Query psy7778
Match_columns 117
No_of_seqs 101 out of 170
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 18:38:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7778hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05158 RNA_pol_Rpc34: RNA po 100.0 7.8E-38 1.7E-42 257.6 7.4 103 3-105 57-178 (327)
2 KOG3233|consensus 100.0 9.1E-35 2E-39 237.1 5.1 104 2-105 56-178 (297)
3 COG5111 RPC34 DNA-directed RNA 100.0 1.5E-31 3.2E-36 216.0 6.3 106 2-107 57-181 (301)
4 PF12802 MarR_2: MarR family; 98.1 1.8E-05 3.9E-10 49.0 6.6 56 27-82 2-57 (62)
5 COG2512 Predicted membrane-ass 98.0 1.3E-05 2.9E-10 65.0 6.4 57 24-81 189-245 (258)
6 PF13412 HTH_24: Winged helix- 98.0 2.7E-05 5.8E-10 46.9 5.9 48 28-77 1-48 (48)
7 PF13730 HTH_36: Helix-turn-he 98.0 3.3E-05 7.1E-10 47.4 6.2 51 26-76 1-55 (55)
8 PF04182 B-block_TFIIIC: B-blo 98.0 2.5E-05 5.4E-10 52.0 5.6 53 29-81 1-53 (75)
9 PF01978 TrmB: Sugar-specific 97.8 2.7E-05 5.9E-10 49.9 4.1 52 27-80 5-56 (68)
10 smart00550 Zalpha Z-DNA-bindin 97.8 0.00015 3.3E-09 47.4 6.7 58 30-88 6-63 (68)
11 PF01047 MarR: MarR family; I 97.7 0.00021 4.6E-09 44.0 6.4 53 28-82 1-53 (59)
12 TIGR01889 Staph_reg_Sar staphy 97.6 0.00022 4.8E-09 49.7 6.4 57 27-83 22-80 (109)
13 COG1846 MarR Transcriptional r 97.5 0.00044 9.4E-09 46.1 6.1 54 28-83 20-73 (126)
14 PF13463 HTH_27: Winged helix 97.3 0.00085 1.8E-08 42.0 5.8 55 28-83 1-55 (68)
15 PRK10870 transcriptional repre 97.3 0.0008 1.7E-08 50.9 6.2 59 25-83 50-108 (176)
16 smart00347 HTH_MARR helix_turn 97.3 0.0012 2.7E-08 42.9 6.1 54 26-81 6-59 (101)
17 PF02082 Rrf2: Transcriptional 97.1 0.003 6.4E-08 42.1 6.6 52 40-91 18-70 (83)
18 TIGR00498 lexA SOS regulatory 97.0 0.0026 5.6E-08 48.0 6.8 64 26-89 2-69 (199)
19 PRK11512 DNA-binding transcrip 97.0 0.0025 5.5E-08 45.9 6.4 56 26-83 36-91 (144)
20 PRK13777 transcriptional regul 96.9 0.0031 6.7E-08 48.9 6.3 57 25-83 40-96 (185)
21 TIGR02337 HpaR homoprotocatech 96.9 0.0039 8.5E-08 43.4 6.2 56 26-83 24-79 (118)
22 PRK03573 transcriptional regul 96.9 0.0041 8.9E-08 44.5 6.4 58 25-83 26-83 (144)
23 PF01726 LexA_DNA_bind: LexA D 96.9 0.0046 1E-07 40.5 6.0 57 26-82 2-62 (65)
24 TIGR02944 suf_reg_Xantho FeS a 96.6 0.0064 1.4E-07 43.2 5.9 52 34-85 13-64 (130)
25 PF12840 HTH_20: Helix-turn-he 96.6 0.0092 2E-07 37.5 6.0 48 31-80 11-58 (61)
26 PF08784 RPA_C: Replication pr 96.6 0.0072 1.6E-07 41.5 5.5 53 26-78 43-97 (102)
27 PRK00215 LexA repressor; Valid 96.5 0.0096 2.1E-07 45.1 6.5 54 28-81 2-59 (205)
28 cd00090 HTH_ARSR Arsenical Res 96.5 0.014 2.9E-07 35.4 6.0 50 30-82 7-56 (78)
29 PRK11920 rirA iron-responsive 96.5 0.0089 1.9E-07 44.5 6.1 72 31-102 7-80 (153)
30 TIGR02010 IscR iron-sulfur clu 96.4 0.016 3.4E-07 41.8 6.6 55 31-85 7-64 (135)
31 COG1959 Predicted transcriptio 96.4 0.015 3.3E-07 43.3 6.6 61 31-91 7-70 (150)
32 smart00344 HTH_ASNC helix_turn 96.2 0.02 4.2E-07 39.0 6.0 53 28-82 1-53 (108)
33 PRK11014 transcriptional repre 96.2 0.021 4.5E-07 41.4 6.3 60 31-90 7-69 (141)
34 TIGR01884 cas_HTH CRISPR locus 96.2 0.022 4.7E-07 43.6 6.6 55 25-81 138-192 (203)
35 PF01325 Fe_dep_repress: Iron 96.1 0.023 5E-07 36.5 5.6 44 34-79 12-55 (60)
36 smart00420 HTH_DEOR helix_turn 96.1 0.032 7E-07 32.5 5.9 46 33-80 3-48 (53)
37 COG3355 Predicted transcriptio 96.0 0.03 6.6E-07 41.6 6.5 69 25-94 22-92 (126)
38 TIGR01610 phage_O_Nterm phage 96.0 0.033 7.3E-07 38.3 6.3 57 24-80 19-81 (95)
39 PF02295 z-alpha: Adenosine de 95.8 0.027 5.9E-07 37.1 4.9 58 30-88 4-61 (66)
40 PF09339 HTH_IclR: IclR helix- 95.7 0.022 4.8E-07 34.8 4.0 44 34-78 7-50 (52)
41 cd00092 HTH_CRP helix_turn_hel 95.6 0.047 1E-06 33.7 5.3 36 45-80 24-59 (67)
42 cd07153 Fur_like Ferric uptake 95.6 0.046 1E-06 37.6 5.7 56 33-89 4-64 (116)
43 TIGR00738 rrf2_super rrf2 fami 95.5 0.04 8.6E-07 38.7 5.4 55 31-85 7-64 (132)
44 PRK10857 DNA-binding transcrip 95.5 0.037 8E-07 41.9 5.5 55 31-85 7-64 (164)
45 PF13601 HTH_34: Winged helix 95.5 0.021 4.6E-07 38.4 3.7 42 44-85 12-53 (80)
46 COG1522 Lrp Transcriptional re 95.3 0.071 1.5E-06 38.0 6.2 57 26-84 4-60 (154)
47 PF14947 HTH_45: Winged helix- 95.3 0.057 1.2E-06 35.8 5.3 45 34-78 7-51 (77)
48 PF10007 DUF2250: Uncharacteri 95.1 0.083 1.8E-06 37.2 5.9 53 28-82 5-57 (92)
49 PRK04172 pheS phenylalanyl-tRN 95.0 0.059 1.3E-06 46.7 6.0 53 27-81 3-55 (489)
50 PF04703 FaeA: FaeA-like prote 94.8 0.11 2.4E-06 34.0 5.5 50 34-84 4-53 (62)
51 TIGR02702 SufR_cyano iron-sulf 94.7 0.089 1.9E-06 40.2 5.6 47 33-81 4-50 (203)
52 smart00345 HTH_GNTR helix_turn 94.7 0.073 1.6E-06 31.7 4.1 35 46-80 19-54 (60)
53 smart00418 HTH_ARSR helix_turn 94.6 0.12 2.6E-06 30.4 5.0 38 44-81 8-45 (66)
54 smart00346 HTH_ICLR helix_turn 94.6 0.11 2.5E-06 33.9 5.2 45 34-79 9-53 (91)
55 TIGR02698 CopY_TcrY copper tra 94.2 0.17 3.7E-06 36.8 5.8 52 27-80 1-56 (130)
56 PF01022 HTH_5: Bacterial regu 93.9 0.25 5.4E-06 29.6 5.2 41 35-78 7-47 (47)
57 smart00419 HTH_CRP helix_turn_ 93.8 0.15 3.3E-06 29.4 4.0 33 47-79 9-41 (48)
58 PF00325 Crp: Bacterial regula 93.6 0.13 2.8E-06 29.9 3.5 30 47-76 3-32 (32)
59 PF01475 FUR: Ferric uptake re 93.6 0.18 3.9E-06 35.1 4.9 62 28-90 6-72 (120)
60 smart00421 HTH_LUXR helix_turn 93.5 0.36 7.9E-06 27.9 5.4 43 26-72 2-44 (58)
61 COG1378 Predicted transcriptio 93.4 0.26 5.6E-06 39.6 6.1 52 27-80 13-64 (247)
62 cd07377 WHTH_GntR Winged helix 93.4 0.32 7E-06 29.4 5.2 33 48-80 27-59 (66)
63 PRK09391 fixK transcriptional 93.1 0.29 6.4E-06 37.5 5.8 53 25-77 150-210 (230)
64 PRK12423 LexA repressor; Provi 93.1 0.47 1E-05 36.4 6.9 55 27-81 3-61 (202)
65 PF03965 Penicillinase_R: Peni 92.6 0.63 1.4E-05 32.5 6.4 52 28-81 1-56 (115)
66 PRK03902 manganese transport t 92.5 0.4 8.6E-06 34.6 5.5 44 34-79 12-55 (142)
67 PF13545 HTH_Crp_2: Crp-like h 92.5 0.32 7E-06 30.8 4.5 32 46-77 28-59 (76)
68 smart00529 HTH_DTXR Helix-turn 92.5 0.21 4.6E-06 33.1 3.7 32 50-81 3-34 (96)
69 PF13936 HTH_38: Helix-turn-he 92.4 0.21 4.6E-06 30.0 3.3 43 24-69 1-43 (44)
70 PRK09462 fur ferric uptake reg 92.1 0.72 1.6E-05 33.6 6.5 63 27-89 14-81 (148)
71 COG1321 TroR Mn-dependent tran 92.1 0.45 9.8E-06 35.8 5.5 52 34-89 14-65 (154)
72 PRK10141 DNA-binding transcrip 91.7 0.4 8.8E-06 34.7 4.7 58 22-81 7-65 (117)
73 PRK14165 winged helix-turn-hel 91.6 0.43 9.2E-06 38.0 5.2 39 43-81 18-56 (217)
74 PRK11169 leucine-responsive tr 91.5 0.42 9.1E-06 35.4 4.7 55 26-82 10-64 (164)
75 PRK11050 manganese transport r 91.4 0.63 1.4E-05 34.4 5.5 53 34-90 41-93 (152)
76 TIGR03697 NtcA_cyano global ni 91.3 0.55 1.2E-05 34.0 5.1 53 26-78 111-175 (193)
77 PRK11753 DNA-binding transcrip 91.2 0.66 1.4E-05 34.1 5.5 54 25-78 136-200 (211)
78 COG0735 Fur Fe2+/Zn2+ uptake r 90.9 0.8 1.7E-05 33.8 5.7 62 27-89 18-84 (145)
79 PRK06474 hypothetical protein; 90.6 0.75 1.6E-05 35.0 5.5 56 25-81 5-62 (178)
80 PRK11161 fumarate/nitrate redu 90.6 0.68 1.5E-05 34.9 5.2 54 25-78 151-216 (235)
81 PRK13918 CRP/FNR family transc 90.4 0.75 1.6E-05 33.7 5.1 53 25-77 116-180 (202)
82 PRK10402 DNA-binding transcrip 90.0 1 2.2E-05 34.3 5.7 53 27-79 148-202 (226)
83 PF04545 Sigma70_r4: Sigma-70, 89.9 1.3 2.9E-05 26.4 5.2 42 25-69 2-43 (50)
84 PRK10430 DNA-binding transcrip 89.9 1.4 3.1E-05 33.3 6.5 58 26-83 157-216 (239)
85 PRK10163 DNA-binding transcrip 89.4 0.75 1.6E-05 36.6 4.8 51 28-79 21-73 (271)
86 PRK09954 putative kinase; Prov 89.4 1.1 2.3E-05 36.5 5.7 48 28-77 1-48 (362)
87 PF05732 RepL: Firmicute plasm 89.3 0.54 1.2E-05 35.7 3.8 49 32-80 58-109 (165)
88 PRK09334 30S ribosomal protein 89.3 0.57 1.2E-05 32.8 3.6 47 34-80 27-75 (86)
89 PF08279 HTH_11: HTH domain; 89.1 2.5 5.3E-05 25.4 6.0 40 34-74 4-43 (55)
90 TIGR02431 pcaR_pcaU beta-ketoa 88.9 0.79 1.7E-05 35.6 4.5 44 34-78 13-56 (248)
91 TIGR03879 near_KaiC_dom probab 88.7 0.72 1.6E-05 31.3 3.6 53 21-75 9-61 (73)
92 COG1414 IclR Transcriptional r 88.2 1.3 2.8E-05 35.1 5.4 46 34-80 8-53 (246)
93 PF03297 Ribosomal_S25: S25 ri 88.1 0.84 1.8E-05 32.9 3.9 57 33-89 44-102 (105)
94 PF09202 Rio2_N: Rio2, N-termi 88.0 1.2 2.6E-05 30.5 4.4 54 25-78 1-56 (82)
95 PHA00738 putative HTH transcri 87.9 1.6 3.4E-05 31.9 5.2 47 33-81 15-61 (108)
96 PRK10434 srlR DNA-bindng trans 87.8 3.5 7.6E-05 32.7 7.7 46 33-80 8-53 (256)
97 cd06170 LuxR_C_like C-terminal 87.6 2.4 5.2E-05 24.6 5.1 41 28-72 1-41 (57)
98 smart00531 TFIIE Transcription 87.2 0.63 1.4E-05 34.3 2.9 61 46-106 15-81 (147)
99 PRK15090 DNA-binding transcrip 87.2 1.2 2.7E-05 34.8 4.7 44 34-79 18-61 (257)
100 PF05158 RNA_pol_Rpc34: RNA po 87.0 1.3 2.8E-05 37.1 5.0 62 27-89 6-69 (327)
101 PF09012 FeoC: FeoC like trans 86.7 1.2 2.6E-05 28.6 3.7 47 35-83 5-51 (69)
102 PF08220 HTH_DeoR: DeoR-like h 86.7 3.9 8.4E-05 25.5 5.9 45 33-79 3-47 (57)
103 PRK11569 transcriptional repre 86.4 1.5 3.2E-05 34.9 4.8 45 34-79 32-76 (274)
104 PF03444 HrcA_DNA-bdg: Winged 86.3 4.4 9.5E-05 27.9 6.4 59 28-86 2-63 (78)
105 PRK09834 DNA-binding transcrip 86.0 1.7 3.6E-05 34.3 4.9 46 34-80 15-60 (263)
106 PRK10046 dpiA two-component re 86.0 3.1 6.7E-05 31.2 6.1 47 32-79 164-210 (225)
107 cd06171 Sigma70_r4 Sigma70, re 86.0 2.8 6E-05 23.4 4.7 45 24-71 7-51 (55)
108 PRK11179 DNA-binding transcrip 85.7 3.7 8.1E-05 30.0 6.3 52 27-80 6-57 (153)
109 PF00392 GntR: Bacterial regul 85.5 1.7 3.8E-05 27.2 3.9 34 48-81 26-59 (64)
110 PHA02701 ORF020 dsRNA-binding 85.4 3.5 7.5E-05 32.6 6.3 62 31-94 5-66 (183)
111 COG1725 Predicted transcriptio 85.0 1.6 3.6E-05 32.3 4.1 45 45-91 34-78 (125)
112 PF02002 TFIIE_alpha: TFIIE al 84.5 2.1 4.6E-05 29.4 4.3 49 30-80 13-61 (105)
113 COG3888 Predicted transcriptio 84.2 2 4.3E-05 36.4 4.7 51 29-80 4-54 (321)
114 PRK10906 DNA-binding transcrip 84.0 6.2 0.00013 31.4 7.3 56 32-92 7-62 (252)
115 COG1733 Predicted transcriptio 83.8 1.6 3.5E-05 31.5 3.6 34 46-79 35-70 (120)
116 COG3398 Uncharacterized protei 83.6 2.5 5.4E-05 34.7 4.9 50 32-83 103-152 (240)
117 PF01638 HxlR: HxlR-like helix 83.5 2.2 4.7E-05 28.6 3.9 35 47-81 19-54 (90)
118 PF06163 DUF977: Bacterial pro 82.6 4.5 9.8E-05 30.3 5.6 84 27-116 4-90 (127)
119 PRK10736 hypothetical protein; 82.6 3.3 7.2E-05 35.6 5.6 51 27-80 305-355 (374)
120 TIGR02325 C_P_lyase_phnF phosp 81.9 3.1 6.7E-05 31.6 4.6 50 33-82 11-68 (238)
121 PRK09483 response regulator; P 81.3 4.7 0.0001 28.8 5.2 45 25-73 146-190 (217)
122 PF04492 Phage_rep_O: Bacterio 81.2 7.7 0.00017 27.4 6.2 53 25-77 27-85 (100)
123 cd04761 HTH_MerR-SF Helix-Turn 81.2 1.3 2.9E-05 25.6 2.0 42 48-93 2-43 (49)
124 PRK13509 transcriptional repre 80.8 6.9 0.00015 31.0 6.4 49 33-86 8-56 (251)
125 TIGR00122 birA_repr_reg BirA b 80.5 7.3 0.00016 24.6 5.4 44 34-80 4-47 (69)
126 PHA02943 hypothetical protein; 80.4 4.2 9.1E-05 31.7 4.9 71 34-107 15-85 (165)
127 PRK09764 DNA-binding transcrip 80.3 8.4 0.00018 29.7 6.7 58 34-93 9-74 (240)
128 PRK06266 transcription initiat 80.2 6.6 0.00014 30.2 6.0 50 29-80 21-70 (178)
129 PRK00411 cdc6 cell division co 79.9 5.5 0.00012 32.4 5.8 59 23-81 289-360 (394)
130 PRK10336 DNA-binding transcrip 79.9 5.3 0.00012 28.4 5.1 56 27-82 149-212 (219)
131 TIGR02404 trehalos_R_Bsub treh 79.9 5.2 0.00011 30.6 5.3 48 35-82 5-60 (233)
132 PRK14999 histidine utilization 79.8 8.7 0.00019 29.6 6.6 59 34-94 16-82 (241)
133 PF00538 Linker_histone: linke 79.8 13 0.00029 24.3 6.6 55 29-83 3-68 (77)
134 PRK10840 transcriptional regul 79.7 5.6 0.00012 29.3 5.3 44 26-73 149-192 (216)
135 COG2188 PhnF Transcriptional r 79.4 4.5 9.7E-05 31.6 4.9 49 34-82 11-67 (236)
136 PF00888 Cullin: Cullin family 78.6 1.8 3.8E-05 37.0 2.6 64 27-92 517-580 (588)
137 PRK10411 DNA-binding transcrip 78.3 11 0.00023 29.8 6.8 55 32-91 6-60 (240)
138 TIGR00373 conserved hypothetic 78.0 7.8 0.00017 29.1 5.7 48 31-80 15-62 (158)
139 PRK11886 bifunctional biotin-- 77.7 7.1 0.00015 31.6 5.8 48 32-81 6-54 (319)
140 cd04789 HTH_Cfa Helix-Turn-Hel 77.6 1.9 4.1E-05 29.8 2.1 44 47-94 2-45 (102)
141 COG2865 Predicted transcriptio 77.6 5.3 0.00011 35.5 5.3 51 42-92 412-462 (467)
142 PRK11402 DNA-binding transcrip 77.3 6.1 0.00013 30.4 5.1 56 34-91 13-76 (241)
143 PRK10651 transcriptional regul 77.2 8.2 0.00018 27.1 5.3 45 25-73 153-197 (216)
144 TIGR03433 padR_acidobact trans 77.1 5.8 0.00013 27.2 4.4 48 32-79 6-58 (100)
145 PRK09392 ftrB transcriptional 75.9 9.8 0.00021 28.7 5.8 52 25-76 144-203 (236)
146 PRK15481 transcriptional regul 75.8 7.5 0.00016 32.2 5.5 50 32-81 7-64 (431)
147 PF05584 Sulfolobus_pRN: Sulfo 75.5 6.9 0.00015 26.6 4.3 44 41-85 14-57 (72)
148 PF13384 HTH_23: Homeodomain-l 75.5 5 0.00011 23.6 3.3 30 46-75 17-46 (50)
149 PRK10100 DNA-binding transcrip 75.3 7.6 0.00017 30.1 5.1 45 25-73 153-197 (216)
150 PF08221 HTH_9: RNA polymerase 75.0 4.9 0.00011 25.7 3.4 44 34-79 17-60 (62)
151 PF14502 HTH_41: Helix-turn-he 75.0 7.3 0.00016 24.7 4.0 39 49-87 9-47 (48)
152 COG3388 Predicted transcriptio 74.7 2 4.3E-05 31.1 1.6 45 33-79 17-61 (101)
153 PRK11083 DNA-binding response 74.5 13 0.00029 26.4 5.9 58 25-82 152-222 (228)
154 TIGR03338 phnR_burk phosphonat 74.0 7.9 0.00017 28.9 4.8 48 34-81 15-69 (212)
155 PF08281 Sigma70_r4_2: Sigma-7 73.9 9.5 0.00021 22.7 4.3 43 23-68 6-48 (54)
156 COG1654 BirA Biotin operon rep 73.3 14 0.0003 25.2 5.5 50 32-83 5-54 (79)
157 PHA03103 double-strand RNA-bin 72.6 15 0.00033 28.9 6.2 61 34-95 14-75 (183)
158 cd04781 HTH_MerR-like_sg6 Heli 71.2 3.3 7.1E-05 29.2 2.0 50 48-101 2-52 (120)
159 PRK03837 transcriptional regul 71.1 12 0.00025 28.5 5.2 49 34-82 17-73 (241)
160 cd00592 HTH_MerR-like Helix-Tu 70.9 3.6 7.9E-05 27.6 2.1 42 48-93 2-43 (100)
161 PF14163 SieB: Superinfection 70.5 6.8 0.00015 28.6 3.7 49 23-82 74-122 (151)
162 PRK13719 conjugal transfer tra 70.4 11 0.00024 30.3 5.1 46 24-73 140-185 (217)
163 PRK09802 DNA-binding transcrip 70.3 14 0.00031 29.6 5.8 54 32-90 19-72 (269)
164 PRK04214 rbn ribonuclease BN/u 70.2 12 0.00026 31.7 5.6 44 35-78 297-342 (412)
165 PRK11523 DNA-binding transcrip 70.0 10 0.00022 29.4 4.8 49 34-82 12-68 (253)
166 cd04777 HTH_MerR-like_sg1 Heli 69.8 4 8.6E-05 28.1 2.2 40 48-92 2-41 (107)
167 TIGR02018 his_ut_repres histid 69.5 7.8 0.00017 29.6 3.9 56 34-91 5-68 (230)
168 PF01418 HTH_6: Helix-turn-hel 69.4 9.7 0.00021 24.9 3.9 50 24-73 10-61 (77)
169 PF08222 HTH_CodY: CodY helix- 69.4 7.3 0.00016 25.9 3.2 51 51-103 9-59 (61)
170 PTZ00326 phenylalanyl-tRNA syn 69.1 14 0.00031 33.0 5.9 53 30-83 6-58 (494)
171 PF04967 HTH_10: HTH DNA bindi 68.0 27 0.00058 22.1 5.5 46 28-73 1-50 (53)
172 PRK11534 DNA-binding transcrip 67.3 14 0.00031 27.9 4.9 49 34-82 11-66 (224)
173 PF00126 HTH_1: Bacterial regu 67.3 6.3 0.00014 24.4 2.5 36 34-73 5-40 (60)
174 smart00422 HTH_MERR helix_turn 67.3 5.3 0.00011 24.7 2.2 42 48-93 2-44 (70)
175 cd04783 HTH_MerR1 Helix-Turn-H 67.1 4.5 9.8E-05 28.7 2.1 43 48-94 2-45 (126)
176 TIGR03337 phnR transcriptional 67.0 17 0.00036 27.4 5.3 41 49-91 28-68 (231)
177 PRK04984 fatty acid metabolism 67.0 16 0.00034 27.8 5.2 49 34-82 11-67 (239)
178 PF14394 DUF4423: Domain of un 66.9 17 0.00037 27.6 5.3 57 24-81 9-76 (171)
179 cd01282 HTH_MerR-like_sg3 Heli 66.9 4.8 0.0001 28.2 2.1 41 48-92 2-42 (112)
180 COG4189 Predicted transcriptio 66.8 11 0.00025 31.6 4.6 56 21-78 13-69 (308)
181 PRK11475 DNA-binding transcrip 66.0 18 0.0004 27.8 5.4 45 25-73 132-176 (207)
182 cd04775 HTH_Cfa-like Helix-Tur 65.4 5 0.00011 27.6 2.0 44 47-94 2-45 (102)
183 TIGR02036 dsdC D-serine deamin 65.1 14 0.0003 28.9 4.6 46 24-73 4-49 (302)
184 PF04218 CENP-B_N: CENP-B N-te 65.1 9.2 0.0002 23.7 3.0 43 24-69 3-45 (53)
185 PRK10360 DNA-binding transcrip 64.8 22 0.00048 24.8 5.3 44 26-73 136-179 (196)
186 PRK10225 DNA-binding transcrip 64.3 11 0.00024 29.1 4.0 49 34-82 13-69 (257)
187 PRK09508 leuO leucine transcri 64.2 21 0.00045 28.0 5.5 45 25-73 19-63 (314)
188 PF08100 Dimerisation: Dimeris 63.8 17 0.00038 22.7 4.0 39 32-70 8-50 (51)
189 PRK10079 phosphonate metabolis 63.6 12 0.00026 28.9 3.9 34 49-82 38-71 (241)
190 PF13744 HTH_37: Helix-turn-he 63.5 13 0.00028 24.4 3.6 36 33-68 18-53 (80)
191 PRK05803 sporulation sigma fac 63.5 16 0.00034 28.1 4.6 45 23-67 171-216 (233)
192 PLN02853 Probable phenylalanyl 63.4 20 0.00043 32.1 5.8 52 31-83 4-55 (492)
193 PF03551 PadR: Transcriptional 63.3 12 0.00027 23.9 3.4 27 57-83 28-54 (75)
194 PRK04424 fatty acid biosynthes 62.9 12 0.00026 28.5 3.8 50 32-83 9-58 (185)
195 COG4901 Ribosomal protein S25 62.5 9.9 0.00021 27.8 3.1 51 31-81 43-94 (107)
196 PF00196 GerE: Bacterial regul 62.2 24 0.00052 21.5 4.5 44 26-73 2-45 (58)
197 TIGR02928 orc1/cdc6 family rep 62.2 22 0.00048 28.5 5.4 59 23-81 281-352 (365)
198 TIGR02154 PhoB phosphate regul 62.1 13 0.00028 26.3 3.7 45 26-70 153-202 (226)
199 TIGR02812 fadR_gamma fatty aci 62.0 22 0.00049 27.0 5.2 48 34-81 10-65 (235)
200 cd01104 HTH_MlrA-CarA Helix-Tu 61.9 6.5 0.00014 24.3 1.9 44 48-94 2-45 (68)
201 PRK15411 rcsA colanic acid cap 61.9 22 0.00048 27.0 5.1 43 27-73 137-179 (207)
202 PRK10216 DNA-binding transcrip 61.7 23 0.0005 27.8 5.4 46 24-73 4-49 (319)
203 PRK10086 DNA-binding transcrip 61.7 16 0.00035 28.7 4.4 45 25-73 11-55 (311)
204 PF03428 RP-C: Replication pro 61.6 42 0.0009 26.0 6.6 67 22-88 35-113 (177)
205 PTZ00034 40S ribosomal protein 61.5 8.9 0.00019 28.6 2.8 53 32-88 9-68 (124)
206 PRK11302 DNA-binding transcrip 61.4 12 0.00027 29.1 3.7 48 23-70 9-58 (284)
207 PF03501 S10_plectin: Plectin/ 60.9 9.8 0.00021 27.2 2.8 52 33-88 7-65 (95)
208 COG3432 Predicted transcriptio 60.8 13 0.00028 26.5 3.3 48 34-81 19-66 (95)
209 PRK15002 redox-sensitivie tran 60.4 6.6 0.00014 29.6 2.0 41 48-92 13-53 (154)
210 PF13404 HTH_AsnC-type: AsnC-t 60.2 34 0.00073 20.3 5.1 42 28-71 1-42 (42)
211 TIGR02846 spore_sigmaK RNA pol 60.1 20 0.00044 27.4 4.7 48 24-71 171-223 (227)
212 PRK10421 DNA-binding transcrip 60.0 15 0.00033 28.4 4.0 54 34-89 6-67 (253)
213 PF13518 HTH_28: Helix-turn-he 59.8 24 0.00051 20.4 4.0 30 45-74 11-40 (52)
214 TIGR02392 rpoH_proteo alternat 59.5 22 0.00048 28.2 4.9 48 23-71 214-265 (270)
215 COG4565 CitB Response regulato 59.2 34 0.00073 27.9 5.9 54 24-78 151-205 (224)
216 PRK06811 RNA polymerase factor 59.0 29 0.00064 25.5 5.2 50 23-75 127-180 (189)
217 PRK09986 DNA-binding transcrip 58.9 16 0.00035 27.8 3.9 46 24-73 3-48 (294)
218 PRK00135 scpB segregation and 58.8 37 0.0008 26.4 6.0 50 25-79 85-134 (188)
219 TIGR00721 tfx DNA-binding prot 58.8 27 0.00059 26.1 5.0 43 25-71 4-50 (137)
220 PRK04217 hypothetical protein; 58.6 24 0.00051 25.5 4.5 43 25-70 40-82 (110)
221 TIGR02719 repress_PhaQ poly-be 58.6 13 0.00027 27.8 3.2 26 57-82 54-79 (138)
222 PRK10710 DNA-binding transcrip 58.6 20 0.00044 25.9 4.2 63 25-87 158-230 (240)
223 PRK05638 threonine synthase; V 58.5 23 0.00049 30.3 5.1 49 28-79 369-419 (442)
224 PRK15201 fimbriae regulatory p 58.0 27 0.00058 28.0 5.1 44 26-73 132-175 (198)
225 smart00351 PAX Paired Box doma 58.0 37 0.00081 24.2 5.5 49 27-78 17-65 (125)
226 cd01279 HTH_HspR-like Helix-Tu 58.0 8.1 0.00018 26.5 1.9 42 48-93 3-44 (98)
227 cd04787 HTH_HMRTR_unk Helix-Tu 57.5 8.2 0.00018 27.7 2.0 41 48-92 2-43 (133)
228 PRK09464 pdhR transcriptional 57.2 18 0.00039 27.9 4.0 55 34-90 14-76 (254)
229 PRK09990 DNA-binding transcrip 57.0 18 0.0004 27.8 4.0 48 34-81 11-66 (251)
230 TIGR03020 EpsA transcriptional 56.8 30 0.00066 27.8 5.3 45 25-73 188-232 (247)
231 KOG1767|consensus 56.6 6.3 0.00014 28.9 1.2 61 24-84 36-98 (110)
232 PRK15369 two component system 56.5 37 0.0008 23.3 5.1 44 26-73 148-191 (211)
233 PF13443 HTH_26: Cro/C1-type H 56.4 12 0.00026 22.7 2.4 27 42-68 6-32 (63)
234 PRK10955 DNA-binding transcrip 56.4 15 0.00032 26.4 3.2 57 26-82 155-224 (232)
235 cd04774 HTH_YfmP Helix-Turn-He 56.2 9.9 0.00021 26.1 2.1 42 48-93 2-43 (96)
236 PRK09652 RNA polymerase sigma 56.0 28 0.0006 24.5 4.5 42 24-68 125-166 (182)
237 TIGR02787 codY_Gpos GTP-sensin 55.4 37 0.0008 28.1 5.6 56 25-80 174-232 (251)
238 PRK03975 tfx putative transcri 55.4 34 0.00073 25.7 5.0 41 25-69 4-44 (141)
239 cd04770 HTH_HMRTR Helix-Turn-H 55.3 11 0.00023 26.4 2.2 42 48-93 2-44 (123)
240 TIGR00635 ruvB Holliday juncti 55.1 37 0.0008 26.6 5.5 53 25-77 233-287 (305)
241 PF09106 SelB-wing_2: Elongati 54.9 13 0.00028 23.1 2.4 36 44-79 15-53 (59)
242 cd00131 PAX Paired Box domain 54.7 45 0.00097 24.0 5.5 50 26-78 16-65 (128)
243 COG2345 Predicted transcriptio 54.4 18 0.00039 29.1 3.6 35 45-79 24-58 (218)
244 COG0640 ArsR Predicted transcr 54.4 48 0.001 20.2 5.3 52 25-78 19-71 (110)
245 PRK11557 putative DNA-binding 54.3 20 0.00044 28.0 3.8 48 23-70 5-54 (278)
246 PRK10403 transcriptional regul 53.8 48 0.001 23.0 5.4 44 26-73 152-195 (215)
247 TIGR02937 sigma70-ECF RNA poly 53.4 34 0.00074 22.6 4.4 46 23-71 106-151 (158)
248 cd04780 HTH_MerR-like_sg5 Heli 53.3 25 0.00055 24.0 3.8 40 48-91 2-42 (95)
249 TIGR02989 Sig-70_gvs1 RNA poly 53.2 32 0.00069 24.0 4.4 44 23-69 107-150 (159)
250 PF06970 RepA_N: Replication i 53.0 39 0.00083 22.7 4.6 47 23-70 14-76 (76)
251 TIGR01950 SoxR redox-sensitive 52.8 10 0.00023 27.9 1.9 40 49-92 4-43 (142)
252 PRK09645 RNA polymerase sigma 52.5 41 0.00089 24.0 5.0 47 23-72 114-164 (173)
253 TIGR00637 ModE_repress ModE mo 52.3 35 0.00076 23.6 4.4 48 28-79 2-52 (99)
254 COG5051 RPL36A Ribosomal prote 52.1 12 0.00026 26.8 2.1 38 24-62 46-83 (97)
255 COG0478 RIO-like serine/threon 51.8 43 0.00093 28.5 5.6 84 21-105 4-90 (304)
256 PF06969 HemN_C: HemN C-termin 51.3 25 0.00055 21.7 3.3 35 44-78 18-53 (66)
257 PRK00082 hrcA heat-inducible t 50.9 48 0.001 27.7 5.8 68 26-95 2-83 (339)
258 COG0282 ackA Acetate kinase [E 50.8 11 0.00023 33.1 1.9 91 5-104 5-114 (396)
259 TIGR03541 reg_near_HchA LuxR f 50.8 35 0.00076 26.4 4.7 45 25-73 169-213 (232)
260 PRK04158 transcriptional repre 50.5 16 0.00036 30.1 2.9 55 24-78 176-233 (256)
261 cd00569 HTH_Hin_like Helix-tur 50.4 30 0.00066 16.8 4.4 36 27-66 5-41 (42)
262 TIGR01321 TrpR trp operon repr 49.9 38 0.00081 24.0 4.3 43 28-70 33-79 (94)
263 PRK05572 sporulation sigma fac 49.6 38 0.00082 26.4 4.7 43 23-68 198-240 (252)
264 PF08461 HTH_12: Ribonuclease 49.4 46 0.001 21.4 4.4 44 35-79 3-51 (66)
265 PF06971 Put_DNA-bind_N: Putat 48.6 33 0.00071 21.5 3.4 33 35-67 17-49 (50)
266 TIGR03787 marine_sort_RR prote 48.6 49 0.0011 23.7 4.9 57 26-82 155-221 (227)
267 PRK00135 scpB segregation and 48.5 47 0.001 25.8 5.1 42 31-72 5-46 (188)
268 PRK12529 RNA polymerase sigma 48.5 41 0.0009 24.5 4.5 42 24-68 124-165 (178)
269 PRK08301 sporulation sigma fac 48.5 43 0.00092 25.5 4.8 49 23-71 174-227 (234)
270 PRK11482 putative DNA-binding 48.5 32 0.00069 27.3 4.2 46 24-73 25-70 (317)
271 COG1349 GlpR Transcriptional r 48.4 69 0.0015 25.4 6.1 59 32-95 7-65 (253)
272 COG1339 Transcriptional regula 48.2 40 0.00087 27.3 4.7 35 45-79 18-52 (214)
273 PRK09958 DNA-binding transcrip 48.0 63 0.0014 22.7 5.3 46 25-74 141-186 (204)
274 TIGR03339 phn_lysR aminoethylp 47.6 15 0.00033 27.5 2.1 21 53-73 18-38 (279)
275 TIGR02531 yecD_yerC TrpR-relat 47.3 39 0.00084 23.3 4.0 27 43-69 47-73 (88)
276 COG0664 Crp cAMP-binding prote 47.3 70 0.0015 22.5 5.5 55 26-80 139-205 (214)
