||||||.|+||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 222688899999999999999999999 899999999999999 99999999999999999999666
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1.1e-18 Score=156.66 Aligned_cols=73 Identities=23% Similarity=0.314 Sum_probs=66.8
Q ss_pred ccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCC
Q 027250 83 VASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (226)
Q Consensus 83 ~~~~~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~ 160 (226)
+....+||+|+.||.||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||......+
T Consensus 164 ~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 164 YQRSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred cccCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 3445568899999999999999999999999 999999999999999 999999999999999999998877433
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=7.7e-19 Score=154.49 Aligned_cols=69 Identities=23% Similarity=0.322 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCCC
Q 027250 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 161 (226)
Q Consensus 88 ~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~~ 161 (226)
..+.||.||.||..|+.+||+.|+.+ +|.++..|.+||..| .|+|+||||||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34578999999999999999999999 999999999999999 9999999999999999999988776443
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.74 E-value=1e-18 Score=131.77 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 88 ~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
.++.||-||+|+..||.+||+.|... +||++-.|++||.++ .|++.+|+|||||||+|.||+.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 34678899999999999999999999 999999999999999 9999999999999999999987653
No 5
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.70 E-value=1.5e-17 Score=141.29 Aligned_cols=69 Identities=26% Similarity=0.393 Sum_probs=64.8
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 85 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 85 ~~~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
.++.||.|+.||.++..||..|.+.|+++ .|+..++|.+||..| ||+.+||||||||||.|.||..+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhcC
Confidence 45677888999999999999999999999 999999999999999 9999999999999999999999843
No 6
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.69 E-value=1.9e-18 Score=150.98 Aligned_cols=144 Identities=17% Similarity=0.195 Sum_probs=118.9
Q ss_pred CCcccchhhhhhhccCCCCCCCc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccCCCCCCCCCCcc
Q 027250 7 NFQQGGEMERQFQQDGGDTSNGL---CVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFV 83 (226)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~g~~---~~~~~t~~~~~~lr~qi~~~~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~ 83 (226)
-|+|++++.+-+|+|||-++..| .+..+||.+||+|+-+-++-.+|--..+.++.||.++..-.......+... ..
T Consensus 225 rFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~-~l 303 (385)
T KOG1168|consen 225 RFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDIN-EL 303 (385)
T ss_pred HHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchh-hc
Confidence 37899999999999999987777 888999999999999999999999999999999998865222111111111 11
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 84 ASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 84 ~~~~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
-+++ .++|+||.+..-....||.+|... +.|+.+.|..||++| +|....|+|||||.|+|.||.....
T Consensus 304 ~~~~--ekKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 304 LPGG--EKKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cCcc--ccccccccccCcccccHHHHhccC-CCCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhhh
Confidence 1222 367788999999999999999999 899999999999999 9999999999999999999966543
No 7
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.69 E-value=1.4e-17 Score=148.12 Aligned_cols=67 Identities=25% Similarity=0.372 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCC
Q 027250 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (226)
Q Consensus 88 ~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~ 159 (226)
..++||.|..|+..|+.+||+.|.+. +|++.++|+.||..| +|+++||||||||||-|.||+++...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhh
Confidence 45778889999999999999999999 999999999999999 99999999999999999999988763
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.69 E-value=3.3e-17 Score=138.54 Aligned_cols=68 Identities=29% Similarity=0.488 Sum_probs=65.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 86 ~~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
.++++.||.||+|+..|+.+||.+|.++ .||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT-qYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT-QYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh-cCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 6788899999999999999999999999 999999999999999 9999999999999999999988874
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.69 E-value=3e-17 Score=134.88 Aligned_cols=64 Identities=36% Similarity=0.450 Sum_probs=61.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 90 ~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
+.+|.||.|+++||..||.+|+.+ +|....+|+.||..| +|++.||+|||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 788999999999999999999999 999999999999999 9999999999999999999988774
No 10
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.67 E-value=2e-17 Score=144.56 Aligned_cols=112 Identities=23% Similarity=0.300 Sum_probs=99.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhccccccccCCCCCCCCCCcccCC---------CCCCCCCCCCCCCHHHHHHHHHHHhhc
Q 027250 43 RKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG---------SQKLTARQRWTPTPAQLQILEHVYDEC 113 (226)
Q Consensus 43 r~qi~~~~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~---------~~~~~rr~Rt~~s~~Ql~~Le~~F~~~ 113 (226)
++|..||...|.+++.+.+.|.+.++++-|..+...|.-..... +....+|+||+++..||+.|..+|...
T Consensus 110 kAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~S 189 (383)
T KOG4577|consen 110 KAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTS 189 (383)
T ss_pred HhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCC
Confidence 78999999999999999999999999999988877776544322 344578999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCC
Q 027250 114 KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (226)
Q Consensus 114 ~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~ 159 (226)
+.|.+.-|+.|+.+. ||.-+.|||||||||||+||.++..-
T Consensus 190 -pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 190 -PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred -CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcc
Confidence 899999999999999 99999999999999999999887753
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.66 E-value=7.9e-17 Score=143.43 Aligned_cols=66 Identities=27% Similarity=0.303 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 87 ~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
..+..|++|..+|..|+.+||+.|..| .|.+++.|.+|++.| +|+++||+|||||||+|.||..++
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhh
Confidence 346788899999999999999999999 899999999999999 999999999999999999998764
No 12
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.65 E-value=1.2e-16 Score=134.73 Aligned_cols=68 Identities=28% Similarity=0.367 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCC
Q 027250 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (226)
Q Consensus 87 ~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~ 159 (226)
+..++++.||+|+..|+..||..|+.. +|.+..+|..||+.| .|+|.||+|||||||.||||+-....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 344788899999999999999999999 999999999999999 99999999999999999999876643
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.64 E-value=1.3e-16 Score=133.75 Aligned_cols=67 Identities=33% Similarity=0.412 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 87 ~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
+++..|+.||.||..||..||+.|... +|.++++|.+++..| .|+++||+|||||||+|.||.+...
