Query psy12847
Match_columns 188
No_of_seqs 192 out of 1358
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 21:17:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12847hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00901 methylated-DNA--prote 100.0 3.6E-52 7.7E-57 333.0 16.3 151 22-177 2-154 (155)
2 PRK10286 O-6-alkylguanine-DNA: 100.0 3E-49 6.5E-54 320.3 15.9 155 21-178 3-170 (171)
3 COG0350 Ada Methylated DNA-pro 100.0 2.3E-48 4.9E-53 314.7 13.0 152 22-176 2-168 (168)
4 PRK15435 bifunctional DNA-bind 100.0 1.2E-46 2.7E-51 334.8 16.7 158 17-177 184-351 (353)
5 KOG4062|consensus 100.0 2.7E-37 5.9E-42 245.7 12.6 152 22-176 5-169 (178)
6 TIGR00589 ogt O-6-methylguanin 100.0 5.5E-37 1.2E-41 220.8 9.3 80 95-174 1-80 (80)
7 PF01035 DNA_binding_1: 6-O-me 100.0 3.1E-36 6.8E-41 218.9 9.1 85 95-179 1-85 (85)
8 PRK03887 methylated-DNA--prote 100.0 1.5E-35 3.2E-40 239.8 13.4 107 67-177 61-171 (175)
9 cd06445 ATase The DNA repair p 100.0 9.3E-33 2E-37 197.9 9.2 79 97-175 1-79 (79)
10 COG3695 Predicted methylated D 99.9 2.6E-26 5.5E-31 170.3 8.6 92 94-185 4-95 (103)
11 PF02870 Methyltransf_1N: 6-O- 99.4 4E-13 8.7E-18 94.7 2.8 69 21-92 1-77 (77)
12 PF13936 HTH_38: Helix-turn-he 83.7 1.4 3.1E-05 27.6 2.9 39 95-139 6-44 (44)
13 PF01726 LexA_DNA_bind: LexA D 83.3 1.5 3.3E-05 30.0 3.1 42 95-137 5-48 (65)
14 PF12324 HTH_15: Helix-turn-he 78.6 5.4 0.00012 28.6 4.7 35 106-142 31-65 (77)
15 PF10771 DUF2582: Protein of u 76.4 3.9 8.3E-05 28.3 3.3 40 99-141 11-52 (65)
16 PF13730 HTH_36: Helix-turn-he 64.4 18 0.00038 22.9 4.4 42 95-138 4-48 (55)
17 PF04545 Sigma70_r4: Sigma-70, 61.4 22 0.00049 22.2 4.4 28 95-126 6-33 (50)
18 PF08765 Mor: Mor transcriptio 61.2 15 0.00032 27.3 4.0 63 65-138 31-95 (108)
19 PF13404 HTH_AsnC-type: AsnC-t 60.7 19 0.00041 22.4 3.8 35 97-136 4-38 (42)
20 PF10743 Phage_Cox: Regulatory 58.2 15 0.00032 27.0 3.4 37 111-153 10-46 (87)
21 PF08784 RPA_C: Replication pr 56.4 20 0.00043 26.0 3.9 43 93-137 44-87 (102)
22 PRK04257 hypothetical protein; 54.9 5.9 0.00013 28.2 0.9 10 143-152 53-62 (78)
23 PF13412 HTH_24: Winged helix- 53.9 33 0.00072 21.1 4.2 37 96-137 3-39 (48)
24 PF04457 DUF504: Protein of un 47.2 9.7 0.00021 25.3 0.9 11 142-152 34-44 (56)
25 PRK13239 alkylmercury lyase; P 47.2 42 0.00091 28.3 4.9 46 106-160 29-74 (206)
26 PF08279 HTH_11: HTH domain; 46.5 41 0.00089 21.2 3.9 37 98-138 2-38 (55)
27 PF03444 HrcA_DNA-bdg: Winged 46.3 34 0.00074 24.5 3.7 45 95-139 3-50 (78)
28 smart00344 HTH_ASNC helix_turn 45.9 39 0.00084 24.2 4.1 29 96-127 3-31 (108)
29 TIGR03879 near_KaiC_dom probab 45.6 28 0.00061 24.6 3.1 41 95-140 17-57 (73)
30 PF00392 GntR: Bacterial regul 45.1 57 0.0012 21.4 4.5 27 100-126 8-37 (64)
31 PF08281 Sigma70_r4_2: Sigma-7 44.1 29 0.00063 21.8 2.8 25 110-136 23-47 (54)
32 TIGR00498 lexA SOS regulatory 43.5 37 0.0008 27.4 4.0 32 95-126 5-38 (199)
33 smart00550 Zalpha Z-DNA-bindin 43.5 57 0.0012 22.0 4.4 41 95-138 5-45 (68)
34 PF06301 Lambda_Kil: Bacteriop 41.0 12 0.00027 23.8 0.6 30 117-149 12-41 (43)
35 cd00090 HTH_ARSR Arsenical Res 39.9 76 0.0016 20.0 4.5 42 94-139 5-48 (78)
36 PF06056 Terminase_5: Putative 38.2 46 0.00099 22.2 3.1 37 112-150 12-48 (58)
37 PF13518 HTH_28: Helix-turn-he 38.0 76 0.0016 19.4 4.0 22 111-136 12-33 (52)
38 cd06170 LuxR_C_like C-terminal 37.5 89 0.0019 18.9 4.3 35 96-137 3-37 (57)
39 PF09339 HTH_IclR: IclR helix- 36.6 25 0.00054 22.3 1.6 35 100-136 7-43 (52)
40 PF14120 YhzD: YhzD-like prote 35.9 19 0.00042 24.6 1.0 34 126-160 26-59 (61)
41 TIGR01557 myb_SHAQKYF myb-like 35.8 1E+02 0.0022 20.5 4.5 43 95-137 8-51 (57)
42 COG1531 Uncharacterized protei 35.7 17 0.00036 26.1 0.7 10 143-152 54-63 (77)
43 PF12840 HTH_20: Helix-turn-he 34.8 27 0.0006 22.8 1.6 31 94-127 8-38 (61)
44 PRK12423 LexA repressor; Provi 33.8 50 0.0011 27.0 3.4 44 95-138 5-52 (202)
45 PRK00215 LexA repressor; Valid 33.4 37 0.0008 27.5 2.5 42 95-136 3-49 (205)
46 PF05225 HTH_psq: helix-turn-h 32.8 27 0.00058 22.0 1.2 29 100-129 4-32 (45)
47 TIGR00721 tfx DNA-binding prot 32.4 85 0.0019 24.7 4.3 28 94-126 7-34 (137)
48 KOG1182|consensus 32.3 25 0.00055 32.0 1.4 18 144-161 61-78 (432)
49 COG1522 Lrp Transcriptional re 32.0 86 0.0019 23.7 4.3 39 95-138 7-45 (154)
50 PF12802 MarR_2: MarR family; 31.3 1.2E+02 0.0026 19.1 4.3 42 95-137 4-47 (62)
51 PRK10100 DNA-binding transcrip 31.0 92 0.002 25.8 4.5 36 94-136 156-191 (216)
52 PRK15411 rcsA colanic acid cap 30.4 85 0.0018 25.6 4.2 62 67-137 110-174 (207)
53 PF08280 HTH_Mga: M protein tr 30.3 73 0.0016 20.8 3.1 36 98-138 7-42 (59)
54 TIGR02393 RpoD_Cterm RNA polym 30.3 1.1E+02 0.0025 25.3 5.0 16 111-126 194-209 (238)
55 PRK09640 RNA polymerase sigma 29.6 94 0.002 24.5 4.3 40 96-137 123-172 (188)
56 PF01498 HTH_Tnp_Tc3_2: Transp 28.7 77 0.0017 21.1 3.1 34 108-141 8-44 (72)
57 cd06171 Sigma70_r4 Sigma70, re 28.7 1.3E+02 0.0028 17.5 4.3 35 95-135 12-46 (55)
58 PF02796 HTH_7: Helix-turn-hel 28.6 70 0.0015 19.7 2.7 23 114-138 22-44 (45)
59 PF04967 HTH_10: HTH DNA bindi 28.0 1.8E+02 0.0039 19.1 4.6 41 95-137 2-45 (53)
60 PRK03975 tfx putative transcri 27.3 1.2E+02 0.0026 24.0 4.3 29 94-127 7-35 (141)
61 PF00325 Crp: Bacterial regula 27.1 99 0.0022 18.3 3.0 23 114-138 3-25 (32)
62 PF01325 Fe_dep_repress: Iron 26.9 1.8E+02 0.0038 19.2 4.6 37 97-138 9-45 (60)
63 PRK09652 RNA polymerase sigma 26.2 1.1E+02 0.0024 23.2 4.0 24 111-136 142-165 (182)
64 PRK11083 DNA-binding response 26.0 1.7E+02 0.0036 22.6 5.0 31 94-125 155-185 (228)
65 PRK12514 RNA polymerase sigma 25.9 72 0.0016 24.8 2.9 35 101-137 123-167 (179)
66 TIGR01764 excise DNA binding d 25.7 1.5E+02 0.0032 17.4 3.9 31 114-150 2-32 (49)
67 PRK08295 RNA polymerase factor 25.5 76 0.0017 25.2 3.0 27 110-138 167-193 (208)
68 PRK08301 sporulation sigma fac 25.4 1.5E+02 0.0033 24.2 4.9 22 112-135 197-218 (234)
69 PRK12513 RNA polymerase sigma 25.3 78 0.0017 25.0 3.0 35 100-136 132-176 (194)
70 PRK06759 RNA polymerase factor 25.2 1.3E+02 0.0027 22.6 4.1 24 111-136 120-143 (154)
71 PF01978 TrmB: Sugar-specific 25.2 75 0.0016 21.0 2.5 30 95-127 7-36 (68)
72 TIGR02950 SigM_subfam RNA poly 25.1 82 0.0018 23.6 3.0 36 100-137 98-143 (154)
73 PF01381 HTH_3: Helix-turn-hel 24.3 1.2E+02 0.0025 18.8 3.2 23 114-138 10-32 (55)
74 TIGR02844 spore_III_D sporulat 24.1 1.4E+02 0.0031 21.2 3.9 37 97-139 7-43 (80)
75 PRK15201 fimbriae regulatory p 23.9 1.4E+02 0.0031 25.0 4.3 37 94-137 134-170 (198)
76 PF13384 HTH_23: Homeodomain-l 23.8 1E+02 0.0022 18.9 2.8 24 113-138 17-40 (50)
77 TIGR02859 spore_sigH RNA polym 23.7 87 0.0019 24.6 3.1 25 112-138 164-188 (198)
78 PRK12518 RNA polymerase sigma 23.6 88 0.0019 24.1 3.0 35 101-137 114-158 (175)
79 PRK09647 RNA polymerase sigma 23.4 1.2E+02 0.0026 24.6 3.9 35 101-137 132-176 (203)
80 PRK10840 transcriptional regul 23.3 1.5E+02 0.0033 23.5 4.4 37 94-137 151-187 (216)
81 PRK13919 putative RNA polymera 23.3 88 0.0019 24.4 3.0 36 100-137 128-173 (186)
82 PF04539 Sigma70_r3: Sigma-70 23.3 71 0.0015 21.5 2.1 27 110-138 17-43 (78)
83 PRK11179 DNA-binding transcrip 22.8 74 0.0016 24.7 2.4 29 95-126 8-36 (153)
84 PRK11014 transcriptional repre 22.7 1.8E+02 0.0039 22.2 4.5 45 95-139 7-52 (141)
85 PRK12515 RNA polymerase sigma 22.7 93 0.002 24.5 3.0 36 100-137 124-169 (189)
86 PRK12520 RNA polymerase sigma 22.5 95 0.0021 24.5 3.0 34 101-136 125-168 (191)
87 TIGR02989 Sig-70_gvs1 RNA poly 22.4 1.5E+02 0.0031 22.3 4.0 36 99-136 103-148 (159)
88 PRK02866 cyanate hydratase; Va 22.3 94 0.002 24.9 2.9 16 110-125 15-30 (147)
89 PRK09642 RNA polymerase sigma 22.0 1E+02 0.0022 23.4 3.1 35 100-136 99-143 (160)
90 PRK12512 RNA polymerase sigma 21.9 99 0.0021 24.1 3.0 37 99-137 123-169 (184)
91 PRK12526 RNA polymerase sigma 21.9 98 0.0021 25.0 3.0 26 110-137 166-191 (206)
92 PF13463 HTH_27: Winged helix 21.9 2.2E+02 0.0049 18.1 4.3 40 98-139 5-46 (68)
93 PRK09648 RNA polymerase sigma 21.8 1.4E+02 0.0031 23.3 3.9 36 100-137 132-177 (189)
94 smart00354 HTH_LACI helix_turn 21.8 1.2E+02 0.0025 20.4 3.0 24 115-140 2-25 (70)
95 COG1414 IclR Transcriptional r 21.7 79 0.0017 26.7 2.5 52 100-163 8-61 (246)
96 PRK05949 RNA polymerase sigma 21.6 1.8E+02 0.004 25.7 5.0 16 111-126 284-299 (327)
97 PRK12530 RNA polymerase sigma 21.5 1E+02 0.0022 24.4 3.1 34 101-136 128-171 (189)
98 PRK11169 leucine-responsive tr 21.4 1.2E+02 0.0025 23.9 3.3 39 95-138 13-51 (164)
99 PRK05672 dnaE2 error-prone DNA 21.4 94 0.002 32.3 3.4 57 76-139 380-442 (1046)
100 COG3784 Uncharacterized protei 21.2 53 0.0012 24.8 1.2 36 101-138 52-87 (109)
101 TIGR02980 SigBFG RNA polymeras 20.9 1.5E+02 0.0033 24.1 4.0 25 110-136 191-215 (227)
102 PRK12537 RNA polymerase sigma 20.5 1E+02 0.0023 24.1 2.9 36 100-137 126-171 (182)
103 PRK09047 RNA polymerase factor 20.5 1.2E+02 0.0025 22.9 3.1 35 100-136 99-143 (161)
104 PF04492 Phage_rep_O: Bacterio 20.4 2E+02 0.0044 21.2 4.2 41 96-138 32-77 (100)
105 cd06571 Bac_DnaA_C C-terminal 20.3 1.2E+02 0.0027 21.4 3.0 39 97-138 30-68 (90)
106 PRK12547 RNA polymerase sigma 20.3 1.2E+02 0.0025 23.4 3.1 37 100-138 105-151 (164)
107 PF00356 LacI: Bacterial regul 20.3 1.6E+02 0.0035 18.5 3.2 23 115-139 1-23 (46)
108 PRK09651 RNA polymerase sigma 20.2 1.2E+02 0.0025 23.6 3.1 25 110-136 132-156 (172)
109 smart00345 HTH_GNTR helix_turn 20.1 2.2E+02 0.0048 17.3 4.4 20 107-126 13-33 (60)
No 1
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=100.00 E-value=3.6e-52 Score=332.99 Aligned_cols=151 Identities=36% Similarity=0.622 Sum_probs=137.3
Q ss_pred EEEEEEeccCccceEEEEEecccccc-cc-cccchhhhhhcccCChhHHHHHHHHHHHhcCCCCCCcccccccCCChhHH
Q psy12847 22 MLIAYYDKSCIIQAIMFGANPEYLYV-DL-TKLYSHIEYIKMFESKQSRDIIDRLEAYIVNPKQNCLDIKFKIEGTDFQK 99 (188)
Q Consensus 22 ~~~~~~~tP~~~G~i~i~a~~~gL~~-~f-d~~~~~~~~~~~~~~~~l~~~~~qL~~YF~G~~~~~F~lpl~~~gt~f~~ 99 (188)
++|.+|+|| ||.+.+++++++|+. .| +..... .....+++.+.++.+||++||+|++.+ |++|+++.||+||+
T Consensus 2 ~~~~~~~tp--~G~~~i~~~~~~l~~l~f~~~~~~~--~~~~~~~~~~~~~~~~l~~Yf~G~~~~-f~lpl~~~gt~fq~ 76 (155)
T PRK00901 2 NNIYFYETP--IGKIGIAENGTAITHLCFGEDKIPK--DVTILETDLLKEANKQLEEYFEGKRKK-FDLPLAPQGTEFQK 76 (155)
T ss_pred CeeEEEeCC--CEEEEEEEECCEEEEEEecCCcchh--hccccCcHHHHHHHHHHHHHHcCCCcC-CceeecCCCChHHH
Confidence 478899999 999999999999999 88 432210 111234568889999999999999999 99999999999999
Q ss_pred HHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHHHHHHHhccc
Q psy12847 100 LVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKETLIKIEQKI 177 (188)
Q Consensus 100 ~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~E~~~ 177 (188)
+||++|++||||+|+||+|||+++|.|+++||||+||++||++++|||||||+++|+++||+||.+.|++||++|+..