277 cd04766 HTH_HspR Helix-Turn-He 47.1 17 0.00037 24.3 2.1 41 48-92 3-43 (91)
278 PRK11151 DNA-binding transcrip 46.8 55 0.0012 25.3 5.2 39 31-73 4-42 (305)
279 CHL00148 orf27 Ycf27; Reviewed 46.8 40 0.00087 24.3 4.2 47 25-71 159-216 (240)
280 COG1695 Predicted transcriptio 46.8 27 0.00058 24.7 3.2 69 32-100 11-88 (138)
281 PRK11639 zinc uptake transcrip 46.8 76 0.0016 23.8 5.8 53 28-81 24-81 (169)
282 PRK10188 DNA-binding transcrip 46.6 49 0.0011 26.0 4.9 44 26-73 178-221 (240)
283 PRK11414 colanic acid/biofilm 46.4 29 0.00062 26.2 3.5 55 26-81 8-69 (221)
284 TIGR02835 spore_sigmaE RNA pol 46.0 46 0.001 25.6 4.7 45 23-67 174-219 (234)
285 PRK09791 putative DNA-binding 46.0 63 0.0014 24.9 5.4 43 27-73 4-46 (302)
286 PRK10082 cell density-dependen 45.4 18 0.0004 28.1 2.4 45 25-73 8-52 (303)
287 cd04769 HTH_MerR2 Helix-Turn-H 45.3 17 0.00038 25.4 2.0 42 48-93 2-43 (116)
288 COG1167 ARO8 Transcriptional r 45.3 48 0.001 28.4 5.1 49 33-81 7-63 (459)
289 TIGR02394 rpoS_proteo RNA poly 45.1 49 0.0011 26.3 4.8 45 23-67 218-263 (285)
290 PRK13919 putative RNA polymera 45.0 53 0.0011 23.7 4.6 46 23-71 131-180 (186)
291 PRK10161 transcriptional regul 44.6 58 0.0013 23.5 4.8 45 27-71 154-207 (229)
292 PRK12539 RNA polymerase sigma 44.4 62 0.0013 23.5 4.9 45 24-71 128-176 (184)
293 PRK09333 30S ribosomal protein 44.3 31 0.00068 26.4 3.4 56 23-80 38-115 (150)
294 PRK09390 fixJ response regulat 44.3 48 0.001 22.6 4.1 44 24-71 138-181 (202)
295 PRK12527 RNA polymerase sigma 44.3 57 0.0012 23.0 4.6 46 23-71 101-150 (159)
296 PRK12427 flagellar biosynthesi 44.2 51 0.0011 25.6 4.7 46 24-72 180-225 (231)
297 PRK07037 extracytoplasmic-func 44.2 55 0.0012 23.0 4.5 42 24-68 106-147 (163)
298 PRK08629 coproporphyrinogen II 43.7 73 0.0016 27.4 5.9 52 27-78 339-391 (433)
299 PF13613 HTH_Tnp_4: Helix-turn 43.5 74 0.0016 19.3 5.2 44 27-72 2-45 (53)
300 PRK11337 DNA-binding transcrip 43.4 34 0.00074 27.0 3.6 48 23-70 21-70 (292)
301 PRK06288 RNA polymerase sigma 43.3 51 0.0011 25.9 4.6 41 24-67 209-249 (268)
302 PRK10094 DNA-binding transcrip 43.2 21 0.00045 28.2 2.3 41 29-73 3-43 (308)
303 TIGR02063 RNase_R ribonuclease 43.0 68 0.0015 29.3 5.9 48 32-79 4-55 (709)
304 TIGR02980 SigBFG RNA polymeras 42.9 62 0.0013 24.5 4.9 43 24-69 175-217 (227)
305 PRK00118 putative DNA-binding 42.7 81 0.0018 22.5 5.1 41 26-69 16-56 (104)
306 TIGR02044 CueR Cu(I)-responsiv 42.6 21 0.00045 25.3 2.1 41 48-92 2-43 (127)
307 COG1693 Repressor of nif and g 42.6 36 0.00077 29.2 3.8 55 28-82 4-62 (325)
308 COG2197 CitB Response regulato 42.3 70 0.0015 24.5 5.1 44 26-73 147-190 (211)
309 PRK15479 transcriptional regul 42.2 84 0.0018 22.1 5.2 56 27-82 148-213 (221)
310 COG2996 Predicted RNA-bindinin 41.9 53 0.0011 27.8 4.6 52 27-78 222-278 (287)
311 PF13411 MerR_1: MerR HTH fami 41.8 19 0.00041 22.2 1.6 42 48-93 2-43 (69)
312 PRK12547 RNA polymerase sigma 41.8 64 0.0014 23.0 4.6 43 23-68 108-150 (164)
313 TIGR02424 TF_pcaQ pca operon t 41.3 23 0.0005 27.2 2.3 42 28-73 3-44 (300)
314 TIGR02952 Sig70_famx2 RNA poly 41.3 64 0.0014 22.6 4.5 42 23-67 118-159 (170)
315 PRK10837 putative DNA-binding 41.2 20 0.00044 27.2 2.0 42 28-73 3-44 (290)
316 PRK15421 DNA-binding transcrip 40.7 78 0.0017 25.1 5.3 42 28-73 2-43 (317)
317 PRK11233 nitrogen assimilation 40.6 23 0.0005 27.6 2.2 22 52-73 21-42 (305)
318 PRK08583 RNA polymerase sigma 40.5 63 0.0014 25.1 4.7 43 23-68 201-243 (257)
319 PRK09642 RNA polymerase sigma 40.4 68 0.0015 22.5 4.5 44 24-70 103-150 (160)
320 PRK03635 chromosome replicatio 40.2 24 0.00053 27.3 2.3 50 30-83 4-56 (294)
321 PF13542 HTH_Tnp_ISL3: Helix-t 39.9 77 0.0017 18.4 4.6 37 32-69 14-50 (52)
322 PRK10632 transcriptional regul 39.8 26 0.00056 27.5 2.4 21 53-73 23-43 (309)
323 TIGR03418 chol_sulf_TF putativ 39.7 27 0.00058 26.7 2.4 36 34-73 7-42 (291)
324 TIGR02393 RpoD_Cterm RNA polym 39.7 67 0.0015 24.7 4.7 45 24-68 173-218 (238)
325 PRK12679 cbl transcriptional r 39.7 23 0.0005 27.9 2.1 23 51-73 21-43 (316)
326 PRK09906 DNA-binding transcrip 39.4 21 0.00047 27.3 1.9 37 33-73 6-42 (296)
327 COG1675 TFA1 Transcription ini 39.1 1E+02 0.0022 24.0 5.6 60 31-92 19-84 (176)
328 cd04788 HTH_NolA-AlbR Helix-Tu 39.1 25 0.00055 23.8 2.0 41 48-92 2-43 (96)
329 cd04763 HTH_MlrA-like Helix-Tu 39.0 26 0.00057 21.8 2.0 43 48-94 2-45 (68)
330 cd04784 HTH_CadR-PbrR Helix-Tu 39.0 25 0.00055 24.8 2.1 51 48-102 2-54 (127)
331 cd04768 HTH_BmrR-like Helix-Tu 39.0 26 0.00056 23.8 2.0 41 49-93 3-44 (96)
332 PF04157 EAP30: EAP30/Vps36 fa 38.9 57 0.0012 25.3 4.2 49 28-76 172-220 (223)
333 PRK03601 transcriptional regul 38.3 28 0.0006 26.8 2.4 39 31-73 4-42 (275)
334 TIGR02948 SigW_bacill RNA poly 38.2 63 0.0014 23.1 4.1 43 23-68 132-174 (187)
335 PRK13348 chromosome replicatio 38.2 26 0.00057 26.9 2.2 44 31-78 5-51 (294)
336 PRK09801 transcriptional activ 38.0 28 0.00061 27.5 2.4 39 31-73 9-47 (310)
337 PRK11013 DNA-binding transcrip 37.9 64 0.0014 25.2 4.4 43 27-73 3-45 (309)
338 PRK11924 RNA polymerase sigma 37.7 75 0.0016 22.2 4.4 44 23-69 121-164 (179)
339 TIGR02479 FliA_WhiG RNA polyme 37.7 81 0.0018 23.9 4.8 42 23-67 171-212 (224)
340 PF10557 Cullin_Nedd8: Cullin 37.6 43 0.00093 21.4 2.8 37 34-80 28-64 (68)
341 cd01108 HTH_CueR Helix-Turn-He 37.5 27 0.00058 24.8 2.0 43 48-94 2-45 (127)
342 PRK14997 LysR family transcrip 37.5 30 0.00065 26.6 2.4 41 29-73 3-43 (301)
343 TIGR02885 spore_sigF RNA polym 37.3 85 0.0018 23.8 4.9 44 23-69 179-222 (231)
344 PRK12524 RNA polymerase sigma 37.3 78 0.0017 23.3 4.6 44 24-70 133-180 (196)
345 COG4465 CodY Pleiotropic trans 37.2 62 0.0013 26.8 4.3 79 24-104 179-260 (261)
346 cd01105 HTH_GlnR-like Helix-Tu 37.2 28 0.00061 23.3 2.0 42 47-92 2-44 (88)
347 TIGR02051 MerR Hg(II)-responsi 37.1 26 0.00056 24.9 1.9 40 49-92 2-42 (124)
348 PRK12681 cysB transcriptional 37.1 27 0.00058 27.9 2.2 26 53-78 23-51 (324)
349 COG3177 Fic family protein [Fu 37.0 56 0.0012 27.3 4.1 43 43-85 301-343 (348)
350 cd01109 HTH_YyaN Helix-Turn-He 36.9 68 0.0015 22.1 4.0 41 48-92 2-43 (113)
351 PRK06930 positive control sigm 36.8 77 0.0017 23.9 4.5 44 24-70 111-154 (170)
352 PRK12682 transcriptional regul 36.6 28 0.00061 27.1 2.2 22 52-73 22-43 (309)
353 TIGR02941 Sigma_B RNA polymera 36.5 85 0.0018 24.3 4.8 43 23-68 201-243 (255)
354 PRK09514 zntR zinc-responsive 36.5 28 0.0006 25.4 2.0 42 48-93 3-45 (140)
355 PRK11074 putative DNA-binding 36.5 31 0.00067 26.8 2.4 40 30-73 4-43 (300)
356 cd04779 HTH_MerR-like_sg4 Heli 36.4 28 0.0006 25.6 2.0 42 48-93 2-43 (134)
357 TIGR02147 Fsuc_second hypothet 36.4 1.2E+02 0.0026 24.8 5.9 58 23-80 106-173 (271)
358 PRK12683 transcriptional regul 36.2 28 0.00061 27.4 2.1 21 53-73 23-43 (309)
359 TIGR03184 DNA_S_dndE DNA sulfu 36.2 52 0.0011 23.5 3.3 56 50-105 12-75 (105)
360 PRK13824 replication initiatio 35.9 73 0.0016 27.6 4.7 66 22-87 47-124 (404)
361 TIGR00331 hrcA heat shock gene 35.8 93 0.002 26.0 5.3 50 33-82 6-59 (337)
362 cd04767 HTH_HspR-like_MBC Heli 35.8 30 0.00064 25.3 2.0 41 47-92 2-42 (120)
363 PRK13413 mpi multiple promoter 35.8 74 0.0016 23.9 4.3 37 29-69 159-195 (200)
364 COG2963 Transposase and inacti 35.2 1.1E+02 0.0024 20.9 4.8 70 26-103 6-76 (116)
365 TIGR03298 argP transcriptional 35.0 35 0.00075 26.2 2.4 49 31-83 4-55 (292)
366 PRK12512 RNA polymerase sigma 34.8 80 0.0017 22.8 4.2 42 23-67 127-168 (184)
367 TIGR02985 Sig70_bacteroi1 RNA 34.8 1.1E+02 0.0024 20.8 4.8 44 23-69 109-152 (161)
368 PF01090 Ribosomal_S19e: Ribos 34.7 43 0.00093 25.3 2.8 56 23-80 37-114 (139)
369 PF02984 Cyclin_C: Cyclin, C-t 34.7 98 0.0021 20.2 4.3 38 35-72 50-87 (118)
370 cd04782 HTH_BltR Helix-Turn-He 34.6 36 0.00079 23.1 2.2 42 48-93 2-44 (97)
371 PRK06986 fliA flagellar biosyn 34.6 87 0.0019 24.0 4.6 41 24-67 181-221 (236)
372 PRK15431 ferrous iron transpor 34.5 89 0.0019 21.5 4.1 44 35-80 7-50 (78)
373 PRK11242 DNA-binding transcrip 34.5 33 0.00072 26.1 2.2 39 31-73 4-42 (296)
374 PF10771 DUF2582: Protein of u 34.4 48 0.001 21.9 2.7 41 34-76 12-52 (65)
375 TIGR02984 Sig-70_plancto1 RNA 34.3 97 0.0021 22.1 4.6 42 24-68 137-178 (189)
376 PF02796 HTH_7: Helix-turn-hel 34.2 50 0.0011 19.4 2.6 31 38-68 13-43 (45)
377 COG2390 DeoR Transcriptional r 34.2 57 0.0012 27.5 3.7 48 31-78 11-58 (321)
378 COG2771 CsgD DNA-binding HTH d 33.8 1E+02 0.0022 18.1 4.8 44 26-73 3-46 (65)
379 PF00356 LacI: Bacterial regul 33.7 49 0.0011 20.1 2.5 20 49-68 2-21 (46)
380 PRK12546 RNA polymerase sigma 33.4 81 0.0018 23.5 4.1 45 23-70 109-157 (188)
381 PF09862 DUF2089: Protein of u 33.4 1.2E+02 0.0027 22.0 4.9 46 23-72 29-75 (113)
382 COG3413 Predicted DNA binding 33.4 1.4E+02 0.0029 22.9 5.5 48 26-73 154-205 (215)
383 PRK08599 coproporphyrinogen II 33.4 1.4E+02 0.0029 24.7 5.8 52 26-77 297-350 (377)
384 PRK08208 coproporphyrinogen II 33.3 1.2E+02 0.0025 25.9 5.5 79 26-104 340-423 (430)
385 PRK09047 RNA polymerase factor 33.3 88 0.0019 21.8 4.1 44 24-70 103-150 (161)
386 PRK10341 DNA-binding transcrip 33.2 36 0.00079 26.6 2.3 41 29-73 8-48 (312)
387 PRK11139 DNA-binding transcrip 32.9 38 0.00083 26.1 2.4 39 31-73 9-47 (297)
388 PRK12684 transcriptional regul 32.6 33 0.00072 27.0 2.0 21 53-73 23-43 (313)
389 PRK08215 sporulation sigma fac 32.5 1E+02 0.0023 24.0 4.8 42 24-68 206-247 (258)
390 PRK01381 Trp operon repressor; 32.4 66 0.0014 23.1 3.3 46 25-70 29-79 (99)
391 PF01381 HTH_3: Helix-turn-hel 32.2 47 0.001 19.4 2.2 26 44-69 7-32 (55)
392 TIGR03209 P21_Cbot clostridium 32.0 37 0.00081 23.5 2.0 39 24-65 104-142 (142)
393 KOG0081|consensus 32.0 15 0.00033 29.4 -0.0 14 88-101 29-42 (219)
394 COG1737 RpiR Transcriptional r 31.8 68 0.0015 25.7 3.7 48 23-70 11-60 (281)
395 PRK13752 putative transcriptio 31.2 38 0.00083 25.0 2.0 42 47-92 8-50 (144)
396 TIGR00180 parB_part ParB-like 31.2 1.5E+02 0.0033 22.2 5.3 27 45-71 119-145 (187)
397 PRK09935 transcriptional regul 31.2 1.4E+02 0.0031 20.7 4.9 43 27-73 149-191 (210)
398 smart00530 HTH_XRE Helix-turn- 31.2 60 0.0013 17.2 2.4 23 45-67 9-31 (56)
399 PRK05602 RNA polymerase sigma 31.1 93 0.002 22.5 4.1 42 23-67 124-165 (186)
400 PRK12680 transcriptional regul 31.1 38 0.00083 27.1 2.1 21 53-73 23-43 (327)
401 PRK09638 RNA polymerase sigma 31.1 53 0.0011 23.4 2.7 44 24-70 123-170 (176)
402 smart00526 H15 Domain in histo 31.0 1.4E+02 0.003 18.7 5.7 52 30-81 6-66 (66)
403 COG5625 Predicted transcriptio 30.7 52 0.0011 24.2 2.6 52 25-77 16-67 (113)
404 PRK11062 nhaR transcriptional 30.7 44 0.00095 25.9 2.4 42 28-73 4-45 (296)
405 PRK09416 lstR lineage-specific 30.7 1.2E+02 0.0026 22.8 4.6 61 27-88 40-105 (135)
406 cd04785 HTH_CadR-PbrR-like Hel 30.6 42 0.0009 23.8 2.1 43 48-94 2-45 (126)
407 COG3132 Uncharacterized protei 30.6 27 0.00059 28.1 1.2 28 56-83 48-75 (215)
408 PRK09639 RNA polymerase sigma 30.6 1.3E+02 0.0027 21.2 4.6 41 23-67 108-148 (166)
409 COG1542 Uncharacterized conser 30.5 45 0.00098 30.5 2.7 55 27-81 422-477 (593)
410 PRK10681 DNA-binding transcrip 30.4 1.5E+02 0.0033 23.3 5.4 44 28-73 3-48 (252)
411 PRK07500 rpoH2 RNA polymerase 30.3 1.2E+02 0.0025 24.5 4.8 42 25-67 225-266 (289)
412 PRK11716 DNA-binding transcrip 30.3 43 0.00092 24.8 2.2 18 56-73 1-18 (269)
413 TIGR02939 RpoE_Sigma70 RNA pol 30.2 1.1E+02 0.0024 21.8 4.3 46 23-71 134-183 (190)
414 PRK12519 RNA polymerase sigma 30.2 1E+02 0.0023 22.3 4.2 46 24-72 138-187 (194)
415 PRK15243 transcriptional regul 30.2 44 0.00095 27.0 2.4 39 31-73 7-45 (297)
416 COG2186 FadR Transcriptional r 30.2 64 0.0014 25.3 3.2 69 34-102 14-104 (241)
417 PRK06759 RNA polymerase factor 30.2 1.3E+02 0.0028 20.8 4.5 43 23-68 102-144 (154)
418 PF09904 HTH_43: Winged helix- 30.0 1.4E+02 0.003 21.2 4.5 53 48-100 23-81 (90)
419 PRK06596 RNA polymerase factor 30.0 1.2E+02 0.0026 24.3 4.9 46 23-69 226-271 (284)
420 PRK15092 DNA-binding transcrip 30.0 45 0.00098 26.5 2.4 43 27-73 10-52 (310)
421 COG0583 LysR Transcriptional r 29.9 43 0.00094 24.9 2.1 21 53-73 22-42 (297)
422 PRK15482 transcriptional regul 29.8 87 0.0019 24.7 3.9 47 24-70 10-58 (285)
423 cd04786 HTH_MerR-like_sg7 Heli 29.6 45 0.00097 24.2 2.1 51 48-102 2-54 (131)
424 PRK12534 RNA polymerase sigma 29.5 1.1E+02 0.0025 22.0 4.3 41 24-67 134-174 (187)
425 TIGR02043 ZntR Zn(II)-responsi 29.4 45 0.00097 23.9 2.1 41 48-92 3-44 (131)
426 PRK13347 coproporphyrinogen II 29.1 1.9E+02 0.0041 24.8 6.2 53 26-78 360-416 (453)
427 TIGR02047 CadR-PbrR Cd(II)/Pb( 29.0 48 0.001 23.6 2.2 49 49-101 3-53 (127)
428 PF01853 MOZ_SAS: MOZ/SAS fami 28.8 1.4E+02 0.0029 23.7 4.8 45 34-81 137-182 (188)
429 PRK08295 RNA polymerase factor 28.8 1.3E+02 0.0029 21.9 4.6 41 25-69 153-193 (208)
430 PF10141 ssDNA-exonuc_C: Singl 28.7 2.7E+02 0.0058 21.2 7.1 55 23-77 89-147 (195)
431 PRK11923 algU RNA polymerase s 28.7 98 0.0021 22.5 3.8 46 23-71 134-183 (193)
432 cd00073 H15 linker histone 1 a 28.6 1.8E+02 0.004 19.4 6.2 55 28-82 4-67 (88)
433 cd04762 HTH_MerR-trunc Helix-T 28.6 47 0.001 18.2 1.7 41 49-93 3-43 (49)
434 PRK08898 coproporphyrinogen II 28.5 1.6E+02 0.0036 24.7 5.6 51 27-77 318-369 (394)
435 cd01111 HTH_MerD Helix-Turn-He 28.3 48 0.001 23.2 2.0 40 49-92 3-43 (107)
436 PRK13749 transcriptional regul 28.2 73 0.0016 23.1 3.0 42 48-93 5-47 (121)
437 TIGR02999 Sig-70_X6 RNA polyme 28.2 1.6E+02 0.0035 21.0 4.9 40 25-67 132-171 (183)
438 PF09397 Ftsk_gamma: Ftsk gamm 28.0 1.2E+02 0.0027 19.8 3.9 38 45-82 19-56 (65)
439 TIGR02983 SigE-fam_strep RNA p 28.0 1.4E+02 0.0031 20.8 4.5 43 23-68 106-148 (162)
440 CHL00180 rbcR LysR transcripti 28.0 45 0.00098 25.9 2.0 42 28-73 5-46 (305)
441 PF00440 TetR_N: Bacterial reg 27.6 1.1E+02 0.0024 17.7 3.3 34 35-68 5-38 (47)
442 PRK12513 RNA polymerase sigma 27.6 65 0.0014 23.5 2.7 45 24-71 136-184 (194)
443 KOG3233|consensus 27.5 2E+02 0.0044 24.4 5.9 62 27-88 7-69 (297)
444 PRK12543 RNA polymerase sigma 27.3 1.2E+02 0.0025 22.0 4.0 45 23-70 113-161 (179)
445 PRK11832 putative DNA-binding 27.3 82 0.0018 25.1 3.4 30 52-81 166-195 (207)
446 PF12926 MOZART2: Mitotic-spin 27.3 1.9E+02 0.0041 20.5 4.8 53 23-75 18-74 (88)
447 cd01110 HTH_SoxR Helix-Turn-He 26.6 48 0.001 24.2 1.8 40 49-92 4-43 (139)
448 PRK05911 RNA polymerase sigma 26.4 1.5E+02 0.0032 23.4 4.7 42 24-68 202-243 (257)
449 TIGR02850 spore_sigG RNA polym 26.3 1.6E+02 0.0035 22.9 4.9 43 23-68 202-244 (254)
450 PRK11517 transcriptional regul 26.3 2E+02 0.0043 20.3 5.0 31 25-55 145-175 (223)
451 COG2524 Predicted transcriptio 26.1 2.2E+02 0.0047 24.2 5.8 60 26-85 2-64 (294)
452 PF01371 Trp_repressor: Trp re 26.1 2.2E+02 0.0047 19.7 4.9 44 28-71 27-74 (87)
453 PRK07157 acetate kinase; Provi 26.0 58 0.0013 28.5 2.5 46 59-104 61-115 (400)
454 COG1497 Predicted transcriptio 25.9 93 0.002 26.0 3.6 47 33-80 13-59 (260)
455 PRK14101 bifunctional glucokin 25.8 98 0.0021 27.7 4.0 49 23-71 349-399 (638)
456 PRK05660 HemN family oxidoredu 25.7 2.1E+02 0.0045 23.9 5.7 51 27-77 301-352 (378)
457 COG0789 SoxR Predicted transcr 25.7 94 0.002 21.1 3.1 40 49-92 3-43 (124)
458 cd01107 HTH_BmrR Helix-Turn-He 25.6 60 0.0013 22.4 2.1 41 48-92 2-44 (108)
459 PRK12531 RNA polymerase sigma 25.6 1.7E+02 0.0036 21.5 4.6 41 24-67 138-178 (194)
460 PF12759 HTH_Tnp_IS1: InsA C-t 25.5 93 0.002 19.5 2.7 31 38-69 14-44 (46)
461 COG1777 Predicted transcriptio 25.5 90 0.002 25.4 3.3 36 47-82 29-65 (217)
462 PF05331 DUF742: Protein of un 25.4 2.7E+02 0.0058 20.2 5.5 70 25-101 38-107 (114)
463 PRK09641 RNA polymerase sigma 25.4 1.4E+02 0.0031 21.2 4.2 41 24-67 133-173 (187)
464 TIGR02954 Sig70_famx3 RNA poly 25.0 1.6E+02 0.0035 20.8 4.4 45 23-70 115-163 (169)
465 PRK12538 RNA polymerase sigma 25.0 1.3E+02 0.0029 23.3 4.1 46 23-71 167-216 (233)
466 PRK12440 acetate kinase; Revie 24.8 63 0.0014 28.2 2.5 46 59-104 64-115 (397)
467 PRK07122 RNA polymerase sigma 24.7 1.7E+02 0.0036 23.3 4.7 42 24-68 212-253 (264)
468 PRK12516 RNA polymerase sigma 24.6 1.6E+02 0.0036 21.7 4.5 45 23-70 112-160 (187)
469 COG5340 Predicted transcriptio 24.5 1.1E+02 0.0024 25.6 3.7 53 27-81 13-65 (269)
470 PRK07670 RNA polymerase sigma 24.5 1.7E+02 0.0037 22.7 4.7 42 23-67 197-238 (251)
471 COG4738 Predicted transcriptio 24.3 1.1E+02 0.0024 22.9 3.3 42 37-78 32-73 (124)
472 PRK12528 RNA polymerase sigma 24.3 1.8E+02 0.004 20.3 4.5 43 24-69 110-152 (161)
473 PRK04841 transcriptional regul 24.3 1.7E+02 0.0038 26.2 5.2 44 26-73 837-880 (903)
474 PRK12515 RNA polymerase sigma 24.2 1.7E+02 0.0037 21.2 4.5 40 24-66 128-167 (189)
475 PF13814 Replic_Relax: Replica 24.0 1.1E+02 0.0023 22.3 3.3 33 49-81 12-47 (191)
476 TIGR02959 SigZ RNA polymerase 23.9 1.8E+02 0.0039 20.9 4.5 40 24-66 97-136 (170)
477 COG1420 HrcA Transcriptional r 23.8 2.2E+02 0.0048 24.3 5.5 74 27-100 3-88 (346)
478 PRK12523 RNA polymerase sigma 23.8 1.9E+02 0.0041 20.7 4.5 41 24-67 116-156 (172)
479 PRK05657 RNA polymerase sigma 23.7 1.7E+02 0.0038 24.1 4.8 45 23-67 258-303 (325)
480 PRK12397 propionate kinase; Re 23.7 69 0.0015 28.1 2.5 47 59-105 61-116 (404)
481 KOG2593|consensus 23.7 66 0.0014 28.7 2.4 57 31-92 30-86 (436)
482 PRK12533 RNA polymerase sigma 23.6 1.5E+02 0.0032 22.8 4.2 42 24-68 131-172 (216)
483 PF05225 HTH_psq: helix-turn-h 23.6 1.7E+02 0.0038 17.4 4.5 36 37-72 7-42 (45)
484 KOG2313|consensus 23.6 1.2E+02 0.0027 21.9 3.4 41 10-52 49-92 (100)
485 cd01106 HTH_TipAL-Mta Helix-Tu 23.5 1.5E+02 0.0032 20.0 3.8 44 48-95 2-46 (103)
486 smart00413 ETS erythroblast tr 23.5 95 0.0021 21.7 2.8 33 48-81 43-75 (87)
487 cd04772 HTH_TioE_rpt1 First He 23.4 73 0.0016 21.8 2.2 50 49-102 3-54 (99)
488 PF12872 OST-HTH: OST-HTH/LOTU 23.3 85 0.0018 19.5 2.3 28 28-55 3-32 (74)
489 PRK12525 RNA polymerase sigma 23.1 1.8E+02 0.0039 20.8 4.3 42 24-68 115-156 (168)
490 cd00093 HTH_XRE Helix-turn-hel 23.1 1.1E+02 0.0024 16.2 2.6 24 45-68 11-34 (58)
491 PF13453 zf-TFIIB: Transcripti 23.1 14 0.00031 21.6 -1.3 12 84-95 26-37 (41)
492 PTZ00095 40S ribosomal protein 23.0 79 0.0017 24.7 2.5 22 59-80 118-139 (169)
493 cd07287 PX_RPK118_like The pho 22.9 83 0.0018 22.6 2.5 26 80-107 69-94 (118)
494 PF05043 Mga: Mga helix-turn-h 22.8 1.4E+02 0.003 19.3 3.4 41 32-72 15-56 (87)
495 TIGR00281 segregation and cond 22.7 3.7E+02 0.008 20.9 6.9 69 13-86 61-140 (186)
496 PF13551 HTH_29: Winged helix- 22.7 1.3E+02 0.0028 19.6 3.3 32 44-75 9-41 (112)
497 PRK12379 propionate/acetate ki 22.6 75 0.0016 27.7 2.6 47 59-105 60-112 (396)
498 TIGR01387 cztR_silR_copR heavy 22.6 2.4E+02 0.0053 19.7 4.8 58 25-82 145-214 (218)
499 PRK07408 RNA polymerase sigma 22.6 1.8E+02 0.004 22.8 4.6 42 24-68 200-241 (256)
500 COG2973 TrpR Trp operon repres 22.6 1.3E+02 0.0027 21.9 3.3 43 28-70 38-84 (103)
No 1
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=100.00 E-value=7.8e-38 Score=257.56 Aligned_cols=103 Identities=45% Similarity=0.662 Sum_probs=65.6
Q ss_pred ccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 3 ANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 3 ~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
..+++.+++++|+++++++|+++++|+++|++||++|++|||+|||++|||.+||||+++|+||||+||+|+|||+||||
T Consensus 57 ~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv 136 (327)
T PF05158_consen 57 LKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSV 136 (327)
T ss_dssp EEEEE-SSSEEEEE--SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--S
T ss_pred EEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence 45778889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred c-------------------CCcccccCccccccchhhhhhh
Q psy7778 83 A-------------------NIEYLTEGTVNAMVLPSRKKRE 105 (117)
Q Consensus 83 ~-------------------gg~wYtdg~~D~~fI~~l~~~~ 105 (117)
+ ||+||+||+||++||+.|++.-
T Consensus 137 ~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~ 178 (327)
T PF05158_consen 137 KNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQC 178 (327)
T ss_dssp S-SS--EEEESSS-----------------------------
T ss_pred CCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHH
Confidence 7 9999999999999999998753
No 2
>KOG3233|consensus
Probab=100.00 E-value=9.1e-35 Score=237.14 Aligned_cols=104 Identities=43% Similarity=0.624 Sum_probs=100.3
Q ss_pred cccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 2 LANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 2 ~~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+.+++++++++.|+.+++..|++.++++++|++||++|++|||+|||+++||.+||||+++|+||||+||+|+|||+|||
T Consensus 56 ~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233|consen 56 LLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred cchhhccCCcceEeccCchhhcccccCChHHHHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc-------------------CCcccccCccccccchhhhhhh
Q psy7778 82 VA-------------------NIEYLTEGTVNAMVLPSRKKRE 105 (117)
Q Consensus 82 V~-------------------gg~wYtdg~~D~~fI~~l~~~~ 105 (117)
|+ ||+|||||+||.+||+.|++.-
T Consensus 136 v~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c 178 (297)
T KOG3233|consen 136 VKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQIC 178 (297)
T ss_pred hcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHH
Confidence 97 9999999999999999999864
No 3
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=99.97 E-value=1.5e-31 Score=216.00 Aligned_cols=106 Identities=31% Similarity=0.473 Sum_probs=102.6
Q ss_pred cccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 2 LANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 2 ~~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
|+.+|++++.|.|+.+-..+|++...|+++|.+||++|+++|++|||.|+|+.|||||++++-||||+||+|++||+|||
T Consensus 57 li~l~rq~~vL~y~~v~~~ea~~~~tm~~~E~~vYs~i~~SG~EGiW~Ktik~rTNlh~~vV~kcLkSlESkr~vKSvKs 136 (301)
T COG5111 57 LISLFRQKGVLYYKGVLESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRTNLHHNVVGKCLKSLESKRIVKSVKS 136 (301)
T ss_pred hhhHHhcCCEEEEeeeecccCCcccccchHHHHHHHHHHhcCCCceehhhhhhhccCcHHHHHHHHHHHHHHHHHHHhhh
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc-------------------CCcccccCccccccchhhhhhhhh
Q psy7778 82 VA-------------------NIEYLTEGTVNAMVLPSRKKREER 107 (117)
Q Consensus 82 V~-------------------gg~wYtdg~~D~~fI~~l~~~~~~ 107 (117)
|+ ||+|||||++|.+||+.|++--+|
T Consensus 137 vKnptRKiYmLYdlvPS~eiTGGpWFtD~elDvEfi~~ll~ii~r 181 (301)
T COG5111 137 VKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIER 181 (301)
T ss_pred hcCCCceEEEEecccccccccCCCccccCcccHHHHHHHHHHHHH
Confidence 97 999999999999999999987766
No 4
>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=98.09 E-value=1.8e-05 Score=48.99 Aligned_cols=56 Identities=11% Similarity=0.184 Sum_probs=51.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
+||+.+..|+..|...+..++-..+|...++++.+.++++++.||.+|||....+-
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 68999999999999999999999999999999999999999999999999887654
No 5
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=98.03 E-value=1.3e-05 Score=64.99 Aligned_cols=57 Identities=28% Similarity=0.451 Sum_probs=52.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
...+|+++|+.|..+|.+.|+. |=.+||++++|+|.+++.|+|+.||++|||+..|.