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 455677889999999999999999999 999999999999999 9999999999999999999977654
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=99.63 E-value=3.5e-16 Score=106.41 Aligned_cols=57 Identities=39% Similarity=0.634 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 92 rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
|+.|+.|+.+|+.+|+.+|..+ +||+..+++.||..| ||+..+|++||+|||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-ccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 5778999999999999999998 999999999999999 99999999999999999986
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=6e-16 Score=133.55 Aligned_cols=65 Identities=28% Similarity=0.414 Sum_probs=60.0
Q ss_pred CCCCCC-CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 89 KLTARQ-RWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 89 ~~~rr~-Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
+++||. ||.||..|+.+||+.|+.. +||+...|+-||..+ .|.|.+|+|||||||+||||..++-
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhc
Confidence 334454 9999999999999999999 999999999999999 9999999999999999999988874
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.54 E-value=1.7e-15 Score=131.27 Aligned_cols=61 Identities=28% Similarity=0.361 Sum_probs=57.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 93 r~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
+-|.++|+.|+.+||+.|..+ +|.++..+.+||.-| +|+|+||+|||||||+|+||..+..
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 458899999999999999999 999999999999999 9999999999999999999876654
No 17
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.52 E-value=4.7e-15 Score=120.40 Aligned_cols=67 Identities=30% Similarity=0.420 Sum_probs=62.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCCC
Q 027250 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 161 (226)
Q Consensus 90 ~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~~ 161 (226)
++++.|++|+..|+..||+.|+.. +|.+.++|.+||..| +|++.||+.||||||+|.||.++...+.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 566789999999999999999999 999999999999999 9999999999999999999999887643
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.49 E-value=3.9e-14 Score=97.28 Aligned_cols=53 Identities=17% Similarity=0.375 Sum_probs=50.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHHhhCCCcccccccchhhhH
Q 027250 91 TARQRWTPTPAQLQILEHVYDECKGT----PRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (226)
Q Consensus 91 ~rr~Rt~~s~~Ql~~Le~~F~~~~~~----p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRR 148 (226)
++|.||.||++|+..||..|+.+ +| |+..+|.+||..| ||++.+|+|||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 37889999999999999999999 99 9999999999999 999999999999964
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=4e-14 Score=95.50 Aligned_cols=55 Identities=40% Similarity=0.649 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHH
Q 027250 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (226)
Q Consensus 93 r~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~K 152 (226)
+.|+.++..|+.+|+..|..+ +||+..++..||..| ||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN-PYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 467789999999999999999 899999999999999 9999999999999998854
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=99.48 E-value=5.8e-14 Score=95.36 Aligned_cols=57 Identities=40% Similarity=0.672 Sum_probs=53.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 93 r~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
+.|+.++..++.+||.+|..+ +||+..++..||..+ ||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN-PYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 467889999999999999999 999999999999999 999999999999999998763
No 21
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.46 E-value=7.9e-14 Score=118.03 Aligned_cols=116 Identities=22% Similarity=0.308 Sum_probs=84.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCCCCCCchhh
Q 027250 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPNNAESEAE 168 (226)
Q Consensus 89 ~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~~~~~~~~~ 168 (226)
.+++..|.+|+..|+..||+.|+.. +|+-.++|.+||..| |+++.+|+|||||||.||||+...+..+....
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmasakkk--- 236 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMASAKKK--- 236 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhhcccc---
Confidence 4666779999999999999999999 999999999999999 99999999999999999999876643221110
Q ss_pred hhcchhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCcccchhhhhhhhcccccc
Q 027250 169 TVTHAESRKQNPESIQSLEDSAPPPRDEDIYPQSPDLGNKFFCFNVLLNKYKLI 222 (226)
Q Consensus 169 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sp~~~s~~~~~~~~~~~~~~~ 222 (226)
........--+++.+..++.|...-+-.|+-..|..+|.++++.
T Consensus 237 ----------qds~ae~~~gg~~~eeeDDeYNkPLDPnSDDEKIt~LLkKHk~s 280 (288)
T KOG0847|consen 237 ----------QDSGAERGAGGAPSEEEDDEYNKPLDPNSDDEKITLLLKKHKAS 280 (288)
T ss_pred ----------CCCcccccccCCCccccccccCCCCCCCcchHHHHHHHHhcccc
Confidence 00111112222344445555555445557777888888888753
No 22
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.45 E-value=9.6e-14 Score=120.11 Aligned_cols=62 Identities=32% Similarity=0.504 Sum_probs=58.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 91 ~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
-+|.||.|+.+||..|...|+.+ +|.+...|.+||.+| +|.|.||+|||||+|+|.||....
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 46889999999999999999999 999999999999999 999999999999999999985544
No 23
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.43 E-value=4.9e-14 Score=124.24 Aligned_cols=65 Identities=28% Similarity=0.380 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCC
Q 027250 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (226)
Q Consensus 89 ~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~ 158 (226)
..-||-||.||.+|+..||+.|-+- .|-+++.|.+||..| +|+|..|+|||||||+|+||++-..