T Consensus 77 ~Vw~~l~~Ip~G~t~tY~~lA~~~g~p~a~RAVg~A~~~NP~~iiIPCHRVv~~~G~lggy~gG~~~K~~LL~~E~~~ 154 (155)
T PRK00901 77 KVWKALQEIPYGETRSYKEIAVNIGNPKACRAVGLANNKNPIPIFIPCHRVIGANGKLVGYAGGLDIKEKLLKLEKEN 154 (155)
T ss_pred HHHHHHccCCCCCcCCHHHHHHHHCCCchHHHHHHHHHhCCCCCccCCceEECCCCCCCCCCCcHHHHHHHHHHhcCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999863
No 2
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=100.00 E-value=3e-49 Score=320.30 Aligned_cols=155 Identities=28% Similarity=0.503 Sum_probs=134.7
Q ss_pred eEEEEEEeccCccceEEEEEecc-cccc-cc-cccch--hh-hhhcc------cCChhHHHHHHHHHHHhcCCCCCCcc-
Q psy12847 21 KMLIAYYDKSCIIQAIMFGANPE-YLYV-DL-TKLYS--HI-EYIKM------FESKQSRDIIDRLEAYIVNPKQNCLD- 87 (188)
Q Consensus 21 ~~~~~~~~tP~~~G~i~i~a~~~-gL~~-~f-d~~~~--~~-~~~~~------~~~~~l~~~~~qL~~YF~G~~~~~F~- 87 (188)
.|+|.+++|| +|.+.++++++ +|+. .| +.... .. ..... ...+...++.+||++||+|++.. |+
T Consensus 3 ~~~~~~~~sP--iG~l~i~~~~~~~l~~l~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~Yf~g~~~~-f~~ 79 (171)
T PRK10286 3 RLLEEKIATP--LGPLWVICDEQFRLRAVEWEEYSERMVQLLDIHYRKEGYERISATNPGGLSDKLRDYFAGNLSI-IDT 79 (171)
T ss_pred cccceeeeCC--CeeEEEEEeCCCcEEEEEecCCccchhhhccccccccccccccccCHHHHHHHHHHHHCCCCCC-CCc
Confidence 4789999999 99999999999 6999 88 43211 10 00000 11123357899999999999999 96
Q ss_pred cccccCCChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHH
Q psy12847 88 IKFKIEGTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIK 167 (188)
Q Consensus 88 lpl~~~gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k 167 (188)
+|+++.||+||++||++|++||||+|+||+|||+.+|.|+++||||+||++||++++|||||||+++|+|+||+||.+.|
T Consensus 80 ~pl~~~gt~fq~~V~~~l~~IP~G~~~tYg~iA~~~g~p~aaRaVG~A~~~Np~~i~iPCHRVv~~~G~l~gy~gG~~~K 159 (171)
T PRK10286 80 LPTATGGTPFQREVWQTLRTIPCGQVMHYGQLAEQLGRPGAARAVGAANGSNPISIVVPCHRVIGRNGTMTGYAGGVQRK 159 (171)
T ss_pred ccccCCCCHHHHHHHHHHHcCCCCCcEeHHHHHHHhCCCChHHHHHHHHHhCCCCCccCCceEECCCCCcCCCCCcHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccc
Q psy12847 168 ETLIKIEQKIV 178 (188)
Q Consensus 168 ~~LL~~E~~~~ 178 (188)
++||++|++.+
T Consensus 160 ~~LL~~E~~~~ 170 (171)
T PRK10286 160 EWLLRHEGYLL 170 (171)
T ss_pred HHHHHHcCCcc
Confidence 99999999853
No 3
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.3e-48 Score=314.66 Aligned_cols=152 Identities=32% Similarity=0.598 Sum_probs=131.9
Q ss_pred EEEEEEeccCccceEEEEEeccc-ccc-cc-cccc--h---hhhhh-----cccCChhHHHHHHHHHHHhcCCCCCCcc-
Q psy12847 22 MLIAYYDKSCIIQAIMFGANPEY-LYV-DL-TKLY--S---HIEYI-----KMFESKQSRDIIDRLEAYIVNPKQNCLD- 87 (188)
Q Consensus 22 ~~~~~~~tP~~~G~i~i~a~~~g-L~~-~f-d~~~--~---~~~~~-----~~~~~~~l~~~~~qL~~YF~G~~~~~F~- 87 (188)
++|..++|| +|.+.+++++.+ ++. .| +... . ..... ...+.+.+....+||++||+|++.. |+
T Consensus 2 ~~~~~~~s~--~G~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~yf~g~~~~-~~~ 78 (168)
T COG0350 2 LYYALMLSP--LGPELLALSYGYGLVALIFDDQGDVETYLDLAQALGPSALDPGAARALGGLLRELEAYFNGKEPD-FDP 78 (168)
T ss_pred chhhcccCC--cccEEEEEeCCCcEEEEEcCCcccHHHHhhhhccccccccCccchhhHHHHHHHHHHHHcCCCcc-cCC
Confidence 567889999 999999996655 777 88 5311 1 11111 1234467889999999999999888 88
Q ss_pred -cccccCCChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHH
Q psy12847 88 -IKFKIEGTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYI 166 (188)
Q Consensus 88 -lpl~~~gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~ 166 (188)
+|+++.||+||++||++|++||||+|+||+|||+++|.|+++||||+||++||++|+|||||||++||+|+||+||.++
T Consensus 79 ~l~l~~~gt~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig~p~a~rAVG~A~~~NPl~IiIPCHRVig~~G~L~Gy~~G~~~ 158 (168)
T COG0350 79 PLPLVLHGTGFQGRVWQALREIPYGETVTYGEIARRLGRPTAVRAVGNANGANPLPIIIPCHRVIGADGDLGGYAGGLER 158 (168)
T ss_pred ccccccCCChHHHHHHHHHhcCCCCCcEeHHHHHHHhCCCcHHHHHHHHhccCCceEEecCeEeEcCCCCccCccchHHH
Confidence 7777789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcc
Q psy12847 167 KETLIKIEQK 176 (188)
Q Consensus 167 k~~LL~~E~~ 176 (188)
|+|||++|+.
T Consensus 159 K~~LL~~E~~ 168 (168)
T COG0350 159 KKWLLELEGA 168 (168)
T ss_pred HHHHHHhhcC
Confidence 9999999984
No 4
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=100.00 E-value=1.2e-46 Score=334.82 Aligned_cols=158 Identities=30% Similarity=0.469 Sum_probs=141.3
Q ss_pred ccceeEEEEEEeccCccceEEEEEecccccc-cc-cccc---hhhhhhc-----ccCChhHHHHHHHHHHHhcCCCCCCc
Q psy12847 17 CIGTKMLIAYYDKSCIIQAIMFGANPEYLYV-DL-TKLY---SHIEYIK-----MFESKQSRDIIDRLEAYIVNPKQNCL 86 (188)
Q Consensus 17 ~~g~~~~~~~~~tP~~~G~i~i~a~~~gL~~-~f-d~~~---~~~~~~~-----~~~~~~l~~~~~qL~~YF~G~~~~~F 86 (188)
..+..+.|.+++|| +|.+.++++++||+. .| +... ..+...+ ...++.+.++.+||++||+|++.. |
T Consensus 184 ~~~~~i~~~~~~tp--~G~~~i~~~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~yf~g~~~~-f 260 (353)
T PRK15435 184 GENLAVRYALADCE--LGRCLVAESERGICAILLGDDDAALISELQQMFPAADNAPADLTFQQHVREVIASLNQRDTP-L 260 (353)
T ss_pred CCcccceeEEEecc--ceEEEEEEcCCceeEEEecCCcchHHHHHHhhcccccccCCchHHHHHHHHHHHHHcCCCCC-C
Confidence 45678999999999 999999999999999 88 4321 1122221 123457888899999999999999 9
Q ss_pred ccccccCCChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHH
Q psy12847 87 DIKFKIEGTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYI 166 (188)
Q Consensus 87 ~lpl~~~gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~ 166 (188)
++||++.||+||++||++|++||||+|+||+|||+.+|.|+++||||+||++||++++|||||||+++|+||||+||.+.
T Consensus 261 ~lpl~~~gt~f~~~v~~~l~~ip~G~~~tY~~~a~~~g~p~a~ravg~a~~~np~~~~iPchRvv~~~g~l~g~~~g~~~ 340 (353)
T PRK15435 261 TLPLDIRGTAFQQQVWQALRTIPCGETVSYQQLANAIGKPKAVRAVASACAANKLAIVIPCHRVVRGDGALSGYRWGVSR 340 (353)
T ss_pred CccccCCCCHHHHHHHHHHhcCCCCCcCcHHHHHHHhCCCChHHHHHHHHHhCCCCcccCCceeECCCCCcCCCCCcHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccc
Q psy12847 167 KETLIKIEQKI 177 (188)
Q Consensus 167 k~~LL~~E~~~ 177 (188)
|++||++|+..