T Consensus 189 ~~~~L~~~e~~il~~i~~~GGr-i~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 189 NEYDLNEDEKEILDLIRERGGR-ITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred ccCCCCHHHHHHHHHHHHhCCE-EeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence 3478999999999999988864 88999999999999999999999999999999874
No 6
>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=98.00 E-value=2.7e-05 Score=46.92 Aligned_cols=48 Identities=25% Similarity=0.410 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
|++-++.|+.+|.+ +.++-.++|..++|++.+.+++.|+.|+.+|+|+
T Consensus 1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 56778889999998 6669999999999999999999999999999996
No 7
>PF13730 HTH_36: Helix-turn-helix domain
Probab=97.98 E-value=3.3e-05 Score=47.42 Aligned_cols=51 Identities=22% Similarity=0.356 Sum_probs=45.0
Q ss_pred cCCCHHHHHHHHHHHHhc--CCccc--HHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778 26 KDSDNEEKVVYKIIEEAG--NKGIW--MRDIRFKSNLMPTQLNKILKQLETKKII 76 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AG--n~GIW--tkdIk~ktnL~~~~l~K~LK~LE~k~LI 76 (117)
++|++.|++||..|..-- +.|.| .++|-..+|+..++|.|+|+.||.+|+|
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 479999999999988764 45566 6999999999999999999999999987
No 8
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=97.95 E-value=2.5e-05 Score=51.95 Aligned_cols=53 Identities=21% Similarity=0.210 Sum_probs=50.0
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
|+.++.|+..|-.|+.+|||+.||-..+|+....+...+|.|+.+|||.....
T Consensus 1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 1 TDIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred CchHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 46789999999999999999999999999999999999999999999988766
No 9
>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=97.83 E-value=2.7e-05 Score=49.93 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=47.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
+|++.|..||..+- .+.+.-..+|...+|++.+++.++|+.|+.+|||....
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 68889999998887 56678899999999999999999999999999999876
No 10
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.75 E-value=0.00015 Score=47.40 Aligned_cols=58 Identities=16% Similarity=0.189 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
+-+..|+.++..+|.+|+-..+|-.+.|++...++++|..|+.+|+|-...+ ..+.|.
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~-~~~~W~ 63 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG-TPPLWK 63 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC-CCCceE
Confidence 3567899999999999999999999999999999999999999999977554 556775
No 11
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=97.69 E-value=0.00021 Score=44.02 Aligned_cols=53 Identities=21% Similarity=0.321 Sum_probs=46.9
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
||..|..+...|.+.|+ +-..+|...+++..+.++++++.||.+|||..-.+-
T Consensus 1 lt~~q~~iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp STHHHHHHHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CCHHHHHHHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 57789999999998776 899999999999999999999999999999877654
No 12
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=97.62 E-value=0.00022 Score=49.71 Aligned_cols=57 Identities=19% Similarity=0.232 Sum_probs=53.0
Q ss_pred CCCHHHHHHHHHHH--HhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 27 DSDNEEKVVYKIIE--EAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie--~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
+|+..|..|...|. .+.+.|+-..+|...++++.+.++++++.||.+|+|..+.+-.
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~ 80 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSED 80 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcc
Confidence 79999999999998 6677889999999999999999999999999999999998865
No 13
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.48 E-value=0.00044 Score=46.12 Aligned_cols=54 Identities=20% Similarity=0.318 Sum_probs=51.0
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
|+..|..|+..|...+..+. .+|..++++..+.+++.++.||.+|||+..++-.
T Consensus 20 lt~~q~~~L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~ 73 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPE 73 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcc
Confidence 89999999999999998888 9999999999999999999999999999998865
No 14
>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=97.34 E-value=0.00085 Score=41.99 Aligned_cols=55 Identities=13% Similarity=0.230 Sum_probs=43.1
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
||..|..|...|. ..+.++-..+|...++++.+.+++.|+.|+.+|||....+-.
T Consensus 1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 1 LTRPQWQVLRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp --HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred CCHHHHHHHHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 5678888888888 667788889999999999999999999999999998777654
No 15
>PRK10870 transcriptional repressor MprA; Provisional
Probab=97.29 E-value=0.0008 Score=50.86 Aligned_cols=59 Identities=15% Similarity=0.127 Sum_probs=54.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
--+||..+..|...|...++.++-..+|...++++.++++++++.||++|||....+-.
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~ 108 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN 108 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 35789999999999998889999999999999999999999999999999999988764
No 16
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.26 E-value=0.0012 Score=42.94 Aligned_cols=54 Identities=20% Similarity=0.391 Sum_probs=48.7
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
-+|+..|..|+.+|...| ++-.++|...++++++.+++.|+.|+++++|...++
T Consensus 6 ~~l~~~~~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 6 LGLTPTQFLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred cCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence 468899999999999866 688889999999999999999999999999987755
No 17
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=97.07 E-value=0.003 Score=42.09 Aligned_cols=52 Identities=17% Similarity=0.245 Sum_probs=43.6
Q ss_pred HHhcCCc-ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 40 EEAGNKG-IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 40 e~AGn~G-IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
...++.+ +-.++|..++|+|.+.+.+++..|+..|+|++.++.+||-+....
T Consensus 18 a~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~ 70 (83)
T PF02082_consen 18 ARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARP 70 (83)
T ss_dssp HCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-
T ss_pred HhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCC
Confidence 3334444 999999999999999999999999999999999999999877653
No 18
>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=97.04 E-value=0.0026 Score=48.04 Aligned_cols=64 Identities=20% Similarity=0.175 Sum_probs=54.3
Q ss_pred cCCCHHHHHHHHHHHHh---cCCcccHHHHHhhcCCC-hHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 26 KDSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSNLM-PTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~-~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
++||+.|..|+..|.+. +..+.-.++|-..+|+. .+++.+.|+.||.+|+|+...+...|.++.
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~~ 69 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRIL 69 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeEEeC
Confidence 46899999999999955 45568899999999999 999999999999999999877665455444
No 19
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.03 E-value=0.0025 Score=45.88 Aligned_cols=56 Identities=14% Similarity=0.058 Sum_probs=50.9
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
-+||..+..|...|.. +.|+-..+|...+++..+.+++.|+.||.+|||....+-.
T Consensus 36 ~glt~~q~~vL~~l~~--~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~ 91 (144)
T PRK11512 36 LDITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPN 91 (144)
T ss_pred cCCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcc
Confidence 4799999999888864 5689999999999999999999999999999999998865
No 20
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=96.90 E-value=0.0031 Score=48.88 Aligned_cols=57 Identities=18% Similarity=0.096 Sum_probs=50.7
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
--+|+..|..|+.+|... .|+-.++|-..++++.++++++|+.||.+|||...++-.
T Consensus 40 ~~gLt~~q~~iL~~L~~~--~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~ 96 (185)
T PRK13777 40 PYDLNINEHHILWIAYHL--KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKED 96 (185)
T ss_pred HCCCCHHHHHHHHHHHhC--CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence 358999999999888664 589999999999999999999999999999999887654
No 21
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=96.89 E-value=0.0039 Score=43.37 Aligned_cols=56 Identities=14% Similarity=0.290 Sum_probs=49.8
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
-+|+..+..|...|.. +.|+-..+|-..+++..+.+++.|+.||.+|||....+-.
T Consensus 24 ~~lt~~q~~iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~ 79 (118)
T TIGR02337 24 HGLTEQQWRILRILAE--QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN 79 (118)
T ss_pred cCCCHHHHHHHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC
Confidence 5789999988888876 4478889999999999999999999999999999987764
No 22
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.88 E-value=0.0041 Score=44.48 Aligned_cols=58 Identities=16% Similarity=0.083 Sum_probs=50.3
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
--+|+..+..|...|...+ .|+-..+|...+++..++++++++.||.+|||....+-.
T Consensus 26 ~~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~ 83 (144)
T PRK03573 26 PLELTQTHWVTLHNIHQLP-PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCAS 83 (144)
T ss_pred hcCCCHHHHHHHHHHHHcC-CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCC
Confidence 3479999988888887653 467789999999999999999999999999999998754
No 23
>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=96.87 E-value=0.0046 Score=40.53 Aligned_cols=57 Identities=26% Similarity=0.293 Sum_probs=45.1
Q ss_pred cCCCHHHHHHHHHHHHhcC-Ccc--cHHHHHhhcCCC-hHHHHHHHHHHhhcCCeeeeccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGN-KGI--WMRDIRFKSNLM-PTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn-~GI--WtkdIk~ktnL~-~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
+.||+-|+.||..|.+--. .|. -.++|....|+. .+.+.+.|+.||.+|+|+...+.
T Consensus 2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 2 KELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp ----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCCC
Confidence 5789989999999887433 455 579999999998 99999999999999999987664
No 24
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=96.65 E-value=0.0064 Score=43.18 Aligned_cols=52 Identities=21% Similarity=0.274 Sum_probs=43.8
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
.+...+..+++..+-..+|..+.++|.+.+.++|+.|+..|+|.+.++..||
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~gg 64 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGG 64 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCC
Confidence 4444555566678999999999999999999999999999999988776655
No 25
>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=96.64 E-value=0.0092 Score=37.55 Aligned_cols=48 Identities=15% Similarity=0.259 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.=..|+..+ +.+.+.-..+|...+|++++++.+.|+.|+.-|||+.++
T Consensus 11 ~R~~Il~~L--~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 11 TRLRILRLL--ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHH--HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHH--hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 344788888 788999999999999999999999999999999999875
No 26
>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=96.55 E-value=0.0072 Score=41.49 Aligned_cols=53 Identities=15% Similarity=0.243 Sum_probs=44.2
Q ss_pred cCCCHHHHHHHHHHHH--hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 26 KDSDNEEKVVYKIIEE--AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~--AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.+|++-.+.||++|++ ..+.|+-..+|..+.+|+...|.++|..|...|+|=+
T Consensus 43 ~~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 43 SGLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp --S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred cCCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence 3799999999999998 3469999999999999999999999999999998843
No 27
>PRK00215 LexA repressor; Validated
Probab=96.52 E-value=0.0096 Score=45.13 Aligned_cols=54 Identities=20% Similarity=0.238 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHHH---hcCCcccHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeecc
Q psy7778 28 SDNEEKVVYKIIEE---AGNKGIWMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 28 L~~eE~lVY~~Ie~---AGn~GIWtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
||+.|..|+..|.+ .++.++-.++|-..+|+ +.+++++.|+.||.+|+|....+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCC
Confidence 67889999999984 45677889999999999 99999999999999999976543
No 28
>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=96.52 E-value=0.014 Score=35.41 Aligned_cols=50 Identities=12% Similarity=0.246 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
..+..|+..|...+ +-..+|...++++.+.+++.|+.|++.++|....+-
T Consensus 7 ~~~~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 7 PTRLRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred hHHHHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 45677888777654 889999999999999999999999999999987654
No 29
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=96.51 E-value=0.0089 Score=44.51 Aligned_cols=72 Identities=15% Similarity=0.143 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhh
Q psy7778 31 EEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRK 102 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~ 102 (117)
-++.|.-++.-|.+.+ +-+++|-.+.|+|.+.|.|++..|...|||.++++.+||-+....-=+-.+-|.+.
T Consensus 7 ~~YAlr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~eItl~dIi~ 80 (153)
T PRK11920 7 TNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVR 80 (153)
T ss_pred HhHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHHCcHHHHHH
Confidence 4666777777665433 67899999999999999999999999999999999999988765544444444443
No 30
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=96.37 E-value=0.016 Score=41.82 Aligned_cols=55 Identities=15% Similarity=0.235 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 31 EEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 31 eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
.++.+.-++.-| +..-+-.++|..++++|.+.+.|+|..|...|||.++++..||
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Gg 64 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGG 64 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCC
Confidence 455555555555 3334788999999999999999999999999999999888766
No 31
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.35 E-value=0.015 Score=43.28 Aligned_cols=61 Identities=21% Similarity=0.245 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHhcCCc---ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 31 EEKVVYKIIEEAGNKG---IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~G---IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
-++.|--++.-|.+.| +-..+|..+.|+|.+.|.|++..|...|||+++++.+||-...--
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~ 70 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARP 70 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCC
Confidence 4667777777776544 668999999999999999999999999999999999988765443
No 32
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.22 E-value=0.02 Score=38.97 Aligned_cols=53 Identities=21% Similarity=0.376 Sum_probs=46.0
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
|++.++.|+.++...+ .+-..+|-.++|++.+++.+.++.|+.+|+|+.+..+
T Consensus 1 ld~~D~~il~~L~~~~--~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~ 53 (108)
T smart00344 1 LDEIDRKILEELQKDA--RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAV 53 (108)
T ss_pred CCHHHHHHHHHHHHhC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEE
Confidence 5677888888998865 5889999999999999999999999999999965543
No 33
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=96.18 E-value=0.021 Score=41.41 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHhcC-Cc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778 31 EEKVVYKIIEEAGN-KG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE 90 (117)
Q Consensus 31 eE~lVY~~Ie~AGn-~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd 90 (117)
-++.+-.+|..|.. .| +-.++|-.+.|++.+.|.|+|..|+..|||+++++..||-....
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 56777778877743 33 66799999999999999999999999999999999998877764
No 34
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=96.15 E-value=0.022 Score=43.56 Aligned_cols=55 Identities=20% Similarity=0.292 Sum_probs=48.9
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
..++++.+..|+..|...| ++-..+|...++++.+++++.|+.|+.+|+|...+.
T Consensus 138 ~~~ls~~~~~IL~~l~~~g--~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 138 LAGLSREELKVLEVLKAEG--EKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred hcCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 4578888899999997654 688999999999999999999999999999998864
No 35
>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=96.11 E-value=0.023 Score=36.49 Aligned_cols=44 Identities=20% Similarity=0.413 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.||.+-+ ++..+-+.+|....|..++.++..++.|+.+|||.-.
T Consensus 12 ~Iy~l~~--~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 12 AIYELSE--EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHH--CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHc--CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 6887776 8889999999999999999999999999999999754
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.10 E-value=0.032 Score=32.47 Aligned_cols=46 Identities=9% Similarity=0.239 Sum_probs=39.4
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
..|+..+.+. .++-..+|....+++.+.+.+.|+.|+.+++|....
T Consensus 3 ~~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3577777653 579999999999999999999999999999997654
No 37
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.98 E-value=0.03 Score=41.59 Aligned_cols=69 Identities=14% Similarity=0.117 Sum_probs=57.7
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc-c-CCcccccCccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV-A-NIEYLTEGTVN 94 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV-~-gg~wYtdg~~D 94 (117)
.=+|++-|..||..+=+ -|.+.-+-+|..+.|+..++++|+|++|...|||...|-- . ||..|-=-..|
T Consensus 22 ~~GLs~~Dv~v~~~LL~-~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~ 92 (126)
T COG3355 22 VYGLSELDVEVYKALLE-ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID 92 (126)
T ss_pred HhCCcHHHHHHHHHHHh-hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC
Confidence 45789999999998887 6788899999999999999999999999999999988865 3 66666543333
No 38
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.97 E-value=0.033 Score=38.30 Aligned_cols=57 Identities=19% Similarity=0.110 Sum_probs=46.8
Q ss_pred cccCCCHHHHHHHHHHHH-h-----cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 24 KLKDSDNEEKVVYKIIEE-A-----GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~-A-----Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
...++++.+..++-.|-. . ...++-..+|-..+|+..++++|+|+.||.+|+|..-.
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence 466777777766665542 1 47889999999999999999999999999999998544
No 39
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=95.75 E-value=0.027 Score=37.10 Aligned_cols=58 Identities=12% Similarity=0.162 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
+.|..|+++++++|..++....+-...+.|...||++|=.|+.+|.|..... ....|+
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~-~PP~W~ 61 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGG-TPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECS-SSTEEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCC-CCCceE
Confidence 4577999999999999999999999999999999999999999999975433 344453
No 40
>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=95.68 E-value=0.022 Score=34.84 Aligned_cols=44 Identities=14% Similarity=0.283 Sum_probs=35.3
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.|..++.+++ .|+-..+|-.++|+|.+++.+.|++|+..|++..
T Consensus 7 ~iL~~l~~~~-~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESG-GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTB-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 3455555554 4478899999999999999999999999999975
No 41
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.59 E-value=0.047 Score=33.65 Aligned_cols=36 Identities=19% Similarity=0.188 Sum_probs=32.8
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
..+-..+|...+|++...++++|+.|+.+|+|....
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 457788999999999999999999999999998765
No 42
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=95.56 E-value=0.046 Score=37.57 Aligned_cols=56 Identities=9% Similarity=0.161 Sum_probs=45.0
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
..|+.++.++ +.-+-..+|-.+. ++..++|-|+|+.|+..|+|..+..-.+..+|.
T Consensus 4 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~ 64 (116)
T cd07153 4 LAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE 64 (116)
T ss_pred HHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence 4688888776 4556666666555 689999999999999999999998777767774
No 43
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=95.54 E-value=0.04 Score=38.71 Aligned_cols=55 Identities=16% Similarity=0.265 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHhc---CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 31 EEKVVYKIIEEAG---NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 31 eE~lVY~~Ie~AG---n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
.+..+.-++.-|. ...+-..+|...+++|.+.+.++|..|+..|+|.+..+-.||
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~gg 64 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGG 64 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCC
Confidence 3444444444443 346899999999999999999999999999999987665544
No 44
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=95.52 E-value=0.037 Score=41.92 Aligned_cols=55 Identities=13% Similarity=0.218 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 31 EEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 31 eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
.+..+.-++.-| +...+-.++|..+.|+|.+.+.|+|..|...|||.+..+..||
T Consensus 7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GG 64 (164)
T PRK10857 7 GRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGG 64 (164)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCC
Confidence 455555555444 3345788999999999999999999999999999999888765
No 45
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=95.50 E-value=0.021 Score=38.42 Aligned_cols=42 Identities=21% Similarity=0.250 Sum_probs=35.9
Q ss_pred CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
+..+.-++|+..+++++..+++.|+.||..|+|+.-|...++
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 678999999999999999999999999999999998877644
No 46
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.32 E-value=0.071 Score=38.00 Aligned_cols=57 Identities=19% Similarity=0.376 Sum_probs=50.6
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccC
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN 84 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~g 84 (117)
..|++-++.+++++..-+. +-.++|..+.|++.+.+.+.++.||..|+|+-..-+-+
T Consensus 4 ~~lD~~D~~IL~~L~~d~r--~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 4 MKLDDIDRRILRLLQEDAR--ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred ccccHHHHHHHHHHHHhCC--CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEEC
Confidence 4588888888888888877 88999999999999999999999999999998877653
No 47
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=95.30 E-value=0.057 Score=35.79 Aligned_cols=45 Identities=33% Similarity=0.523 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
+|+++++...+.|.=..+|-..+||+...+.+.|+.|+++|||+.
T Consensus 7 Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 7 IIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp HHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence 678888887788888899999999999999999999999999954
No 48
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=95.13 E-value=0.083 Score=37.22 Aligned_cols=53 Identities=15% Similarity=0.186 Sum_probs=46.6
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
+++.+..|..++..+|.+=.|+ |-..+++|...+..+++.||..|||..|.+=
T Consensus 5 ~~~l~~~IL~hl~~~~~Dy~k~--ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 5 LDPLDLKILQHLKKAGPDYAKS--IARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred cChhHHHHHHHHHHHCCCcHHH--HHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 5667889999999999998875 4667899999999999999999999998753
No 49
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=95.05 E-value=0.059 Score=46.72 Aligned_cols=53 Identities=23% Similarity=0.275 Sum_probs=47.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+|++.|..|...|...| ++-+.+|-.++++..+.++++++.|+++|||.....
T Consensus 3 ~Lt~~e~~vL~~L~~~~--~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~ 55 (489)
T PRK04172 3 ELHPNEKKVLKALKELK--EATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEER 55 (489)
T ss_pred CCCHHHHHHHHHHHhCC--CCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEee
Confidence 68998888998996544 789999999999999999999999999999997654
No 50
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.81 E-value=0.11 Score=34.03 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccC
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN 84 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~g 84 (117)
.|++.|.+. +.++-|+||-..++|...++.+.|..||+.|.|+.++.=+|
T Consensus 4 ~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG 53 (62)
T PF04703_consen 4 KILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRG 53 (62)
T ss_dssp CHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSS
T ss_pred HHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCC
Confidence 366777776 77899999999999999999999999999999998775443
No 51
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=94.73 E-value=0.089 Score=40.18 Aligned_cols=47 Identities=17% Similarity=0.221 Sum_probs=40.5
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
..|+..+...|. +-..+|...++++.+++++.|+.||.+|||.....
T Consensus 4 ~~IL~~L~~~~~--~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~ 50 (203)
T TIGR02702 4 EDILSYLLKQGQ--ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAV 50 (203)
T ss_pred HHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeec
Confidence 456777766554 99999999999999999999999999999988753
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.66 E-value=0.073 Score=31.70 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=31.4
Q ss_pred cc-cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 46 GI-WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 46 GI-WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
-+ -.++|....+++.+.+.++|+.|++.|+|..+.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 45 689999999999999999999999999987654
No 53
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.65 E-value=0.12 Score=30.41 Aligned_cols=38 Identities=11% Similarity=0.204 Sum_probs=33.9
Q ss_pred CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+..+-..+|...++++.+.++++|+.|+++++|.....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 55678889999999999999999999999999986653
No 54
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=94.56 E-value=0.11 Score=33.85 Aligned_cols=45 Identities=13% Similarity=0.268 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.|..+|...+ .++-..+|-..++++.+++.+.|+.|+..|+|...
T Consensus 9 ~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 9 AVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 4666675542 47999999999999999999999999999999874
No 55
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=94.21 E-value=0.17 Score=36.78 Aligned_cols=52 Identities=19% Similarity=0.207 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhh----cCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK----SNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k----tnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.||+-|..|..+|=..| ++-.++|... .++..+++...|+.|+.||+|..-+
T Consensus 1 ~Lt~~E~~VM~vlW~~~--~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 1 SISDAEWEVMRVVWTLG--ETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred CCCHHHHHHHHHHHcCC--CCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeec
Confidence 37888999999998766 4677885544 5799999999999999999998654
No 56
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=93.88 E-value=0.25 Score=29.64 Aligned_cols=41 Identities=15% Similarity=0.306 Sum_probs=32.6
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
|...+.+ .-.-..+|...++++++++++.|+.|+..|+|++
T Consensus 7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 3444444 3466789999999999999999999999999974
No 57
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=93.76 E-value=0.15 Score=29.40 Aligned_cols=33 Identities=21% Similarity=0.260 Sum_probs=29.6
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
+-.++|...++++.+.++++|+.|+..|+|...
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 456789999999999999999999999999753
No 58
>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=93.62 E-value=0.13 Score=29.91 Aligned_cols=30 Identities=30% Similarity=0.376 Sum_probs=25.5
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKII 76 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LI 76 (117)
+-..||-.-.|+...+++|+|+.|+.+|+|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 346789999999999999999999999997
No 59
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=93.59 E-value=0.18 Score=35.11 Aligned_cols=62 Identities=11% Similarity=0.139 Sum_probs=45.7
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE 90 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd 90 (117)
+|+.-..|+.+|.++.. -.--.+|-.. .++..++|=|+|+.|+..|+|..+..-.+..+|.=
T Consensus 6 ~T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~ 72 (120)
T PF01475_consen 6 LTPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYEL 72 (120)
T ss_dssp HHHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE
T ss_pred CCHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEee
Confidence 35566799999999987 4444443333 47889999999999999999999988766666653
No 60
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=93.46 E-value=0.36 Score=27.95 Aligned_cols=43 Identities=12% Similarity=0.244 Sum_probs=35.8
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
..||++|+.++.++. .|...++|-..++++.+++.+.++.+..
T Consensus 2 ~~l~~~e~~i~~~~~----~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 2 ASLTPREREVLRLLA----EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 358888888777652 6789999999999999999999887754
No 61
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=93.44 E-value=0.26 Score=39.65 Aligned_cols=52 Identities=19% Similarity=0.287 Sum_probs=46.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
|||..|-.||-.+=.-|.. --++|-..+|+|++.+-.+|++||.||+|....
T Consensus 13 Glt~yEa~vY~aLl~~g~~--tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~ 64 (247)
T COG1378 13 GLTEYEAKVYLALLCLGEA--TAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE 64 (247)
T ss_pred CCCHHHHHHHHHHHHhCCc--cHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC
Confidence 7899999999988887764 458999999999999999999999999999873
No 62
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=93.37 E-value=0.32 Score=29.38 Aligned_cols=33 Identities=15% Similarity=0.254 Sum_probs=29.9
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
-.++|...++++.+.+++.|+.|+..|+|....