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhhc
Confidence 3568889999999999999999888 699999999999999 9999999999999999999987653
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.42 E-value=2.2e-13 Score=111.25 Aligned_cols=65 Identities=31% Similarity=0.452 Sum_probs=59.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCC
Q 027250 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (226)
Q Consensus 91 ~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~ 160 (226)
.+++|...+..|+.+|++.|+.+ +||+...|..|+..| +|+++.|+|||||||++.|+.......
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred CcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccchh
Confidence 56667778999999999999999 999999999999999 999999999999999999998777543
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.41 E-value=1.2e-13 Score=122.14 Aligned_cols=66 Identities=27% Similarity=0.414 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCC
Q 027250 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (226)
Q Consensus 89 ~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~ 159 (226)
+|.||.||.|+..||.+||..|.++ +||+...|++||.-. +|+|.+|+|||.|||+||||..+...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 3788999999999999999999999 999999999999999 99999999999999999998776643
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.39 E-value=1.5e-13 Score=116.08 Aligned_cols=62 Identities=29% Similarity=0.412 Sum_probs=56.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcCCCC
Q 027250 94 QRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (226)
Q Consensus 94 ~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~~~~ 160 (226)
++.+++.+|...||+.|+.. .+....++..||+.| ||.++||.|||||||||||.++.....
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~d~ 114 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEKDY 114 (198)
T ss_pred ccccccHHHHHHhHHhhccc-cccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhhhH
Confidence 33459999999999999999 899999999999999 999999999999999999998877543
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.31 E-value=2.2e-12 Score=110.02 Aligned_cols=104 Identities=19% Similarity=0.201 Sum_probs=77.5
Q ss_pred HHHHHHHHHHHHhhhhhccccccccCCCCCCCCCCcccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Q 027250 47 AVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT 126 (226)
Q Consensus 47 ~~~~~ic~q~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA 126 (226)
..|..-|-.+..+...+......... .|..++..........+.|+.|+.|+..|+.+||+.|+.. +||+...++.||
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la 94 (235)
T KOG0490|consen 17 RYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLA 94 (235)
T ss_pred HHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHh
Confidence 34455555555555555411111112 4555554443332245678999999999999999999999 999999999999
Q ss_pred HHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 127 AELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 127 ~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
..+ ++++..|+|||||||+||+++.+
T Consensus 95 ~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 95 LLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 999 99999999999999999998875
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.01 E-value=2.9e-10 Score=104.23 Aligned_cols=66 Identities=30% Similarity=0.476 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 87 ~~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
..++.+|.||+|+..|+..||+.|+.+ +||+...|+.||.++ ++++..|+|||+|||++++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 345677889999999999999999999 899999999999999 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=98.80 E-value=2.5e-10 Score=82.02 Aligned_cols=59 Identities=15% Similarity=0.120 Sum_probs=53.6
Q ss_pred CcccchhhhhhhccCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccc
Q 027250 8 FQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (226)
Q Consensus 8 ~~~~~~~~~~~q~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~ic~q~~~~~~~l~~~ 66 (226)
|.+.++..+..|+|||.++|.+||+++|+++||+|+++..+++++|+..|.+.+||.++
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 56778888999999999999999999999999999999999999999999999999764
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.75 E-value=3.2e-08 Score=86.60 Aligned_cols=56 Identities=23% Similarity=0.345 Sum_probs=49.4
Q ss_pred CCCCCCCHHH---------HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 93 RQRWTPTPAQ---------LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 93 r~Rt~~s~~Q---------l~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
-+||.+..++ +..|..+|..+ +||+..++.+||+.+ ||+..||-+||+|||+|+|-
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~~~-~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYLQN-PYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHhcC-CCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 3577665554 56899999999 999999999999999 99999999999999999983
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.56 E-value=6.5e-07 Score=78.07 Aligned_cols=102 Identities=21% Similarity=0.320 Sum_probs=73.8
Q ss_pred cCCHHHHHHHHHHHHH-HHHHHHHHHHhh--hhhccccccccCCCCCCCCCCcccCCCCCCCCCCCCCCCHHHHHHHHHH
Q 027250 33 VMTDEQMELLRKQIAV-YAMICEQLVQMH--KVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHV 109 (226)
Q Consensus 33 ~~t~~~~~~lr~qi~~-~~~ic~q~~~~~--~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~rr~Rt~~s~~Ql~~Le~~ 109 (226)
..+...+++++.-|+- |..||-++-+.. +.+.-- ...-..||+|..|+..-..+|..+
T Consensus 146 Pi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr-------------------~r~ldarRKRRNFsK~aTeiLney 206 (334)
T KOG0774|consen 146 PIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILR-------------------SRFLDARRKRRNFSKQATEILNEY 206 (334)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHhhcccchhHHHHHHHH
Confidence 4455667777766665 667666654311 110000 000125677888999999999999
Q ss_pred Hhh--cCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 110 YDE--CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 110 F~~--~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
|.. +++||+.+..++||+++ +++..||-.||.|+|-+.||....