T Consensus 341 k~~Ll~~e~~~ 351 (353)
T PRK15435 341 KAQLLRREAEN 351 (353)
T ss_pred HHHHHHHhccc
Confidence 99999999864
No 5
>KOG4062|consensus
Probab=100.00 E-value=2.7e-37 Score=245.65 Aligned_cols=152 Identities=29% Similarity=0.506 Sum_probs=122.1
Q ss_pred EEEEEEeccCccce--EEEEEecccccc-cc-ccc-ch----hhhhhcc--cCChhHHHHHHHHHHHhcCCCCCCcccc-
Q psy12847 22 MLIAYYDKSCIIQA--IMFGANPEYLYV-DL-TKL-YS----HIEYIKM--FESKQSRDIIDRLEAYIVNPKQNCLDIK- 89 (188)
Q Consensus 22 ~~~~~~~tP~~~G~--i~i~a~~~gL~~-~f-d~~-~~----~~~~~~~--~~~~~l~~~~~qL~~YF~G~~~~~F~lp- 89 (188)
.+|.+..|- .|. |.+....+|+.. .+ ++. .. ..+..+. ...+....++.++++||.-.... ..+|
T Consensus 5 c~y~f~etd--~gqa~l~~~~~~qglv~i~Ll~d~l~~~~~~Evqd~~p~l~~~k~~~t~k~~i~~yf~~le~~-~~~p~ 81 (178)
T KOG4062|consen 5 CEYKFTETD--SGQAKLELSGCEQGLVEIKLLGDGLSAADAVEVQDPAPVLGGPKPLMTCKAWINAYFHQLEAI-EEFPV 81 (178)
T ss_pred eEEEEEEec--cCceeEEEecccccchhhhhcccchhhhhhhhccccchhhcCCCcchHHHHHHHHHHhChhhc-ccCCc
Confidence 456777776 664 555555777777 44 222 11 1111111 12245677899999999987654 4555
Q ss_pred -cccCCChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHH
Q psy12847 90 -FKIEGTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKE 168 (188)
Q Consensus 90 -l~~~gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~ 168 (188)
..+.||+||++||++|..||+|+|+||+|||+.+|+|+++||||+||+.|+++++|||||||+++|.+++|.||...|+
T Consensus 82 ~~~~~~t~F~~kVw~al~~i~~Gev~tY~~iA~~iG~PsaaRaVg~A~~~n~la~lvPcHRVv~s~g~~s~y~wg~a~k~ 161 (178)
T KOG4062|consen 82 HPVMRGTDFQRKVWDALCEIPYGEVSTYGQIARRIGNPSAARAVGSAMAHNNLAILVPCHRVVGSNGTLSKYDWGAALKR 161 (178)
T ss_pred cceeccchHHHHHHHHHhccCCCceeeHHHHHHHhCCcHHHHHHHHHHccCCCcEEecceeeecCCCCccccchhHHHHH
Confidence 4567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcc
Q psy12847 169 TLIKIEQK 176 (188)
Q Consensus 169 ~LL~~E~~ 176 (188)
+||++|+.
T Consensus 162 ~ll~~E~~ 169 (178)
T KOG4062|consen 162 QLLALEGE 169 (178)
T ss_pred HHHhhccc
Confidence 99999997
No 6
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5.5e-37 Score=220.84 Aligned_cols=80 Identities=48% Similarity=0.850 Sum_probs=78.8
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHHHHHHHh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKETLIKIE 174 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~E 174 (188)
|+||++||++|.+||+|+|+||++||+.+|.|+++|+||+||++||++++|||||||+++|++++|.+|...|++||++|
T Consensus 1 t~f~~~V~~~l~~IP~G~v~TYg~iA~~~g~p~~~RaVg~al~~np~~~~iPcHRVv~s~G~l~~y~~g~~~k~~lL~~E 80 (80)
T TIGR00589 1 TPFQQRVWQALRTIPYGETKSYGQLAARIGNPKAVRAVGGANGRNPLAILVPCHRVIGKNGSLTGYAGGVELKKFLLEHE 80 (80)
T ss_pred ChHHHHHHHHHhCCCCCCcCCHHHHHHHhCCCChHHHHHHHHHhCCCCCCCCCceeECCCCCCCCCCCcHHHHHHHHhcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999988
No 7
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=100.00 E-value=3.1e-36 Score=218.89 Aligned_cols=85 Identities=48% Similarity=0.888 Sum_probs=78.3
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHHHHHHHh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKETLIKIE 174 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~E 174 (188)
|+||++||++|++||+|+|+||++||+.+|.|+++|+||+||+.||.+++|||||||+++|++++|++|...|++||+.|
T Consensus 1 T~f~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~ar~Vg~al~~np~~~~iP~HRVv~~~G~l~~~~~g~~~k~~lL~~E 80 (85)
T PF01035_consen 1 TPFQRRVWEAVRQIPYGKVTTYGEIARLLGRPKAARAVGSALARNPIPIIIPCHRVVNSDGSLGGYRGGIERKRALLEAE 80 (85)
T ss_dssp -HHHHHHHHHHTTS-TT-BEEHHHHHHHTT-TTCHHHHHHHHHTSSCTTTSGGGGEEBTTSBECTTTTCHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHcCCCCceEeHHHHHHHHhhcccHHHHHHHhccccccCCCCeEEEECCCCCcCCCCCcHHHHHHHHHHh
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q psy12847 175 QKIVS 179 (188)
Q Consensus 175 ~~~~~ 179 (188)
|+.|+
T Consensus 81 gv~~~ 85 (85)
T PF01035_consen 81 GVPFK 85 (85)
T ss_dssp TSS--
T ss_pred CCccC
Confidence 99874
No 8
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=100.00 E-value=1.5e-35 Score=239.77 Aligned_cols=107 Identities=27% Similarity=0.477 Sum_probs=98.5
Q ss_pred HHHHHHHHHHHhcCCCCCCcc--cccccCC-ChhHHHHHHHhc-ccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCC
Q psy12847 67 SRDIIDRLEAYIVNPKQNCLD--IKFKIEG-TDFQKLVWSELC-KIPFGSLCSYADVARNIGRPKSARAVANACGQNNIP 142 (188)
Q Consensus 67 l~~~~~qL~~YF~G~~~~~F~--lpl~~~g-t~f~~~V~~~l~-~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~ 142 (188)
..+..+++.+||.|...+ |+ .+++..| |+||++||++|. +||+|+|+||+|||+++|. ++||||+||++||++
T Consensus 61 ~~~~~~~l~~~l~g~~~~-~~~~~~l~~~g~T~Fq~rV~~~Lv~~IP~G~v~TYgqIA~~~G~--aaRAVG~Al~~NP~~ 137 (175)
T PRK03887 61 PSDYPELVFKVLIGKISN-EEGLEELSFEGLTPFERKVYEWLTKNVKRGEVITYGELAKALNT--SPRAVGGAMKRNPYP 137 (175)
T ss_pred ChhHHHHHHHHHcCCccc-cccCcccCcCCCCHHHHHHHHHHHHhCCCCCCCcHHHHHHHHCc--hHHHHHHHHHhCCCC
Confidence 345678889999999998 87 5688888 999999999765 8999999999999999996 799999999999999
Q ss_pred CCCCceeeeCCCCCcCCCCCcHHHHHHHHHHhccc
Q psy12847 143 ILIPCHRVIRSDGSYGGYSSGKYIKETLIKIEQKI 177 (188)
Q Consensus 143 ~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~E~~~ 177 (188)
++|||||||+++| +++|++|...|++||++||+.
T Consensus 138 i~IPCHRVV~s~G-~ggy~~G~~~K~~LL~~EGv~ 171 (175)
T PRK03887 138 IIVPCHRVVGRKN-PGLYTPKPEYKKFLLEVEGVK 171 (175)
T ss_pred CccCCeeEECCCC-CcCCCCCHHHHHHHHHHcCCc
Confidence 9999999999999 689999999999999999975
No 9
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=99.98 E-value=9.3e-33 Score=197.88 Aligned_cols=79 Identities=51% Similarity=0.951 Sum_probs=77.6
Q ss_pred hHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHHHHHHHhc
Q psy12847 97 FQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKETLIKIEQ 175 (188)
Q Consensus 97 f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~E~ 175 (188)
||++||+.|.+||+|+++||++||+.+|.|.++|+||+||++||.+++|||||||+++|.+++|.+|...|++||++||
T Consensus 1 ~~~~V~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~Vg~al~~np~~~~vP~HRVv~~~g~~~~~~~g~~~q~~lL~~Eg 79 (79)
T cd06445 1 FQRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRSDGGLGGYRGGLERKRELLELEG 79 (79)
T ss_pred CHHHHHHHHhcCCCCCcCcHHHHHHHHCCCCcHHHHHHHHHhCCCCCCCCceeEECCCCCcCCCCCcHHHHHHHHHhcC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999999999997
No 10
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=99.93 E-value=2.6e-26 Score=170.32 Aligned_cols=92 Identities=26% Similarity=0.365 Sum_probs=87.3
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCcHHHHHHHHHH
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGYSSGKYIKETLIKI 173 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g~~~k~~LL~~ 173 (188)
..+|.++||+.+.+||+|+|+||||||+.+|.|++||.||.+|+.-|....+||||||+++|.|+-+..+..+|+.||..
T Consensus 4 ~def~~~v~~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~il~~l~~~s~lPWhRVvns~G~isl~~~~~~~Q~~lL~a 83 (103)
T COG3695 4 ADEFTQRVLDVVAAIPEGKVSTYGDIAKLAGLPRAARQVGRILKHLPEGSDLPWHRVVNSDGRISLPGPDKQRQRELLLA 83 (103)
T ss_pred hhHHHHHHHHHHHhCCCCceeeHHHHHHHhCCChhHHHHHHHHhhCCCCCCCChhheecCCCcccCCCccHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999887788899999999
Q ss_pred hccccccccccc
Q psy12847 174 EQKIVSEKIQVH 185 (188)
Q Consensus 174 E~~~~~~~~~v~ 185 (188)
||+.+++.++++
T Consensus 84 EGv~~~~~g~i~ 95 (103)
T COG3695 84 EGVEFSDTGRID 95 (103)
T ss_pred cCceeccCceee
Confidence 999999988764
No 11
>PF02870 Methyltransf_1N: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; InterPro: IPR008332 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources []. This group of proteins are characterised by having an N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity (IPR001497 from INTERPRO).; GO: 0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A.
Probab=99.35 E-value=4e-13 Score=94.73 Aligned_cols=69 Identities=12% Similarity=0.240 Sum_probs=50.9
Q ss_pred eEEEEEEeccCccceEEEEEecccccc-cc-cccch---hhhhhc-ccC-ChhHHHHHHHHHHHhcCCCC-CCccccccc
Q psy12847 21 KMLIAYYDKSCIIQAIMFGANPEYLYV-DL-TKLYS---HIEYIK-MFE-SKQSRDIIDRLEAYIVNPKQ-NCLDIKFKI 92 (188)
Q Consensus 21 ~~~~~~~~tP~~~G~i~i~a~~~gL~~-~f-d~~~~---~~~~~~-~~~-~~~l~~~~~qL~~YF~G~~~-~~F~lpl~~ 92 (188)
+|+|.+++|| +|.+.|+++++|||+ .| +.... ...... ..+ .+.+..+.+||++||+|+|. . |++||++
T Consensus 1 ~l~y~~~~sP--lG~l~l~a~e~gL~~i~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qL~eYF~G~r~~~-F~lPld~ 77 (77)
T PF02870_consen 1 MLYYTTIDSP--LGPLLLAASEKGLCGIDFEDQDFELMADLPKWFPQDDEAPLLAEAKQQLDEYFAGERTPE-FDLPLDI 77 (77)
T ss_dssp --EEEEEEET--TEEEEEEEETTCEEEEEEEC-HHHCCHHHCCCTTTSCCHCCHHHHHHHHHHHHHHHHS---B-SHCHH
T ss_pred CeEEEEecCC--CeEEEEEEECCeEEEEEECCCcchhhhhhhhhhhcccccccHHHHHHHHHHHHcCCCCCC-CcCCccC
Confidence 4799999999 999999999999999 88 43321 111111 112 35899999999999999999 8 9999974
No 12
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=83.69 E-value=1.4 Score=27.63 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=21.7
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQN 139 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~N 139 (188)
|+.++.....+.+ +-.|+.+||+.+|. +.-.|.+.+.+|
T Consensus 6 t~~eR~~I~~l~~----~G~s~~~IA~~lg~--s~sTV~relkR~ 44 (44)
T PF13936_consen 6 TPEERNQIEALLE----QGMSIREIAKRLGR--SRSTVSRELKRN 44 (44)
T ss_dssp ------HHHHHHC----S---HHHHHHHTT----HHHHHHHHHHH
T ss_pred hhhHHHHHHHHHH----cCCCHHHHHHHHCc--CcHHHHHHHhcC
Confidence 4556666666644 44899999999997 777888888765
No 13
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=83.31 E-value=1.5 Score=30.04 Aligned_cols=42 Identities=24% Similarity=0.166 Sum_probs=29.9
Q ss_pred ChhHHHHHHHhcc--cCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 95 TDFQKLVWSELCK--IPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 95 t~f~~~V~~~l~~--IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
|+-|++|++.+.+ --.|..=|+.|||+.+|. ++...|-..|.
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~-~S~~tv~~~L~ 48 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPTVREIAEALGL-KSTSTVQRHLK 48 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-SSHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-CChHHHHHHHH
Confidence 7889999999877 456888899999999997 35666665554
No 14
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=78.57 E-value=5.4 Score=28.60 Aligned_cols=35 Identities=14% Similarity=0.099 Sum_probs=24.9
Q ss_pred cccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCC
Q psy12847 106 CKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIP 142 (188)
Q Consensus 106 ~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~ 142 (188)
+.+-.|+-+|-.+||..+|. ..-.|..++...|-.