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 388999999999999999999999999987653
No 63
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=93.10 E-value=0.29 Score=37.46 Aligned_cols=53 Identities=25% Similarity=0.270 Sum_probs=41.9
Q ss_pred ccCCCHHHHHHHHHHHHhcCCc--------ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKG--------IWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~G--------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
+...+.++|++.-+.+.+...| +-.++|-.-.|+...+++|+|+.|+..|+|+
T Consensus 150 l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 150 LGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred HcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 3456778988777766543322 3358999999999999999999999999996
No 64
>PRK12423 LexA repressor; Provisional
Probab=93.06 E-value=0.47 Score=36.38 Aligned_cols=55 Identities=15% Similarity=0.163 Sum_probs=46.4
Q ss_pred CCCHHHHHHHHHHHHhc-CCcc--cHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeecc
Q psy7778 27 DSDNEEKVVYKIIEEAG-NKGI--WMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AG-n~GI--WtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.||+-++.||+.|.+.= ..|+ -.++|-...|+ ..+.+.+.|+.|+.+|+|..-.+
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 48899999999999862 2344 78999999995 88999999999999999987554
No 65
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=92.58 E-value=0.63 Score=32.50 Aligned_cols=52 Identities=19% Similarity=0.219 Sum_probs=43.0
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
|++-|..|..+|=+.|. +-.++|....+ .+.+++...|+.|+.||+|..-+.
T Consensus 1 Ls~~E~~IM~~lW~~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 1 LSDLELEIMEILWESGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp --HHHHHHHHHHHHHSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCHHHHHHHHHHHhCCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec
Confidence 57789999999999998 88888887754 779999999999999999998764
No 66
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.51 E-value=0.4 Score=34.56 Aligned_cols=44 Identities=23% Similarity=0.396 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.||.+++..| .+-..+|....++..+.+++.|+.|+.+|||...
T Consensus 12 ~I~~l~~~~~--~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 12 QIYLLIEEKG--YARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHhcCC--CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 6777766443 4577999999999999999999999999999854
No 67
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=92.50 E-value=0.32 Score=30.80 Aligned_cols=32 Identities=22% Similarity=0.289 Sum_probs=29.5
Q ss_pred cccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 46 GIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 46 GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
.+-..+|-.-+|++...++++|+.|+..|+|.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34588999999999999999999999999998
No 68
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.49 E-value=0.21 Score=33.07 Aligned_cols=32 Identities=22% Similarity=0.388 Sum_probs=29.7
Q ss_pred HHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 50 RDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 50 kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
++|-..++++.+.++++|+.|+++|||....+
T Consensus 3 ~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 57889999999999999999999999999775
No 69
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=92.35 E-value=0.21 Score=29.96 Aligned_cols=43 Identities=26% Similarity=0.308 Sum_probs=22.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+++-||++|+.. |+.--+.|.-.+.|-...|.+.++|.+.||.
T Consensus 1 ~~~~Lt~~eR~~---I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 1 KYKHLTPEERNQ---IEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp -----------H---HHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred CccchhhhHHHH---HHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 356789988865 4444568999999999999999999999873
No 70
>PRK09462 fur ferric uptake regulator; Provisional
Probab=92.09 E-value=0.72 Score=33.57 Aligned_cols=63 Identities=10% Similarity=0.172 Sum_probs=50.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
.+|++=..|+.++.++.+.-+-..+|-.+ .++..++|-|+|+.|+..|+|..+..-.+..+|.
T Consensus 14 r~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~ 81 (148)
T PRK09462 14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE 81 (148)
T ss_pred CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence 36788889999999876667777766544 3578899999999999999999997656666774
No 71
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=92.05 E-value=0.45 Score=35.80 Aligned_cols=52 Identities=21% Similarity=0.300 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
.||.+++ ...-+=++||-...|..++.+++.++.|++.|||.-++. +|.+.|
T Consensus 14 ~Iy~l~~--~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y--~gi~LT 65 (154)
T COG1321 14 TIYELLE--EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPY--GGVTLT 65 (154)
T ss_pred HHHHHHh--ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecC--CCeEEC
Confidence 6777777 334489999999999999999999999999999998775 444444
No 72
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=91.72 E-value=0.4 Score=34.74 Aligned_cols=58 Identities=14% Similarity=0.200 Sum_probs=47.2
Q ss_pred cccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 22 NEKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 22 a~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
++.++-|.++-| .|+.++...| +.-..+|-..++++++++++.|+.|+.-|||..-+.
T Consensus 7 ~~~fkaLadptRl~IL~~L~~~~--~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~ 65 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLRESG--ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ 65 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE
Confidence 456777888766 6777776544 466789999999999999999999999999987654
No 73
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=91.65 E-value=0.43 Score=38.05 Aligned_cols=39 Identities=21% Similarity=0.173 Sum_probs=35.0
Q ss_pred cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 43 GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 43 Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
++.+|-..+|...+++.++++++.|+.||.+|||....+
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~ 56 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIV 56 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEc
Confidence 345799999999999999999999999999999987654
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.48 E-value=0.42 Score=35.44 Aligned_cols=55 Identities=18% Similarity=0.320 Sum_probs=46.1
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
..|++-++.|..++..-|... .++|-.+.|+..+++.+-++.|+..|.|+.+..+
T Consensus 10 ~~lD~~D~~IL~~Lq~d~R~s--~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~ 64 (164)
T PRK11169 10 KDLDRIDRNILNELQKDGRIS--NVELSKRVGLSPTPCLERVRRLERQGFIQGYTAL 64 (164)
T ss_pred hhHHHHHHHHHHHhccCCCCC--HHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEE
Confidence 457777888888887766654 4999999999999999999999999999865543
No 75
>PRK11050 manganese transport regulator MntR; Provisional
Probab=91.36 E-value=0.63 Score=34.38 Aligned_cols=53 Identities=19% Similarity=0.234 Sum_probs=41.5
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE 90 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd 90 (117)
.|+.+|.. +.++-..+|-..+++.++.+++.|+.||.+|+|..-. ..|.+.|+
T Consensus 41 ~I~~~l~~--~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~--~~~v~LT~ 93 (152)
T PRK11050 41 LIADLIAE--VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRP--YRGVFLTP 93 (152)
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec--CCceEECc
Confidence 56666654 3578889999999999999999999999999997643 23444554
No 76
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=91.34 E-value=0.55 Score=33.98 Aligned_cols=53 Identities=19% Similarity=0.283 Sum_probs=41.0
Q ss_pred cCCCHHHHHHHHHHHHh---c---CCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 26 KDSDNEEKVVYKIIEEA---G---NKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~A---G---n~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
...+.++|+..-+...+ | +.| +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus 111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 44566788776655432 2 234 46889999999999999999999999999974
No 77
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=91.18 E-value=0.66 Score=34.10 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=40.1
Q ss_pred ccCCCHHHHHHHHHHHHh---c----CCcc----cHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 25 LKDSDNEEKVVYKIIEEA---G----NKGI----WMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~A---G----n~GI----WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
+...+..+|+.+-+.+-+ + ..|+ -.++|...+|++..+++|+|+.|+..|+|+.
T Consensus 136 ~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~ 200 (211)
T PRK11753 136 LAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISA 200 (211)
T ss_pred HHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence 344556788766554433 2 1233 3589999999999999999999999999974
No 78
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=90.86 E-value=0.8 Score=33.81 Aligned_cols=62 Identities=11% Similarity=0.148 Sum_probs=52.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
.+|++-..|++++.++++- .--.+|=.+ -++..++|-+.|+.|+..|+|..+..-.+..+|.
T Consensus 18 r~T~qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~ 84 (145)
T COG0735 18 RLTPQRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYE 84 (145)
T ss_pred CcCHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEe
Confidence 4688888999999999887 777766544 4488899999999999999999999988888884
No 79
>PRK06474 hypothetical protein; Provisional
Probab=90.61 E-value=0.75 Score=35.04 Aligned_cols=56 Identities=11% Similarity=0.127 Sum_probs=45.1
Q ss_pred ccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 25 LKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 25 ~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+.-|....| .|++.+...+. +.-..+|-... +++++++.+.|+.|+..|||..++.
T Consensus 5 ~~~La~p~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 334555444 78888877643 48889998888 7999999999999999999999875
No 80
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=90.58 E-value=0.68 Score=34.87 Aligned_cols=54 Identities=15% Similarity=0.186 Sum_probs=42.1
Q ss_pred ccCCCHHHHHHHHHHHHhc------CCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 25 LKDSDNEEKVVYKIIEEAG------NKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AG------n~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
+...+.++|+..-+.+.+. ..| +-.++|-.-.|++...++|+|+.|+++|+|+-
T Consensus 151 l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 151 LSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAV 216 (235)
T ss_pred HhCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 3456778887766665442 122 56789999999999999999999999999984
No 81
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=90.39 E-value=0.75 Score=33.69 Aligned_cols=53 Identities=11% Similarity=0.223 Sum_probs=42.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCC-------c-----ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNK-------G-----IWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~-------G-----IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
+...+.++|+.+-+++-+... + +-..+|-.-.|+....++|+|+.|+..|+|+
T Consensus 116 l~~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 116 LVGQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred HHhCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 345567888888777655321 1 3578899999999999999999999999997
No 82
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=89.98 E-value=1 Score=34.26 Aligned_cols=53 Identities=11% Similarity=-0.058 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 27 DSDNEEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.++.++|+.+-+...+.... .-..+|-...|+...+|+|+|+.|+..|+|..-
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 44678998887776554332 346899999999999999999999999999753
No 83
>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=89.90 E-value=1.3 Score=26.37 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=34.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+..||++|+.|..+.. -+|.-..+|-...|++...+.++.+.
T Consensus 2 l~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 2 LDQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HCTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hhhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 5689999998887777 78899999999999999998877654
No 84
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=89.86 E-value=1.4 Score=33.30 Aligned_cols=58 Identities=12% Similarity=0.084 Sum_probs=49.0
Q ss_pred cCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCe-eeecccc
Q psy7778 26 KDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKII-KAVKSVA 83 (117)
Q Consensus 26 ~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LI-K~VKsV~ 83 (117)
..|++.|. .+..+|++--+.|..+++|-.+.|+...++.+.+..|-+.++. ..++...
T Consensus 157 ~~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~ 216 (239)
T PRK10430 157 KGLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHYGV 216 (239)
T ss_pred CCCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeeccC
Confidence 35888774 5667887777899999999999999999999999999999998 5666654
No 85
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.39 E-value=0.75 Score=36.59 Aligned_cols=51 Identities=18% Similarity=0.292 Sum_probs=41.0
Q ss_pred CCHHHH--HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 28 SDNEEK--VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 28 L~~eE~--lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
...-++ .|..++...+ .++-..+|-.+++||.+++.+.|++|+..|++..-
T Consensus 21 ~~sl~r~l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 21 AQALERGIAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred chHHHHHHHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 444444 6777776543 56778999999999999999999999999999653
No 86
>PRK09954 putative kinase; Provisional
Probab=89.36 E-value=1.1 Score=36.54 Aligned_cols=48 Identities=21% Similarity=0.182 Sum_probs=42.1
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
|++-++.|+.++.+.+ =|-..+|..+.|+..+++.+.|+.|+++|+|+
T Consensus 1 ~~~~~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 1 MNNREKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred CChHHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 4566777888888665 48999999999999999999999999999995
No 87
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=89.31 E-value=0.54 Score=35.74 Aligned_cols=49 Identities=24% Similarity=0.386 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhcCCcc---cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 32 EKVVYKIIEEAGNKGI---WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GI---WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
-++++-+++.....+. -.++|-..+++..+++.|++|.|+.+++|..++
T Consensus 58 ~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~ 109 (165)
T PF05732_consen 58 FRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR 109 (165)
T ss_pred HHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc
Confidence 3455556666665553 357799999999999999999999999999875
No 88
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=89.28 E-value=0.57 Score=32.79 Aligned_cols=47 Identities=17% Similarity=0.192 Sum_probs=37.4
Q ss_pred HHHHHHH-HhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 34 VVYKIIE-EAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 34 lVY~~Ie-~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
..|+-|. +..+ +=|---.|-.+.++.-+.-.++|+.||.+|+||.|.
T Consensus 27 ~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 27 ELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred HHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEe
Confidence 3444443 4443 666777889999999999999999999999999993
No 89
>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=89.13 E-value=2.5 Score=25.42 Aligned_cols=40 Identities=13% Similarity=0.195 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcC
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKK 74 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~ 74 (117)
.|..++.++++. +-..+|..+.|+...+|.+-|+.|+..+
T Consensus 4 ~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 455566555555 9999999999999999999999999888
No 90
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=88.89 E-value=0.79 Score=35.64 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.|..++.. .+.|+-..+|-.++|||.+++.+.|++|+..|++..
T Consensus 13 ~IL~~l~~-~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGA-ERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHHhc-CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 45556644 357888999999999999999999999999999975
No 91
>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=88.66 E-value=0.72 Score=31.31 Aligned_cols=53 Identities=13% Similarity=0.015 Sum_probs=45.6
Q ss_pred ccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCC
Q psy7778 21 TNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKI 75 (117)
Q Consensus 21 ~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L 75 (117)
-|+.+..|++..+.+|.+- .-.+|.-.++|-..+|++.+++...++.+++.+-
T Consensus 9 ~~~~l~~l~~~~r~af~L~--R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~ 61 (73)
T TIGR03879 9 LAERLTWVDSLAEAAAALA--REEAGKTASEIAEELGRTEQTVRNHLKGETKAGG 61 (73)
T ss_pred HHHHHhcCCHHHHHHHHHH--HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccch
Confidence 3567889999999999887 3458999999999999999999999999887653
No 92
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=88.23 E-value=1.3 Score=35.09 Aligned_cols=46 Identities=13% Similarity=0.313 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.|.+++.. +..|+-..+|-.++|||.+++.+.|.+|+..||+..-.
T Consensus 8 ~iL~~l~~-~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~ 53 (246)
T COG1414 8 AILDLLAE-GPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP 53 (246)
T ss_pred HHHHHHHh-CCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 56777777 66777899999999999999999999999999998755
No 93
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=88.08 E-value=0.84 Score=32.88 Aligned_cols=57 Identities=25% Similarity=0.199 Sum_probs=43.3
Q ss_pred HHHHHHHH-H-hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 33 KVVYKIIE-E-AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 33 ~lVY~~Ie-~-AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
.-.|+-|. + -.-+=|-.-.|-.+.++..+.-.++|+.|+++|+|+.|..=++-.=||
T Consensus 44 ~~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 44 KETYDKLLKEVPKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp CHHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HHHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 34566554 2 334668888999999999999999999999999999994434444443
No 94
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=87.99 E-value=1.2 Score=30.47 Aligned_cols=54 Identities=24% Similarity=0.216 Sum_probs=40.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
++.|+++|.-|...||..-.+= +=...|...++++..-+.++|+.|...+||..
T Consensus 1 ~r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 1 LRYLSKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp --T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred CCcCCHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 3578999999999999643322 22568999999999999999999999999998
No 95
>PHA00738 putative HTH transcription regulator
Probab=87.90 E-value=1.6 Score=31.89 Aligned_cols=47 Identities=23% Similarity=0.169 Sum_probs=37.8
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+.|...+.. +.+.-.-+|-..++|.++.|++.||.|+.-|||.+-+.
T Consensus 15 r~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~ 61 (108)
T PHA00738 15 RKILELIAE--NYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKE 61 (108)
T ss_pred HHHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEE
Confidence 455666644 23477789999999999999999999999999987653
No 96
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=87.81 E-value=3.5 Score=32.75 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=40.2
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
..|.+++.+-|. +-..||-..++....++.|=|+.||+.|+|+.+.
T Consensus 8 ~~Il~~L~~~~~--v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 8 AAILEYLQKQGK--TSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHcCC--EEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 367777777554 8999999999999999999999999999998864
No 97
>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=87.60 E-value=2.4 Score=24.60 Aligned_cols=41 Identities=12% Similarity=0.193 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
||+.|+.++.++. .|+-.++|-..+|++..++.+.++.+..
T Consensus 1 l~~~e~~i~~~~~----~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 1 LTPREREVLRLLA----EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5677777777763 6789999999999999999998887644
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.22 E-value=0.63 Score=34.30 Aligned_cols=61 Identities=23% Similarity=0.168 Sum_probs=43.9
Q ss_pred cccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee----ccccCCcccccC-ccc-cccchhhhhhhh
Q psy7778 46 GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV----KSVANIEYLTEG-TVN-AMVLPSRKKREE 106 (117)
Q Consensus 46 GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V----KsV~gg~wYtdg-~~D-~~fI~~l~~~~~ 106 (117)
-+--.||...+||+.+.|.|+|-.|...++++.. +.-.+|+||+-= .+| ..+++.++-|-.
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~ 81 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLD 81 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHH
Confidence 3667899999999999999999999997776543 444466566543 255 466676665543
No 99
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=87.21 E-value=1.2 Score=34.80 Aligned_cols=44 Identities=9% Similarity=0.218 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.|..++.. ..++-..+|-.+++||.+++.+.|++|+..|++..-
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 56666654 346788999999999999999999999999999764
No 100
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=87.04 E-value=1.3 Score=37.11 Aligned_cols=62 Identities=19% Similarity=0.197 Sum_probs=49.6
Q ss_pred CCCHHHHHHHHHHHHh-cCCcccHHHHHhh-cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 27 DSDNEEKVVYKIIEEA-GNKGIWMRDIRFK-SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~k-tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
++.+-|..||+++.++ +.+|+-.+||... .+++...+-.+|..|.+.++|+-++ ..++..|.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~ 69 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYK 69 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEE
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEE
Confidence 4556688999999999 8999999999999 7899999999999999999999999 55555654
No 101
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=86.72 E-value=1.2 Score=28.57 Aligned_cols=47 Identities=17% Similarity=0.289 Sum_probs=36.0
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
|.++|++. .-+-..+|-.+.++++..|.-.|..|+.+|.|..+..-.
T Consensus 5 i~~~l~~~--~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 5 IRDYLRER--GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHS---SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 44455543 347789999999999999999999999999999887654
No 102
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=86.66 E-value=3.9 Score=25.53 Aligned_cols=45 Identities=13% Similarity=0.306 Sum_probs=38.5
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
..|+++|.+. .-+-+.+|-..+|....++.+=|..|+..++|+.+
T Consensus 3 ~~Il~~l~~~--~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 3 QQILELLKEK--GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHc--CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3567777775 46788999999999999999999999999997654
No 103
>PRK11569 transcriptional repressor IclR; Provisional
Probab=86.36 E-value=1.5 Score=34.89 Aligned_cols=45 Identities=13% Similarity=0.332 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.|..++.+ .+.++-..+|-..+|||.+++.++|.+|+..|++...
T Consensus 32 ~IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~ 76 (274)
T PRK11569 32 KLLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV 76 (274)
T ss_pred HHHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 56666655 4677889999999999999999999999999999753
No 104
>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=86.26 E-value=4.4 Score=27.94 Aligned_cols=59 Identities=10% Similarity=0.160 Sum_probs=45.1
Q ss_pred CCHHHHHHHH-HHHH--hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCc
Q psy7778 28 SDNEEKVVYK-IIEE--AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIE 86 (117)
Q Consensus 28 L~~eE~lVY~-~Ie~--AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~ 86 (117)
||+-++.|+. +|+. ....=|=+++|-.+.+....+|...+..||.-|||.++.+-.+|-
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~Gr 63 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGR 63 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCC
Confidence 5664444433 3332 235668899999999999999999999999999999887766664
No 105
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=86.03 E-value=1.7 Score=34.35 Aligned_cols=46 Identities=13% Similarity=0.247 Sum_probs=38.6
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.|+.++.+. +.++-..+|-.++|+|.+++.|+|++|+..|++....
T Consensus 15 ~iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~ 60 (263)
T PRK09834 15 MVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA 60 (263)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 456666543 4468899999999999999999999999999998664
No 106
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=85.98 E-value=3.1 Score=31.24 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
++.|+++|. .|..|.-+++|-.+.++...++.+.+..|++.|++.+-
T Consensus 164 ~r~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 164 LNAVRKLFK-EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEE
Confidence 357888886 55668899999999999999999999999999998764
No 107
>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=85.98 E-value=2.8 Score=23.45 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=36.5
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
.+..|+++++.++..... .|.-.++|-..+|++..++.+.+....
T Consensus 7 ~~~~l~~~~~~~~~~~~~---~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 7 ALDKLPEREREVILLRFG---EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred HHHhCCHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 456789988887766653 677889999999999999999887653
No 108
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=85.71 E-value=3.7 Score=29.96 Aligned_cols=52 Identities=12% Similarity=0.224 Sum_probs=45.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.|++-++.|...+..-|. +-..+|-.+.|++.+++.+-++.|+..|.|+...
T Consensus 6 ~lD~~D~~Il~~Lq~d~R--~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~ 57 (153)
T PRK11179 6 QIDNLDRGILEALMENAR--TPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTR 57 (153)
T ss_pred ccCHHHHHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEE
Confidence 488888889888887755 5679999999999999999999999999998554
No 109
>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=85.49 E-value=1.7 Score=27.18 Aligned_cols=34 Identities=18% Similarity=0.274 Sum_probs=29.4
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
-.++|-.+.+.+.+++.++|+.|++.|+|....+
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 5688999999999999999999999999987654
No 110
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=85.36 E-value=3.5 Score=32.55 Aligned_cols=62 Identities=11% Similarity=0.153 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D 94 (117)
-|++|..++...|.+ +=-.+|.++.||..+.+||+|=.|...+.|..+. =+...||..-+-|
T Consensus 5 ~~~~i~~~l~~~~~~-~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~-~~pP~W~~~~~~~ 66 (183)
T PHA02701 5 CASLILTLLSSSGDK-LPAKRIAKELGISKHEANRCLYRLLESDAVSCED-GCPPLWSVECEPD 66 (183)
T ss_pred HHHHHHHHHHhcCCC-CcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCC-CCCCccccccCCC
Confidence 478999999998877 9999999999999999999999999999998774 3577899877766
No 111
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=84.96 E-value=1.6 Score=32.26 Aligned_cols=45 Identities=18% Similarity=0.313 Sum_probs=38.7
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
+==.+|++-..+++++++++|+.+.||..|+|.+..+ -|.|-++.
T Consensus 34 kLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg--~G~fV~~~ 78 (125)
T COG1725 34 KLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG--KGTFVTED 78 (125)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC--eeEEEcCC
Confidence 3345899999999999999999999999999998876 47777766
No 112
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=84.52 E-value=2.1 Score=29.37 Aligned_cols=49 Identities=20% Similarity=0.281 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
++...|..++-..| .+--.+|...+||+.+.+.++|-.|...+||+..+
T Consensus 13 ~~~~~Il~~L~~~~--~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 13 EEAVRILDALLRKG--ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp STTHHHHHHHHHH----B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred chHHHHHHHHHHcC--CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEE
Confidence 35567777776554 58889999999999999999999999999996664
No 113
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=84.18 E-value=2 Score=36.36 Aligned_cols=51 Identities=27% Similarity=0.362 Sum_probs=44.2
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
+.-|+ +....+.||..||-.-.|-.=+|+..++++-+|+.||.+|.||.=|
T Consensus 4 ~~rek-lir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rrk 54 (321)
T COG3888 4 SLREK-LIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRK 54 (321)
T ss_pred cHHHH-HHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeee
Confidence 33453 4467899999999999999999999999999999999999998643
No 114
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=84.00 E-value=6.2 Score=31.41 Aligned_cols=56 Identities=11% Similarity=0.192 Sum_probs=45.0
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
...|..++.+.| -+-..+|....++...++.|=|+.||++|+|+. ++||--+.+..
T Consensus 7 ~~~Il~~l~~~~--~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r---~~GGa~~~~~~ 62 (252)
T PRK10906 7 HDAIIELVKQQG--YVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR---HHGGAALPSSS 62 (252)
T ss_pred HHHHHHHHHHcC--CEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCCEEecCCC
Confidence 346777776644 489999999999999999999999999999865 67776555443
No 115
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=83.80 E-value=1.6 Score=31.51 Aligned_cols=34 Identities=26% Similarity=0.463 Sum_probs=28.7
Q ss_pred ccc-HHHHHhhcC-CChHHHHHHHHHHhhcCCeeee
Q psy7778 46 GIW-MRDIRFKSN-LMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 46 GIW-tkdIk~ktn-L~~~~l~K~LK~LE~k~LIK~V 79 (117)
|-+ -.+|++..+ +.+.+|++.||.||..|+|...
T Consensus 35 g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~ 70 (120)
T COG1733 35 GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERV 70 (120)
T ss_pred CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEee
Confidence 543 367888888 9999999999999999999754
No 116
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=83.57 E-value=2.5 Score=34.66 Aligned_cols=50 Identities=22% Similarity=0.334 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
-.-+|+.|.. |-|....+++...+++..+++=.|+.||+.++|++.+.-.
T Consensus 103 R~~Iy~~i~~--nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g 152 (240)
T COG3398 103 RDGIYNYIKP--NPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGG 152 (240)
T ss_pred HHHHHHHhcc--CCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCC
Confidence 3468999876 4588889999999999999999999999999999987554
No 117
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=83.54 E-value=2.2 Score=28.64 Aligned_cols=35 Identities=17% Similarity=0.330 Sum_probs=29.0
Q ss_pred ccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 47 IWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 47 IWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.=-.+|+.+. ++++.+|++.|+.||..|||.....
T Consensus 19 ~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~ 54 (90)
T PF01638_consen 19 MRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVY 54 (90)
T ss_dssp EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccc
Confidence 3447889998 9999999999999999999977643
No 118
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=82.61 E-value=4.5 Score=30.31 Aligned_cols=84 Identities=18% Similarity=0.197 Sum_probs=59.9
Q ss_pred CCCHHHH--HHHHHHHHhcCCc-ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhh
Q psy7778 27 DSDNEEK--VVYKIIEEAGNKG-IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKK 103 (117)
Q Consensus 27 ~L~~eE~--lVY~~Ie~AGn~G-IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~ 103 (117)
..|++|+ +...+||-+-..| +-++++...||++-+++.+.++.|+..|-|-. +=.-|.|=++. .++|-.++
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~--~G~~GvF~seq----A~~dw~~~ 77 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR--HGRSGVFPSEQ----ARKDWDKA 77 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe--CCCccccccHH----HHHHHHHh
Confidence 4566655 6667777666655 78899999999999999999999999876643 11115565553 56777788
Q ss_pred hhhhhhccccccc
Q psy7778 104 REERQDRGVLLKL 116 (117)
Q Consensus 104 ~~~~~~~~~~~~~ 116 (117)
|+..-|.+.+.+|
T Consensus 78 ~~~~~~~~~~~~~ 90 (127)
T PF06163_consen 78 RKKLVDPDLIWKL 90 (127)
T ss_pred HHhhccchhhhhC
Confidence 8877776655543
No 119
>PRK10736 hypothetical protein; Provisional
Probab=82.61 E-value=3.3 Score=35.55 Aligned_cols=51 Identities=12% Similarity=-0.012 Sum_probs=43.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.++.++..||+.+.. .++-..+|-.+++|+...+.-+|=.||-+|+|.+..
T Consensus 305 ~~~~~~~~v~~~l~~---~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~ 355 (374)
T PRK10736 305 EVALPFPELLANVGD---EVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVP 355 (374)
T ss_pred cccchHHHHHHhcCC---CCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcC
Confidence 466677888888853 466789999999999999999999999999999874
No 120
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=81.87 E-value=3.1 Score=31.61 Aligned_cols=50 Identities=10% Similarity=0.144 Sum_probs=42.3
Q ss_pred HHHHHHHHHhcCCcccH--------HHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 33 KVVYKIIEEAGNKGIWM--------RDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWt--------kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
..|++.|.+.=..|.|. ++|-.+.|....+|.++|..|+..|+|....+.
T Consensus 11 ~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~ 68 (238)
T TIGR02325 11 RQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGR 68 (238)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 35677777776667663 689999999999999999999999999998774
No 121
>PRK09483 response regulator; Provisional
Probab=81.32 E-value=4.7 Score=28.80 Aligned_cols=45 Identities=22% Similarity=0.277 Sum_probs=39.8
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+..||+-|+.|+.++. +|.-.++|-.+.++..++|...++.+-.|
T Consensus 146 ~~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 146 FASLSERELQIMLMIT----KGQKVNEISEQLNLSPKTVNSYRYRMFSK 190 (217)
T ss_pred ccccCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5679999999998883 88999999999999999999999888765
No 122
>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=81.22 E-value=7.7 Score=27.42 Aligned_cols=53 Identities=17% Similarity=0.117 Sum_probs=42.3
Q ss_pred ccCCCHHHHHHHHHHHHh------cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 25 LKDSDNEEKVVYKIIEEA------GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~A------Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
..+|+.-|..||-.|--- ..+-|-.-.+-..|+++.+.++++++.|+..++|.
T Consensus 27 ~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 27 RADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred hccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 368888777666555332 34567788899999999999999999999999993
No 123
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=81.18 E-value=1.3 Score=25.61 Aligned_cols=42 Identities=7% Similarity=0.218 Sum_probs=30.1
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
++.++...+|++..+|. ..+.+|+|.+.+...+.-+|+..++
T Consensus 2 ~~~e~a~~~gv~~~tlr----~~~~~g~l~~~~~~~~~~~y~~~~v 43 (49)
T cd04761 2 TIGELAKLTGVSPSTLR----YYERIGLLSPARTEGGYRLYSDADL 43 (49)
T ss_pred cHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCEEeCHHHH
Confidence 46677888899887654 6688999997666666666665443
No 124
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=80.78 E-value=6.9 Score=31.01 Aligned_cols=49 Identities=10% Similarity=0.202 Sum_probs=40.6
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCc
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIE 86 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~ 86 (117)
..|..++.+ +.-+-.++|-..+|....++.|=|+.||+.|+|.. ++||-
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r---~~gga 56 (251)
T PRK13509 8 QILLELLAQ--LGFVTVEKVIERLGISPATARRDINKLDESGKLKK---VRNGA 56 (251)
T ss_pred HHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCCc
Confidence 367777775 44578899999999999999999999999999976 45554
No 125
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=80.46 E-value=7.3 Score=24.59 Aligned_cols=44 Identities=9% Similarity=0.039 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.+..++.++ -+-..+|..+.++..+++.+.++.|+..|+.-...