T Consensus 207 F~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 207 FYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhh
Confidence 964 36999999999999999 999999999999999999885443
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=98.17 E-value=9.8e-07 Score=56.20 Aligned_cols=33 Identities=27% Similarity=0.586 Sum_probs=28.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHH
Q 027250 114 KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (226)
Q Consensus 114 ~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak 150 (226)
++||+..++..||..+ ||+..||..||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 4899999999999999 99999999999999865
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.02 E-value=5.5e-06 Score=70.49 Aligned_cols=64 Identities=34% Similarity=0.545 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 88 ~~~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
..+.++.|+.+...|+..|+..|..+ ++|+...+..|+..+ |+++..|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 34678889999999999999999999 899999999999999 99999999999999999998665
No 34
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=97.93 E-value=2e-06 Score=61.91 Aligned_cols=59 Identities=14% Similarity=0.076 Sum_probs=53.9
Q ss_pred CcccchhhhhhhccCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccc
Q 027250 8 FQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (226)
Q Consensus 8 ~~~~~~~~~~~q~~~~~~~g~~~~~~~t~~~~~~lr~qi~~~~~ic~q~~~~~~~l~~~ 66 (226)
+.+.+...+..|++++-++|.+||..+|+.+|++|+....+++++|+..|.+.+|+.++
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 34556677889999999999999999999999999999999999999999999999764
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.82 E-value=1.8e-05 Score=75.30 Aligned_cols=57 Identities=25% Similarity=0.401 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHH
Q 027250 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (226)
Q Consensus 90 ~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~ 151 (226)
..++.|.+|++.|+..|..+|+.+ ++|+.+..+.|+.+| +|....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 456779999999999999999999 999999999999999 999999999999988775
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.22 E-value=0.00031 Score=72.79 Aligned_cols=62 Identities=24% Similarity=0.379 Sum_probs=57.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 90 ~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
.+|+.|+.++..||.++...|... .||...+.+.|...+ +++.+.|++||||-|+|.|+...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhh
Confidence 367789999999999999999999 999999999999999 99999999999999999988665
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.18 E-value=0.0024 Score=43.52 Aligned_cols=42 Identities=21% Similarity=0.439 Sum_probs=30.8
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHH
Q 027250 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (226)
Q Consensus 103 l~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRa 149 (226)
+..|+++|... +.+...+...|+.+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~h-~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKH-KQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHc-CCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 34699999999 899999999999999 9999999999976543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.72 E-value=0.031 Score=50.81 Aligned_cols=59 Identities=24% Similarity=0.290 Sum_probs=47.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 91 TARQRWTPTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 91 ~rr~Rt~~s~~Ql~~Le~~F~~~--~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
..|.+..+......+|+.+.... .+||+..+...||.++ ||+..+|-+||-|.|-|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCC
Confidence 34445578888888998774432 3799999999999999 99999999999999877544
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.91 E-value=0.079 Score=52.71 Aligned_cols=50 Identities=16% Similarity=0.380 Sum_probs=45.7
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 103 l~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
+..|..+|..| ..|+..+...||..+ ||+.+.|+.||+++++......+.
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccC
Confidence 67888899999 899999999999999 999999999999999998876644
No 40
>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=89.09 E-value=0.71 Score=30.77 Aligned_cols=47 Identities=19% Similarity=0.234 Sum_probs=34.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhH
Q 027250 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (226)
Q Consensus 92 rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRR 148 (226)
+|+|..+|-++...+-..++.+ . ....||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 4678889998888877788777 3 356899999 999999999998853
No 41
>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=88.60 E-value=0.58 Score=29.15 Aligned_cols=22 Identities=32% Similarity=0.468 Sum_probs=19.7
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 027250 33 VMTDEQMELLRKQIAVYAMICE 54 (226)
Q Consensus 33 ~~t~~~~~~lr~qi~~~~~ic~ 54 (226)
.||.+|+..||+||..|..+.+
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5899999999999999988655
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=65.47 E-value=7.8 Score=25.96 Aligned_cols=39 Identities=31% Similarity=0.451 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHhhCCCcccccc
Q 027250 98 PTPAQLQILEHVYDECKG--TPRKQKIQDMTAELAKHGQISETNVY 141 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~--~p~~~~r~~LA~~L~~~~~ls~~~V~ 141 (226)
+|+.|+.+|..+|+.+ - +|-.....+||..| |++..-|-
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 4788999999999877 2 35556778899999 99987543
No 43
>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=63.11 E-value=13 Score=23.72 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHH
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak 150 (226)
.+++.+..+|...|-.+ ....++|..+ |++...|+.+...=..|
T Consensus 4 ~L~~~er~vi~~~y~~~------~t~~eIa~~l----g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG------LTLEEIAERL----GISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC------CCHHHHHHHH----CCcHHHHHHHHHHHHHH
Confidence 46788899999988554 1345899999 99999998876544443
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=60.97 E-value=8.9 Score=23.58 Aligned_cols=43 Identities=12% Similarity=0.173 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak 150 (226)
+++.+..+++..|..+ + ....+|..+ |++...|+.|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 5677778888777544 2 245789999 99999999998655443
No 45
>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=57.08 E-value=8.8 Score=26.47 Aligned_cols=44 Identities=23% Similarity=0.437 Sum_probs=28.2
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhh
Q 027250 93 RQRWTPTPAQLQILEHVY-DECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (226)
Q Consensus 93 r~Rt~~s~~Ql~~Le~~F-~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQN 146 (226)
+.|..|++++...+-..+ ..+ ..+..+|..+ ||++..+..|-.-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~----gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY----GISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH----TS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc----ccccccccHHHHH
Confidence 346679998777665555 333 4577899999 9999999999753
No 46
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=51.80 E-value=18 Score=23.31 Aligned_cols=41 Identities=22% Similarity=0.207 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRR 148 (226)
+++.+..++...|-.+ ....++|..+ |+++..|+.|...=|
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHH
Confidence 5566777777766555 2455889999 999999999987433
No 47
>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=49.96 E-value=31 Score=18.65 Aligned_cols=37 Identities=16% Similarity=0.423 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccch
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWF 144 (226)
++......+...|... + ....+|..+ +++...|..|.