T Consensus 31 r~LA~G~PVt~~~LA~a~g~--~~e~v~~~L~~~p~t 65 (77)
T PF12324_consen 31 RLLAKGQPVTVEQLAAALGW--PVEEVRAALAAMPDT 65 (77)
T ss_dssp HHHTTTS-B-HHHHHHHHT----HHHHHHHHHH-TTS
T ss_pred HHHHcCCCcCHHHHHHHHCC--CHHHHHHHHHhCCCc
Confidence 33555999999999999997 577899999988854
No 15
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=76.37 E-value=3.9 Score=28.30 Aligned_cols=40 Identities=20% Similarity=0.262 Sum_probs=29.4
Q ss_pred HHHHHHhcccCCCceeCHHHHHHHhCCCC--cHHHHHHHHhhCCC
Q psy12847 99 KLVWSELCKIPFGSLCSYADVARNIGRPK--SARAVANACGQNNI 141 (188)
Q Consensus 99 ~~V~~~l~~IP~G~~~TY~~lA~~~g~p~--~~RaVg~a~~~Np~ 141 (188)
-+||++|.. ....||++|++..|... -..|+|.-.+.|-+
T Consensus 11 G~Vw~~L~~---~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI 52 (65)
T PF10771_consen 11 GKVWQLLNE---NGEWSVSELKKATGLSDKEVYLAIGWLARENKI 52 (65)
T ss_dssp HHHHHHHCC---SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSE
T ss_pred HHHHHHHhh---CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCce
Confidence 469999998 56799999999999743 34666666666654
No 16
>PF13730 HTH_36: Helix-turn-helix domain
Probab=64.40 E-value=18 Score=22.94 Aligned_cols=42 Identities=29% Similarity=0.355 Sum_probs=30.7
Q ss_pred ChhHHHHHHHhcccC--CCc-eeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 95 TDFQKLVWSELCKIP--FGS-LCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 95 t~f~~~V~~~l~~IP--~G~-~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
++-+..||-.|..-. .|. .-|+.+||+.+|. +.|.|-+++..
T Consensus 4 s~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~--s~~Tv~~~i~~ 48 (55)
T PF13730_consen 4 SPTAKLVYLYLASYANKNGGCFPSQETLAKDLGV--SRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCc--CHHHHHHHHHH
Confidence 566777887776653 333 3389999999997 68888887764
No 17
>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=61.43 E-value=22 Score=22.17 Aligned_cols=28 Identities=11% Similarity=0.010 Sum_probs=20.1
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRP 126 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p 126 (188)
++-+++|....- .+-.||.|||+.+|.+
T Consensus 6 ~~~er~vi~~~y----~~~~t~~eIa~~lg~s 33 (50)
T PF04545_consen 6 PPREREVIRLRY----FEGLTLEEIAERLGIS 33 (50)
T ss_dssp -HHHHHHHHHHH----TST-SHHHHHHHHTSC
T ss_pred CHHHHHHHHHHh----cCCCCHHHHHHHHCCc
Confidence 566667665443 8889999999999984
No 18
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=61.15 E-value=15 Score=27.28 Aligned_cols=63 Identities=16% Similarity=0.130 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHHhcCCCCCCcccccccCC--ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 65 KQSRDIIDRLEAYIVNPKQNCLDIKFKIEG--TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 65 ~~l~~~~~qL~~YF~G~~~~~F~lpl~~~g--t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.+-.++...|.+||.|.. +.+|-...- ..-.+.+|+... | .++.+||++.|. +.|.|-+.+++
T Consensus 31 ~ig~~~~~~L~~~~gG~~---iyiP~~~~~~~~~R~~~I~~~f~----G--~n~~eLA~kygl--S~r~I~~Ii~~ 95 (108)
T PF08765_consen 31 IIGEEVALKLCRYFGGQQ---IYIPKCDRLLRALRNREIRREFN----G--MNVRELARKYGL--SERQIYRIIKR 95 (108)
T ss_dssp TSHHHHHHHHHHHH-SS---------SHHHHHHHHHHHHHHH------S--S-HHHHHHHHT----HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCEe---EEeeCccHHHHHHHHHHHHHHhC----C--CCHHHHHHHHCc--CHHHHHHHHHH
Confidence 456678889999999984 456643321 222345666555 4 468999999997 88999888765
No 19
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=60.68 E-value=19 Score=22.41 Aligned_cols=35 Identities=23% Similarity=0.284 Sum_probs=22.9
Q ss_pred hHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 97 FQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 97 f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
+-+++++.|+.= -..||.+||+.+|. ++.+|..-+
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lgl--S~~~v~~Ri 38 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELGL--SESTVRRRI 38 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHTS---HHHHHHHH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHCc--CHHHHHHHH
Confidence 445666666654 56899999999997 566665544
No 20
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=58.19 E-value=15 Score=26.96 Aligned_cols=37 Identities=19% Similarity=0.343 Sum_probs=28.3
Q ss_pred CceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCC
Q psy12847 111 GSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRS 153 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~ 153 (188)
..-+||...|+.+|. ...||-..+.+|-+ |.|..-..
T Consensus 10 ~d~v~~~~FA~~IGK--t~sAVr~Mi~~gKL----P~i~~~dP 46 (87)
T PF10743_consen 10 SDAVTYEKFAEYIGK--TPSAVRKMIKAGKL----PVIEMRDP 46 (87)
T ss_pred ccccCHHHHHHHHCC--CHHHHHHHHHcCCC----CeEeccCC
Confidence 456899999999996 67799999998855 45555443
No 21
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=56.37 E-value=20 Score=25.96 Aligned_cols=43 Identities=14% Similarity=0.083 Sum_probs=30.4
Q ss_pred CCChhHHHHHHHhcc-cCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 93 EGTDFQKLVWSELCK-IPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 93 ~gt~f~~~V~~~l~~-IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
..++.|++|++.|+. -..-+-++..+||+.++.| ...|-.||.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~--~~~v~~al~ 87 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMS--ENEVRKALD 87 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS---HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcC--HHHHHHHHH
Confidence 348999999999999 4455569999999999774 556666654
No 22
>PRK04257 hypothetical protein; Provisional
Probab=54.87 E-value=5.9 Score=28.22 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=8.5
Q ss_pred CCCCceeeeC
Q psy12847 143 ILIPCHRVIR 152 (188)
Q Consensus 143 ~~iPcHRVv~ 152 (188)
-.||.|||+.
T Consensus 53 ~~IP~HRI~~ 62 (78)
T PRK04257 53 THIPYHRILE 62 (78)
T ss_pred CcccceEEEE
Confidence 5799999974
No 23
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=53.87 E-value=33 Score=21.12 Aligned_cols=37 Identities=19% Similarity=0.209 Sum_probs=26.2
Q ss_pred hhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 96 DFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 96 ~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
+-+.+|+..|.+=|. +|-.+||+.+|. +..+|.+.+.
T Consensus 3 ~~~~~Il~~l~~~~~---~t~~ela~~~~i--s~~tv~~~l~ 39 (48)
T PF13412_consen 3 ETQRKILNYLRENPR---ITQKELAEKLGI--SRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHHHHCTT---S-HHHHHHHHTS---HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCC---CCHHHHHHHhCC--CHHHHHHHHH
Confidence 457788888888433 999999999997 5556665554
No 24
>PF04457 DUF504: Protein of unknown function (DUF504); InterPro: IPR007547 This is a family of uncharacterised proteins.
Probab=47.20 E-value=9.7 Score=25.30 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=8.9
Q ss_pred CCCCCceeeeC
Q psy12847 142 PILIPCHRVIR 152 (188)
Q Consensus 142 ~~~iPcHRVv~ 152 (188)
...||-|||+.
T Consensus 34 ~~~IP~HRI~~ 44 (56)
T PF04457_consen 34 ETFIPYHRIVE 44 (56)
T ss_pred ccCcCCeeEEE
Confidence 45899999974
No 25
>PRK13239 alkylmercury lyase; Provisional
Probab=47.18 E-value=42 Score=28.27 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=33.4
Q ss_pred cccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCC
Q psy12847 106 CKIPFGSLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRVIRSDGSYGGY 160 (188)
Q Consensus 106 ~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy 160 (188)
+.+-.|+-.|-.+||+.+|. ...+|-.+|..-+.. ++..+|++-||
T Consensus 29 r~la~G~pvt~~~lA~~~~~--~~~~v~~~L~~l~~~-------~~d~~g~iv~~ 74 (206)
T PRK13239 29 RLLAKGRPVSVTTLAAALGW--PVEEVEAVLEAMPDT-------EYDEDGRIIGY 74 (206)
T ss_pred HHHHcCCCCCHHHHHHHhCC--CHHHHHHHHHhCCCe-------EECCCCCEEec
Confidence 33458999999999999998 456777777775532 45666666665
No 26
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=46.46 E-value=41 Score=21.16 Aligned_cols=37 Identities=19% Similarity=0.195 Sum_probs=26.2
Q ss_pred HHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 98 QKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 98 ~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
|.+++..|.+=.. .+|-.+||+.+|. +.|.|-+.+..
T Consensus 2 ~~~il~~L~~~~~--~it~~eLa~~l~v--S~rTi~~~i~~ 38 (55)
T PF08279_consen 2 QKQILKLLLESKE--PITAKELAEELGV--SRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHHTTT--SBEHHHHHHHCTS---HHHHHHHHHH
T ss_pred HHHHHHHHHHcCC--CcCHHHHHHHhCC--CHHHHHHHHHH
Confidence 4566666644333 3999999999997 77888877765
No 27
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=46.34 E-value=34 Score=24.51 Aligned_cols=45 Identities=22% Similarity=0.317 Sum_probs=36.4
Q ss_pred ChhHHHHHHHhcc--cCCCceeCHHHHHHHhCC-CCcHHHHHHHHhhC
Q psy12847 95 TDFQKLVWSELCK--IPFGSLCSYADVARNIGR-PKSARAVANACGQN 139 (188)
Q Consensus 95 t~f~~~V~~~l~~--IP~G~~~TY~~lA~~~g~-p~~~RaVg~a~~~N 139 (188)
|+-|++|+++|.+ +--|+.+.-.+||+.++. |...|-+-.+|...
T Consensus 3 t~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~l 50 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEEL 50 (78)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 6789999998866 788999999999999985 44567777777665
No 28
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.86 E-value=39 Score=24.24 Aligned_cols=29 Identities=24% Similarity=0.420 Sum_probs=21.8
Q ss_pred hhHHHHHHHhcccCCCceeCHHHHHHHhCCCC
Q psy12847 96 DFQKLVWSELCKIPFGSLCSYADVARNIGRPK 127 (188)
Q Consensus 96 ~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~ 127 (188)
+..++|...|.. +...|+.+||+.+|.+.
T Consensus 3 ~~D~~il~~L~~---~~~~~~~~la~~l~~s~ 31 (108)
T smart00344 3 EIDRKILEELQK---DARISLAELAKKVGLSP 31 (108)
T ss_pred HHHHHHHHHHHH---hCCCCHHHHHHHHCcCH
Confidence 455777777765 33589999999999753
No 29
>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=45.61 E-value=28 Score=24.56 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=28.6
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhCC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQNN 140 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~Np 140 (188)
.+..++++...+.+ +-.||.|||+.+|. +..+|-+-+..++
T Consensus 17 ~~~~r~af~L~R~~---eGlS~kEIAe~LGI--S~~TVk~~l~~~~ 57 (73)
T TIGR03879 17 DSLAEAAAALAREE---AGKTASEIAEELGR--TEQTVRNHLKGET 57 (73)
T ss_pred CHHHHHHHHHHHHH---cCCCHHHHHHHHCc--CHHHHHHHHhcCc
Confidence 44556666554222 55799999999997 6778888777653
No 30
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=45.11 E-value=57 Score=21.38 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=19.1
Q ss_pred HHHHHhc--ccCCCcee-CHHHHHHHhCCC
Q psy12847 100 LVWSELC--KIPFGSLC-SYADVARNIGRP 126 (188)
Q Consensus 100 ~V~~~l~--~IP~G~~~-TY~~lA~~~g~p 126 (188)
.+.+.+. .+|+|+.. |-.+||+.+|..
T Consensus 8 ~l~~~I~~g~~~~g~~lps~~~la~~~~vs 37 (64)
T PF00392_consen 8 QLRQAILSGRLPPGDRLPSERELAERYGVS 37 (64)
T ss_dssp HHHHHHHTTSS-TTSBE--HHHHHHHHTS-
T ss_pred HHHHHHHcCCCCCCCEeCCHHHHHHHhccC
Confidence 3445554 49999999 999999999973
No 31
>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=44.07 E-value=29 Score=21.80 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=15.3
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
|-+-.||.|||+.+|. +..+|-+.+
T Consensus 23 ~~~g~s~~eIa~~l~~--s~~~v~~~l 47 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGI--SESTVKRRL 47 (54)
T ss_dssp HTS---HHHHHHHCTS---HHHHHHHH
T ss_pred HHHCcCHHHHHHHHCc--CHHHHHHHH
Confidence 4566789999999997 455555444
No 32
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=43.54 E-value=37 Score=27.37 Aligned_cols=32 Identities=25% Similarity=0.168 Sum_probs=26.7
Q ss_pred ChhHHHHHHHhcc--cCCCceeCHHHHHHHhCCC
Q psy12847 95 TDFQKLVWSELCK--IPFGSLCSYADVARNIGRP 126 (188)
Q Consensus 95 t~f~~~V~~~l~~--IP~G~~~TY~~lA~~~g~p 126 (188)
|+-|.+|++.|.+ -.-|...|..+||+.+|..