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~ 47 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV 47 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 344454433 24589999999999999999999999999955444
No 126
>PHA02943 hypothetical protein; Provisional
Probab=80.39 E-value=4.2 Score=31.71 Aligned_cols=71 Identities=11% Similarity=0.045 Sum_probs=49.8
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhhhhhh
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREER 107 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~~~~~ 107 (117)
.|+.+| .+-+--+.+|-..+|+...++.-+|+.||..|.|++|+==...-|+-+-+==+..|..++..-.|
T Consensus 15 eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~day~~~v~~~~Relwr 85 (165)
T PHA02943 15 KTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDEDAYTNLVFEIKRELWR 85 (165)
T ss_pred HHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChHHHHHHHHHHHHHHHH
Confidence 566777 22235688999999999999999999999999999987444556765553112225555544443
No 127
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=80.31 E-value=8.4 Score=29.74 Aligned_cols=58 Identities=17% Similarity=0.264 Sum_probs=45.6
Q ss_pred HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.||+.|.+.=..|-| -++|..+.|..-.+|.++|..|+..|+|..+.+. |.|-....+
T Consensus 9 qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~--GtfV~~~~~ 74 (240)
T PRK09764 9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGS--GTYVKEERV 74 (240)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc--eeEEccccc
Confidence 566667666555554 3899999999999999999999999999998875 566555443
No 128
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.24 E-value=6.6 Score=30.16 Aligned_cols=50 Identities=20% Similarity=0.250 Sum_probs=40.8
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
++....|..++-..|. +-..+|...+||+.+.+.|+|-.|+..|||...+
T Consensus 21 ~~~~~~Vl~~L~~~g~--~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 21 DEEGFEVLKALIKKGE--VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred CccHhHHHHHHHHcCC--cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence 3345567776666663 7889999999999999999999999999999543
No 129
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=79.92 E-value=5.5 Score=32.38 Aligned_cols=59 Identities=19% Similarity=0.209 Sum_probs=47.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcC---CcccHHHHHhh-------cCCCh---HHHHHHHHHHhhcCCeeeecc
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGN---KGIWMRDIRFK-------SNLMP---TQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn---~GIWtkdIk~k-------tnL~~---~~l~K~LK~LE~k~LIK~VKs 81 (117)
..+.+||..|++++..|-..+. ..+-+.++-.+ .|+.+ +.+...+..|+..|||....+
T Consensus 289 ~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~~~ 360 (394)
T PRK00411 289 EVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYS 360 (394)
T ss_pred HHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence 4588999999988888876653 56888888754 67754 899999999999999998764
No 130
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=79.91 E-value=5.3 Score=28.38 Aligned_cols=56 Identities=13% Similarity=0.175 Sum_probs=44.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcC-----CChHHHHHHHHHHhhc---CCeeeeccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN-----LMPTQLNKILKQLETK---KIIKAVKSV 82 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn-----L~~~~l~K~LK~LE~k---~LIK~VKsV 82 (117)
.||+-|..|..++-...+++.-.++|..+.. ...+++...+..|.+| .+|+.|.++
T Consensus 149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~~~i~t~~g~ 212 (219)
T PRK10336 149 TLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGSDFIRTVHGI 212 (219)
T ss_pred ecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCCCcEEEecCc
Confidence 5999999999999999999999999999975 7777777777666554 456655554
No 131
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=79.85 E-value=5.2 Score=30.55 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=38.9
Q ss_pred HHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 35 VYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 35 VY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
|++.|.+.=..|-| -++|-.+.|..-.+|.++|..|+..|+|..+.+.
T Consensus 5 i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~ 60 (233)
T TIGR02404 5 IYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQGK 60 (233)
T ss_pred HHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCc
Confidence 45555555555555 4789999999999999999999999999998875
No 132
>PRK14999 histidine utilization repressor; Provisional
Probab=79.82 E-value=8.7 Score=29.60 Aligned_cols=59 Identities=15% Similarity=0.259 Sum_probs=46.6
Q ss_pred HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778 34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D 94 (117)
.|++.|.+.=..|.| -++|-.+.|....+|.++|..|+..|+|....+. |+|-......
T Consensus 16 qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~Gk--GTfV~~~~~~ 82 (241)
T PRK14999 16 TVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGV--GTFVAEPKGQ 82 (241)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc--EEEECCCCcc
Confidence 566667666555555 5889999999999999999999999999988874 6666555543
No 133
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=79.78 E-value=13 Score=24.29 Aligned_cols=55 Identities=22% Similarity=0.266 Sum_probs=43.5
Q ss_pred CHHHHHHHHHHHHhcC-CcccHHHHHhh----c--CCCh----HHHHHHHHHHhhcCCeeeecccc
Q psy7778 29 DNEEKVVYKIIEEAGN-KGIWMRDIRFK----S--NLMP----TQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn-~GIWtkdIk~k----t--nL~~----~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
|+-..||...|.+.+. .|.....|++- . +++. +.|.++||.+..+|.+..++..-
T Consensus 3 P~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G 68 (77)
T PF00538_consen 3 PPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKG 68 (77)
T ss_dssp SCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCST
T ss_pred CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccC
Confidence 4567799999998777 89988887653 3 3554 67999999999999999999543
No 134
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=79.68 E-value=5.6 Score=29.33 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=39.3
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+-|+.|..++. +|.-+++|-.+.++...++...++.+-.|
T Consensus 149 ~~Lt~rE~evl~~~~----~G~s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 149 KRLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 469999999999996 89999999999999999998888887654
No 135
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=79.39 E-value=4.5 Score=31.58 Aligned_cols=49 Identities=14% Similarity=0.130 Sum_probs=44.3
Q ss_pred HHHHHHHHhcCCcccH--------HHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGIWM--------RDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWt--------kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.|++.|++.=..|.|. ++|-.+.|..-.+|.|+|..|++.|+|....+.
T Consensus 11 qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~ 67 (236)
T COG2188 11 QIAEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK 67 (236)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC
Confidence 6888889888999996 579999999999999999999999999988764
No 136
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=78.60 E-value=1.8 Score=37.01 Aligned_cols=64 Identities=16% Similarity=0.274 Sum_probs=47.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
.+|..+..|..+..+ +.++-..+|...|||+...+.++|+.|...+++...++-++.++-.+..
T Consensus 517 ~~s~~q~~iLl~Fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~ 580 (588)
T PF00888_consen 517 TVSTLQAAILLLFND--NDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDE 580 (588)
T ss_dssp EEEHHHHHHHHGGGS--SSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-E
T ss_pred EeeHHHHHHHHHHcc--CCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCE
Confidence 466778888776655 7789999999999999999999999999999998886555555554444
No 137
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=78.31 E-value=11 Score=29.83 Aligned_cols=55 Identities=9% Similarity=0.119 Sum_probs=45.2
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
+..|++++.+ +..+-..+|-...++...++.|-|+.|+..++|+. ++||--|.++
T Consensus 6 ~~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r---~~Gga~~~~~ 60 (240)
T PRK10411 6 QQAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR---NHGRAKYIHR 60 (240)
T ss_pred HHHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCeEEEecC
Confidence 4568888885 45799999999999999999999999999998876 5666655443
No 138
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=77.95 E-value=7.8 Score=29.09 Aligned_cols=48 Identities=15% Similarity=0.120 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
+...|...+-..| .+-..+|...+||+.+.|+|+|..|...|||.-.+
T Consensus 15 ~~v~Vl~aL~~~~--~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 15 EVGLVLFSLGIKG--EFTDEEISLELGIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred hHHHHHHHHhccC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeee
Confidence 4455666555444 47889999999999999999999999999996444
No 139
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=77.67 E-value=7.1 Score=31.62 Aligned_cols=48 Identities=13% Similarity=0.071 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCC-eeeecc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKI-IKAVKS 81 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L-IK~VKs 81 (117)
++.|..++.+ +..+-..+|..+.+++.+.+.++|+.|+..|+ |.+..+
T Consensus 6 ~~~il~~L~~--~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~ 54 (319)
T PRK11886 6 MLQLLSLLAD--GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKG 54 (319)
T ss_pred HHHHHHHHHc--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecC
Confidence 3455566653 46777789999999999999999999999999 877643
No 140
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=77.58 E-value=1.9 Score=29.82 Aligned_cols=44 Identities=9% Similarity=0.177 Sum_probs=34.9
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D 94 (117)
+.+.++-..+|++.++| +..|..|||.+..+-+|--+|++..++
T Consensus 2 ~~i~eva~~~gvs~~tl----R~ye~~Gll~~~r~~~g~R~Y~~~~l~ 45 (102)
T cd04789 2 YTISELAEKAGISRSTL----LYYEKLGLITGTRNANGYRLYPDSDLQ 45 (102)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCeeCCHHHHH
Confidence 35778889999998765 488999999997777777888877643
No 141
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=77.57 E-value=5.3 Score=35.46 Aligned_cols=51 Identities=14% Similarity=0.244 Sum_probs=47.3
Q ss_pred hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 42 AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 42 AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
+.|.=+-.+.|+..+++....++|.|..|..+++++.+=+.+.|.||-.++
T Consensus 412 ~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~~~ 462 (467)
T COG2865 412 KENGKVTARELREILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVKGE 462 (467)
T ss_pred hhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEecCC
Confidence 345679999999999999999999999999999999999999999998876
No 142
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=77.33 E-value=6.1 Score=30.39 Aligned_cols=56 Identities=9% Similarity=0.195 Sum_probs=46.4
Q ss_pred HHHHHHHHhcCCcccH--------HHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 34 VVYKIIEEAGNKGIWM--------RDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWt--------kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
.|++.|.+.=..|.|. ++|-.+.|..-.+|.++|..|+..|||....+ -|+|-...
T Consensus 13 qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G--~GTfV~~~ 76 (241)
T PRK11402 13 TVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQG--KGTFVQSQ 76 (241)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC--ceeEECCC
Confidence 5778888888888885 68999999999999999999999999998866 34554433
No 143
>PRK10651 transcriptional regulator NarL; Provisional
Probab=77.17 E-value=8.2 Score=27.09 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=38.7
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
...||+.|+.|..++. +|.-.++|..+.+++..+|...++.|-.|
T Consensus 153 ~~~Lt~rE~~vl~~l~----~g~~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 153 VNQLTPRERDILKLIA----QGLPNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred cccCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3469999999998875 67789999999999999999999988665
No 144
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=77.06 E-value=5.8 Score=27.16 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhcCCcccHHHH-Hhh----cCCChHHHHHHHHHHhhcCCeeee
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDI-RFK----SNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdI-k~k----tnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
+.+|..++.....-|-+.... ... ..+.+.+|..+|+.||.+|+|.+.
T Consensus 6 ~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 6 DLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEE
Confidence 556777776655566665443 222 368899999999999999999984
No 145
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=75.89 E-value=9.8 Score=28.66 Aligned_cols=52 Identities=13% Similarity=0.211 Sum_probs=41.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCc--------ccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKG--------IWMRDIRFKSNLMPTQLNKILKQLETKKII 76 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~G--------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LI 76 (117)
+...+.++++.+-+.+.+-..| +-.++|-.-.|++..+++|+|+.|+.+|++
T Consensus 144 ~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~ 203 (236)
T PRK09392 144 QKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVH 203 (236)
T ss_pred hhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeE
Confidence 3456778888887777665444 224789999999999999999999999963
No 146
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=75.81 E-value=7.5 Score=32.23 Aligned_cols=50 Identities=12% Similarity=0.182 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 32 EKVVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
...||+.|...=-.|.| .+.|..+.|+..+++.+++..|+..|+|.+...
T Consensus 7 ~~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~ 64 (431)
T PRK15481 7 ANEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGR 64 (431)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45678888887777766 689999999999999999999999999987543
No 147
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=75.49 E-value=6.9 Score=26.63 Aligned_cols=44 Identities=14% Similarity=0.059 Sum_probs=36.8
Q ss_pred HhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 41 EAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 41 ~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
-|++ .+-..+|-.+||++.+.+...|..|..+|+|..=-..-+|
T Consensus 14 ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~~~g 57 (72)
T PF05584_consen 14 LSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRKFGG 57 (72)
T ss_pred HHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEEecC
Confidence 4555 9999999999999999999999999999999865443333
No 148
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=75.46 E-value=5 Score=23.57 Aligned_cols=30 Identities=13% Similarity=0.285 Sum_probs=19.7
Q ss_pred cccHHHHHhhcCCChHHHHHHHHHHhhcCC
Q psy7778 46 GIWMRDIRFKSNLMPTQLNKILKQLETKKI 75 (117)
Q Consensus 46 GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L 75 (117)
|.-.++|-..+|++.+++.+.++..+..|+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 999999999999999999999999877663
No 149
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=75.27 E-value=7.6 Score=30.07 Aligned_cols=45 Identities=16% Similarity=0.050 Sum_probs=39.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+..||+-|+.|..++.. |...++|-.+.+++..+++..+..+-.|
T Consensus 153 ~~~Lt~rE~~Vl~l~~~----G~s~~eIA~~L~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 153 SALLTHREKEILNKLRI----GASNNEIARSLFISENTVKTHLYNLFKK 197 (216)
T ss_pred cCCCCHHHHHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45699999999999976 8899999999999999988888877554
No 150
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=74.97 E-value=4.9 Score=25.75 Aligned_cols=44 Identities=23% Similarity=0.366 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.|+..+-..|. .-.++|-..|+|+.+++.++|-.|.+.+++.-.
T Consensus 17 ~V~~~Ll~~G~--ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 17 KVGEVLLSRGR--LTLREIVRRTGLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHHC-S--EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHcCC--cCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeee
Confidence 45555555553 457999999999999999999999999998643
No 151
>PF14502 HTH_41: Helix-turn-helix domain
Probab=74.97 E-value=7.3 Score=24.65 Aligned_cols=39 Identities=18% Similarity=0.099 Sum_probs=32.5
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEY 87 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~w 87 (117)
..++..+.++..-+|.++||.||..+-|+-.+-=+.|+|
T Consensus 9 I~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh~GTf 47 (48)
T PF14502_consen 9 ISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGHLGTF 47 (48)
T ss_pred HHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCcCccc
Confidence 457788999999999999999999999987766555554
No 152
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=74.70 E-value=2 Score=31.09 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
-.|...+-+-+.-||- .|...||||.+.+.=.|+.||+.++|++=
T Consensus 17 l~Vl~~v~eeqPiGI~--klS~~TGmp~HKVRYSLRVLEq~~iI~PS 61 (101)
T COG3388 17 LSVLKVVLEEQPIGII--KLSDETGMPEHKVRYSLRVLEQENIISPS 61 (101)
T ss_pred HHHHHHHHHhCCceeE--eechhcCCchhhhhhhhhhhhhcCccCcc
Confidence 3677777788888885 46889999999999999999999999863
No 153
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=74.50 E-value=13 Score=26.42 Aligned_cols=58 Identities=9% Similarity=-0.035 Sum_probs=42.6
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCC-----h----HHHHHHHHHHhhc----CCeeeeccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLM-----P----TQLNKILKQLETK----KIIKAVKSV 82 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~-----~----~~l~K~LK~LE~k----~LIK~VKsV 82 (117)
...||+-|+.|..++-...++|.-.++|-...... . +.+.++.+.|... .+|+.|.++
T Consensus 152 ~~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~~~~~~~~i~t~~g~ 222 (228)
T PRK11083 152 PLTLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAINPDLSPINTHRGM 222 (228)
T ss_pred EeecCHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCCCeEEEeCce
Confidence 44699999999999999999999999999988874 3 3356666666432 345555443
No 154
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=73.97 E-value=7.9 Score=28.91 Aligned_cols=48 Identities=21% Similarity=0.237 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCccc-------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 34 VVYKIIEEAGNKGIW-------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW-------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.||+.|++.=-.|-| ..+|-.+.|+..+.|..+|+.|+..|||...++
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 15 LVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred HHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 588888887555544 478999999999999999999999999987664
No 155
>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=73.92 E-value=9.5 Score=22.68 Aligned_cols=43 Identities=9% Similarity=0.185 Sum_probs=31.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
+.+..||++++.|+.+..- .|.-.++|-..+|++.+.+.+.+.
T Consensus 6 ~~l~~L~~~~r~i~~l~~~---~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 6 QALAQLPERQREIFLLRYF---QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHCS-HHHHHHHHHHHT---S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHHH---HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3567899999998887765 678899999999999999877664
No 156
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=73.31 E-value=14 Score=25.22 Aligned_cols=50 Identities=12% Similarity=0.117 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
...++.+.-.+++.=+.=.+|..+.|+.-+.|.|++++|+..|+ .|.+|.
T Consensus 5 ~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~--~I~s~~ 54 (79)
T COG1654 5 SQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGV--DIESVR 54 (79)
T ss_pred HHHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCC--ceEecC
Confidence 34677777788888888999999999999999999999999887 344443
No 157
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=72.56 E-value=15 Score=28.87 Aligned_cols=61 Identities=21% Similarity=0.290 Sum_probs=50.0
Q ss_pred HHHHHHHHhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcccc
Q psy7778 34 VVYKIIEEAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNA 95 (117)
Q Consensus 34 lVY~~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~ 95 (117)
+|-.+|+.-|. +++--.+|.++.||+-+.+||+|=.|...+.+..+.+ +...||.+-+=|+
T Consensus 14 lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~-~pp~w~~~~~~~~ 75 (183)
T PHA03103 14 LVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDS-NPPKWFKTTEADN 75 (183)
T ss_pred HHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCC-CCCCcccccCCCC
Confidence 55566666675 8999999999999999999999999999999987744 4677887766544
No 158
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=71.15 E-value=3.3 Score=29.25 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=37.2
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc-cccchhh
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN-AMVLPSR 101 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D-~~fI~~l 101 (117)
.+.++-..+|++.. .|+..|+.||+.++..-+|--.|++..++ ..+|..+
T Consensus 2 ~IgevA~~~gvs~~----tlRyYe~~GLl~p~~~~~gyR~Y~~~~l~~l~~I~~l 52 (120)
T cd04781 2 DIAEVARQSGLPAS----TLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALG 52 (120)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCceecCHHHHHHHHHHHHH
Confidence 56788899999984 56889999999998876666888887633 2344333
No 159
>PRK03837 transcriptional regulator NanR; Provisional
Probab=71.06 E-value=12 Score=28.48 Aligned_cols=49 Identities=14% Similarity=0.117 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.||+.|.+.=-.|- --++|..+.|...+.|..+|+.|+..|||....+.
T Consensus 17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~ 73 (241)
T PRK03837 17 EVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGE 73 (241)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 57777777655544 46899999999999999999999999999987653
No 160
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=70.92 E-value=3.6 Score=27.59 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=31.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.++++...+|++.++|. ..++.|+|.+.++-.|.-.|++.++
T Consensus 2 ~~~eva~~~gi~~~tlr----~~~~~Gll~~~~~~~g~r~y~~~dv 43 (100)
T cd00592 2 TIGEVAKLLGVSVRTLR----YYEEKGLLPPERSENGYRLYSEEDL 43 (100)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCcCCCcCCCCCcccCHHHH
Confidence 57788899999997765 4577899997776666666776553
No 161
>PF14163 SieB: Superinfection exclusion protein B
Probab=70.54 E-value=6.8 Score=28.63 Aligned_cols=49 Identities=29% Similarity=0.327 Sum_probs=38.0
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
+.+.+||++|+.|..-.-.+|+.=++. ..+ +-+.++|+++|+|-...|+
T Consensus 74 ~~l~~Lt~~EkavL~~~~~~~~~~~~l-------p~~----~~~v~~L~~~gIl~~~~~~ 122 (151)
T PF14163_consen 74 KKLNSLTPEEKAVLREFYIQGNNTLTL-------PYN----NPAVKSLLQKGILERASNV 122 (151)
T ss_pred HHHHhCCHHHHHHHHHHHHCCCCeEEe-------cCC----CHHHHHHHHCCCeEecCcc
Confidence 568999999998887777777655532 223 4567899999999999998
No 162
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=70.36 E-value=11 Score=30.33 Aligned_cols=46 Identities=9% Similarity=-0.000 Sum_probs=39.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
-...||+-|+.|..+|.+ |..+++|..+.++...++.+.++.+-.|
T Consensus 140 ~~~~LS~RE~eVL~Lia~----G~SnkEIA~~L~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 140 AKNKVTKYQNDVFILYSF----GFSHEYIAQLLNITVGSSKNKISEILKF 185 (217)
T ss_pred ccCCCCHHHHHHHHHHHC----CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 356799999999999974 9999999999999999988888777554
No 163
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=70.31 E-value=14 Score=29.61 Aligned_cols=54 Identities=11% Similarity=0.168 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE 90 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd 90 (117)
...|.+++.+.|. +-..+|-..++....++.|=|..||+.|+++. ++||-+..+
T Consensus 19 ~~~Il~~L~~~~~--vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r---~~GGa~~~~ 72 (269)
T PRK09802 19 REQIIQRLRQQGS--VQVNDLSALYGVSTVTIRNDLAFLEKQGIAVR---AYGGALICD 72 (269)
T ss_pred HHHHHHHHHHcCC--EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEE---EeCCEEecC
Confidence 3377888888766 99999999999999999999999999999984 458876653
No 164
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=70.23 E-value=12 Score=31.74 Aligned_cols=44 Identities=14% Similarity=0.216 Sum_probs=36.9
Q ss_pred HHHHHH--HhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 35 VYKIIE--EAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 35 VY~~Ie--~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
|..++. ..+.++.-..+|..++++|...++++|..|++.|+|..
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~ 342 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRR 342 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEe
Confidence 444453 34557999999999999999999999999999999974
No 165
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=70.03 E-value=10 Score=29.36 Aligned_cols=49 Identities=18% Similarity=0.210 Sum_probs=41.2
Q ss_pred HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.||+.|.+.=-.|-| -++|..+.|+..+.|.-+|+.|+..|||....+.
T Consensus 12 ~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~ 68 (253)
T PRK11523 12 QLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGS 68 (253)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 577777776555544 3789999999999999999999999999988764
No 166
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.82 E-value=4 Score=28.14 Aligned_cols=40 Identities=8% Similarity=0.069 Sum_probs=30.2
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
.+.++...+|++.. .|+-.|+.|||.+. ..+|+-.|++..
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYe~~GLl~p~-~~~g~r~Y~~~~ 41 (107)
T cd04777 2 KIGKFAKKNNITID----TVRHYIDLGLLIPE-KKGGQYFFDEKC 41 (107)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCcCCc-cCCCccccCHHH
Confidence 46778888999874 67899999999984 445666676654
No 167
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=69.50 E-value=7.8 Score=29.61 Aligned_cols=56 Identities=16% Similarity=0.258 Sum_probs=42.3
Q ss_pred HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
.|++.|.+.=..|-| -++|-.+.|....+|.++|..|+..|+|..+.+. |+|-...
T Consensus 5 qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~--GtfV~~~ 68 (230)
T TIGR02018 5 RIKQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQGV--GTFVAEP 68 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC--EEEEccC
Confidence 355555555444544 4689999999999999999999999999998874 5554433
No 168
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=69.41 E-value=9.7 Score=24.89 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=37.4
Q ss_pred cccCCCHHHHHHHHHHHHhcC--CcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGN--KGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..||+-|+.|.+.|-+.-. .-+-+.+|-..++..+++|.|..|.|-=.
T Consensus 10 ~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 10 QYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 467899989988888876544 46788999999999999999999988433
No 169
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=69.36 E-value=7.3 Score=25.88 Aligned_cols=51 Identities=18% Similarity=0.253 Sum_probs=32.1
Q ss_pred HHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhh
Q psy7778 51 DIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKK 103 (117)
Q Consensus 51 dIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~ 103 (117)
.|-.+.|+..+++-.+|+.||+-|+|-+=..=--|.+-. -+|..|.++|++
T Consensus 9 ~iAd~~GiTRSvIVNALRKleSaGvIesrSlGmKGT~ik--vlN~~~~~el~k 59 (61)
T PF08222_consen 9 KIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIK--VLNDYFLDELEK 59 (61)
T ss_dssp HHHHHHT--HHHHHHHHHHHHHTTSEEEEETTSS-EEEE--E--THHHHHHCC
T ss_pred HHHHHhCccHHHHHHHHHHHHhcCceeecccCCCceeee--eecHHHHHHHHh
Confidence 577889999999999999999999998644322333321 245555555543
No 170
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=69.08 E-value=14 Score=33.02 Aligned_cols=53 Identities=17% Similarity=0.145 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
..|..|+..+++. +..+-+.+|-.++|+....|..++++|+++++|+.-..+.
T Consensus 6 ~~e~~iL~~l~~~-~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~ 58 (494)
T PTZ00326 6 LEENTILSKLESE-NEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKS 58 (494)
T ss_pred HHHHHHHHHHHhc-CCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEE
Confidence 4577777777764 3447788999999999999999999999999998766554
No 171
>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=67.98 E-value=27 Score=22.11 Aligned_cols=46 Identities=15% Similarity=0.267 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHHhc----CCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAG----NKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AG----n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
||+.|+.+...--+.| ..++-..+|-...|+..++++..|+.-|+|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5777777666666666 678999999999999999999999887754
No 172
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=67.32 E-value=14 Score=27.91 Aligned_cols=49 Identities=18% Similarity=0.202 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCCcc-------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGI-------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GI-------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.||+.|.+.=-.|- =..+|-.+.|+..+.|.-+|+.|++.|||..+.+.
T Consensus 11 ~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~ 66 (224)
T PRK11534 11 DGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK 66 (224)
T ss_pred HHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence 47777777644443 36789999999999999999999999999987654
No 173
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=67.31 E-value=6.3 Score=24.40 Aligned_cols=36 Identities=17% Similarity=0.312 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.++..|.+.|+ ...--...|+.++.|++.|+.||..
T Consensus 5 ~~f~~v~~~gs----~~~AA~~l~is~~~vs~~i~~LE~~ 40 (60)
T PF00126_consen 5 RYFLAVAETGS----ISAAAEELGISQSAVSRQIKQLEEE 40 (60)
T ss_dssp HHHHHHHHHSS----HHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCC----HHHHHHHhhccchHHHHHHHHHHHH
Confidence 44555555553 2334678999999999999999973
No 174
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=67.29 E-value=5.3 Score=24.69 Aligned_cols=42 Identities=5% Similarity=0.095 Sum_probs=30.3
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~ 93 (117)
.++++...+|++..+|.+ .+..|+|.+. ++-.|.-+|++.++
T Consensus 2 s~~eva~~~gvs~~tlr~----~~~~gli~~~~~~~~g~r~y~~~dl 44 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRY----YERIGLLPPPIRTEGGYRLYSDEDL 44 (70)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCCEecCHHHH
Confidence 356788899999877664 4679999987 56555556666553
No 175
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=67.07 E-value=4.5 Score=28.71 Aligned_cols=43 Identities=7% Similarity=0.142 Sum_probs=33.2
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCee-eeccccCCcccccCccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIK-AVKSVANIEYLTEGTVN 94 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK-~VKsV~gg~wYtdg~~D 94 (117)
.+.++-..+|++.++| +..|..|||. +.++-+|--+|++..+.
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~~~~l~ 45 (126)
T cd04783 2 TIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYPEETVT 45 (126)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecCHHHHH
Confidence 4678888999998766 8899999999 56666666677776544
No 176
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=67.03 E-value=17 Score=27.43 Aligned_cols=41 Identities=20% Similarity=0.199 Sum_probs=35.0
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG 91 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg 91 (117)
-++|..+.|++..++.++|..|+..|+|...... |.|-...
T Consensus 28 E~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g~--Gt~V~~~ 68 (231)
T TIGR03337 28 ERDLGERFNTTRVTIREALQQLEAEGLIYREDRR--GWFVSPP 68 (231)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCCC--EEEECCc
Confidence 6889999999999999999999999999998875 5554433
No 177
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=67.03 E-value=16 Score=27.84 Aligned_cols=49 Identities=14% Similarity=0.080 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.||+.|.+.=-.|- --++|-.+.|+..+.|..+|+.|+..|||....+.
T Consensus 11 ~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~ 67 (239)
T PRK04984 11 FAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK 67 (239)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 47777776655553 46799999999999999999999999999987663
No 178
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=66.89 E-value=17 Score=27.61 Aligned_cols=57 Identities=18% Similarity=0.111 Sum_probs=42.2
Q ss_pred cccCCCHHHHHHH---------HHHHHhcCCcccHHHHHhhc--CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 24 KLKDSDNEEKVVY---------KIIEEAGNKGIWMRDIRFKS--NLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 24 k~~~L~~eE~lVY---------~~Ie~AGn~GIWtkdIk~kt--nL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+.+.|+.++...| .++.-.+..+ =...|-+++ +++...+.++|..|+.-|||+.-.+
T Consensus 9 ~~~~l~~~~~~~~~~W~~~~ir~l~~l~~~~~-d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 9 KVRVLDEDEFEYYSSWYHPAIRELLPLMPFAP-DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred ceeeccHHHHHHHhhhHHHHHHHHhhcCCCCC-CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 4556666665543 3444444433 456788899 9999999999999999999998877
No 179
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=66.86 E-value=4.8 Score=28.17 Aligned_cols=41 Identities=10% Similarity=0.178 Sum_probs=32.9
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
.+.++-..+|++.. .|+..|..|||.+..+-+|--+|++..
T Consensus 2 ~i~eva~~~gvs~~----tlR~Ye~~GLl~p~r~~~g~R~Y~~~~ 42 (112)
T cd01282 2 RIGELAARTGVSVR----SLRYYEEQGLLVPERSANGYRDYDEAA 42 (112)
T ss_pred CHHHHHHHHCCCHH----HHHHHHHCCCCCCCcCCCCCeecCHHH
Confidence 46778888999985 467889999999988766778888765
No 180
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=66.79 E-value=11 Score=31.58 Aligned_cols=56 Identities=16% Similarity=0.286 Sum_probs=42.4
Q ss_pred ccccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 21 TNEKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 21 ~a~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
+..-++.|-..-| .|.++...+|..- ...|....+|||++++--+|.||.-|||..
T Consensus 13 ~~dv~kalaS~vRv~Il~lL~~k~plN--vneiAe~lgLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 13 SLDVLKALASKVRVAILQLLHRKGPLN--VNEIAEALGLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhCCCC--HHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence 3334444544333 6777887777544 589999999999999999999999999953
No 181
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=65.96 E-value=18 Score=27.83 Aligned_cols=45 Identities=11% Similarity=0.089 Sum_probs=40.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
...||+-|+.|..+|- +|--.++|-.+.++...++...+.++-.|
T Consensus 132 ~~~LT~RE~eVL~ll~----~G~snkeIA~~L~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 132 SRMLSPTEREILRFMS----RGYSMPQIAEQLERNIKTIRAHKFNVMSK 176 (207)
T ss_pred cCCCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4569999999999997 58999999999999999999998888665
No 182
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=65.44 E-value=5 Score=27.64 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=32.6
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D 94 (117)
.++.++...+|++.++| +..|..|||.+..+-+|--.|++..++
T Consensus 2 ~~i~eva~~~gvs~~tL----R~ye~~Gll~~~r~~~g~R~Y~~~dl~ 45 (102)
T cd04775 2 YTIGQMSRKFGVSRSTL----LYYESIGLIPSARSEANYRLYSEADLS 45 (102)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCeeeCHHHHH
Confidence 46788999999999766 889999999665554444567766543
No 183
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=65.12 E-value=14 Score=28.95 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=36.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+.+++-.+..++..|-+.|+= ..=-.+.|+.|+.|++.|+.||+.
T Consensus 4 ~~~~~~l~~L~~F~~va~~gs~----s~AA~~L~isQpavS~~I~~LE~~ 49 (302)
T TIGR02036 4 RLNSFQLSKMHTFEVAARHQSF----SLAAEELSLTPSAISHRINQLEEE 49 (302)
T ss_pred cccCcCHHHHHHHHHHHHhCCH----HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4677888888888888888762 222678999999999999999984
No 184
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=65.12 E-value=9.2 Score=23.70 Aligned_cols=43 Identities=33% Similarity=0.364 Sum_probs=27.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+-+.||-+|++ ++|+.. ..|--.++|-.+.|++.++|..++|.
T Consensus 3 kR~~LTl~eK~--~iI~~~-e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 3 KRKSLTLEEKL--EIIKRL-EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSS--HHHHH--HHHHHH-HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCccCCHHHHH--HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 34568887762 344443 23448999999999999999999986
No 185
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=64.79 E-value=22 Score=24.84 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=37.8
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+.|+.|..++.+ |.-.++|..+.++..+++...++.|..|
T Consensus 136 ~~Lt~~E~~il~~l~~----g~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ----GMAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC----CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4699999999988774 6889999999999999999888888665
No 186
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=64.32 E-value=11 Score=29.14 Aligned_cols=49 Identities=20% Similarity=0.190 Sum_probs=40.2
Q ss_pred HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.||..|.+.=-.|-| -++|-.+.|+..+.|.-+|+.|++.|||....+.