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 5566666666666543 2 345788899 99998888773
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=47.99 E-value=25 Score=29.69 Aligned_cols=50 Identities=32% Similarity=0.368 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhc-CCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHH
Q 027250 97 TPTPAQLQILEHVYDEC-KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~-~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~K 152 (226)
.+|+.|+.+|..+|+.+ =-||-.....+||+.| |+++.- +|.-=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~l----GISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKEL----GISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHh----CCCHHH--HHHHHHHHHHH
Confidence 69999999999999877 0145555677899999 999875 44555565544
No 49
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=45.96 E-value=15 Score=36.36 Aligned_cols=50 Identities=20% Similarity=0.231 Sum_probs=32.1
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHH---hhCCCcccccccchhhhHHHHHHhhcC
Q 027250 107 EHVYDECKGTPRKQKIQDMTAELA---KHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 107 e~~F~~~~~~p~~~~r~~LA~~L~---~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
+..|.++ ..+....+.+..+++- -.-..+...|+.||.|||+++|+.+..
T Consensus 708 ~~w~~k~-~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKT-RSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecc-cCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 3445555 5677666665554440 001235678999999999999986654
No 50
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.95 E-value=41 Score=27.10 Aligned_cols=50 Identities=18% Similarity=0.190 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 96 t~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
..+++.|..+|... ..+ + ...+||..| |++...|..|-.+.+.+.++...
T Consensus 5 ~~Lt~rqreVL~lr-~~G--l----Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG--L----TQQEIADIL----GTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHH-HcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999874 333 2 234899999 99999999999877777665443
No 51
>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=38.58 E-value=15 Score=25.34 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=16.6
Q ss_pred HHHHHHHHHhhCCCcccccccch
Q 027250 122 IQDMTAELAKHGQISETNVYNWF 144 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWF 144 (226)
-.+||.+| |+++.+|..|=
T Consensus 25 lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHh
Confidence 44789999 99999999994
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=37.21 E-value=38 Score=26.19 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHH
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~K 152 (226)
.+++.+..++...|-.+ ....+||..| |++...|+.|...=|.+-|
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 34555666665555444 2356899999 9999999998865444443
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.96 E-value=45 Score=27.22 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
+++.+..+|...|-.+ ....+||+.| |++...|+++...-|.+.|+.
T Consensus 143 L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHH
Confidence 4555555655544333 2345789999 999999999987656555543
No 54
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=36.69 E-value=21 Score=22.55 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchh
Q 027250 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (226)
Q Consensus 96 t~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQ 145 (226)
..+|.++...++..+..+ ....+||+.| |.+...|..+.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G------~s~~~IA~~l----g~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG------MSIREIAKRL----GRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC------CCHHHHHHHH----CcCcHHHHHHHh
Confidence 357888888999888766 2345799999 999988877653
No 55
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=36.39 E-value=50 Score=25.99 Aligned_cols=48 Identities=10% Similarity=0.011 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
.+++.+..+|...|-.+ + ...+||..| |+++..|+.|...=+.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG--L----SYEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35666666666655433 2 244789999 999999999988555555543
No 56
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=33.86 E-value=63 Score=24.77 Aligned_cols=41 Identities=10% Similarity=0.303 Sum_probs=27.2
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchh
Q 027250 95 RWTPTPAQLQ-ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (226)
Q Consensus 95 Rt~~s~~Ql~-~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQ 145 (226)
|..|+.+... ++...+..+ + ...++|..+ |+++..|+.|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--~----sv~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--M----TVSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--C----CHHHHHHHH----CcCHHHHHHHHH
Confidence 3447776644 444444433 2 244789999 999999999964
No 57
>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=32.84 E-value=69 Score=20.91 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHH
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~ 151 (226)
.+|+.++.+|.-...-. ...++|..+ ++++..|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 47888888887665333 245899999 999999999887655554
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=32.08 E-value=60 Score=26.90 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhCCCcccccccchhhhHHHHHHhh
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~ 155 (226)
...+||..| |+++..|+++...-+.+.++..
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 355789999 9999999998876666655543
No 59
>PRK09480 slmA division inhibitor protein; Provisional
Probab=31.77 E-value=40 Score=26.95 Aligned_cols=36 Identities=14% Similarity=0.329 Sum_probs=28.8
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHH
Q 027250 108 HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (226)
Q Consensus 108 ~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRa 149 (226)
..|... +. .......||++. |++...++.+|.|+-.
T Consensus 21 ~l~~~~-~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESP-PG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhc-CC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 335444 45 777888999999 9999999999999763
No 60
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=31.44 E-value=73 Score=25.53 Aligned_cols=50 Identities=24% Similarity=0.248 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
+++.+..++...|-.+ ....+||..| |++...|+.++..=|.+.|+.-..
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKL----SMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhhc
Confidence 4444555555544333 2345789999 999999999998777776665443
No 61
>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=31.42 E-value=63 Score=24.02 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++...|-.+ + ...+||..+ |+++..|+.+...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~~g--~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLEG--L----SYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 4566666665554333 2 345789999 99999999988765555443
No 62
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.39 E-value=73 Score=24.83 Aligned_cols=48 Identities=15% Similarity=0.096 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~ 155 (226)
+++.+..++...|-.+ ....+||..| |+++..|++....-|.+-|+.-
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE------KSYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 4445555555544333 1244789999 9999999999876666655543
No 63
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=29.59 E-value=91 Score=25.45 Aligned_cols=50 Identities=10% Similarity=-0.031 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
+++.+..++.-.|-.+ + ...+||..| |+++..|+++...=|.+.|+....