T Consensus 5 t~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~ 38 (199)
T TIGR00498 5 TARQQEVLDLIRAHIESTGYPPSIREIARAVGLR 38 (199)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC
Confidence 7899999999985 2346668999999999985
No 33
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=43.46 E-value=57 Score=22.05 Aligned_cols=41 Identities=17% Similarity=0.230 Sum_probs=30.1
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.+-.++|++.|..-+ ++..|=++||+.+|.++ ++|-++|.+
T Consensus 5 ~~~~~~IL~~L~~~g-~~~~ta~eLa~~lgl~~--~~v~r~L~~ 45 (68)
T smart00550 5 DSLEEKILEFLENSG-DETSTALQLAKNLGLPK--KEVNRVLYS 45 (68)
T ss_pred hHHHHHHHHHHHHCC-CCCcCHHHHHHHHCCCH--HHHHHHHHH
Confidence 345678999998773 22588999999999854 466666653
No 34
>PF06301 Lambda_Kil: Bacteriophage lambda Kil protein; InterPro: IPR010444 This family consists of several Bacteriophage lambda Kil protein like sequences. A cessation of division, followed by one or two fairly synchronous cell divisions in Escherichia coli is due to two genetically separable events: a temporary block of cell division and, at the same time, a block to the initiation of new rounds of DNA replication. The cell division block is a result of the transient expression of the lambda kil gene []. The lambda kil gene has been shown to be responsible for premature lysis on the addition of chloramphenicol between 15 and 20 min after thermal induction of a lambda prophage []. Induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of functions from the lambda p(L) operon. The kil gene causes cell death and filamentation [].
Probab=41.00 E-value=12 Score=23.80 Aligned_cols=30 Identities=30% Similarity=0.367 Sum_probs=19.7
Q ss_pred HHHHHHhCCCCcHHHHHHHHhhCCCCCCCCcee
Q psy12847 117 ADVARNIGRPKSARAVANACGQNNIPILIPCHR 149 (188)
Q Consensus 117 ~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHR 149 (188)
--||.-+|.. .---.|+..-...|.+||||
T Consensus 12 ~~IA~flGD~---~mw~eA~e~~k~ai~~pwyR 41 (43)
T PF06301_consen 12 AAIARFLGDE---KMWSEANEAMKIAIGMPWYR 41 (43)
T ss_pred HHHHHHHccH---HHHHHHHHHHHHHhCcchhc
Confidence 3578888863 33444444445568899998
No 35
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=39.86 E-value=76 Score=19.99 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=27.0
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCc--HHHHHHHHhhC
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKS--ARAVANACGQN 139 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~--~RaVg~a~~~N 139 (188)
++..+..|+..+..=| .|..+||+.+|.+.. .|++-.-...+
T Consensus 5 ~~~~~~~il~~l~~~~----~~~~ei~~~~~i~~~~i~~~l~~L~~~g 48 (78)
T cd00090 5 SDPTRLRILRLLLEGP----LTVSELAERLGLSQSTVSRHLKKLEEAG 48 (78)
T ss_pred cChHHHHHHHHHHHCC----cCHHHHHHHHCcCHhHHHHHHHHHHHCC
Confidence 3556777877766533 999999999987543 24444433333
No 36
>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=38.19 E-value=46 Score=22.18 Aligned_cols=37 Identities=24% Similarity=0.303 Sum_probs=25.4
Q ss_pred ceeCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceee
Q psy12847 112 SLCSYADVARNIGRPKSARAVANACGQNNIPILIPCHRV 150 (188)
Q Consensus 112 ~~~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRV 150 (188)
+-.|+.+||+.+|.| .+.|-+-..+.-..-.-|-+||
T Consensus 12 ~G~~~~eIA~~Lg~~--~~TV~~W~~r~~W~~~~~~~rv 48 (58)
T PF06056_consen 12 QGWSIKEIAEELGVP--RSTVYSWKDRYKWDELLPIERV 48 (58)
T ss_pred cCCCHHHHHHHHCCC--hHHHHHHHHhhCccccCchhhH
Confidence 346789999999986 6777776666554444455554
No 37
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.00 E-value=76 Score=19.37 Aligned_cols=22 Identities=32% Similarity=0.382 Sum_probs=16.3
Q ss_pred CceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 111 GSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
|. |+.++|+.+|. +.+.|.+-+
T Consensus 12 g~--s~~~~a~~~gi--s~~tv~~w~ 33 (52)
T PF13518_consen 12 GE--SVREIAREFGI--SRSTVYRWI 33 (52)
T ss_pred CC--CHHHHHHHHCC--CHhHHHHHH
Confidence 66 99999999997 445555444
No 38
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.51 E-value=89 Score=18.95 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=22.1
Q ss_pred hhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 96 DFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 96 ~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
+.++++...+. .| .|+.+||+.+|. +.+.|-..+.
T Consensus 3 ~~e~~i~~~~~---~~--~s~~eia~~l~~--s~~tv~~~~~ 37 (57)
T cd06170 3 PREREVLRLLA---EG--KTNKEIADILGI--SEKTVKTHLR 37 (57)
T ss_pred HHHHHHHHHHH---cC--CCHHHHHHHHCC--CHHHHHHHHH
Confidence 44555554432 23 599999999997 4555555543
No 39
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=36.63 E-value=25 Score=22.29 Aligned_cols=35 Identities=23% Similarity=0.320 Sum_probs=22.2
Q ss_pred HHHHHhcccCCCceeCHHHHHHHhCCCCc--HHHHHHHH
Q psy12847 100 LVWSELCKIPFGSLCSYADVARNIGRPKS--ARAVANAC 136 (188)
Q Consensus 100 ~V~~~l~~IP~G~~~TY~~lA~~~g~p~~--~RaVg~a~ 136 (188)
+|++.+..=+.+ .|-+|||+.+|.|++ .|.+.+-.
T Consensus 7 ~iL~~l~~~~~~--~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 7 RILEALAESGGP--LTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHHCHHCTBSC--EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCC--CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 355555555444 699999999999865 35544433
No 40
>PF14120 YhzD: YhzD-like protein
Probab=35.90 E-value=19 Score=24.65 Aligned_cols=34 Identities=15% Similarity=0.163 Sum_probs=22.0
Q ss_pred CCcHHHHHHHHhhCCCCCCCCceeeeCCCCCcCCC
Q psy12847 126 PKSARAVANACGQNNIPILIPCHRVIRSDGSYGGY 160 (188)
Q Consensus 126 p~~~RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy 160 (188)
...|+..|..+-+.- .+.=--||+|++.|+|--|
T Consensus 26 D~eAK~~G~~~L~Ek-~~~~~THR~v~~~GKLiLF 59 (61)
T PF14120_consen 26 DEEAKEIGEQKLKEK-GYEEKTHRCVSSSGKLILF 59 (61)
T ss_pred HHHHHHHHHHHHHHC-ChhhcceeeeCCCCcEEEe
Confidence 346677776665432 2345679999999987533
No 41
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=35.76 E-value=1e+02 Score=20.46 Aligned_cols=43 Identities=9% Similarity=-0.004 Sum_probs=35.1
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCC-cHHHHHHHHh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPK-SARAVANACG 137 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~-~~RaVg~a~~ 137 (188)
.+.+.+..+++..+..|...|=..|++.++.+. +...|.+-+-
T Consensus 8 ~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~Q 51 (57)
T TIGR01557 8 EDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQ 51 (57)
T ss_pred HHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHH
Confidence 356777889999999999999999999998777 7888877553
No 42
>COG1531 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.73 E-value=17 Score=26.08 Aligned_cols=10 Identities=40% Similarity=0.926 Sum_probs=8.3
Q ss_pred CCCCceeeeC
Q psy12847 143 ILIPCHRVIR 152 (188)
Q Consensus 143 ~~iPcHRVv~ 152 (188)
-.||-||||.
T Consensus 54 ~~IP~HRIve 63 (77)
T COG1531 54 TYIPYHRIVE 63 (77)
T ss_pred ceeeeEEEEE
Confidence 3599999986
No 43
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=34.79 E-value=27 Score=22.77 Aligned_cols=31 Identities=10% Similarity=0.129 Sum_probs=23.9
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCC
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPK 127 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~ 127 (188)
+.|-+.+|++.| ..+...|.++||+.+|.|.
T Consensus 8 ~~p~R~~Il~~L---~~~~~~t~~ela~~l~~~~ 38 (61)
T PF12840_consen 8 SDPTRLRILRLL---ASNGPMTVSELAEELGISQ 38 (61)
T ss_dssp TSHHHHHHHHHH---HHCSTBEHHHHHHHHTS-H
T ss_pred CCHHHHHHHHHH---hcCCCCCHHHHHHHHCCCH
Confidence 457777888777 5577889999999999754
No 44
>PRK12423 LexA repressor; Provisional
Probab=33.79 E-value=50 Score=27.01 Aligned_cols=44 Identities=23% Similarity=0.215 Sum_probs=28.8
Q ss_pred ChhHHHHHHHhcc-cCC-CceeCHHHHHHHhCC--CCcHHHHHHHHhh
Q psy12847 95 TDFQKLVWSELCK-IPF-GSLCSYADVARNIGR--PKSARAVANACGQ 138 (188)
Q Consensus 95 t~f~~~V~~~l~~-IP~-G~~~TY~~lA~~~g~--p~~~RaVg~a~~~ 138 (188)
|+-|+++++.|.+ |-. |-.-|+.|||+.+|. +.+.|.-=.+|.+
T Consensus 5 t~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 5 TPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 7889999998876 322 223599999999993 3344433334433
No 45
>PRK00215 LexA repressor; Validated
Probab=33.36 E-value=37 Score=27.51 Aligned_cols=42 Identities=17% Similarity=0.066 Sum_probs=30.3
Q ss_pred ChhHHHHHHHhccc--CCCceeCHHHHHHHhCC-CCc--HHHHHHHH
Q psy12847 95 TDFQKLVWSELCKI--PFGSLCSYADVARNIGR-PKS--ARAVANAC 136 (188)
Q Consensus 95 t~f~~~V~~~l~~I--P~G~~~TY~~lA~~~g~-p~~--~RaVg~a~ 136 (188)
|+-|.+|+..|.+- -.|...|.+|||+.+|. +++ .|.+.+-.
T Consensus 3 t~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 3 TKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 67788999888753 35777899999999997 543 35544433
No 46
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=32.77 E-value=27 Score=22.00 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=20.5
Q ss_pred HHHHHhcccCCCceeCHHHHHHHhCCCCcH
Q psy12847 100 LVWSELCKIPFGSLCSYADVARNIGRPKSA 129 (188)
Q Consensus 100 ~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~ 129 (188)
++-.+|..|--|+ .|+.+.|+..|.|.+.
T Consensus 4 ~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sT 32 (45)
T PF05225_consen 4 DLQKAIEAVKNGK-MSIRKAAKKYGVPRST 32 (45)
T ss_dssp HHHHHHHHHHTTS-S-HHHHHHHHT--HHH
T ss_pred HHHHHHHHHHhCC-CCHHHHHHHHCcCHHH
Confidence 4456677777899 9999999999998754
No 47
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=32.40 E-value=85 Score=24.67 Aligned_cols=28 Identities=18% Similarity=0.013 Sum_probs=22.5
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCC
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRP 126 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p 126 (188)
-++.|++|.... -+-.||.+||+.+|..
T Consensus 7 Lte~qr~VL~Lr-----~~GlTq~EIAe~LgiS 34 (137)
T TIGR00721 7 LTERQIKVLELR-----EKGLSQKEIAKELKTT 34 (137)
T ss_pred CCHHHHHHHHHH-----HcCCCHHHHHHHHCcC
Confidence 378899998774 2556999999999974
No 48
>KOG1182|consensus
Probab=32.27 E-value=25 Score=31.97 Aligned_cols=18 Identities=39% Similarity=0.445 Sum_probs=15.2
Q ss_pred CCCceeeeCCCCCcCCCC
Q psy12847 144 LIPCHRVIRSDGSYGGYS 161 (188)
Q Consensus 144 ~iPcHRVv~~~G~l~gy~ 161 (188)
-|||.||+..+|.|..-+
T Consensus 61 ~iPiYRV~d~~G~ii~~s 78 (432)
T KOG1182|consen 61 RIPIYRVMDADGQIIDKS 78 (432)
T ss_pred CCceEEEecCCCcccCcc
Confidence 599999999999986543
No 49
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.05 E-value=86 Score=23.72 Aligned_cols=39 Identities=21% Similarity=0.206 Sum_probs=28.0
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.+.-.++++.|+.=.. .||.+||+++|. ++.+|..-+.+
T Consensus 7 D~~D~~IL~~L~~d~r---~~~~eia~~lgl--S~~~v~~Ri~~ 45 (154)
T COG1522 7 DDIDRRILRLLQEDAR---ISNAELAERVGL--SPSTVLRRIKR 45 (154)
T ss_pred cHHHHHHHHHHHHhCC---CCHHHHHHHHCC--CHHHHHHHHHH
Confidence 4566778888876433 999999999997 55566655544
No 50
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=31.33 E-value=1.2e+02 Score=19.13 Aligned_cols=42 Identities=26% Similarity=0.193 Sum_probs=28.4
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCc--HHHHHHHHh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKS--ARAVANACG 137 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~--~RaVg~a~~ 137 (188)
|+-|..|+..|..=|.+ ..|-++||+.+|.+++ .|.|..-..