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 69 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGA 69 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 577777766444433 5689999999999999999999999999988763
No 187
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=64.15 E-value=21 Score=28.02 Aligned_cols=45 Identities=11% Similarity=0.148 Sum_probs=36.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
++.|+-.+..++..|.+.|+- ..--.+.|+.|+.|++.|+.||..
T Consensus 19 ~~~~~l~~L~~f~avae~gs~----s~AA~~L~isQpavS~~I~~LE~~ 63 (314)
T PRK09508 19 LRMVDLNLLTVFDAVMQEQNI----TRAAHNLGMSQPAVSNAVARLKVM 63 (314)
T ss_pred ccccChHHHHHHHHHHhcCCH----HHHHHHhCCCHHHHHHHHHHHHHh
Confidence 566777788888888888872 333678999999999999999984
No 188
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=63.80 E-value=17 Score=22.72 Aligned_cols=39 Identities=26% Similarity=0.373 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcC-CCh---HHHHHHHHHH
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSN-LMP---TQLNKILKQL 70 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktn-L~~---~~l~K~LK~L 70 (117)
|--|.++|..+|+..++-.+|-.++. .|+ ..|.|+++.|
T Consensus 8 eLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 8 ELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred HcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 44588999999999999999999887 443 3578888876
No 189
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=63.60 E-value=12 Score=28.86 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=31.1
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
-++|-.+.|....++.++|..|+..|+|....+.
T Consensus 38 E~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~ 71 (241)
T PRK10079 38 EQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGV 71 (241)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3789999999999999999999999999988764
No 190
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=63.49 E-value=13 Score=24.42 Aligned_cols=36 Identities=8% Similarity=0.207 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.++..+++.-...|+-.+++-..+|++++.|+++++
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 467778888888999999999999999999999885
No 191
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=63.45 E-value=16 Score=28.09 Aligned_cols=45 Identities=24% Similarity=0.228 Sum_probs=37.8
Q ss_pred ccccCCCHHHHHHHHHHHHhcC-CcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGN-KGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
+.+..||+.++.|+.+..-..+ +|.-.++|-..+|++.++|.+.+
T Consensus 171 ~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~ 216 (233)
T PRK05803 171 KKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIE 216 (233)
T ss_pred HHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999774444 89999999999999999876654
No 192
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=63.43 E-value=20 Score=32.14 Aligned_cols=52 Identities=10% Similarity=0.045 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
.|..|+..+...+. .+-+.++-..+|+....+..++++|+++++|+.-..+.
T Consensus 4 ~e~~iL~~l~~~~~-~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~~ 55 (492)
T PLN02853 4 AEEALLGALSNNEE-ISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIKR 55 (492)
T ss_pred HHHHHHHHHHhcCC-CCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEE
Confidence 35666666655321 26788999999999999999999999999998765553
No 193
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=63.33 E-value=12 Score=23.88 Aligned_cols=27 Identities=26% Similarity=0.351 Sum_probs=23.9
Q ss_pred CCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 57 NLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 57 nL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
+++...|-.+|+.||.+|+|.+.....
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~ 54 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEE 54 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEE
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeecc
Confidence 577899999999999999999887763
No 194
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=62.94 E-value=12 Score=28.53 Aligned_cols=50 Identities=20% Similarity=0.163 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
+..|..++...|- +-..+|-...|.+..++.|=|..|+..|++..+.+|.
T Consensus 9 ~~~Il~~l~~~~~--~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~~~~~ 58 (185)
T PRK04424 9 QKALQELIEENPF--ITDEELAEKFGVSIQTIRLDRMELGIPELRERIKHVA 58 (185)
T ss_pred HHHHHHHHHHCCC--EEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHHHHHH
Confidence 4478888888554 7899999999999999999999999999998887764
No 195
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=62.45 E-value=9.9 Score=27.79 Aligned_cols=51 Identities=16% Similarity=0.252 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHhcCCcccHH-HHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMR-DIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtk-dIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+|.++=.+-.+-++.-+=|. -|-.++|+..++-.++|+.||..|.|+.|.-
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsk 94 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSK 94 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeecc
Confidence 45566667777788665554 5788999999999999999999999998854
No 196
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=62.25 E-value=24 Score=21.45 Aligned_cols=44 Identities=11% Similarity=0.210 Sum_probs=35.8
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+.|..|..++- .|--.++|-...|+...+|...++.+-.|
T Consensus 2 ~~LT~~E~~vl~~l~----~G~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 2 PSLTERELEVLRLLA----QGMSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp GSS-HHHHHHHHHHH----TTS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHHHHHHH----hcCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 579999998888875 57788999999999999999988888654
No 197
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=62.19 E-value=22 Score=28.48 Aligned_cols=59 Identities=14% Similarity=0.221 Sum_probs=44.0
Q ss_pred ccccCCCHHHHHHHHHHH---HhcCCcccHHHHHhh-------cC---CChHHHHHHHHHHhhcCCeeeecc
Q psy7778 23 EKLKDSDNEEKVVYKIIE---EAGNKGIWMRDIRFK-------SN---LMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie---~AGn~GIWtkdIk~k-------tn---L~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+.+.+||..+++++..|. .+++..+-..++-.+ .| +..+.+..+|..||.-|||....+
T Consensus 281 ~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 281 ELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 467899999987777665 235566666655543 23 777899999999999999998653
No 198
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=62.10 E-value=13 Score=26.35 Aligned_cols=45 Identities=4% Similarity=-0.024 Sum_probs=33.4
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHH-----HhhcCCChHHHHHHHHHH
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDI-----RFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdI-----k~ktnL~~~~l~K~LK~L 70 (117)
..||+-|+.|..++-..-++|+-...| ....++..++|...++.|
T Consensus 153 ~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l 202 (226)
T TIGR02154 153 LSLGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRL 202 (226)
T ss_pred EEcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHH
Confidence 459999999999999988888887777 445666666655544444
No 199
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=61.96 E-value=22 Score=27.01 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=39.1
Q ss_pred HHHHHHHHhcCCc-------c-cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 34 VVYKIIEEAGNKG-------I-WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 34 lVY~~Ie~AGn~G-------I-WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.||+.|.+.=-.| + --++|-.+.|+..+.|.-+|+.|+..|||...++
T Consensus 10 ~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~ 65 (235)
T TIGR02812 10 FAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 65 (235)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4666666653333 4 5679999999999999999999999999998875
No 200
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=61.90 E-value=6.5 Score=24.27 Aligned_cols=44 Identities=9% Similarity=0.099 Sum_probs=32.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D 94 (117)
.++++...+|++..+|.+..+. .+++.+..+-.|.-+|++.++.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~---~g~~~~~r~~~~~r~yt~~~v~ 45 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR---YGLPAPQRTDGGHRLYSEADVA 45 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh---CCCCCCCcCCCCCeecCHHHHH
Confidence 3578889999999999887653 2777776655677888886543
No 201
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=61.87 E-value=22 Score=27.00 Aligned_cols=43 Identities=12% Similarity=0.104 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.||+-|+.|++++- +|.-.++|-.+.++...++...++.+-.|
T Consensus 137 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWM----AGQGTIQISDQMNIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 49999999999996 58899999999999999998888877554
No 202
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=61.67 E-value=23 Score=27.80 Aligned_cols=46 Identities=15% Similarity=0.206 Sum_probs=37.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.++.|+-.+..++..|.+.|+- ..=-.+.++.|+.|++.|+.||+.
T Consensus 4 ~~~~mdl~~L~~f~av~e~gs~----t~AA~~L~iSQpavS~~I~~LE~~ 49 (319)
T PRK10216 4 SLTTLDLNLLLCLQLLMQERSV----TKAAKRMNVTPSAVSKSLAKLRAW 49 (319)
T ss_pred chhhcCHHHHHHHHHHHHhCCH----HHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4677888888888888888862 223578999999999999999984
No 203
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=61.66 E-value=16 Score=28.69 Aligned_cols=45 Identities=13% Similarity=0.203 Sum_probs=36.3
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+.+|+-.+..+|..|-+.|+-.- =-.+.|+.|+.|++.|+.||+.
T Consensus 11 ~~~~~l~~L~~f~~va~~gs~s~----AA~~L~iSQpavS~~I~~LE~~ 55 (311)
T PRK10086 11 LNGWQLSKLHTFEVAARHQSFAL----AADELSLTPSAVSHRINQLEEE 55 (311)
T ss_pred hcCCcHHHHHHHHHHHHcCCHHH----HHHHHCCCHHHHHHHHHHHHHH
Confidence 56788888888888888877432 2567899999999999999984
No 204
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=61.57 E-value=42 Score=25.99 Aligned_cols=67 Identities=12% Similarity=0.107 Sum_probs=50.6
Q ss_pred cccccCCCHHHHHHHHHHHHhcCCccc-----------HHHHHhhc-CCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 22 NEKLKDSDNEEKVVYKIIEEAGNKGIW-----------MRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 22 a~k~~~L~~eE~lVY~~Ie~AGn~GIW-----------tkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
|...-+|++-...|.+..-.--...-| ..+|-.++ ||+.++|.++|..|...|||..=-|-+|.-|.
T Consensus 35 a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~ 113 (177)
T PF03428_consen 35 ARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYA 113 (177)
T ss_pred HHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccC
Confidence 344556777666665555444444444 47899999 99999999999999999999988888876664
No 205
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=61.53 E-value=8.9 Score=28.64 Aligned_cols=53 Identities=19% Similarity=0.457 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhc-------CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 32 EKVVYKIIEEAG-------NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 32 E~lVY~~Ie~AG-------n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
-+.||..+..-| -.+.|..+| ++|--.+-|++++|.|||++|+.-+=..-=||
T Consensus 9 r~~Iye~LfkeGVlvakKd~~~~~h~el----~vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~ 68 (124)
T PTZ00034 9 RKAIYRYLFKEGVIVCKKDPKGPWHPEL----NVPNLHVMMLMRSLKSRGLVKEQFAWQHYYYY 68 (124)
T ss_pred HHHHHHHHhhCceEEEecCCCCCCCCcc----CCccHHHHHHHHccccCCceEEEEeeEEEEEE
Confidence 347888776654 234555555 57777899999999999999999887766665
No 206
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=61.40 E-value=12 Score=29.08 Aligned_cols=48 Identities=15% Similarity=0.224 Sum_probs=42.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCC--cccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNK--GIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~--GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
+.+.+||+-|+.|.++|-+-.+. -+-.++|-.++|..+++|.|-.|.|
T Consensus 9 ~~~~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 9 SRLEHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred HHHhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 45778999999999999888775 5778999999999999999999998
No 207
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=60.89 E-value=9.8 Score=27.17 Aligned_cols=52 Identities=12% Similarity=0.115 Sum_probs=35.6
Q ss_pred HHHHHHHHHhcCC-------cccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 33 KVVYKIIEEAGNK-------GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 33 ~lVY~~Ie~AGn~-------GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
..||..+..-|-. .-...+ .|.|.=.+-|++++|.|+|++|+.-+=..-=||
T Consensus 7 ~~Iye~LFkeGVlvakKD~~~~~H~e----l~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~ 65 (95)
T PF03501_consen 7 IAIYEYLFKEGVLVAKKDFHMPKHPE----LNVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWY 65 (95)
T ss_dssp HHHHHHHHHHSEEEEES-TTSCS-TT----TSSBHHHHHHHHHHHHHCTSEEEEECTTEEEEE
T ss_pred HHHHHHHhhcceEEEEccCCCCCCCc----cCCCcHHHHHHHhcccchhhhcCeecceEEEEE
Confidence 4677777655421 112333 378888899999999999999998766555454
No 208
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=60.77 E-value=13 Score=26.49 Aligned_cols=48 Identities=21% Similarity=0.362 Sum_probs=41.6
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+|+.+++..-+.|+=...|=...||+-....+.++.|+.+|+|+.-++
T Consensus 19 Ii~dIL~~~~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~ 66 (95)
T COG3432 19 IIFDILKAISEGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDN 66 (95)
T ss_pred HHHHHHHHhcCCCCCceeeeeecCcCHHHHHHHHHHHHhCCCEEeccC
Confidence 788999877777777788999999999999999999999997776543
No 209
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=60.41 E-value=6.6 Score=29.57 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=31.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
-+.++-+.+|++.. .|+..|+.|||.+..+-.|+-+|++..
T Consensus 13 ~IgevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y~~~~ 53 (154)
T PRK15002 13 TPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKRDV 53 (154)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECHHH
Confidence 35667777777764 567899999999988877778887755
No 210
>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=60.21 E-value=34 Score=20.30 Aligned_cols=42 Identities=14% Similarity=0.337 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
|++-++.|...+..-|. +--.+|-.+.|+..+.+.+-++.||
T Consensus 1 lD~~D~~Il~~Lq~d~r--~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 1 LDELDRKILRLLQEDGR--RSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp --HHHHHHHHHHHH-TT--S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC--ccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 45667788888887766 4568999999999999999999886
No 211
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=60.11 E-value=20 Score=27.41 Aligned_cols=48 Identities=21% Similarity=0.206 Sum_probs=38.8
Q ss_pred cccCCCHHHHHHHHHHHHhcC-CcccHHHHHhhcCCChHHHHH----HHHHHh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGN-KGIWMRDIRFKSNLMPTQLNK----ILKQLE 71 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K----~LK~LE 71 (117)
.+..||+.++.|+.+..-.+. +|.-.++|-..+|++.+++.+ +++.|.
T Consensus 171 ~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 171 KLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred HHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 478999999999988775554 899999999999999998654 455554
No 212
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=59.97 E-value=15 Score=28.43 Aligned_cols=54 Identities=11% Similarity=0.209 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCC-----c--c-cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778 34 VVYKIIEEAGNK-----G--I-WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT 89 (117)
Q Consensus 34 lVY~~Ie~AGn~-----G--I-WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt 89 (117)
.||+.|.+.=-. | + --++|-.+.|+..+.|.-+|+.||..|||...++ .|.|-.
T Consensus 6 ~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~--~G~~V~ 67 (253)
T PRK10421 6 EVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG--GGTFIR 67 (253)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCC--CeEEEe
Confidence 456666554322 3 3 3579999999999999999999999999998765 455543
No 213
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.79 E-value=24 Score=20.42 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=27.2
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcC
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKK 74 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~ 74 (117)
+|.-.+++-.+.|++.++|.+.++..+..|
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 356899999999999999999999999877
No 214
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=59.46 E-value=22 Score=28.16 Aligned_cols=48 Identities=8% Similarity=0.182 Sum_probs=38.2
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE 71 (117)
..+..||+.|+.|..+-.-. .+|.-.++|-...|+++..|. ++|+.|.
T Consensus 214 ~al~~L~~rer~vl~l~y~~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 214 NALGSLDARSRRIIEARWLD-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred HHHHcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35678999999888876632 579999999999999999988 5555553
No 215
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=59.17 E-value=34 Score=27.91 Aligned_cols=54 Identities=13% Similarity=0.154 Sum_probs=49.0
Q ss_pred cccCCCH-HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 24 KLKDSDN-EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 24 k~~~L~~-eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
-.+|++. -.+.|-+.|+ ..+.+--+-++-..+|+..++..|-|..|++.+.+++
T Consensus 151 LPkGi~~~Tl~~i~~~~~-~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a 205 (224)
T COG4565 151 LPKGLDELTLQKVREALK-EPDQELTAEELAQALGISRVTARRYLEYLVSNGILEA 205 (224)
T ss_pred CCCCcCHHHHHHHHHHHh-CcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeE
Confidence 4578887 5778999999 9999999999999999999999999999999998875
No 216
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=59.03 E-value=29 Score=25.45 Aligned_cols=50 Identities=18% Similarity=0.220 Sum_probs=38.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHH----HHHHHHHHhhcCC
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQ----LNKILKQLETKKI 75 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~----l~K~LK~LE~k~L 75 (117)
+.+..||++++.|+.+..- .|.-.++|-..+|++.++ +.|+.+.|....|
T Consensus 127 ~~l~~L~~~~r~i~~l~~~---~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 127 KLINDLEKLDREIFIRRYL---LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HHHHhCCHHHHHHHHHHHH---ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 4578899999988876543 478899999999999987 4566666665544
No 217
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=58.86 E-value=16 Score=27.82 Aligned_cols=46 Identities=17% Similarity=0.140 Sum_probs=35.1
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
++..|+-....++..|-+.|+ +- -=-.+.++.|+.|++.||.||+.
T Consensus 3 ~~~~~~l~~l~~f~~v~~~gs--~t--~AA~~L~itq~avS~~i~~LE~~ 48 (294)
T PRK09986 3 RLYRIDLKLLRYFLAVAEELH--FG--RAAARLNISQPPLSIHIKELEDQ 48 (294)
T ss_pred hhhhhhHHHHHHHHHHHHhcC--HH--HHHHHhCCCCCHHHHHHHHHHHH
Confidence 455677677778888888775 22 22667899999999999999984
No 218
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=58.85 E-value=37 Score=26.39 Aligned_cols=50 Identities=22% Similarity=0.163 Sum_probs=44.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
...||.-...++.+|.- +..|-..+|...+|... +.+++.|..+|||+++
T Consensus 85 ~~~LS~aaLEtLaiIay--~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 85 KQSLSQAALEVLAIIAY--KQPITRIEIDEIRGVNS---DGALQTLLAKGLIKEV 134 (188)
T ss_pred cCCCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEc
Confidence 34799999999999965 56999999999999996 8999999999999875
No 219
>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=58.80 E-value=27 Score=26.07 Aligned_cols=43 Identities=12% Similarity=0.191 Sum_probs=35.6
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHh
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLE 71 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE 71 (117)
..-||+.|+.|+.+. .+|.-.++|-.+.|++.+.+. ++++.|.
T Consensus 4 ~~~Lte~qr~VL~Lr----~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELR----EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 456899999999994 389999999999999999987 5555554
No 220
>PRK04217 hypothetical protein; Provisional
Probab=58.63 E-value=24 Score=25.46 Aligned_cols=43 Identities=9% Similarity=-0.024 Sum_probs=34.7
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
.+.|+++|+.++. ...-+|+-.++|...+|++.++|.+.|+..
T Consensus 40 ~~~Lt~eereai~---l~~~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 40 PIFMTYEEFEALR---LVDYEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred cccCCHHHHHHHH---HHHHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6678888876554 445588899999999999999988887754
No 221
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=58.62 E-value=13 Score=27.84 Aligned_cols=26 Identities=15% Similarity=0.288 Sum_probs=22.1
Q ss_pred CCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 57 NLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 57 nL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.+.+.+|..+|+.||..|+|.+-...
T Consensus 54 ~v~~GtLYp~L~RLE~~GlI~~~~~~ 79 (138)
T TIGR02719 54 SVDQGNVYRTLRKLEKDNLISSQWDT 79 (138)
T ss_pred CCCcChHHHHHHHHHHCCCEEEEeee
Confidence 57889999999999999999975433
No 222
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=58.56 E-value=20 Score=25.85 Aligned_cols=63 Identities=13% Similarity=0.165 Sum_probs=43.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC-----CCh----HHHHHHHHHHhhcC-CeeeeccccCCcc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN-----LMP----TQLNKILKQLETKK-IIKAVKSVANIEY 87 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn-----L~~----~~l~K~LK~LE~k~-LIK~VKsV~gg~w 87 (117)
.-.||+.|+.|..++-...++|+-..+|-.+.. ... +.++++.+.|+..+ -...+++|.|.-|
T Consensus 158 ~~~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~~~~~~~~i~~~~~~Gy 230 (240)
T PRK10710 158 MLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGY 230 (240)
T ss_pred EeecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhcCCCCCCcEEEeCCCce
Confidence 346999999999999999999999999988865 444 34666667776432 1223455554333
No 223
>PRK05638 threonine synthase; Validated
Probab=58.47 E-value=23 Score=30.28 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcC--CChHHHHHHHHHHhhcCCeeee
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSN--LMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn--L~~~~l~K~LK~LE~k~LIK~V 79 (117)
+++-...|+.++..- -+---+|....+ +.+.++.++|+.||..|||.+-
T Consensus 369 ~~~~r~~IL~~L~~~---~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~ 419 (442)
T PRK05638 369 IGGTKLEILKILSER---EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEA 419 (442)
T ss_pred ccchHHHHHHHHhhC---CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEe
Confidence 334566788888743 366788999888 8999999999999999999764
No 224
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=58.05 E-value=27 Score=28.05 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=37.6
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+-|+.|+.+|.+ |.-.++|-.+.++...++...++.+-.|
T Consensus 132 ~~LSpRErEVLrLLAq----GkTnKEIAe~L~IS~rTVkth~srImkK 175 (198)
T PRK15201 132 RHFSVTERHLLKLIAS----GYHLSETAALLSLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCCHHHHHHHHHHHC----CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4599999999999975 8889999999999999988877776443
No 225
>smart00351 PAX Paired Box domain.
Probab=58.01 E-value=37 Score=24.19 Aligned_cols=49 Identities=24% Similarity=0.259 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.++.+++. .+|..+. .|.-.++|-.++|+..+++.|+++.....|.+++
T Consensus 17 ~~s~~~R~--riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 17 PLPDEERQ--RIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred CCCHHHHH--HHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 47777663 2233332 6888999999999999999999999998887665
No 226
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=57.98 E-value=8.1 Score=26.51 Aligned_cols=42 Identities=5% Similarity=0.038 Sum_probs=30.2
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.+.++-..+|++.++|. ..|..|+|.+..+-.|.-+|++.++
T Consensus 3 ~i~eva~~~gVs~~tLR----~ye~~Gli~p~r~~~g~R~Ys~~dv 44 (98)
T cd01279 3 PISVAAELLGIHPQTLR----VYDRLGLVSPARTNGGGRRYSNNDL 44 (98)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeECHHHH
Confidence 45677788888887655 5588999999776555556666554
No 227
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=57.46 E-value=8.2 Score=27.74 Aligned_cols=41 Identities=5% Similarity=0.203 Sum_probs=30.4
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc-cCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV-ANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV-~gg~wYtdg~ 92 (117)
.+.++-..+|++..+ |+..|+.|||++...- +|--.|++..
T Consensus 2 ~IgE~A~~~gvs~~T----LRyYE~~GLl~p~r~~~~gyR~Y~~~~ 43 (133)
T cd04787 2 KVKELANAAGVTPDT----VRFYTRIGLLRPTRDPVNGYRLYSEKD 43 (133)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeeCCHHH
Confidence 467888899999865 5788999999997654 3445666655
No 228
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=57.24 E-value=18 Score=27.89 Aligned_cols=55 Identities=15% Similarity=0.189 Sum_probs=42.9
Q ss_pred HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778 34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE 90 (117)
Q Consensus 34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd 90 (117)
.||+.|++.=-.|- --++|-.+.|+.-+.|.-+|+.|+..|||...++ .|.|-..
T Consensus 14 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~--~G~~V~~ 76 (254)
T PRK09464 14 VIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG--GGTFVQS 76 (254)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC--ceeEEec
Confidence 47777776544442 4578999999999999999999999999998875 4555544
No 229
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=56.96 E-value=18 Score=27.77 Aligned_cols=48 Identities=23% Similarity=0.189 Sum_probs=38.9
Q ss_pred HHHHHHHHhcC-------Ccc-cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 34 VVYKIIEEAGN-------KGI-WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 34 lVY~~Ie~AGn-------~GI-WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.||+.|.+.=- .-+ --++|-.+.|+..+.|.-+|+.|+..|||....+
T Consensus 11 ~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 11 VVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 46666665422 334 4589999999999999999999999999998876
No 230
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=56.76 E-value=30 Score=27.82 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=39.3
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
...||+.|+.|..++. +|.-.++|-...|++..++...++.+-.|
T Consensus 188 ~~~LT~RE~evl~l~a----~G~s~~eIA~~L~IS~~TVk~hl~~i~~K 232 (247)
T TIGR03020 188 AGLITAREAEILAWVR----DGKTNEEIAAILGISSLTVKNHLQHIFKK 232 (247)
T ss_pred ccCCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5689999999998863 88999999999999999999999887554
No 231
>KOG1767|consensus
Probab=56.63 E-value=6.3 Score=28.91 Aligned_cols=61 Identities=18% Similarity=0.223 Sum_probs=41.5
Q ss_pred cccCCCHHHHHHHH-HHHHhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccC
Q psy7778 24 KLKDSDNEEKVVYK-IIEEAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN 84 (117)
Q Consensus 24 k~~~L~~eE~lVY~-~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~g 84 (117)
++..+---+...|. +-.++++ +=|----|-.+.++.-+.-..+|+.|..+|+|+.|..=..
T Consensus 36 kvnn~Vlfdqatydkl~kevp~~k~it~svl~dRlkIngsLAr~alr~L~~kG~Ik~Vs~h~~ 98 (110)
T KOG1767|consen 36 KVNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAALRELSNKGVIKQVSKHSK 98 (110)
T ss_pred HhhhheeecHHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHHHHHHHhcchHHHHhhcch
Confidence 44444442233343 3445555 4455555677899999999999999999999999865443
No 232
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=56.46 E-value=37 Score=23.28 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=35.0
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+.|+.|+.++. +|.-.++|-.+.+++..+|...++.+-.|
T Consensus 148 ~~lt~~e~~vl~l~~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 148 PLLTPRERQILKLIT----EGYTNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred cCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 459999999999874 45568999999999998887777766544
No 233
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=56.39 E-value=12 Score=22.72 Aligned_cols=27 Identities=26% Similarity=0.487 Sum_probs=20.1
Q ss_pred hcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 42 AGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 42 AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
...+||-..+|..++|++.+++++.++
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 446789999999999999999999886
No 234
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=56.39 E-value=15 Score=26.43 Aligned_cols=57 Identities=5% Similarity=0.128 Sum_probs=37.0
Q ss_pred cCCCHHHHHHHHHHHHhcC---------CcccHHHHHhhcCCChHHHHHHHHHHhhc----CCeeeeccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGN---------KGIWMRDIRFKSNLMPTQLNKILKQLETK----KIIKAVKSV 82 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn---------~GIWtkdIk~ktnL~~~~l~K~LK~LE~k----~LIK~VKsV 82 (117)
..||+-|..|+.++-..-+ .-+|-.++....+--.+.+.++.+.|+.+ .+|+.|.++
T Consensus 155 ~~Lt~~E~~~l~~l~~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~~~~~~~~i~tv~g~ 224 (232)
T PRK10955 155 LELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDRKDGHPWFKTLRGR 224 (232)
T ss_pred ecCCHHHHHHHHHHHhCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhcccCCCCCCeEEEeccc
Confidence 3699988877777766555 36777765444455556677777777643 356666554
No 235
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=56.18 E-value=9.9 Score=26.09 Aligned_cols=42 Identities=14% Similarity=0.185 Sum_probs=32.4
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
++.++...+|++.++| +.-|+.|||.++.+-+|--.|++..+
T Consensus 2 ~I~e~a~~~gvs~~tL----R~ye~~Gll~p~r~~~g~R~Y~~~dv 43 (96)
T cd04774 2 KVDEVAKRLGLTKRTL----KYYEEIGLVSPERSEGRYRLYSEEDL 43 (96)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCEEECHHHH
Confidence 5678889999998765 45588999998887666668887664
No 236
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.99 E-value=28 Score=24.52 Aligned_cols=42 Identities=10% Similarity=0.040 Sum_probs=33.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.++.|+.+..- .|.-.++|-..+|++.++|...+.
T Consensus 125 ~l~~L~~~~r~vl~l~~~---~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 125 AIESLPEELRTAITLREI---EGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 477899999888766543 689999999999999998754443
No 237
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=55.44 E-value=37 Score=28.13 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=42.8
Q ss_pred ccCCCHHHH-HHHHHHHHhcC--CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 25 LKDSDNEEK-VVYKIIEEAGN--KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 25 ~~~L~~eE~-lVY~~Ie~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
+..||=-|. .|=.+++.-.. --+-..+|-.+.|+..+.+..+++.||+.|+|+.-.
T Consensus 174 i~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 174 INTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 555664333 44445555444 357789999999999999999999999999999876
No 238
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=55.35 E-value=34 Score=25.67 Aligned_cols=41 Identities=12% Similarity=0.087 Sum_probs=34.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
..-||+.|+.|+.+. .+|.-.++|-...|++.+.+.+..+.
T Consensus 4 ~~~Lt~rqreVL~lr----~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 4 ESFLTERQIEVLRLR----ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred ccCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 456999999999884 38999999999999999887666554
No 239
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=55.33 E-value=11 Score=26.42 Aligned_cols=42 Identities=10% Similarity=0.191 Sum_probs=31.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~ 93 (117)
.+.++...+|++..+ |+..|..|||.+. .+-+|--+|++..+
T Consensus 2 ~I~eva~~~gvs~~t----LRyYe~~GLl~p~~r~~~gyR~Y~~~~i 44 (123)
T cd04770 2 KIGELAKAAGVSPDT----IRYYERIGLLPPPQRSENGYRLYGEADL 44 (123)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCCCCCCCccCCHHHH
Confidence 357788899999865 4679999999964 45455568887763
No 240
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=55.06 E-value=37 Score=26.62 Aligned_cols=53 Identities=8% Similarity=0.097 Sum_probs=43.8
Q ss_pred ccCCCHHHHHHHH-HHHHhcCCcccHHHHHhhcCCChHHHHHHHH-HHhhcCCee
Q psy7778 25 LKDSDNEEKVVYK-IIEEAGNKGIWMRDIRFKSNLMPTQLNKILK-QLETKKIIK 77 (117)
Q Consensus 25 ~~~L~~eE~lVY~-~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK-~LE~k~LIK 77 (117)
..+++..|+..+. ++..-++...-..+|....|.+...+...+. .|-.++||-
T Consensus 233 ~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 233 ELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc
Confidence 4678888876666 6665555567789999999999999999999 699999995
No 241
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=54.91 E-value=13 Score=23.14 Aligned_cols=36 Identities=22% Similarity=0.340 Sum_probs=30.4
Q ss_pred CCcccHHHHHhhc---CCChHHHHHHHHHHhhcCCeeee
Q psy7778 44 NKGIWMRDIRFKS---NLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 44 n~GIWtkdIk~kt---nL~~~~l~K~LK~LE~k~LIK~V 79 (117)
..|+=...+|.+. +++....+.+|..|+.+|.|+.-
T Consensus 15 r~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 15 RPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVE 53 (59)
T ss_dssp SS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEE
T ss_pred ccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeE
Confidence 4788889999888 88999999999999999999864
No 242
>cd00131 PAX Paired Box domain
Probab=54.73 E-value=45 Score=24.02 Aligned_cols=50 Identities=22% Similarity=0.246 Sum_probs=39.0
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
+.||.+.+. .+|..+ .+|.-.++|-.++++..++|.++++.....|-+++
T Consensus 16 ~~lS~d~R~--rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 16 RPLPDSIRQ--RIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred CcCCHHHHH--HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 357776653 223333 37999999999999999999999999999886665
No 243
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=54.42 E-value=18 Score=29.11 Aligned_cols=35 Identities=11% Similarity=0.253 Sum_probs=32.4
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.++--.+|-.+.+++.+.+.+.|..||.+|+|-..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 46788999999999999999999999999999876
No 244
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=54.39 E-value=48 Score=20.22 Aligned_cols=52 Identities=13% Similarity=0.233 Sum_probs=38.1
Q ss_pred ccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 25 LKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 25 ~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
++.|.++.+ .++...... ...-..+|...+++.++.++..|+.|+..++|..