T Consensus 117 Lp~~~r~i~~L~~~~g--~----s~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 117 LPDDQREAIILVGASG--F----AYEEAAEIC----GCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3444555554444333 1 244789999 999999999987666666665443
No 64
>PRK04217 hypothetical protein; Provisional
Probab=29.23 E-value=78 Score=24.35 Aligned_cols=51 Identities=14% Similarity=0.102 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 96 t~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
..++.++..++...|... - ...+||+.+ |++...|+..+..-+.+.+..-.
T Consensus 41 ~~Lt~eereai~l~~~eG-l-----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG-L-----TQEEAGKRM----GVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcC-C-----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 458888888888777555 2 356899999 99999999998877766665443
No 65
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=29.21 E-value=54 Score=26.56 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
...+||..+ |++...|+.|+..-|.+.|+.
T Consensus 159 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 159 SQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 456889999 999999999997666665553
No 66
>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=29.13 E-value=29 Score=23.46 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=17.5
Q ss_pred HHHHHHHHHhhCCCcccccccchh
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQ 145 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQ 145 (226)
..+||..| |++...|+.|-+
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH
Confidence 45899999 999999999974
No 67
>PRK00118 putative DNA-binding protein; Validated
Probab=29.03 E-value=78 Score=24.10 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
.++.|..++...|..+ ....+||..+ |++...|+.|...-|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg------~S~~EIAe~l----GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDD------YSLGEIAEEF----NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4566777776666555 1245799999 99999999998766666554
No 68
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.95 E-value=76 Score=24.98 Aligned_cols=49 Identities=12% Similarity=0.018 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
+++.+..++...|-.+ ....+||..| |+++..|++|...=|.+.|+.-.
T Consensus 109 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVHE------LTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHhc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444555554433222 2345788999 99999999999866666665443
No 69
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.60 E-value=62 Score=24.18 Aligned_cols=39 Identities=13% Similarity=0.048 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccc
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVY 141 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~ 141 (226)
++++|...-...|+.+ --.+.-..+++|..| ++++..|+
T Consensus 3 Ln~eq~~~Tk~elqan-~el~~LS~~~iA~~L----n~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQAN-FELCPLSDEEIATAL----NWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHh-hhhccccHHHHHHHh----CCCHHHHH
Confidence 5667766655555555 445556677899999 98886543
No 70
>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=28.04 E-value=40 Score=21.20 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccch
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWF 144 (226)
.++.++...+-..+... ..+.+||+.+ |++...|+-++
T Consensus 5 ~~~~~~~~~i~~l~~~G------~si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG------MSIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC------CCHHHHHHHH----CcCHHHHHHHH
Confidence 35665666666667665 2366899999 99999888765
No 71
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.77 E-value=91 Score=24.84 Aligned_cols=28 Identities=7% Similarity=0.388 Sum_probs=22.3
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
.++||..| |+++..|+++...=|.+.|+
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 56889999 99999999988765555554
No 72
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=27.72 E-value=74 Score=24.88 Aligned_cols=46 Identities=11% Similarity=-0.052 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.|..++.-.|-.+ + ...+||..| |++...|+.+...=|.+-|+
T Consensus 113 L~~~~r~v~~l~~~~~--~----s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG--F----SYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 5555666665555444 1 245789999 99999999888755555443
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.55 E-value=72 Score=25.46 Aligned_cols=30 Identities=13% Similarity=0.343 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
...++|..| |+++..|+++...-|.+-|..
T Consensus 154 s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 154 SLKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 355789999 999999999997666665543
No 74
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.50 E-value=74 Score=24.89 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=23.2
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
..+||..| |+++..|+.|...=|.+.|+.
T Consensus 144 ~~eIA~~l----gis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 144 YREIAEIL----GVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999998666665543
No 75
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=27.41 E-value=54 Score=35.49 Aligned_cols=61 Identities=21% Similarity=0.315 Sum_probs=53.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhh
Q 027250 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (226)
Q Consensus 90 ~~rr~Rt~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~ 155 (226)
+.++.|...-++++.+|-.+|-.+ --|+...+..|.... ..+.+.+.+||+|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~-~sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQD-NSPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCC-CCHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 455667888889999999999999 579999888898888 8999999999999999988876
No 76
>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=26.94 E-value=80 Score=25.16 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++.-.|-.+ ....+||..| |+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG------LTVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 5555555555555444 1345788999 99999999988765555544
No 77
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.71 E-value=37 Score=21.29 Aligned_cols=23 Identities=30% Similarity=0.788 Sum_probs=18.9
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhH
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRR 148 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRR 148 (226)
..++|..+ |++...|..|.+.-+
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHHHH
Confidence 44689999 999999999997544
No 78
>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=26.35 E-value=35 Score=21.13 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhCCCcccccccchhhh
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNR 147 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNR 147 (226)
..++|+.+ |+++..|+.|.++-
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHCC
Confidence 45788899 99999999997543
No 79
>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=25.82 E-value=1.1e+02 Score=23.43 Aligned_cols=45 Identities=18% Similarity=0.094 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~K 152 (226)
+++.+..+|...|-.+ + ...+||..+ |+++..|+.+...=|.+.|
T Consensus 114 L~~~~r~il~l~~~~~--~----~~~eIA~~l----gis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG--K----SYKEIAEEL----GISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 3445555555544333 2 345788999 9999999988765444444
No 80
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.81 E-value=35 Score=21.45 Aligned_cols=22 Identities=27% Similarity=0.767 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhhCCCcccccccchhh
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQN 146 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQN 146 (226)
...++|+.| |++...|..|.+.