T Consensus 4 t~~q~~vL~~l~~~~~~-~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 4 TPSQFRVLMALARHPGE-ELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp THHHHHHHHHHHHSTTS-GEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHCCCC-CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56677788888777655 5699999999998543 244443333
No 51
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=31.03 E-value=92 Score=25.76 Aligned_cols=36 Identities=25% Similarity=0.210 Sum_probs=27.4
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
-|+-+++|++.+.+ | .|+.|||+.++. +.+.|-+.+
T Consensus 156 Lt~rE~~Vl~l~~~---G--~s~~eIA~~L~i--S~~TVk~~~ 191 (216)
T PRK10100 156 LTHREKEILNKLRI---G--ASNNEIARSLFI--SENTVKTHL 191 (216)
T ss_pred CCHHHHHHHHHHHc---C--CCHHHHHHHhCC--CHHHHHHHH
Confidence 38889999888876 6 679999999997 455554444
No 52
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=30.43 E-value=85 Score=25.57 Aligned_cols=62 Identities=8% Similarity=0.068 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhcCCCCCCccccc--c-cCCChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 67 SRDIIDRLEAYIVNPKQNCLDIKF--K-IEGTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 67 l~~~~~qL~~YF~G~~~~~F~lpl--~-~~gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+...+.++...+|+.. ++-.. . ..-|+.+++|++.+. +=.|++|||+++|. +.+.|-+.+.
T Consensus 110 ~~~L~~aI~~v~~g~~~--~~~~~~~~~~~LT~RE~eVL~lla-----~G~snkeIA~~L~i--S~~TVk~h~~ 174 (207)
T PRK15411 110 PESLDDLLGDILKKETT--ITSFLNLPTLSLSRTESSMLRMWM-----AGQGTIQISDQMNI--KAKTVSSHKG 174 (207)
T ss_pred HHHHHHHHHHHHcCCcc--cCccccCCcccCCHHHHHHHHHHH-----cCCCHHHHHHHcCC--CHHHHHHHHH
Confidence 34445555666666542 21110 1 125899999988875 44679999999996 6676665553
No 53
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=30.28 E-value=73 Score=20.84 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=26.4
Q ss_pred HHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 98 QKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 98 ~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
|.++...|.. ....|+.+||+.+|. +.|.+-+-+..
T Consensus 7 q~~Ll~~L~~---~~~~~~~ela~~l~~--S~rti~~~i~~ 42 (59)
T PF08280_consen 7 QLKLLELLLK---NKWITLKELAKKLNI--SERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHH---HTSBBHHHHHHHCTS---HHHHHHHHHH
T ss_pred HHHHHHHHHc---CCCCcHHHHHHHHCC--CHHHHHHHHHH
Confidence 3445666666 567899999999997 78888777654
No 54
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=30.26 E-value=1.1e+02 Score=25.27 Aligned_cols=16 Identities=13% Similarity=0.293 Sum_probs=14.4
Q ss_pred CceeCHHHHHHHhCCC
Q psy12847 111 GSLCSYADVARNIGRP 126 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p 126 (188)
++-.||.+||+.+|.+
T Consensus 194 ~~~~t~~EIA~~lgis 209 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVT 209 (238)
T ss_pred CCCccHHHHHHHHCCC
Confidence 5889999999999984
No 55
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=29.64 E-value=94 Score=24.46 Aligned_cols=40 Identities=10% Similarity=-0.011 Sum_probs=28.3
Q ss_pred hhHHHHHHHhcccC----------CCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 96 DFQKLVWSELCKIP----------FGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 96 ~f~~~V~~~l~~IP----------~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
..+..+..+|.++| |-+-.||.|||+.+|.+ ..+|.+.+.
T Consensus 123 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis--~~tV~~~l~ 172 (188)
T PRK09640 123 EERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG--LSATKMRYK 172 (188)
T ss_pred HHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCC--HHHHHHHHH
Confidence 33455777788888 45567999999999984 456655544
No 56
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=28.74 E-value=77 Score=21.11 Aligned_cols=34 Identities=12% Similarity=0.185 Sum_probs=20.5
Q ss_pred cCCCceeCHHHHHHHh---CCCCcHHHHHHHHhhCCC
Q psy12847 108 IPFGSLCSYADVARNI---GRPKSARAVANACGQNNI 141 (188)
Q Consensus 108 IP~G~~~TY~~lA~~~---g~p~~~RaVg~a~~~Np~ 141 (188)
|-....+|+.+|+..+ |..-+.+-|.+.|..+-+
T Consensus 8 v~~~p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g~ 44 (72)
T PF01498_consen 8 VRRNPRISAREIAQELQEAGISVSKSTIRRRLREAGL 44 (72)
T ss_dssp --------HHHHHHHT---T--S-HHHHHHHHHHT-E
T ss_pred HHHCCCCCHHHHHHHHHHccCCcCHHHHHHHHHHcCc
Confidence 3344459999999999 988899999999998854
No 57
>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=28.66 E-value=1.3e+02 Score=17.55 Aligned_cols=35 Identities=23% Similarity=0.283 Sum_probs=21.3
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHH
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANA 135 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a 135 (188)
++.++++.... |.+-.|+.+||+.+|.+ .+.|-+.
T Consensus 12 ~~~~~~~~~~~----~~~~~~~~~ia~~~~~s--~~~i~~~ 46 (55)
T cd06171 12 PEREREVILLR----FGEGLSYEEIAEILGIS--RSTVRQR 46 (55)
T ss_pred CHHHHHHHHHH----HhcCCCHHHHHHHHCcC--HHHHHHH
Confidence 44555555433 22457999999999974 4444433
No 58
>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=28.62 E-value=70 Score=19.74 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=14.1
Q ss_pred eCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 114 CSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 114 ~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.|..+||+.+|. +-..|=..+..
T Consensus 22 ~si~~IA~~~gv--sr~TvyR~l~~ 44 (45)
T PF02796_consen 22 MSIAEIAKQFGV--SRSTVYRYLNK 44 (45)
T ss_dssp --HHHHHHHTTS---HHHHHHHHCC
T ss_pred CCHHHHHHHHCc--CHHHHHHHHhc
Confidence 889999999997 44445444443
No 59
>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=28.01 E-value=1.8e+02 Score=19.07 Aligned_cols=41 Identities=17% Similarity=0.219 Sum_probs=24.1
Q ss_pred ChhHHHHHHHhccc---CCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 95 TDFQKLVWSELCKI---PFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 95 t~f~~~V~~~l~~I---P~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
|+-|++++..-..- -+=+-+|.++||+.+|. +.-++..-++
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgi--s~st~~~~LR 45 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELGI--SKSTVSEHLR 45 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCC--CHHHHHHHHH
Confidence 45566666433321 12245788999999997 4445554444
No 60
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=27.25 E-value=1.2e+02 Score=23.99 Aligned_cols=29 Identities=17% Similarity=0.037 Sum_probs=23.1
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCC
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPK 127 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~ 127 (188)
-|+-|++|++.. -+-.|+.|||+.+|.+.
T Consensus 7 Lt~rqreVL~lr-----~~GlTq~EIAe~LGiS~ 35 (141)
T PRK03975 7 LTERQIEVLRLR-----ERGLTQQEIADILGTSR 35 (141)
T ss_pred CCHHHHHHHHHH-----HcCCCHHHHHHHHCCCH
Confidence 488899998763 25689999999999843
No 61
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=27.15 E-value=99 Score=18.29 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=14.9
Q ss_pred eCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 114 CSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 114 ~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.|-.|||..+|. +.-.|.+++++
T Consensus 3 mtr~diA~~lG~--t~ETVSR~l~~ 25 (32)
T PF00325_consen 3 MTRQDIADYLGL--TRETVSRILKK 25 (32)
T ss_dssp --HHHHHHHHTS---HHHHHHHHHH
T ss_pred cCHHHHHHHhCC--cHHHHHHHHHH
Confidence 577899999996 55566666553
No 62
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=26.86 E-value=1.8e+02 Score=19.24 Aligned_cols=37 Identities=19% Similarity=0.244 Sum_probs=24.8
Q ss_pred hHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 97 FQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 97 f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
+=+.+|..-. .|+.++-++||+.+|. ++-.|..++++
T Consensus 9 YL~~Iy~l~~---~~~~v~~~~iA~~L~v--s~~tvt~ml~~ 45 (60)
T PF01325_consen 9 YLKAIYELSE---EGGPVRTKDIAERLGV--SPPTVTEMLKR 45 (60)
T ss_dssp HHHHHHHHHH---CTSSBBHHHHHHHHTS---HHHHHHHHHH
T ss_pred HHHHHHHHHc---CCCCccHHHHHHHHCC--ChHHHHHHHHH
Confidence 3345555544 7899999999999997 44455555543
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.17 E-value=1.1e+02 Score=23.22 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=17.3
Q ss_pred CceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 111 GSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
-+-.||.+||+.+|. +...|.+.+
T Consensus 142 ~~~~s~~eIA~~lgi--s~~tV~~~l 165 (182)
T PRK09652 142 IEGLSYEEIAEIMGC--PIGTVRSRI 165 (182)
T ss_pred HcCCCHHHHHHHHCC--CHHHHHHHH
Confidence 356799999999998 455555444
No 64
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=25.98 E-value=1.7e+02 Score=22.62 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=26.4
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCC
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGR 125 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~ 125 (188)
-|+.+.+|+..|.+ -.|++.|+.+||+.++.
T Consensus 155 Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~ 185 (228)
T PRK11083 155 LTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWE 185 (228)
T ss_pred cCHHHHHHHHHHHh-CCCceECHHHHHHHhcC
Confidence 38888899988887 44999999999999964
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.87 E-value=72 Score=24.78 Aligned_cols=35 Identities=11% Similarity=0.004 Sum_probs=22.8
Q ss_pred HHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 101 VWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 101 V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
+-.+|.++|.- +-.||.+||+.+|. +..+|.+.+.
T Consensus 123 l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgi--s~~tV~~~l~ 167 (179)
T PRK12514 123 IDACLEELEKDRAAAVRRAYLEGLSYKELAERHDV--PLNTMRTWLR 167 (179)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC--ChHHHHHHHH
Confidence 44556666632 34689999999997 4556655543
No 66
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.73 E-value=1.5e+02 Score=17.38 Aligned_cols=31 Identities=23% Similarity=0.287 Sum_probs=22.2
Q ss_pred eCHHHHHHHhCCCCcHHHHHHHHhhCCCCCCCCceee
Q psy12847 114 CSYADVARNIGRPKSARAVANACGQNNIPILIPCHRV 150 (188)
Q Consensus 114 ~TY~~lA~~~g~p~~~RaVg~a~~~Np~~~~iPcHRV 150 (188)
.|-.|+|+.+|. +.+.+-+-+... .+|++++
T Consensus 2 lt~~e~a~~lgi--s~~ti~~~~~~g----~i~~~~~ 32 (49)
T TIGR01764 2 LTVEEAAEYLGV--SKDTVYRLIHEG----ELPAYRV 32 (49)
T ss_pred CCHHHHHHHHCC--CHHHHHHHHHcC----CCCeEEe
Confidence 477899999997 555666666544 4788776
No 67
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=25.51 E-value=76 Score=25.17 Aligned_cols=27 Identities=22% Similarity=0.407 Sum_probs=20.6
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
|=+-.||.|||+.+|. +..+|.+++.+
T Consensus 167 ~~e~~s~~EIA~~lgi--s~~tV~~~l~r 193 (208)
T PRK08295 167 YLDGKSYQEIAEELNR--HVKSIDNALQR 193 (208)
T ss_pred HHccCCHHHHHHHHCC--CHHHHHHHHHH
Confidence 3456899999999997 56677766653
No 68
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.41 E-value=1.5e+02 Score=24.21 Aligned_cols=22 Identities=14% Similarity=0.125 Sum_probs=16.0
Q ss_pred ceeCHHHHHHHhCCCCcHHHHHHH
Q psy12847 112 SLCSYADVARNIGRPKSARAVANA 135 (188)
Q Consensus 112 ~~~TY~~lA~~~g~p~~~RaVg~a 135 (188)
+-.||.|||+.+|.+ ...|-+.