T Consensus 19 ~~~l~~~~r~~il~~l~~~--~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~ 71 (110)
T COG0640 19 LKALADPTRLEILSLLAEG--GELTVGELAEALGLSQSTVSHHLKVLREAGLVEL 71 (110)
T ss_pred HHHhCCHHHHHHHHHHHhc--CCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEE
Confidence 344544433 444444443 3344778888889999999999999999999999
No 245
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=54.26 E-value=20 Score=27.99 Aligned_cols=48 Identities=4% Similarity=0.111 Sum_probs=42.6
Q ss_pred ccccCCCHHHHHHHHHHHHhcCC--cccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNK--GIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~--GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
+.+.+||+-|+.|.+.|-+-.++ .+-+++|-.+++..+++|.|-.|.|
T Consensus 5 ~~~~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkl 54 (278)
T PRK11557 5 QRYPGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKL 54 (278)
T ss_pred HhhhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 35678999999999999887764 5788999999999999999999998
No 246
>PRK10403 transcriptional regulator NarP; Provisional
Probab=53.85 E-value=48 Score=23.04 Aligned_cols=44 Identities=16% Similarity=0.144 Sum_probs=36.9
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+.|..|..++. +|.-.++|-.+.++...+|...+..+..|
T Consensus 152 ~~Lt~~e~~vl~~~~----~g~s~~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 152 SVLTERELDVLHELA----QGLSNKQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 468999998888875 46889999999999999988888877654
No 247
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=53.38 E-value=34 Score=22.59 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=35.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
..+..||+.|+.|..+.-- .|.-.++|-...|++...|.+.++...
T Consensus 106 ~~l~~L~~~~~~ii~~~~~---~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 106 EALEKLPEREREVLVLRYL---EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred HHHHhCCHHHHHHHhhHHh---cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3567899988876544322 488899999999999999888887654
No 248
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=53.34 E-value=25 Score=24.05 Aligned_cols=40 Identities=13% Similarity=0.161 Sum_probs=29.1
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCc-ccccC
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIE-YLTEG 91 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~-wYtdg 91 (117)
.+.++-..+|++.. .|+..|+.|||.+...-.+|. +|++.
T Consensus 2 ~I~eva~~~gvs~~----tlR~Ye~~GLl~p~~r~~~g~r~Y~~~ 42 (95)
T cd04780 2 RMSELSKRSGVSVA----TIKYYLREGLLPEGRRLAPNQAEYSEA 42 (95)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCHH
Confidence 46788888999875 567889999999976555554 44433
No 249
>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=53.23 E-value=32 Score=23.99 Aligned_cols=44 Identities=9% Similarity=0.141 Sum_probs=35.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+.+..||+.++.|+.+.. -.|.-.++|-..+|++.+++...+..
T Consensus 107 ~~i~~L~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 107 GCLEKLPERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HHHHHCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 346789999998887754 36999999999999999987766543
No 250
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=52.97 E-value=39 Score=22.65 Aligned_cols=47 Identities=23% Similarity=0.430 Sum_probs=37.5
Q ss_pred ccccCCCHHHHHHHHHHHH----hcCCccc------------HHHHHhhcCCChHHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEE----AGNKGIW------------MRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~----AGn~GIW------------tkdIk~ktnL~~~~l~K~LK~L 70 (117)
.++++|+++.+++|.+..+ |-.+| | ..+|....|+...++.+++|.|
T Consensus 14 ~~y~~Ls~~Ak~lY~ll~dR~~lS~kn~-wiDe~G~vYi~~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 14 PKYKKLSNDAKILYSLLLDRLRLSLKNG-WIDENGNVYIIFSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred cccccCCHHHHHHHHHHHHHHHhhhhcC-cCCCCCCEEEEeeHHHHHHHHCCCHHHHHHHHHcC
Confidence 4689999999999998754 32333 4 4678899999999999998875
No 251
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=52.76 E-value=10 Score=27.92 Aligned_cols=40 Identities=15% Similarity=0.268 Sum_probs=31.0
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
+.++...+|++.. .|+..|+.|||.+..+-+|.-+|++..
T Consensus 4 IgevA~~~Gvs~~----tLRyYE~~GLl~~~r~~~g~R~Y~~~d 43 (142)
T TIGR01950 4 VGELAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKRDV 43 (142)
T ss_pred HHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECHHH
Confidence 5677788888874 568899999999977766667777655
No 252
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=52.51 E-value=41 Score=23.99 Aligned_cols=47 Identities=15% Similarity=0.112 Sum_probs=36.7
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHHhh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQLET 72 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~LE~ 72 (117)
..+..||+.++.|+.+-.- .|.-.++|-..+|++.+++ .++++.|..
T Consensus 114 ~~l~~L~~~~r~vl~L~~~---~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 114 DALAQLSPEHRAVLVRSYY---RGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3578899988888766543 4888999999999999987 666766643
No 253
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=52.28 E-value=35 Score=23.62 Aligned_cols=48 Identities=8% Similarity=0.123 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc---CCeeee
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK---KIIKAV 79 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k---~LIK~V 79 (117)
++..+..++..|.+.|+---+ -...|+.++.+++.|+.||.. .|+...
T Consensus 2 ~~~~~l~~~~av~~~gSis~A----A~~L~iS~stvs~~I~~LE~~lg~~Lf~R~ 52 (99)
T TIGR00637 2 ADPRRVALLKAIARMGSISQA----AKDAGISYKSAWDYIRAMNNLSGEPLVERA 52 (99)
T ss_pred CCHHHHHHHHHHHHhCCHHHH----HHHHCCCHHHHHHHHHHHHHHhCCCeEEec
Confidence 345666778888887764333 457899999999999999984 455554
No 254
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=52.08 E-value=12 Score=26.76 Aligned_cols=38 Identities=11% Similarity=0.132 Sum_probs=29.0
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQ 62 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~ 62 (117)
-+.+|++.|+-+.++|++++|+-. .+-.|++.|-+...
T Consensus 46 EiaGlsPyErr~i~Lirns~~krA-rKlakKRLGs~kRA 83 (97)
T COG5051 46 EIAGLSPYERRVIELIRNSQDKRA-RKLAKKRLGSLKRA 83 (97)
T ss_pred HHccCCHHHHHHHHHHHhcccHHH-HHHHHHHhhhHHHH
Confidence 578999999999999999999754 45566666655443
No 255
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=51.76 E-value=43 Score=28.46 Aligned_cols=84 Identities=20% Similarity=0.252 Sum_probs=67.4
Q ss_pred ccccccCCCHHHHHHHHHHHHhcCCccc--HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCcccccc
Q psy7778 21 TNEKLKDSDNEEKVVYKIIEEAGNKGIW--MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGTVNAMV 97 (117)
Q Consensus 21 ~a~k~~~L~~eE~lVY~~Ie~AGn~GIW--tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~~D~~f 97 (117)
.++.+..|++++..|...||.--..==| ..-|...+.|+..-+...|+.|..-+||.. +.+. -|-=.|-..+|.--
T Consensus 4 ~~~~~~~l~~~D~rlLraiE~~mR~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l~lv~r-~~~~y~Gy~lT~~GyD~LA 82 (304)
T COG0478 4 VAEAYPKLSKEDFRLLRAIEGGMRSHEWVPLELIKKRARMDEEELLYRLKRLDKLKLVSR-RTISYEGYQLTFSGYDALA 82 (304)
T ss_pred hhhhhhhcCHHHHHHHHHHHhcccccccccHHHHHHHcCCCHHHHHHHHHHHHhcCceec-cCCcceeEEEEecchhHHH
Confidence 3556778999999999999976554444 457999999999999999999999999988 5543 55556777788888
Q ss_pred chhhhhhh
Q psy7778 98 LPSRKKRE 105 (117)
Q Consensus 98 I~~l~~~~ 105 (117)
|..+.+|-
T Consensus 83 L~~l~~r~ 90 (304)
T COG0478 83 LHALVKRG 90 (304)
T ss_pred HHHHHHcC
Confidence 88887763
No 256
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=51.34 E-value=25 Score=21.67 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=27.9
Q ss_pred CCcccHHHHHhhcCCChH-HHHHHHHHHhhcCCeee
Q psy7778 44 NKGIWMRDIRFKSNLMPT-QLNKILKQLETKKIIKA 78 (117)
Q Consensus 44 n~GIWtkdIk~ktnL~~~-~l~K~LK~LE~k~LIK~ 78 (117)
+.||-..+++.+++.+-. ...+.|+.|+..|++.-
T Consensus 18 ~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~ 53 (66)
T PF06969_consen 18 NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEI 53 (66)
T ss_dssp HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE
T ss_pred HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEE
Confidence 689999999999998744 44888999999999953
No 257
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=50.88 E-value=48 Score=27.73 Aligned_cols=68 Identities=7% Similarity=0.185 Sum_probs=47.8
Q ss_pred cCCCHHHHHHHH-----HHHHhcCCcccHHHHHhh--cCCChHHHHHHHHHHhhcCCeeee-------ccccCCcccccC
Q psy7778 26 KDSDNEEKVVYK-----IIEEAGNKGIWMRDIRFK--SNLMPTQLNKILKQLETKKIIKAV-------KSVANIEYLTEG 91 (117)
Q Consensus 26 ~~L~~eE~lVY~-----~Ie~AGn~GIWtkdIk~k--tnL~~~~l~K~LK~LE~k~LIK~V-------KsV~gg~wYtdg 91 (117)
+.|++-++.|.. +|+.+ .=+-+++|..+ .|+...++.+-+..||..|+|... ++-+|=-+|-|.
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~--~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~ 79 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATG--EPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDH 79 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcC--CCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHH
Confidence 346664444443 55554 44667999966 889999999999999999998753 333355688776
Q ss_pred cccc
Q psy7778 92 TVNA 95 (117)
Q Consensus 92 ~~D~ 95 (117)
=++.
T Consensus 80 L~~~ 83 (339)
T PRK00082 80 LLEV 83 (339)
T ss_pred hCCC
Confidence 6554
No 258
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=50.79 E-value=11 Score=33.10 Aligned_cols=91 Identities=21% Similarity=0.287 Sum_probs=59.6
Q ss_pred ceecC-CeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCc---ccH----HHHHhhcCC--ChHHHHHHHHHHhhcC
Q psy7778 5 GFLIG-GNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKG---IWM----RDIRFKSNL--MPTQLNKILKQLETKK 74 (117)
Q Consensus 5 ~~~~~-~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~G---IWt----kdIk~ktnL--~~~~l~K~LK~LE~k~ 74 (117)
+++.| +++-|.+-+.. .+|.+.=.++|.-|..+ .|. ......+.+ |...++.++..|+..+
T Consensus 5 viN~GSSSlKf~l~~~~---------~~~~~~~Gl~Erig~~~~~~~~~~~~~~~~~~~~~~~dh~~al~~l~~~l~~~~ 75 (396)
T COG0282 5 VINAGSSSLKFQLFDMP---------ELEVLASGLAERIGLPDAIITIKFDGKQKLELEADIADHKEALKLLLETLEEHK 75 (396)
T ss_pred EEecCcchheeeEeccC---------cccchhhhhHHHcCCCCceEEEEecCccceeeecCCCCHHHHHHHHHHHHHhcc
Confidence 45544 35777776433 34555555666655542 121 122222322 5667999999999999
Q ss_pred Ceeeeccc--------cCCcccccCc-cccccchhhhhh
Q psy7778 75 IIKAVKSV--------ANIEYLTEGT-VNAMVLPSRKKR 104 (117)
Q Consensus 75 LIK~VKsV--------~gg~wYtdg~-~D~~fI~~l~~~ 104 (117)
.|++...+ +||..|++.. .|.+.++.|++-
T Consensus 76 ii~~~~~I~~vGHRVVhGGe~f~~svli~~eVl~~I~~~ 114 (396)
T COG0282 76 IIKSLDEIDAVGHRVVHGGEKFTESVLIDDEVLKAIEDL 114 (396)
T ss_pred hhcchhhhcEEeeEEEecccccCccEEEcHHHHHHHHhh
Confidence 99886655 5999999999 899999888753
No 259
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=50.77 E-value=35 Score=26.43 Aligned_cols=45 Identities=16% Similarity=0.087 Sum_probs=38.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
...||+.|+.|...+. .|--.++|-...|++.++++..|+....|
T Consensus 169 ~~~Lt~re~evl~~~a----~G~t~~eIa~~l~is~~Tv~~~l~~~~~k 213 (232)
T TIGR03541 169 AGVLSEREREVLAWTA----LGRRQADIAAILGISERTVENHLRSARRK 213 (232)
T ss_pred hccCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4579999999998862 78889999999999999998888877554
No 260
>PRK04158 transcriptional repressor CodY; Validated
Probab=50.49 E-value=16 Score=30.14 Aligned_cols=55 Identities=24% Similarity=0.396 Sum_probs=43.8
Q ss_pred cccCCCHHHH-HHHHHHHH-hcCCcccHH-HHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 24 KLKDSDNEEK-VVYKIIEE-AGNKGIWMR-DIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 24 k~~~L~~eE~-lVY~~Ie~-AGn~GIWtk-dIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.+..||=-|. .|..++++ -|++|+-.+ .|-.+-|+.-++|-.+|+.|||-|.|-+
T Consensus 176 Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIES 233 (256)
T PRK04158 176 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIES 233 (256)
T ss_pred HHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceee
Confidence 3566776444 56656655 688999876 4888999999999999999999999977
No 261
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=50.43 E-value=30 Score=16.77 Aligned_cols=36 Identities=11% Similarity=0.148 Sum_probs=25.2
Q ss_pred CCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHH
Q psy7778 27 DSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKI 66 (117)
Q Consensus 27 ~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~ 66 (117)
.++++++ .|...+ ..|....++....+++.+++.+.
T Consensus 5 ~~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence 3555444 344443 35778999999999999988765
No 262
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=49.88 E-value=38 Score=24.02 Aligned_cols=43 Identities=19% Similarity=0.172 Sum_probs=32.6
Q ss_pred CCHHHHHH----HHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 28 SDNEEKVV----YKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 28 L~~eE~lV----Y~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
||++|+.+ |.++.+-=+.|+--+.|..++|+..++|+|+=+.|
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l 79 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNL 79 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence 78877743 34444333789999999999999999998876555
No 263
>PRK05572 sporulation sigma factor SigF; Validated
Probab=49.63 E-value=38 Score=26.35 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=36.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.-+..||+.++.|+.+... .|.-.++|...+|++.+.|.++.+
T Consensus 198 ~~l~~L~~~~~~v~~l~~~---~~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 198 EAIRELDERERLIVYLRYF---KDKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred HHHHcCCHHHHHHHHHHHh---CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999888763 678999999999999999877544
No 264
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=49.36 E-value=46 Score=21.45 Aligned_cols=44 Identities=14% Similarity=0.299 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCcccHHHHHhhc---C--CChHHHHHHHHHHhhcCCeeee
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKS---N--LMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~kt---n--L~~~~l~K~LK~LE~k~LIK~V 79 (117)
|..++.+++. -+-.+.|.... + +...+|.+.|+.||..||++.+
T Consensus 3 IL~~L~~~~~-P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 3 ILRILAESDK-PLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc
Confidence 5666766653 34444554443 3 4458899999999999998853
No 265
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=48.64 E-value=33 Score=21.49 Aligned_cols=33 Identities=18% Similarity=0.282 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
+.....+.|-+-|.+.+|-..+|++..+|.|=|
T Consensus 17 ~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 17 YLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 345567788899999999999999999998743
No 266
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=48.59 E-value=49 Score=23.75 Aligned_cols=57 Identities=11% Similarity=0.029 Sum_probs=35.1
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHH--HhhcCCChHHHHHH----HHHHhhc----CCeeeeccc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDI--RFKSNLMPTQLNKI----LKQLETK----KIIKAVKSV 82 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdI--k~ktnL~~~~l~K~----LK~LE~k----~LIK~VKsV 82 (117)
-.||+-|+.|..++-...+.=.-..+| ....++..++|... -+.|+.. .+|+.|.++
T Consensus 155 ~~Lt~~E~~il~~l~~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~~~~~~~~i~tv~g~ 221 (227)
T TIGR03787 155 IDLTVTEFWMVHALAKHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQAVDDNFDCIQTVYGM 221 (227)
T ss_pred ecCCHHHHHHHHHHHhCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhccCCCCCCeEEEecce
Confidence 469999998888887765554566777 34455555555544 4455431 356665544
No 267
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=48.54 E-value=47 Score=25.81 Aligned_cols=42 Identities=17% Similarity=0.395 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
-...|-.++..||..|+-.++|..-+++....+..+|..|..
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~ 46 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQE 46 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 355788888899999999999999999999999999999943
No 268
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=48.52 E-value=41 Score=24.48 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=34.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..||++++.|+.+-.- .|.-.++|-..+|++.+++...|.
T Consensus 124 ~l~~Lp~~~R~v~~L~~~---~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 124 LLDTLRPRVKQAFLMATL---DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578899999988877655 788999999999999998665543
No 269
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=48.51 E-value=43 Score=25.52 Aligned_cols=49 Identities=16% Similarity=0.270 Sum_probs=38.4
Q ss_pred ccccCCCHHHHHHHHHHHH-hcCCcccHHHHHhhcCCChHHHHH----HHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEE-AGNKGIWMRDIRFKSNLMPTQLNK----ILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~-AGn~GIWtkdIk~ktnL~~~~l~K----~LK~LE 71 (117)
..+..||+.++.|+.+... ..-.|.-.++|-..+|++..+|.+ +++.|.
T Consensus 174 ~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr 227 (234)
T PRK08301 174 KALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227 (234)
T ss_pred HHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578899999999988652 336899999999999999998744 445553
No 270
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=48.48 E-value=32 Score=27.35 Aligned_cols=46 Identities=13% Similarity=0.134 Sum_probs=35.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..|+-....++..+-+.|+-.-. -.+.++.|+.|++.||.||+.
T Consensus 25 ~~~~m~l~~L~~f~av~e~gs~s~A----A~~L~isQpavS~~I~~LE~~ 70 (317)
T PRK11482 25 TLRNIDLNLLTIFEAVYVHKGIVNA----AKILNLTPSAISQSIQKLRVI 70 (317)
T ss_pred cccccchhHHHHHHHHHHcCCHHHH----HHHhCCChHHHHHHHHHHHHH
Confidence 4566776777778788887764332 567899999999999999983
No 271
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=48.45 E-value=69 Score=25.44 Aligned_cols=59 Identities=12% Similarity=0.233 Sum_probs=48.7
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcccc
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNA 95 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~ 95 (117)
...|.+++.+.|- +-..+|-..+|....++.|=|..||++|+++. ++||-.+.+..-..
T Consensus 7 ~~~Il~~l~~~g~--v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R---~hGGa~~~~~~~~~ 65 (253)
T COG1349 7 HQKILELLKEKGK--VSVEELAELFGVSEMTIRRDLNELEEQGLLLR---VHGGAVLPDSESEY 65 (253)
T ss_pred HHHHHHHHHHcCc--EEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE---EeCCEecCCCcccc
Confidence 3478888888554 78899999999999999999999999999876 57787777766444
No 272
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=48.20 E-value=40 Score=27.33 Aligned_cols=35 Identities=14% Similarity=0.165 Sum_probs=31.9
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V 79 (117)
.++-.+++-++++..+....|+|+.||..++|-.-
T Consensus 18 ~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~ 52 (214)
T COG1339 18 VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRT 52 (214)
T ss_pred ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEE
Confidence 55999999999999999999999999999999643
No 273
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=48.00 E-value=63 Score=22.66 Aligned_cols=46 Identities=22% Similarity=0.154 Sum_probs=38.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcC
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKK 74 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~ 74 (117)
+..||+.|+.|..++.+ |.-.++|....++..++|...++.|-.|=
T Consensus 141 ~~~lt~~E~~vl~~l~~----g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 141 LDSLSKQEISVMRYILD----GKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cccCCHHHHHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 45699989888888873 55699999999999999998888887764
No 274
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=47.56 E-value=15 Score=27.48 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=19.0
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
-.+.++.|+.|++.||.||+.
T Consensus 18 A~~L~isqsavS~~i~~LE~~ 38 (279)
T TIGR03339 18 AERLGLSQPTVTDQVRKLEER 38 (279)
T ss_pred HHHhcCCchHHHHHHHHHHHH
Confidence 567899999999999999984
No 275
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=47.29 E-value=39 Score=23.33 Aligned_cols=27 Identities=11% Similarity=0.177 Sum_probs=23.6
Q ss_pred cCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 43 GNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 43 Gn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
-++|++.++|-..+|++.+++.++.|-
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 447899999999999999999997653
No 276
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=47.28 E-value=70 Score=22.53 Aligned_cols=55 Identities=20% Similarity=0.270 Sum_probs=44.3
Q ss_pred cCCCHHHHHHHHHHHHhcCCc------------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKG------------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~G------------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
...+..+++...+..-+...| +-..+|-.-+|+....+++.++.|...++|..-+
T Consensus 139 ~~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 139 ARKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELRKDGLISVRG 205 (214)
T ss_pred hhccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHHhCCcEeeCC
Confidence 344567888887777776654 6678888889999999999999999999997544
No 277
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.07 E-value=17 Score=24.27 Aligned_cols=41 Identities=12% Similarity=0.130 Sum_probs=28.6
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
.+.++-..+|++..+| +..|..|+|.+..+-.|.-+|++..
T Consensus 3 ~i~e~A~~~gvs~~tL----r~ye~~Gli~p~r~~~g~R~y~~~d 43 (91)
T cd04766 3 VISVAAELSGMHPQTL----RLYERLGLLSPSRTDGGTRRYSERD 43 (91)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCcCCCcCCCCCeeECHHH
Confidence 4677888889988654 5668899999876544445555443
No 278
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=46.82 E-value=55 Score=25.28 Aligned_cols=39 Identities=13% Similarity=0.180 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..++-.|-++|+ ...=-.+.++.|+.|++.||+||..
T Consensus 4 ~~L~~f~~v~~~gS----~s~AA~~L~itQpavS~~i~~LE~~ 42 (305)
T PRK11151 4 RDLEYLVALAEHRH----FRRAADSCHVSQPTLSGQIRKLEDE 42 (305)
T ss_pred HHHHHHHHHHHhCC----HHHHHHHhCCCchHHHHHHHHHHHH
Confidence 44455555656553 2233677999999999999999983
No 279
>CHL00148 orf27 Ycf27; Reviewed
Probab=46.76 E-value=40 Score=24.28 Aligned_cols=47 Identities=9% Similarity=0.019 Sum_probs=35.8
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhc-------CCChHHH----HHHHHHHh
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-------NLMPTQL----NKILKQLE 71 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-------nL~~~~l----~K~LK~LE 71 (117)
...|++-|..|..++-...++|+..+.|-... +...++| +++.+.|.
T Consensus 159 ~~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~ 216 (240)
T CHL00148 159 RIRLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLE 216 (240)
T ss_pred EEEcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhc
Confidence 34599999999999999999999999998876 3454444 45555564
No 280
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=46.75 E-value=27 Score=24.66 Aligned_cols=69 Identities=17% Similarity=0.220 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhcCCcccHH-HHHhhcC----CChHHHHHHHHHHhhcCCeeeeccccCC----cccccCccccccchh
Q psy7778 32 EKVVYKIIEEAGNKGIWMR-DIRFKSN----LMPTQLNKILKQLETKKIIKAVKSVANI----EYLTEGTVNAMVLPS 100 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtk-dIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKsV~gg----~wYtdg~~D~~fI~~ 100 (117)
+..|+.++...-..|-... .+...++ .++.+|-.+|+.||..|||.+..-..++ ..|.-.+-=.+.+..
T Consensus 11 ~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~ 88 (138)
T COG1695 11 ELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAE 88 (138)
T ss_pred HHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHH
Confidence 4556666655555554432 3444444 6788999999999999999997666655 667655543333333
No 281
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=46.75 E-value=76 Score=23.75 Aligned_cols=53 Identities=15% Similarity=0.141 Sum_probs=41.9
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+|++=..|+.++... ..-+-..+|-.+ .++..++|-|.|+.|+..|||..+..
T Consensus 24 ~T~qR~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 24 LTPQRLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred CCHHHHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEec
Confidence 566667999999987 356666665544 35788999999999999999999864
No 282
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=46.61 E-value=49 Score=25.99 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=38.7
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+-|+.|...+. +|--.++|-...++...+|+..++++..|
T Consensus 178 ~~LT~rE~evl~~~a----~G~t~~eIa~~l~is~~TV~~h~~~~~~K 221 (240)
T PRK10188 178 MNFSKREKEILKWTA----EGKTSAEIAMILSISENTVNFHQKNMQKK 221 (240)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 369999999999983 78999999999999999999999888654
No 283
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=46.40 E-value=29 Score=26.23 Aligned_cols=55 Identities=9% Similarity=0.075 Sum_probs=41.7
Q ss_pred cCCCHHHHHHHHHHHHhcCCc-------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKG-------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~G-------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+..+.-| .||+.|.+.=-.| |=..+|-.+.|+.-+.|.-+|+.|+..|||...++
T Consensus 8 ~~~~~~e-~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~ 69 (221)
T PRK11414 8 QHISLTL-QVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPA 69 (221)
T ss_pred CCCCHHH-HHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCC
Confidence 3344434 4777777653333 45688999999999999999999999999987655
No 284
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=46.05 E-value=46 Score=25.57 Aligned_cols=45 Identities=7% Similarity=0.068 Sum_probs=37.2
Q ss_pred ccccCCCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+-.--. -+|.-.++|-..+|++..+|.+.+
T Consensus 174 ~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l 219 (234)
T TIGR02835 174 KALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred HHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 457889999998888766433 489999999999999999987765
No 285
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=45.97 E-value=63 Score=24.91 Aligned_cols=43 Identities=14% Similarity=0.155 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.|+-....++..|.+.|+-. .--.+.|+.|+.|++.||.||..
T Consensus 4 ~~~l~~L~~f~~v~~~gs~s----~AA~~L~isQ~avS~~i~~LE~~ 46 (302)
T PRK09791 4 QVKIHQIRAFVEVARQGSIR----GASRMLNMSQPALTKSIQELEEG 46 (302)
T ss_pred cccHHHHHHHHHHHHcCCHH----HHHHHhCCChHHHHHHHHHHHHH
Confidence 35556667777777777532 23678899999999999999984
No 286
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=45.42 E-value=18 Score=28.08 Aligned_cols=45 Identities=13% Similarity=0.217 Sum_probs=33.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+.+|+-.+..++..|-+.|+ +- .=-.+.|+.|+.|++.||.||+.
T Consensus 8 ~~~m~~~~l~~F~av~e~gS--~t--~AA~~L~iSQpavS~~I~~LE~~ 52 (303)
T PRK10082 8 LHNIETKWLYDFLTLEKCRN--FS--QAAVSRNVSQPAFSRRIRALEQA 52 (303)
T ss_pred ccccchHHHHHHHHHHhcCC--HH--HHHHHhCCChHHHHHHHHHHHHH
Confidence 35566666666666666665 22 22678999999999999999984
No 287
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.32 E-value=17 Score=25.36 Aligned_cols=42 Identities=12% Similarity=0.240 Sum_probs=31.1
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.+.++...+|++.. .|+..|..|||.+++.-.|--.|++..+
T Consensus 2 ~ige~a~~~gvs~~----tLryYe~~GLi~p~~~~~~yR~Y~~~d~ 43 (116)
T cd04769 2 YIGELAQQTGVTIK----AIRLYEEKGLLPSPKRSGNYRVYDAQHV 43 (116)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCceeeCHHHH
Confidence 46778888888875 5678899999999875444466776653
No 288
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=45.27 E-value=48 Score=28.44 Aligned_cols=49 Identities=14% Similarity=0.222 Sum_probs=43.0
Q ss_pred HHHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 33 KVVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
..+|+.|+++=..|.| +|.+-...++..+++.++.+.|+.+|+|-+...
T Consensus 7 ~ql~~~i~~~I~~g~l~~g~rLPs~R~la~~l~vs~~Tv~~ay~~L~~~G~i~~~~g 63 (459)
T COG1167 7 QQLAEQLREAILSGRLKPGDRLPSIRQLAQDLGVSRSTVSRAYEELEARGYIESRPG 63 (459)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCcHHHHHHHhCCcHHHHHHHHHHHHhCcceeeccC
Confidence 4678888888888887 588999999999999999999999999998763
No 289
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=45.05 E-value=49 Score=26.33 Aligned_cols=45 Identities=11% Similarity=0.107 Sum_probs=36.8
Q ss_pred ccccCCCHHHHHHHHHHH-HhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIE-EAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie-~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+.. -..-+|.-.++|-..+|++.+.|.+.+
T Consensus 218 ~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l 263 (285)
T TIGR02394 218 AWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQ 263 (285)
T ss_pred HHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHH
Confidence 458899999999988766 345788999999999999999866544
No 290
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.97 E-value=53 Score=23.70 Aligned_cols=46 Identities=24% Similarity=0.262 Sum_probs=35.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE 71 (117)
+.+..||+.++.|+.+-. =.|.-.++|-..+|++.+.|. |+++.|-
T Consensus 131 ~~l~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 131 RALKALSPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 457788998888776543 358999999999999999876 5555553
No 291
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=44.63 E-value=58 Score=23.47 Aligned_cols=45 Identities=9% Similarity=0.051 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHh-----hcCCChHH----HHHHHHHHh
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRF-----KSNLMPTQ----LNKILKQLE 71 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~-----ktnL~~~~----l~K~LK~LE 71 (117)
.||+-|..|..++-...++|.-...|-. ..++..++ ++++-|.|+
T Consensus 154 ~Lt~~E~~ll~~l~~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~ 207 (229)
T PRK10161 154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALE 207 (229)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhc
Confidence 5999999999999998888888777644 34555555 445555554
No 292
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=44.43 E-value=62 Score=23.55 Aligned_cols=45 Identities=13% Similarity=0.237 Sum_probs=35.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHHh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQLE 71 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~LE 71 (117)
.+..||+.++.|+-+..- .|.-.++|-..+|++..+| .++++.|.
T Consensus 128 ~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 128 LLARLPEKMRLAIQAVKL---EGLSVAEAATRSGMSESAVKVSVHRGLKALA 176 (184)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 568899999988866543 6999999999999999874 55555553
No 293
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=44.32 E-value=31 Score=26.37 Aligned_cols=56 Identities=21% Similarity=0.277 Sum_probs=40.1
Q ss_pred ccccCCCHHH--------HHHHHHHHHhcCCcccHHHHHhhcCC-------ChHH-------HHHHHHHHhhcCCeeeec
Q psy7778 23 EKLKDSDNEE--------KVVYKIIEEAGNKGIWMRDIRFKSNL-------MPTQ-------LNKILKQLETKKIIKAVK 80 (117)
Q Consensus 23 ~k~~~L~~eE--------~lVY~~Ie~AGn~GIWtkdIk~ktnL-------~~~~-------l~K~LK~LE~k~LIK~VK 80 (117)
...+.|++++ -.|.-.|-.-|.-|| ..|+..+|. |.+. +.++|++||.-|||+..+
T Consensus 38 g~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV--~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 38 GVHKERPPEQEDWWYVRAASILRKVYIDGPVGV--ERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred cccccCCCCCCchHHHHHHHHHHHHHHcCCccH--HHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 3566666643 244555555565554 778999998 5555 999999999999999765
No 294
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=44.26 E-value=48 Score=22.62 Aligned_cols=44 Identities=11% Similarity=0.166 Sum_probs=31.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
.+..|++.|+.|+.++.. |.+.+.|....|+..+++...+..+-
T Consensus 138 ~~~~l~~~e~~vl~~~~~----~~~~~~ia~~l~~s~~tv~~~~~~~~ 181 (202)
T PRK09390 138 RIASLSERERQVMDGLVA----GLSNKVIARDLDISPRTVEVYRANVM 181 (202)
T ss_pred HHHhhhhhHHHHHHHHHc----cCchHHHHHHcCCCHHHHHHHHHHHH
Confidence 455688878877775443 66899999999999887665555443
No 295
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=44.26 E-value=57 Score=22.95 Aligned_cols=46 Identities=9% Similarity=0.118 Sum_probs=35.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE 71 (117)
..+..||++++.|+.+.. -.|.-.++|-..+|++.+++. ++++.|.