T Consensus 19 s~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHH----TS-HHHHHHHHT-
T ss_pred CHHHHHHHH----CcCHHHHHHHHHH
Confidence 355899999 9999999999754
No 81
>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=25.58 E-value=84 Score=24.30 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHH
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak 150 (226)
.+++.+..++...|-.+ ....+||..+ |++...|+++...-|.+
T Consensus 111 ~L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALSRLRVR 154 (159)
T ss_pred HCCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 35566666666544333 2355889999 99999999876543333
No 82
>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=25.43 E-value=87 Score=24.97 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
.+++.+..+|.-.|-.+ ....+||..| |+++..|+.+-..=|.+.++...
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666655444 1345889999 99999999988766666555443
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.88 E-value=91 Score=25.14 Aligned_cols=46 Identities=15% Similarity=-0.009 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++...|-.+ ....+||..| |++...|+.+...=|.+.|+
T Consensus 140 L~~~~r~i~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVVG------LSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4455555555544333 2356889999 99999999988654444443
No 84
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.49 E-value=1e+02 Score=24.01 Aligned_cols=47 Identities=13% Similarity=0.185 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~ 155 (226)
+++.+..+|.-.| .+ + ...+||..| |++...|+.+...=|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~g--~----s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG--Y----SYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 5566666666666 44 2 345789999 9999999999876666655543
No 85
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.47 E-value=96 Score=25.04 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~ 155 (226)
+++.+..+|+-.|-.+ ....+||..| |+++..|++-...=|.+.|+.-
T Consensus 132 L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 132 LSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 4445555554444333 1245788999 9999999998876666665543
No 86
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=24.26 E-value=1.7e+02 Score=17.87 Aligned_cols=39 Identities=26% Similarity=0.350 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhh
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQN 146 (226)
.+++.+..++...+ .+ + ...++|..+ +++...|+.|...
T Consensus 3 ~l~~~e~~i~~~~~-~g--~----s~~eia~~l----~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA-EG--L----TNKEIAERL----GISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHH
Confidence 35677777776533 33 2 345789999 9999999988764
No 87
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.11 E-value=1.1e+02 Score=24.69 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
..+||..| |++...|+.+...-|.+.|+.-.
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 45788999 99999999998766666665444
No 88
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=23.01 E-value=28 Score=24.93 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhhCCCcccccccchhh
Q 027250 120 QKIQDMTAELAKHGQISETNVYNWFQN 146 (226)
Q Consensus 120 ~~r~~LA~~L~~~~~ls~~~V~vWFQN 146 (226)
....+||..| |+++..|+.|+.+
T Consensus 33 lS~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHH----CcCHHHHHHHHhc
Confidence 3466899999 9999999999864
No 89
>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=22.84 E-value=1.4e+02 Score=23.21 Aligned_cols=46 Identities=22% Similarity=0.164 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 99 s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
++.+..++...|-.+ ....+||..| |++...|+.+-..-|.+-|+.
T Consensus 112 ~~~~r~i~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 112 PARQRAVVVLRYYED------LSEAQVAEAL----GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHhhhHHHhc------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 445555555544333 2245788999 999999999887666666554
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.42 E-value=1.3e+02 Score=23.21 Aligned_cols=47 Identities=17% Similarity=0.114 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
+++.+..++.-.|-.+ + ...+||..| |++...|++....-|.+.|..
T Consensus 107 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 107 LPARQREAFLLRYWED--M----DVAETAAAM----GCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CCHHHHHHHHHHHHhc--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 4555555555544333 1 245889999 999999998876555555443
No 91
>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=22.19 E-value=1.3e+02 Score=23.47 Aligned_cols=43 Identities=16% Similarity=0.132 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak 150 (226)
+++.+..+|...|-.+ ....+||..| |+++..|+....-=|.+
T Consensus 123 L~~~~r~vl~l~~~~g------~s~~eIA~~l----~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN------LPIAEVARIL----GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHH
Confidence 4444444554433222 2345788999 99999998876433333
No 92
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.98 E-value=1.4e+02 Score=21.51 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHhhc----CCCCCHHHHHHHHHHHHhhCCCcccccccchh
Q 027250 96 WTPTPAQLQILEHVYDEC----KGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (226)
Q Consensus 96 t~~s~~Ql~~Le~~F~~~----~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQ 145 (226)
|-++.+++..|...|..- +.+.+..+...+-..+ ++++..|.-+|.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~~ 51 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIWN 51 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHHH
Confidence 457889999999998763 2456666666655555 788777776663
No 93
>PF05777 Acp26Ab: Drosophila accessory gland-specific peptide 26Ab (Acp26Ab); InterPro: IPR008392 This family consists of accessory gland-specific 26Ab peptides or male accessory gland secretory protein 355B from different Drosophila species. Drosophila males, like males of most other insects, transfer a group of specific proteins (Acp26Ab and Acp26Aa in Drosophila) to the females during mating. These proteins are produced primarily in the accessory gland and are likely to influence the female's reproduction [].; GO: 0007617 mating behavior, 0005576 extracellular region
Probab=21.91 E-value=1e+02 Score=22.63 Aligned_cols=30 Identities=30% Similarity=0.458 Sum_probs=22.2
Q ss_pred hhccCCCCCCCc--------ccccCCHHHHHHHHHHHH
Q 027250 18 FQQDGGDTSNGL--------CVKVMTDEQMELLRKQIA 47 (226)
Q Consensus 18 ~q~~~~~~~g~~--------~~~~~t~~~~~~lr~qi~ 47 (226)
-|.+++.+.|.| ...|||.+++++++.|+.