T Consensus 197 eg~s~~EIA~~lgis--~~tVk~~ 218 (234)
T PRK08301 197 EEKTQKEVADMLGIS--QSYISRL 218 (234)
T ss_pred CCCCHHHHHHHHCCC--HHHHHHH
Confidence 567999999999984 4444333
No 69
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=25.33 E-value=78 Score=24.99 Aligned_cols=35 Identities=14% Similarity=0.117 Sum_probs=24.6
Q ss_pred HHHHHhcccC----------CCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 100 LVWSELCKIP----------FGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 100 ~V~~~l~~IP----------~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
.+..+|.+.| +-+-.||.+||+.+|. +...|.+.+
T Consensus 132 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgi--s~~tV~~~l 176 (194)
T PRK12513 132 RLQAALETLPDEQREVFLLREHGDLELEEIAELTGV--PEETVKSRL 176 (194)
T ss_pred HHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCC--CHHHHHHHH
Confidence 4666666666 4567899999999997 455555443
No 70
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.23 E-value=1.3e+02 Score=22.55 Aligned_cols=24 Identities=8% Similarity=-0.191 Sum_probs=17.2
Q ss_pred CceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 111 GSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
.+-.||.|||+.+|.+ ..+|-+.+
T Consensus 120 ~~~~s~~EIA~~l~is--~~tV~~~~ 143 (154)
T PRK06759 120 FVGKTMGEIALETEMT--YYQVRWIY 143 (154)
T ss_pred hcCCCHHHHHHHHCCC--HHHHHHHH
Confidence 4568999999999984 44554443
No 71
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=25.16 E-value=75 Score=20.97 Aligned_cols=30 Identities=13% Similarity=0.255 Sum_probs=23.9
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPK 127 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~ 127 (188)
++-+.+||..|. .-...|-.+||+.+|.|+
T Consensus 7 s~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~ 36 (68)
T PF01978_consen 7 SENEAKVYLALL---KNGPATAEEIAEELGISR 36 (68)
T ss_dssp HHHHHHHHHHHH---HHCHEEHHHHHHHHTSSH
T ss_pred CHHHHHHHHHHH---HcCCCCHHHHHHHHCcCH
Confidence 567788999887 344578899999999864
No 72
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=25.13 E-value=82 Score=23.56 Aligned_cols=36 Identities=17% Similarity=0.122 Sum_probs=25.4
Q ss_pred HHHHHhcccC----------CCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 100 LVWSELCKIP----------FGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 100 ~V~~~l~~IP----------~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+.+.|.+.| +.+-.||.|||+.+|.| ..+|.+.+.
T Consensus 98 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis--~~tv~~~l~ 143 (154)
T TIGR02950 98 EITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLS--LAKVKSNLF 143 (154)
T ss_pred HHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCC--HHHHHHHHH
Confidence 3566777777 34567999999999984 556655554
No 73
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=24.32 E-value=1.2e+02 Score=18.79 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=16.6
Q ss_pred eCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 114 CSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 114 ~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.|+.++|+.+|. +...|......
T Consensus 10 ls~~~la~~~gi--s~~~i~~~~~g 32 (55)
T PF01381_consen 10 LSQKELAEKLGI--SRSTISRIENG 32 (55)
T ss_dssp S-HHHHHHHHTS---HHHHHHHHTT
T ss_pred CCHHHHHHHhCC--CcchhHHHhcC
Confidence 578999999995 66777777665
No 74
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=24.07 E-value=1.4e+02 Score=21.24 Aligned_cols=37 Identities=11% Similarity=0.051 Sum_probs=27.2
Q ss_pred hHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhhC
Q psy12847 97 FQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQN 139 (188)
Q Consensus 97 f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~N 139 (188)
-+.++.+.|.+ | .+|-.+||+.+|. +...|..++..+
T Consensus 7 R~~~I~e~l~~---~-~~ti~dvA~~~gv--S~~TVsr~L~~~ 43 (80)
T TIGR02844 7 RVLEIGKYIVE---T-KATVRETAKVFGV--SKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHHH---C-CCCHHHHHHHhCC--CHHHHHHHhcCC
Confidence 34556677766 4 4589999999997 777888877544
No 75
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=23.93 E-value=1.4e+02 Score=24.97 Aligned_cols=37 Identities=5% Similarity=-0.065 Sum_probs=28.6
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
-|+-+++|++.+.+ -.|++|||+.++. +.+.|.+.+.
T Consensus 134 LSpRErEVLrLLAq-----GkTnKEIAe~L~I--S~rTVkth~s 170 (198)
T PRK15201 134 FSVTERHLLKLIAS-----GYHLSETAALLSL--SEEQTKSLRR 170 (198)
T ss_pred CCHHHHHHHHHHHC-----CCCHHHHHHHhCC--CHHHHHHHHH
Confidence 38888889888854 4679999999997 6666666554
No 76
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.81 E-value=1e+02 Score=18.89 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=15.9
Q ss_pred eeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 113 LCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 113 ~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
-.|+.+||+.+|. +.+.|.+-+.+
T Consensus 17 G~s~~~ia~~lgv--s~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGV--SRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS---HHHHHHHHT-
T ss_pred CCCHHHHHHHHCc--CHHHHHHHHHH
Confidence 4689999999997 66677666554
No 77
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=23.74 E-value=87 Score=24.55 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=18.9
Q ss_pred ceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 112 SLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 112 ~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
+-.||.+||+.+|.| ...|.+++.+
T Consensus 164 ~~~s~~eIA~~l~~s--~~tV~~~l~r 188 (198)
T TIGR02859 164 DGKSYQEIACDLNRH--VKSIDNALQR 188 (198)
T ss_pred cCCCHHHHHHHHCCC--HHHHHHHHHH
Confidence 357999999999985 5567766653
No 78
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.58 E-value=88 Score=24.07 Aligned_cols=35 Identities=14% Similarity=-0.001 Sum_probs=24.4
Q ss_pred HHHHhcccC----------CCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 101 VWSELCKIP----------FGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 101 V~~~l~~IP----------~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
+.++|...| |-+-.||.|||+.+|.| ..+|.+.+.
T Consensus 114 l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s--~~tv~~~l~ 158 (175)
T PRK12518 114 VQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIP--VGTVKSRLF 158 (175)
T ss_pred HHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCC--HHHHHHHHH
Confidence 455566666 45667999999999984 556665554
No 79
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.42 E-value=1.2e+02 Score=24.57 Aligned_cols=35 Identities=20% Similarity=0.241 Sum_probs=22.7
Q ss_pred HHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 101 VWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 101 V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
+-..|.++|.- +-.||.|||+.+|.+ ..+|-+.+.
T Consensus 132 l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis--~~tV~~~l~ 176 (203)
T PRK09647 132 LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVK--LGTVRSRIH 176 (203)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC--HHHHHHHHH
Confidence 44556666654 457999999999974 344444443
No 80
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=23.34 E-value=1.5e+02 Score=23.48 Aligned_cols=37 Identities=11% Similarity=0.110 Sum_probs=28.4
Q ss_pred CChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 94 GTDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 94 gt~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
-|+-+.+|++.+. +-.|.+|||+.++. +.+.|-+.+.
T Consensus 151 Lt~rE~evl~~~~-----~G~s~~eIA~~l~i--S~~TV~~h~~ 187 (216)
T PRK10840 151 LSPKESEVLRLFA-----EGFLVTEIAKKLNR--SIKTISSQKK 187 (216)
T ss_pred CCHHHHHHHHHHH-----CCCCHHHHHHHHCC--CHHHHHHHHH
Confidence 3888888888875 45899999999996 6666665554
No 81
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=23.33 E-value=88 Score=24.37 Aligned_cols=36 Identities=8% Similarity=-0.034 Sum_probs=24.9
Q ss_pred HHHHHhcccCC----------CceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 100 LVWSELCKIPF----------GSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 100 ~V~~~l~~IP~----------G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+.+++.++|. =+-.||.|||+.+|. +..+|-+.+.
T Consensus 128 ~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi--s~~~V~~~l~ 173 (186)
T PRK13919 128 RLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL--PLGTLKTRAR 173 (186)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc--CHHHHHHHHH
Confidence 35666666664 446799999999998 4556665543
No 82
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=23.27 E-value=71 Score=21.50 Aligned_cols=27 Identities=19% Similarity=0.251 Sum_probs=18.2
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.|+.-|..+||+.+|. +...|-.++..
T Consensus 17 lgr~Pt~eEiA~~lgi--s~~~v~~~l~~ 43 (78)
T PF04539_consen 17 LGREPTDEEIAEELGI--SVEEVRELLQA 43 (78)
T ss_dssp HSS--BHHHHHHHHTS---HHHHHHHHHH
T ss_pred hCCCCCHHHHHHHHcc--cHHHHHHHHHh
Confidence 3888999999999997 45555555554
No 83
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.83 E-value=74 Score=24.71 Aligned_cols=29 Identities=17% Similarity=0.415 Sum_probs=22.1
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRP 126 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p 126 (188)
.++-+++.++|++ .--.||.+||+.+|..
T Consensus 8 D~~D~~Il~~Lq~---d~R~s~~eiA~~lglS 36 (153)
T PRK11179 8 DNLDRGILEALME---NARTPYAELAKQFGVS 36 (153)
T ss_pred CHHHHHHHHHHHH---cCCCCHHHHHHHHCcC
Confidence 3566777777765 4678999999999973
No 84
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=22.72 E-value=1.8e+02 Score=22.17 Aligned_cols=45 Identities=18% Similarity=0.289 Sum_probs=31.5
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCc-HHHHHHHHhhC
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKS-ARAVANACGQN 139 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~-~RaVg~a~~~N 139 (188)
+.+--+..-.+...|.|+..|=.+||+.+|.|.. .|.+=+.|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3344444455667899999999999999998643 35555566655
No 85
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.71 E-value=93 Score=24.46 Aligned_cols=36 Identities=17% Similarity=0.087 Sum_probs=25.3
Q ss_pred HHHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 100 LVWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 100 ~V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+.+++..+|.- +-.||.+||+.+|. +..+|.+.+.
T Consensus 124 ~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi--s~~tV~~~l~ 169 (189)
T PRK12515 124 ALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGI--PESTVKTRMF 169 (189)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc--CHHHHHHHHH
Confidence 355666666654 45799999999997 5666666554
No 86
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.51 E-value=95 Score=24.45 Aligned_cols=34 Identities=6% Similarity=-0.049 Sum_probs=23.1
Q ss_pred HHHHhcccCC----------CceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 101 VWSELCKIPF----------GSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 101 V~~~l~~IP~----------G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
+.++|.+.|. -+-.||.|||+.+|.| ..+|.+.+
T Consensus 125 l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis--~~tV~~~l 168 (191)
T PRK12520 125 LQACVDRLPPRTGRVFMMREWLELETEEICQELQIT--ATNAWVLL 168 (191)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC--HHHHHHHH
Confidence 4566666665 3458999999999984 44554443
No 87
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=22.42 E-value=1.5e+02 Score=22.30 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=24.5
Q ss_pred HHHHHHhcccC----------CCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 99 KLVWSELCKIP----------FGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 99 ~~V~~~l~~IP----------~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
..+.+++.++| +=.-.||.+||+.+|.+ ...|.+.+
T Consensus 103 ~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is--~~tv~~~l 148 (159)
T TIGR02989 103 QALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRT--VNAVYKAL 148 (159)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCC--HHHHHHHH
Confidence 33556666666 45678999999999984 45555444
No 88
>PRK02866 cyanate hydratase; Validated
Probab=22.30 E-value=94 Score=24.87 Aligned_cols=16 Identities=31% Similarity=0.351 Sum_probs=12.5
Q ss_pred CCceeCHHHHHHHhCC
Q psy12847 110 FGSLCSYADVARNIGR 125 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~ 125 (188)
.=+-.|+.+||+.+|.
T Consensus 15 ~~kGLTw~~IA~~iG~ 30 (147)
T PRK02866 15 KEKGLTWADIAEAIGL 30 (147)
T ss_pred HHcCCCHHHHHHHhCC
Confidence 3445789999999986
No 89
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.05 E-value=1e+02 Score=23.35 Aligned_cols=35 Identities=20% Similarity=0.210 Sum_probs=24.3
Q ss_pred HHHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 100 LVWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 100 ~V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
.+.++|.++|.- +-.||.|||+.+|.+ ..+|-+.+
T Consensus 99 ~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis--~~tV~~~l 143 (160)
T PRK09642 99 LIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIE--VKTVEMKL 143 (160)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCC--HHHHHHHH
Confidence 355667777764 468999999999974 45554444
No 90
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.93 E-value=99 Score=24.08 Aligned_cols=37 Identities=24% Similarity=0.084 Sum_probs=24.5
Q ss_pred HHHHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 99 KLVWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 99 ~~V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
..+.++|.+.|.= +-.||.|||+.+|. +..+|.+.+.
T Consensus 123 ~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~i--s~~tV~~~l~ 169 (184)
T PRK12512 123 GDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSM--SEGAVRVALH 169 (184)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC--CHHHHHHHHH
Confidence 3455666666642 35789999999998 4556655544
No 91
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=21.88 E-value=98 Score=24.95 Aligned_cols=26 Identities=12% Similarity=0.059 Sum_probs=20.5
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
|-+-.||.+||+.+|. +..+|.+.+.