T Consensus 51 VqD~vnd~~G~lv~t~ka~fnSDvMSp~e~~~~r~qL~ 88 (90)
T PF05777_consen 51 VQDNVNDASGQLVHTHKADFNSDVMSPDEIERVRQQLI 88 (90)
T ss_pred cccccccCCceEEEeccccCccccCCHHHHHHHHHHhc
Confidence 355566665655 567999999999998764
No 94
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.67 E-value=1.3e+02 Score=24.13 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=20.8
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHH
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~K 152 (226)
..+||..+ |++...|++|-..=|.+.|
T Consensus 152 ~~eIA~~l----gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 152 HAEIAQRL----GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHHHHHHH----CCChhhHHHHHHHHHHHHH
Confidence 45789999 9999999998865444444
No 95
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.63 E-value=1.1e+02 Score=24.79 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
+++.+..+|...|-.+ ....+||..+ |++...|+..+..=|.+.|+.-.
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 4444445554443333 2355789999 99999999988765655555433
No 96
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.32 E-value=1.2e+02 Score=24.74 Aligned_cols=28 Identities=21% Similarity=0.283 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
..+||..| |+++..|+++...=|.+.|+
T Consensus 153 ~~EIA~~l----gis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 153 SEQICQEC----DISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 55889999 99999999998755555544
No 97
>PRK06930 positive control sigma-like factor; Validated
Probab=20.99 E-value=1.2e+02 Score=24.84 Aligned_cols=50 Identities=10% Similarity=0.123 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHhhc
Q 027250 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (226)
Q Consensus 97 ~~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~ 156 (226)
.+++.+..++...|-.+ ....+||..| |++...|+.+...-+.+.++.-.
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYL----NIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 46666666666655444 1245789999 99999999999877777665443
No 98
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.80 E-value=49 Score=21.74 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=17.7
Q ss_pred HHHHHHHHHHhhCCCcccccccchhhhHH
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQNRRA 149 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQNRRa 149 (226)
....||+.+ |++...|..|+.++..
T Consensus 12 t~~~La~~~----gis~~tl~~~~~~~~~ 36 (63)
T PF13443_consen 12 TQKDLARKT----GISRSTLSRILNGKPS 36 (63)
T ss_dssp -HHHHHHHH----T--HHHHHHHHTTT--
T ss_pred CHHHHHHHH----CcCHHHHHHHHhcccc
Confidence 355789999 9999999999987743
No 99
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.6e+02 Score=24.06 Aligned_cols=32 Identities=16% Similarity=0.079 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhCCCcccccccchhhhHHHHHHhhcC
Q 027250 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (226)
Q Consensus 122 r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~~~~ 157 (226)
..++|..| |++...|+++...=|.+.|+.-..
T Consensus 132 ~~EIA~~L----giS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 132 YEEAAEMC----GVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHhc
Confidence 45788999 999999999998766666654443
No 100
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.41 E-value=1.4e+02 Score=23.31 Aligned_cols=46 Identities=15% Similarity=0.093 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++.-.|-.+ ....++|+.| |++...|+.....-|.+.++
T Consensus 110 L~~~~r~v~~l~~~~~------~s~~EIA~~l----gis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 110 LPARTRYAFEMYRLHG------ETQKDIAREL----GVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4455555555444333 1245889999 99999999976655555444
No 101
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 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 certain Bacillus and Clostridium species.
Probab=20.36 E-value=1.4e+02 Score=23.44 Aligned_cols=46 Identities=13% Similarity=0.168 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++...|-.+ ....++|..| |+++..|+++...=|.+.++
T Consensus 120 L~~~~r~i~~l~~~~g------~s~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD------LTIKEIAEVM----NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4444445554444333 2345789999 99999999877655555444
No 102
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.30 E-value=1.5e+02 Score=23.77 Aligned_cols=47 Identities=13% Similarity=-0.002 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
+++.+..+++-.|-.+ ....+||..| |++...|+.+...-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVKLEG------LSVAEAATRS----GMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHHHcC------CcHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4555555555443333 2355889999 999999999886655555543
No 103
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.16 E-value=1.3e+02 Score=23.68 Aligned_cols=46 Identities=13% Similarity=0.067 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccccccchhhhHHHHHH
Q 027250 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (226)
Q Consensus 98 ~s~~Ql~~Le~~F~~~~~~p~~~~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr 153 (226)
+++.+..++.-.|-.+ ....+||..| |+++..|+++...=|.+.|.
T Consensus 113 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 113 LSADQREAIILIGASG------FSYEDAAAIC----GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4445555555544333 2355889999 99999999988755555544
No 104
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=20.12 E-value=1e+02 Score=24.67 Aligned_cols=30 Identities=10% Similarity=0.134 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhhCCCcccccccchhhhHHHHHHh
Q 027250 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (226)
Q Consensus 121 ~r~~LA~~L~~~~~ls~~~V~vWFQNRRak~Kr~ 154 (226)
...+||..| |+++..|+++...=|.+-|+.
T Consensus 156 s~~EIA~~l----gis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 156 SYEDIARIM----DCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 456889999 999999999886555555543
Done!