T Consensus 166 ~~~g~s~~EIA~~lgi--s~~tV~~~l~ 191 (206)
T PRK12526 166 YFQELSQEQLAQQLNV--PLGTVKSRLR 191 (206)
T ss_pred HHcCCCHHHHHHHHCC--CHHHHHHHHH
Confidence 5567899999999998 4677776654
No 92
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=21.87 E-value=2.2e+02 Score=18.13 Aligned_cols=40 Identities=20% Similarity=0.198 Sum_probs=22.2
Q ss_pred HHHHHHHhcccCCCceeCHHHHHHHhCCCC--cHHHHHHHHhhC
Q psy12847 98 QKLVWSELCKIPFGSLCSYADVARNIGRPK--SARAVANACGQN 139 (188)
Q Consensus 98 ~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~--~~RaVg~a~~~N 139 (188)
|-.|+..|. -.+...|-.+||+.++.++ ..|++-..+...
T Consensus 5 q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g 46 (68)
T PF13463_consen 5 QWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKG 46 (68)
T ss_dssp HHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 334444444 3677778899999999743 346665555543
No 93
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.79 E-value=1.4e+02 Score=23.35 Aligned_cols=36 Identities=22% Similarity=0.077 Sum_probs=24.6
Q ss_pred HHHHHhcccCC----------CceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 100 LVWSELCKIPF----------GSLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 100 ~V~~~l~~IP~----------G~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+.++|.+.|. -+-.||.|||+.+|.+ ...|-+.+.
T Consensus 132 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis--~~tV~~~l~ 177 (189)
T PRK09648 132 RMRELLDTLPEKQREILILRVVVGLSAEETAEAVGST--PGAVRVAQH 177 (189)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC--HHHHHHHHH
Confidence 35566777765 3457999999999984 455555443
No 94
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=21.76 E-value=1.2e+02 Score=20.40 Aligned_cols=24 Identities=33% Similarity=0.351 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCCcHHHHHHHHhhCC
Q psy12847 115 SYADVARNIGRPKSARAVANACGQNN 140 (188)
Q Consensus 115 TY~~lA~~~g~p~~~RaVg~a~~~Np 140 (188)
|-.|||+.+|. +...|..+|..++
T Consensus 2 t~~~iA~~~gv--S~~TVSr~ln~~~ 25 (70)
T smart00354 2 TIKDVARLAGV--SKATVSRVLNGNG 25 (70)
T ss_pred CHHHHHHHHCC--CHHHHHHHHCCCC
Confidence 56799999997 7778888887654
No 95
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=21.66 E-value=79 Score=26.72 Aligned_cols=52 Identities=29% Similarity=0.392 Sum_probs=33.9
Q ss_pred HHHHHhcccCCCceeCHHHHHHHhCCCCcH--HHHHHHHhhCCCCCCCCceeeeCCCCCcCCCCCc
Q psy12847 100 LVWSELCKIPFGSLCSYADVARNIGRPKSA--RAVANACGQNNIPILIPCHRVIRSDGSYGGYSSG 163 (188)
Q Consensus 100 ~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~--RaVg~a~~~Np~~~~iPcHRVv~~~G~l~gy~~g 163 (188)
+|++.+..-|.| .|..+||+++|.|++. |-+.+-.. . .-|..+++-+-|.-|
T Consensus 8 ~iL~~l~~~~~~--l~l~ela~~~glpksT~~RlL~tL~~-~---------G~v~~d~~~g~Y~Lg 61 (246)
T COG1414 8 AILDLLAEGPGG--LSLAELAERLGLPKSTVHRLLQTLVE-L---------GYVEQDPEDGRYRLG 61 (246)
T ss_pred HHHHHHHhCCCC--CCHHHHHHHhCcCHHHHHHHHHHHHH-C---------CCEEEcCCCCcEeeh
Confidence 577778774444 8999999999999753 55544333 3 235566655556644
No 96
>PRK05949 RNA polymerase sigma factor; Validated
Probab=21.61 E-value=1.8e+02 Score=25.71 Aligned_cols=16 Identities=25% Similarity=0.283 Sum_probs=14.3
Q ss_pred CceeCHHHHHHHhCCC
Q psy12847 111 GSLCSYADVARNIGRP 126 (188)
Q Consensus 111 G~~~TY~~lA~~~g~p 126 (188)
|+-.||.+||+.+|.+
T Consensus 284 ~e~~Tl~EIa~~lgiS 299 (327)
T PRK05949 284 GKELSLAKVGERLNLS 299 (327)
T ss_pred CCCCCHHHHHHHHCcC
Confidence 4889999999999984
No 97
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.53 E-value=1e+02 Score=24.42 Aligned_cols=34 Identities=9% Similarity=-0.019 Sum_probs=23.4
Q ss_pred HHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 101 VWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 101 V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
+-++|.++|.- +-.||.|||+.+|.| ..+|-+-+
T Consensus 128 l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis--~~tVk~~l 171 (189)
T PRK12530 128 FEACLNHLPAQQARVFMMREYLELSSEQICQECDIS--TSNLHVLL 171 (189)
T ss_pred HHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCC--HHHHHHHH
Confidence 44567777763 457999999999984 44554443
No 98
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=21.44 E-value=1.2e+02 Score=23.92 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=26.3
Q ss_pred ChhHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 95 TDFQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 95 t~f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.++-++++.+|++ .-.+||.+||+++|. +..+|.+-+.+
T Consensus 13 D~~D~~IL~~Lq~---d~R~s~~eiA~~lgl--S~~tv~~Ri~r 51 (164)
T PRK11169 13 DRIDRNILNELQK---DGRISNVELSKRVGL--SPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHhcc---CCCCCHHHHHHHHCc--CHHHHHHHHHH
Confidence 3455667776654 556889999999997 44455544444
No 99
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=21.42 E-value=94 Score=32.26 Aligned_cols=57 Identities=19% Similarity=0.302 Sum_probs=37.5
Q ss_pred HHhcCCCCCCc-ccccccCCChhHHHHHHHhcccCCC-----ceeCHHHHHHHhCCCCcHHHHHHHHhhC
Q psy12847 76 AYIVNPKQNCL-DIKFKIEGTDFQKLVWSELCKIPFG-----SLCSYADVARNIGRPKSARAVANACGQN 139 (188)
Q Consensus 76 ~YF~G~~~~~F-~lpl~~~gt~f~~~V~~~l~~IP~G-----~~~TY~~lA~~~g~p~~~RaVg~a~~~N 139 (188)
++++-+|.. . |+.+|.. ..-+.+|.+.+.+. || +..||+.++.+. +.|.||++++-.
T Consensus 380 RFLnpeR~s-mPDIDiDf~-~~rR~~Vi~Yv~~k-YG~~~VaqI~Tf~T~~ak~----AirDv~Rvlg~~ 442 (1046)
T PRK05672 380 RFLSPERDE-PPDIDVDFE-HDRREEVIQYVYRR-YGRDRAAQVANVITYRPRS----AVRDVAKALGLS 442 (1046)
T ss_pred hccCCcccC-CCceeeecc-cccHHHHHHHHHHH-hCcccEEEEeehhhhHHHH----HHHHHHHHhCCC
Confidence 334444443 2 3444443 44678899988887 77 578999888753 678888888753
No 100
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=53 Score=24.83 Aligned_cols=36 Identities=28% Similarity=0.361 Sum_probs=28.2
Q ss_pred HHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 101 VWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 101 V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.-..+.+|-.++-.+|.|||+.-|. +.-.|+..-+.
T Consensus 52 t~alv~~IN~aR~a~Yq~lA~~n~~--s~~~vak~agq 87 (109)
T COG3784 52 TQALVADINAARAASYQQLAKKNGA--STEEVAKLAGQ 87 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHH
Confidence 3456778999999999999999986 56666666554
No 101
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.86 E-value=1.5e+02 Score=24.10 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=18.2
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
|.+-.||.+||+.+|. +..+|.+.+
T Consensus 191 y~~~~s~~eIA~~lgi--s~~~v~~~~ 215 (227)
T TIGR02980 191 FFEDKTQSEIAERLGI--SQMHVSRLL 215 (227)
T ss_pred HhcCCCHHHHHHHHCc--CHHHHHHHH
Confidence 4567899999999997 445555443
No 102
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.46 E-value=1e+02 Score=24.06 Aligned_cols=36 Identities=19% Similarity=0.215 Sum_probs=24.3
Q ss_pred HHHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHh
Q psy12847 100 LVWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACG 137 (188)
Q Consensus 100 ~V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~ 137 (188)
.+-++|.++|.- +-.||.|||+.+|. +..+|.+.+.
T Consensus 126 ~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgi--s~~tV~~~l~ 171 (182)
T PRK12537 126 KIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGA--PLGTVKAWIK 171 (182)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC--ChhhHHHHHH
Confidence 455666666643 45799999999997 4455555443
No 103
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.45 E-value=1.2e+02 Score=22.89 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=23.4
Q ss_pred HHHHHhcccCC----------CceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 100 LVWSELCKIPF----------GSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 100 ~V~~~l~~IP~----------G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
.+.++|.++|. -+-.||.|||+.+|.+ ..+|-+.+
T Consensus 99 ~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis--~~tV~~~l 143 (161)
T PRK09047 99 LIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCS--EGSVKTHC 143 (161)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCC--HHHHHHHH
Confidence 35556666664 4567999999999974 44444443
No 104
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=20.37 E-value=2e+02 Score=21.24 Aligned_cols=41 Identities=20% Similarity=0.214 Sum_probs=30.5
Q ss_pred hhHHHHHHHhcccCCC-----ceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 96 DFQKLVWSELCKIPFG-----SLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 96 ~f~~~V~~~l~~IP~G-----~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
..|.+|+.++..-+|| ..+|-.++|+..|. +...|..|+..
T Consensus 32 ~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~--~~~~V~~al~~ 77 (100)
T PF04492_consen 32 GRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGL--SRDHVSKALNE 77 (100)
T ss_pred HHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCc--CHHHHHHHHHH
Confidence 3455788888777776 58899999999996 45566666654
No 105
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=20.34 E-value=1.2e+02 Score=21.40 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=25.0
Q ss_pred hHHHHHHHhcccCCCceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 97 FQKLVWSELCKIPFGSLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 97 f~~~V~~~l~~IP~G~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.-++|.-.|..--.| .||.+||+.+|. ....+|.+++.+
T Consensus 30 ~aR~ia~yl~~~~~~--~s~~~Ig~~fg~-r~hStV~~a~~r 68 (90)
T cd06571 30 LARQIAMYLARELTG--LSLPEIGRAFGG-RDHSTVLHAVRK 68 (90)
T ss_pred hHHHHHHHHHHHHhC--CCHHHHHHHhCC-CCHhHHHHHHHH
Confidence 334444444443333 689999999994 366677777764
No 106
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.33 E-value=1.2e+02 Score=23.36 Aligned_cols=37 Identities=19% Similarity=0.125 Sum_probs=25.8
Q ss_pred HHHHHhcccCCC----------ceeCHHHHHHHhCCCCcHHHHHHHHhh
Q psy12847 100 LVWSELCKIPFG----------SLCSYADVARNIGRPKSARAVANACGQ 138 (188)
Q Consensus 100 ~V~~~l~~IP~G----------~~~TY~~lA~~~g~p~~~RaVg~a~~~ 138 (188)
.+..+|.+.|.- +-.||.|||+.+|. +...|.+.+.+
T Consensus 105 ~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi--s~~tV~~~l~R 151 (164)
T PRK12547 105 DFKKALNLLSADQREAIILIGASGFSYEDAAAICGC--AVGTIKSRVSR 151 (164)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC--CHHHHHHHHHH
Confidence 456677777653 34789999999997 46666665543
No 107
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=20.32 E-value=1.6e+02 Score=18.54 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=17.6
Q ss_pred CHHHHHHHhCCCCcHHHHHHHHhhC
Q psy12847 115 SYADVARNIGRPKSARAVANACGQN 139 (188)
Q Consensus 115 TY~~lA~~~g~p~~~RaVg~a~~~N 139 (188)
|-.|||+.+|. +.=.|..++...
T Consensus 1 Ti~dIA~~agv--S~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGV--SKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTS--SHHHHHHHHTTC
T ss_pred CHHHHHHHHCc--CHHHHHHHHhCC
Confidence 45799999997 666788777644
No 108
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.15 E-value=1.2e+02 Score=23.58 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=18.3
Q ss_pred CCceeCHHHHHHHhCCCCcHHHHHHHH
Q psy12847 110 FGSLCSYADVARNIGRPKSARAVANAC 136 (188)
Q Consensus 110 ~G~~~TY~~lA~~~g~p~~~RaVg~a~ 136 (188)
+.+-.||.|||+.+|.+ ...|.+.+
T Consensus 132 ~~~g~s~~EIA~~lgis--~~tV~~~l 156 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVS--VSSVKKYV 156 (172)
T ss_pred hccCCCHHHHHHHhCCC--HHHHHHHH
Confidence 56778999999999974 44444443
No 109
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.12 E-value=2.2e+02 Score=17.31 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=16.5
Q ss_pred ccCCCcee-CHHHHHHHhCCC
Q psy12847 107 KIPFGSLC-SYADVARNIGRP 126 (188)
Q Consensus 107 ~IP~G~~~-TY~~lA~~~g~p 126 (188)
.++.|+.. |-.+||+.+|..
T Consensus 13 ~~~~~~~l~s~~~la~~~~vs 33 (60)
T smart00345 13 ELRPGDKLPSERELAAQLGVS 33 (60)
T ss_pred CCCCCCcCcCHHHHHHHHCCC
Confidence 36778877 999999999974
Done!