T Consensus 101 ~~l~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr 150 (159)
T PRK12527 101 RALAELPPACRDSFLLRK---LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150 (159)
T ss_pred HHHHhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 356789998888877753 578889999999999998754 4555553
No 296
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=44.19 E-value=51 Score=25.61 Aligned_cols=46 Identities=13% Similarity=0.327 Sum_probs=38.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
.+..|++.|+.|..+.. -+|.-.++|-..+|+++..|.++.+.+-.
T Consensus 180 ~l~~L~~~er~vi~l~~---~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 180 ALSQLDEREQLILHLYY---QHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred HHHcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57789998888887776 36788999999999999999988777643
No 297
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=44.17 E-value=55 Score=22.99 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=32.9
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.++.|+.+.. -.|.-.++|...+|++.++|+..+.
T Consensus 106 ~l~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 106 ALSELPARTRYAFEMYR---LHGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 56688888888886654 3488899999999999998766543
No 298
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=43.69 E-value=73 Score=27.44 Aligned_cols=52 Identities=15% Similarity=0.087 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChH-HHHHHHHHHhhcCCeee
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPT-QLNKILKQLETKKIIKA 78 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~-~l~K~LK~LE~k~LIK~ 78 (117)
.++++|++.|.++-.--+.|+....++.++|.... .+.+.+..|+..|++..
T Consensus 339 ~ls~~e~~~~~~~~~L~~~gld~~~f~~~~g~~~~~~~~~~l~~l~~~Gll~~ 391 (433)
T PRK08629 339 NFSKKEVMQYRFLLGMFSGRLSIKYFRETFGVNLDKALFKEMLLLKLIGAIKN 391 (433)
T ss_pred eCCHHHHHHHHHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEE
Confidence 47888888888877777789999999999998754 47789999999999884
No 299
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=43.49 E-value=74 Score=19.26 Aligned_cols=44 Identities=7% Similarity=0.232 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
.||.+|+++..+..-.. |.--.+|-...|+++++++|+.+..+.
T Consensus 2 kLs~~d~lll~L~~LR~--~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRL--NLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred CCCHHHHHHHHHHHHHc--CCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 57889998888887764 566789999999999999999987753
No 300
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=43.43 E-value=34 Score=26.97 Aligned_cols=48 Identities=19% Similarity=0.167 Sum_probs=41.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCC--cccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNK--GIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~--GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
+.+..||+-|+.|.+.|-+-... .+-+++|-.+++...++|.|-.|.|
T Consensus 21 ~~~~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkL 70 (292)
T PRK11337 21 MKQEGLTPLESRVVEWLLKPGDLSEATALKDIAEALAVSEAMIVKVAKKL 70 (292)
T ss_pred HHHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHc
Confidence 45778999999999999765543 3567999999999999999999998
No 301
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=43.27 E-value=51 Score=25.94 Aligned_cols=41 Identities=12% Similarity=0.192 Sum_probs=33.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
-+..|++.++.|+.+.. -.|.-.++|-..+|++...|.+.+
T Consensus 209 ~l~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~~ 249 (268)
T PRK06288 209 AIKTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLH 249 (268)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 46789999888877765 358889999999999999988443
No 302
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=43.19 E-value=21 Score=28.16 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+-++..++..|-+.|+- ..--.+.|+.|+.|++.||.||..
T Consensus 3 ~~~~L~~f~~v~e~gs~----s~AA~~L~iSQpavS~~I~~LE~~ 43 (308)
T PRK10094 3 DPETLRTFIAVAETGSF----SKAAERLCKTTATISYRIKLLEEN 43 (308)
T ss_pred CHHHHHHHHHHHHhCCH----HHHHHHhcCCHHHHHHHHHHHHHH
Confidence 34555666677666652 234678999999999999999984
No 303
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=42.97 E-value=68 Score=29.26 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCCh----HHHHHHHHHHhhcCCeeee
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMP----TQLNKILKQLETKKIIKAV 79 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~----~~l~K~LK~LE~k~LIK~V 79 (117)
+..|.++++++..+++-.++|.++.+++. ..+.++|+.|+..|.|...
T Consensus 4 ~~~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~ 55 (709)
T TIGR02063 4 RELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKN 55 (709)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc
Confidence 34688899999999999999999999974 3599999999999998643
No 304
>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=42.86 E-value=62 Score=24.45 Aligned_cols=43 Identities=9% Similarity=0.107 Sum_probs=34.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
-+..||+.|+.|+.+... .|.-.++|-..+|++.+.+.+.++.
T Consensus 175 ~l~~L~~~~r~vl~l~y~---~~~s~~eIA~~lgis~~~v~~~~~r 217 (227)
T TIGR02980 175 LLAALPERERRILLLRFF---EDKTQSEIAERLGISQMHVSRLLRR 217 (227)
T ss_pred HHHcCCHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467899999888877653 5889999999999999987766543
No 305
>PRK00118 putative DNA-binding protein; Validated
Probab=42.67 E-value=81 Score=22.46 Aligned_cols=41 Identities=7% Similarity=0.011 Sum_probs=32.4
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+.||+.++.++.+- .-.|.-.++|-..+|++.+++.+.++.
T Consensus 16 ~~L~ekqRevl~L~---y~eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 16 SLLTEKQRNYMELY---YLDDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred ccCCHHHHHHHHHH---HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46788888776443 345999999999999999998887764
No 306
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=42.64 E-value=21 Score=25.35 Aligned_cols=41 Identities=15% Similarity=0.182 Sum_probs=31.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~ 92 (117)
.+.++-..+|++.. .|+..|+.|||.+. .+-+|--+|++..
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~~~ 43 (127)
T TIGR02044 2 NIGQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQQH 43 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHH
Confidence 45677888888874 56789999999986 4556777887765
No 307
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=42.62 E-value=36 Score=29.16 Aligned_cols=55 Identities=16% Similarity=0.244 Sum_probs=44.6
Q ss_pred CCHHHHHHHHHHHHhc---CCcccHHHHHhh-cCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 28 SDNEEKVVYKIIEEAG---NKGIWMRDIRFK-SNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AG---n~GIWtkdIk~k-tnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
|+.-+..|..++++|+ ..++=-..|+++ .|+....+.=+||.|+.+||++.|-.+
T Consensus 4 ~~rk~ieIl~il~esd~plgak~Ia~el~kRGy~igeRavRYhlk~lderglt~kvgya 62 (325)
T COG1693 4 LNRKLIEILRILAESDEPLGAKIIALELRKRGYNIGERAVRYHLKKLDERGLTRKVGYA 62 (325)
T ss_pred HHHHHHHHHHHHHhcCCccchHHHHHHHHhcccchhHHHHHHHHHHHhhccchhhcccc
Confidence 4445668999999998 355666777777 678889999999999999999998754
No 308
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=42.35 E-value=70 Score=24.51 Aligned_cols=44 Identities=16% Similarity=0.207 Sum_probs=37.6
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+.|+.|..+|. +|--.++|-.+.++...+|+..+.++-+|
T Consensus 147 ~~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLA----EGLSNKEIAEELNLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHhHHHHHHHHHHHH
Confidence 369999999999996 69999999999999999987777766543
No 309
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=42.24 E-value=84 Score=22.09 Aligned_cols=56 Identities=9% Similarity=0.200 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcC-----CChHH----HHHHHHHHhhcC-Ceeeeccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN-----LMPTQ----LNKILKQLETKK-IIKAVKSV 82 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn-----L~~~~----l~K~LK~LE~k~-LIK~VKsV 82 (117)
.||+-|+.|+.++-...+...-..+|-.... +..++ ++++.+.|...+ +|+.|.++
T Consensus 148 ~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~~~~~i~t~~~~ 213 (221)
T PRK15479 148 ALTPREQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQGSDVRITTLRGL 213 (221)
T ss_pred ecCHHHHHHHHHHHhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCCCCCcEEEeccc
Confidence 5999999888888666666677777776543 44444 555555665443 45555443
No 310
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=41.92 E-value=53 Score=27.75 Aligned_cols=52 Identities=17% Similarity=0.224 Sum_probs=44.3
Q ss_pred CCCHHHHHHHHHHHHhcC-Cccc----HHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 27 DSDNEEKVVYKIIEEAGN-KGIW----MRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn-~GIW----tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
-|+++..+||.+.+..|. .=.| --|||...||...+..|+|=.|-.+|+|+.
T Consensus 222 ~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q 278 (287)
T COG2996 222 MLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ 278 (287)
T ss_pred hhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE
Confidence 356678899999999876 4444 358999999999999999999999999986
No 311
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.85 E-value=19 Score=22.19 Aligned_cols=42 Identities=14% Similarity=0.302 Sum_probs=30.4
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.++++...+|++.++| +..|.++++.+.++.+|-..|++..+
T Consensus 2 ti~eva~~~gvs~~tl----r~y~~~gll~~~~~~~g~r~y~~~dv 43 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTL----RYYEREGLLPPPRDENGYRYYSEEDV 43 (69)
T ss_dssp EHHHHHHHTTTTHHHH----HHHHHTTSSTTBESTTSSEEE-HHHH
T ss_pred cHHHHHHHHCcCHHHH----HHHHHhcCcccccccCceeeccHHHH
Confidence 4678889999998765 56788999988885555566665543
No 312
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=41.82 E-value=64 Score=23.01 Aligned_cols=43 Identities=9% Similarity=0.082 Sum_probs=34.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.-+..||+.++.|+.+..- +|.-.++|-..+|++..++...|.
T Consensus 108 ~~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 108 KALNLLSADQREAIILIGA---SGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4678899999888877655 788899999999999988655443
No 313
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=41.34 E-value=23 Score=27.18 Aligned_cols=42 Identities=12% Similarity=0.126 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|+-....+|..+-+.|+-. .--.+.|+.|+.|++.|++||..
T Consensus 3 m~l~~l~~f~~v~~~gS~s----~AA~~L~isq~avS~~I~~LE~~ 44 (300)
T TIGR02424 3 IKFRHLQCFVEVARQGSVK----RAAEALHITQPAVSKTLRELEEI 44 (300)
T ss_pred ccHHHHHHHHHHHHhCCHH----HHHHHhCCChHHHHHHHHHHHHH
Confidence 4445666777777776532 23567899999999999999984
No 314
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=41.29 E-value=64 Score=22.62 Aligned_cols=42 Identities=7% Similarity=-0.009 Sum_probs=33.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+..- .|.-.++|-..+|++.+++...+
T Consensus 118 ~~l~~L~~~~r~vl~l~~~---~g~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 118 KALKILTPKQQHVIALRFG---QNLPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred HHHHhCCHHHHHHHHHHHh---cCCCHHHHHHHHCCCHHHHHHHH
Confidence 4677899999988887553 57889999999999998865544
No 315
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=41.15 E-value=20 Score=27.21 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|+-.+...+..+-+.|+-. .=-.+.|+.|+.|++.||.||..
T Consensus 3 m~l~~L~~f~~v~e~~s~t----~AA~~L~isqpavS~~I~~LE~~ 44 (290)
T PRK10837 3 ITLRQLEVFAEVLKSGSTT----QASVMLALSQSAVSAALTDLEGQ 44 (290)
T ss_pred CcHHHHHHHHHHHHcCCHH----HHHHHhCCCccHHHHHHHHHHHH
Confidence 3444444555555555422 22568999999999999999984
No 316
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=40.67 E-value=78 Score=25.11 Aligned_cols=42 Identities=10% Similarity=0.150 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|+-.+..++..|-+.|+-. .--.+.|+.|+.|++.||.||..
T Consensus 2 m~l~~L~~f~av~~~gs~s----~AA~~L~iSqpaVS~~Ik~LE~~ 43 (317)
T PRK15421 2 IEVKHLKTLQALRNCGSLA----AAAATLHQTQSALSHQFSDLEQR 43 (317)
T ss_pred ccHHHHHHHHHHHHcCCHH----HHHHHhCCCHHHHHHHHHHHHHH
Confidence 3445666777777777532 23568899999999999999984
No 317
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=40.62 E-value=23 Score=27.63 Aligned_cols=22 Identities=14% Similarity=0.116 Sum_probs=19.5
Q ss_pred HHhhcCCChHHHHHHHHHHhhc
Q psy7778 52 IRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 52 Ik~ktnL~~~~l~K~LK~LE~k 73 (117)
--.+.|+.|+.|++.|++||..
T Consensus 21 AA~~L~isQ~avS~~I~~LE~~ 42 (305)
T PRK11233 21 AAEVLHIAQPALSQQVATLEGE 42 (305)
T ss_pred HHHHhCCCchHHHHHHHHHHHH
Confidence 3678999999999999999984
No 318
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=40.52 E-value=63 Score=25.08 Aligned_cols=43 Identities=7% Similarity=0.111 Sum_probs=35.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
..+..||+.++.|+.+.. -.|.-.++|-..+|++..+|.+.++
T Consensus 201 ~~l~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 201 KILPVLSDREKSIIQCTF---IENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 357789999998887765 4789999999999999999876654
No 319
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=40.39 E-value=68 Score=22.50 Aligned_cols=44 Identities=11% Similarity=0.075 Sum_probs=33.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~L 70 (117)
.+..||+.++.|+.+-. -.|.-.++|-..+|++.+++ .++.+.|
T Consensus 103 ~l~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 103 KLRELPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRARKWI 150 (160)
T ss_pred HHHhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46778887777665543 46889999999999999987 5555555
No 320
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=40.17 E-value=24 Score=27.28 Aligned_cols=50 Identities=10% Similarity=0.154 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc---CCeeeecccc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK---KIIKAVKSVA 83 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k---~LIK~VKsV~ 83 (117)
-.+..++..|-+.|+ +-. =-.+.|+.|+.|++.||.||+. .|+..-+++.
T Consensus 4 ~~~L~~f~~v~e~gs--~s~--AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~ 56 (294)
T PRK03635 4 YKQLEALAAVVREGS--FER--AAQKLHITQSAVSQRIKALEERVGQVLLVRTQPCR 56 (294)
T ss_pred HHHHHHHHHHHHcCC--HHH--HHHHhCCChHHHHHHHHHHHHHhCceeeecCCCCc
Confidence 344455555555554 222 2568999999999999999983 5555534443
No 321
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=39.92 E-value=77 Score=18.44 Aligned_cols=37 Identities=8% Similarity=0.144 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
.++...+++.+.+. .-.+++...+|+..++|.++++.
T Consensus 14 ~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 14 KRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34445566666666 88999999999999999999875
No 322
>PRK10632 transcriptional regulator; Provisional
Probab=39.78 E-value=26 Score=27.47 Aligned_cols=21 Identities=10% Similarity=0.230 Sum_probs=19.0
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
-.+.|+.|+.|++.|+.||..
T Consensus 23 A~~L~isQpavS~~I~~LE~~ 43 (309)
T PRK10632 23 ARQLQMSVSSISQTVSKLEDE 43 (309)
T ss_pred HHHhCCCHHHHHHHHHHHHHH
Confidence 567899999999999999984
No 323
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=39.70 E-value=27 Score=26.72 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..+..|-+.|+ + ..--.+.++.|+.|++.||.||..
T Consensus 7 ~~f~~v~~~gs--~--s~AA~~L~itqpavS~~Ik~LE~~ 42 (291)
T TIGR03418 7 RVFESAARLAS--F--TAAARELGSTQPAVSQQVKRLEEE 42 (291)
T ss_pred HHHHHHHHhCC--H--HHHHHHhCCCHHHHHHHHHHHHHH
Confidence 44445555553 2 223678999999999999999984
No 324
>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=39.69 E-value=67 Score=24.74 Aligned_cols=45 Identities=11% Similarity=0.111 Sum_probs=36.4
Q ss_pred cccCCCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.|+.|..+..--+ .+|.-.++|-...|++...|.++.+
T Consensus 173 ~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 173 VLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred HHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 57789999999888876322 5899999999999999998766543
No 325
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=39.69 E-value=23 Score=27.91 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.1
Q ss_pred HHHhhcCCChHHHHHHHHHHhhc
Q psy7778 51 DIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 51 dIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.--.+.|+.|+.|++.||.||+.
T Consensus 21 ~AA~~L~iSQ~avSr~I~~LE~~ 43 (316)
T PRK12679 21 EVANMLFTSQSGVSRHIRELEDE 43 (316)
T ss_pred HHHHHhcCCchHHHHHHHHHHHH
Confidence 34678999999999999999984
No 326
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=39.41 E-value=21 Score=27.31 Aligned_cols=37 Identities=19% Similarity=0.152 Sum_probs=25.7
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..++-.+.+.|+ + ..--.+.|+.|+.|+|.|+.||..
T Consensus 6 L~~f~~v~~~gs--~--s~AA~~L~isQ~avSr~i~~LE~~ 42 (296)
T PRK09906 6 LRYFVAVAEELN--F--TKAAEKLHTAQPSLSQQIKDLENC 42 (296)
T ss_pred HHHHHHHHhhCC--H--HHHHHHhCCCCcHHHHHHHHHHHH
Confidence 334444444443 2 233678999999999999999983
No 327
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=39.11 E-value=1e+02 Score=24.03 Aligned_cols=60 Identities=15% Similarity=0.151 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc------CCcccccCc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA------NIEYLTEGT 92 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~------gg~wYtdg~ 92 (117)
+-..|+..+..-| =+--.+|...+|+-.+.+.|+|-.|-..|+|.-.+... --.||.+.+
T Consensus 19 ~~~~v~~~l~~kg--e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~ 84 (176)
T COG1675 19 EAVLVVDALLEKG--ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYE 84 (176)
T ss_pred hhhHHHHHHHhcC--CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechH
Confidence 3445666666544 37788899999999999999999999999999888775 344555543
No 328
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.10 E-value=25 Score=23.83 Aligned_cols=41 Identities=5% Similarity=0.137 Sum_probs=29.9
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~ 92 (117)
.+.++-..+|++.. .|+..|..|||.+. .+-+|--.|++..
T Consensus 2 ~i~eva~~~gvs~~----tlR~ye~~Gll~p~~r~~~gyR~Y~~~~ 43 (96)
T cd04788 2 KIGELARRTGLSVR----TLHHYDHIGLLSPSQRTEGGHRLYDRAD 43 (96)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCHHH
Confidence 45678888899885 56788999999985 4445556676655
No 329
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=39.03 E-value=26 Score=21.83 Aligned_cols=43 Identities=12% Similarity=0.302 Sum_probs=30.9
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhc-CCeeeeccccCCcccccCccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETK-KIIKAVKSVANIEYLTEGTVN 94 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k-~LIK~VKsV~gg~wYtdg~~D 94 (117)
.+.++-..+|++.++|. ..|.+ +++.+..+-.|--+|++.+++
T Consensus 2 ~i~e~A~~~gVs~~tlr----~ye~~~gl~~~~r~~~g~R~yt~~di~ 45 (68)
T cd04763 2 TIGEVALLTGIKPHVLR----AWEREFGLLKPQRSDGGHRLFNDADID 45 (68)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHhcCCCCCCcCCCCCcccCHHHHH
Confidence 46778888999987665 66776 999887766666677766543
No 330
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.02 E-value=25 Score=24.79 Aligned_cols=51 Identities=12% Similarity=0.205 Sum_probs=34.9
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCccc-cccchhhh
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTVN-AMVLPSRK 102 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~D-~~fI~~l~ 102 (117)
.+.++-+.+|++. +.|+..|..|||.+. .+-+|--+|++..+. ..+|-.++
T Consensus 2 ~IgevA~~~gvs~----~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr 54 (127)
T cd04784 2 KIGELAKKTGCSV----ETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCR 54 (127)
T ss_pred CHHHHHHHHCcCH----HHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHH
Confidence 3567788888887 467889999999864 555666777776643 33444333
No 331
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.98 E-value=26 Score=23.79 Aligned_cols=41 Identities=10% Similarity=0.170 Sum_probs=31.0
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc-ccCCcccccCcc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS-VANIEYLTEGTV 93 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs-V~gg~wYtdg~~ 93 (117)
+.++...+|++.. .|+..|+.|||.++.. -+|--+|++..+
T Consensus 3 i~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~~l 44 (96)
T cd04768 3 IGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYAQL 44 (96)
T ss_pred HHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHHHH
Confidence 4677788888875 5678899999999864 455578887764
No 332
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=38.88 E-value=57 Score=25.34 Aligned_cols=49 Identities=14% Similarity=0.275 Sum_probs=40.5
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKII 76 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LI 76 (117)
++.+...|+.+++...+.|+-..+|....|.+.....-.|..+|..|++
T Consensus 172 ~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 172 LSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp H-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred hhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 4556678888887778899999999999999999999999999999986
No 333
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=38.33 E-value=28 Score=26.81 Aligned_cols=39 Identities=13% Similarity=0.070 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+...+..|.+.|+ +... -.+.|+.|+.|++.|+.||..
T Consensus 4 ~~l~~f~~v~~~gs--~s~A--A~~L~isqpavS~~I~~LE~~ 42 (275)
T PRK03601 4 ELLKTFLEVSRTRH--FGRA--AESLYLTQSAVSFRIRQLENQ 42 (275)
T ss_pred HHHHHHHHHHHcCC--HHHH--HHHhCCChHHHHHHHHHHHHH
Confidence 34445555555554 3333 678999999999999999983
No 334
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.22 E-value=63 Score=23.12 Aligned_cols=43 Identities=7% Similarity=0.097 Sum_probs=34.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
..+..||+.++.|+.+..- .|.-.++|-..+|++.+.+...|.
T Consensus 132 ~~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 132 QEIQALPPKYRMVIVLKYM---EDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred HHHHhCCHHHhHHhhhHHh---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3577899999988866433 589999999999999988665553
No 335
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=38.18 E-value=26 Score=26.86 Aligned_cols=44 Identities=14% Similarity=0.246 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc---CCeee
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK---KIIKA 78 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k---~LIK~ 78 (117)
.....+..+-+.|+ +- .=-.+.|+.|+.|++.|+.||.. .|+..
T Consensus 5 ~~L~~f~~v~~~gs--~t--~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R 51 (294)
T PRK13348 5 KQLEALAAVVETGS--FE--RAARRLHVTPSAVSQRIKALEESLGQPLLVR 51 (294)
T ss_pred HHHHHHHHHHHcCC--HH--HHHHHhCCCchHHHHHHHHHHHHhCceeeec
Confidence 34445555555553 22 22678999999999999999984 55544
No 336
>PRK09801 transcriptional activator TtdR; Provisional
Probab=37.96 E-value=28 Score=27.47 Aligned_cols=39 Identities=18% Similarity=0.168 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..++..+-+.|+ +... -.+.|+.|+.|++.||.||+.
T Consensus 9 ~~L~~F~~v~~~gs--~t~A--A~~L~iSQpavS~~I~~LE~~ 47 (310)
T PRK09801 9 KDLQVLVEIVHSGS--FSAA--AATLGQTPAFVTKRIQILENT 47 (310)
T ss_pred HHHHHHHHHHHcCC--HHHH--HHHhCcCHHHHHHHHHHHHHH
Confidence 34444444444443 3333 678999999999999999984
No 337
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=37.88 E-value=64 Score=25.17 Aligned_cols=43 Identities=9% Similarity=0.060 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.|+-.+..++-.+.+.|+-.= --.+.|+.|+.|++.||.||..
T Consensus 3 ~~~l~~L~~f~av~~~gS~s~----AAe~L~isqsavS~~Ik~LE~~ 45 (309)
T PRK11013 3 AVSLRHIEIFHAVMTAGSLTE----AARLLHTSQPTVSRELARFEKV 45 (309)
T ss_pred CccHHHHHHHHHHHHhCcHHH----HHHHHCCCcHHHHHHHHHHHHH
Confidence 355566677777777775332 2567899999999999999984
No 338
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.69 E-value=75 Score=22.19 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=35.2
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+.+..||+.++.|+.+..- .|.-..+|-...|++.++|.+.+..
T Consensus 121 ~~l~~L~~~~r~i~~l~~~---~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 121 RCLDALPVKQREVFLLRYV---EGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred HHHHhCCHHHHHHhhHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578899998888776653 5888999999999999987766543
No 339
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=37.68 E-value=81 Score=23.87 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=34.2
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
+-+..|++.++.|+.+.. -.|.-.++|-..+|++...+.+.+
T Consensus 171 ~~l~~L~~~~r~il~l~y---~~~~s~~eIA~~lgis~~tV~~~~ 212 (224)
T TIGR02479 171 EAIESLSEREQLVLSLYY---YEELNLKEIGEVLGLTESRVSQIH 212 (224)
T ss_pred HHHHhCCHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHH
Confidence 357789998888777665 478899999999999999987643
No 340
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=37.58 E-value=43 Score=21.44 Aligned_cols=37 Identities=19% Similarity=0.270 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
++...++...+ ....+...+.++|..|-.+++|+.-.
T Consensus 28 L~~~v~~~l~~----------~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 28 LINEVIEELKK----------RFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHTTT----------TS---HHHHHHHHHHHHHTTSEEEES
T ss_pred HHHHHHHHhcC----------CcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 55555555443 55677789999999999999998643
No 341
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=37.50 E-value=27 Score=24.84 Aligned_cols=43 Identities=9% Similarity=0.132 Sum_probs=32.3
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeee-eccccCCcccccCccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKA-VKSVANIEYLTEGTVN 94 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~-VKsV~gg~wYtdg~~D 94 (117)
.+.++-..+|++.. .|+..|..||+.+ ..+-+|--+|++..++
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~ 45 (127)
T cd01108 2 NIGEAAKLTGLSAK----MIRYYEEIGLIPPPSRSDNGYRVYNQRDIE 45 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHHH
Confidence 45678888998885 5678999999985 5566677778877644
No 342
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=37.48 E-value=30 Score=26.65 Aligned_cols=41 Identities=17% Similarity=0.175 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+-.+..++..|.+.|+-.- --.+.|+.|+.|++.|+.||+.
T Consensus 3 ~l~~L~~f~~va~~gs~s~----AA~~L~isQpavS~~I~~LE~~ 43 (301)
T PRK14997 3 DLNDFAWFVHVVEEGGFAA----AGRALDEPKSKLSRRIAQLEER 43 (301)
T ss_pred cHHHHHHHHHHHHcCCHHH----HHHHhCCCHHHHHHHHHHHHHH
Confidence 3445566666666665322 2567899999999999999984
No 343
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=37.28 E-value=85 Score=23.82 Aligned_cols=44 Identities=14% Similarity=0.151 Sum_probs=35.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
.-+..|++.|+.|+.+... +|.-.++|-..+|+++..|.++.+.
T Consensus 179 ~~l~~L~~~e~~i~~~~~~---~~~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 179 EAISKLDERERQIIMLRYF---KDKTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred HHHHcCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3577999999988877643 5788999999999999998766543
No 344
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=37.26 E-value=78 Score=23.33 Aligned_cols=44 Identities=9% Similarity=0.051 Sum_probs=34.5
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~L 70 (117)
.+..||+.++.|+.+..- .|.-.++|-..+|++.++|. ++++.|
T Consensus 133 ~l~~L~~~~r~i~~L~~~---~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 133 ALAALPERQRQAVVLRHI---EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 577899989888777654 58889999999999998854 455555
No 345
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=37.20 E-value=62 Score=26.85 Aligned_cols=79 Identities=23% Similarity=0.329 Sum_probs=53.8
Q ss_pred cccCCCHHHH-HHHHHHHH-hcCCcccHH-HHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchh
Q psy7778 24 KLKDSDNEEK-VVYKIIEE-AGNKGIWMR-DIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPS 100 (117)
Q Consensus 24 k~~~L~~eE~-lVY~~Ie~-AGn~GIWtk-dIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~ 100 (117)
..+.||--|. .|=.++++ -||+|.-++ -|..+-|+..+++-.+|+.||+-|.|-+=.==--|.|.. -++..|.+.
T Consensus 179 Ai~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSRSLGMKGTyik--vln~~~l~e 256 (261)
T COG4465 179 AISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIK--VLNDKFLDE 256 (261)
T ss_pred HHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeecccCccceeEe--eehhhHHHH
Confidence 3456776554 44444444 588998776 478899999999999999999999997632111333332 366667777
Q ss_pred hhhh
Q psy7778 101 RKKR 104 (117)
Q Consensus 101 l~~~ 104 (117)
|+++
T Consensus 257 l~k~ 260 (261)
T COG4465 257 LEKR 260 (261)
T ss_pred Hhcc
Confidence 6654
No 346
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.17 E-value=28 Score=23.27 Aligned_cols=42 Identities=21% Similarity=0.293 Sum_probs=31.1
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGT 92 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~ 92 (117)
..+.++...+|++..+| +..|.+|+|.+..+-. |.-.|++..
T Consensus 2 ~ti~evA~~~gvs~~tL----R~ye~~Gll~p~r~~~~g~R~Ys~~d 44 (88)
T cd01105 2 IGIGEVSKLTGVSPRQL----RYWEEKGLIKSIRSDGGGQRKYSLAD 44 (88)
T ss_pred cCHHHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCceecCHHH
Confidence 45677888888888665 5669999999877775 666676544
No 347
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=37.12 E-value=26 Score=24.86 Aligned_cols=40 Identities=10% Similarity=0.158 Sum_probs=29.4
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeee-eccccCCcccccCc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKA-VKSVANIEYLTEGT 92 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~-VKsV~gg~wYtdg~ 92 (117)
+.++-.++|++..+| +..|..|||.+ ..+-+|--+|++..
T Consensus 2 I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~g~R~Y~~~~ 42 (124)
T TIGR02051 2 IGELAKAAGVNVETI----RYYERKGLLPEPDRPEGGYRRYPEET 42 (124)
T ss_pred HHHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEeECHHH
Confidence 467788899998765 67799999985 45555666676544
No 348
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=37.08 E-value=27 Score=27.91 Aligned_cols=26 Identities=15% Similarity=0.129 Sum_probs=21.4
Q ss_pred HhhcCCChHHHHHHHHHHhhc---CCeee
Q psy7778 53 RFKSNLMPTQLNKILKQLETK---KIIKA 78 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k---~LIK~ 78 (117)
-.+.++.|+.|++.|+.||+. .|+..
T Consensus 23 A~~L~iSQpavS~~I~~LE~~lG~~LF~R 51 (324)
T PRK12681 23 AEGLYTSQPGISKQVRMLEDELGIQIFAR 51 (324)
T ss_pred HHHhcCCcHHHHHHHHHHHHHhCCEeEEE
Confidence 567899999999999999984 45444
No 349
>COG3177 Fic family protein [Function unknown]
Probab=37.01 E-value=56 Score=27.26 Aligned_cols=43 Identities=16% Similarity=0.089 Sum_probs=37.3
Q ss_pred cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 43 GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 43 Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
.+.++-..++-..++++.++++|.|+.|..+|++.+++.=.-+
T Consensus 301 ~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~ 343 (348)
T COG3177 301 QEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRS 343 (348)
T ss_pred cCCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCc
Confidence 4577888899999999999999999999999999999864433
No 350
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.89 E-value=68 Score=22.10 Aligned_cols=41 Identities=22% Similarity=0.310 Sum_probs=29.0
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~ 92 (117)
.+.++.+.+|++..+ |+..|..|||++...-. |--+|++..
T Consensus 2 ~i~e~a~~~gvs~~t----lr~ye~~gll~~~~r~~~gyR~Y~~~~ 43 (113)
T cd01109 2 TIKEVAEKTGLSADT----LRYYEKEGLLPPVKRDENGIRDFTEED 43 (113)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCccCCHHH
Confidence 356788889998854 56789999998765444 445666655
No 351
>PRK06930 positive control sigma-like factor; Validated
Probab=36.77 E-value=77 Score=23.94 Aligned_cols=44 Identities=18% Similarity=0.241 Sum_probs=35.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
.+..||+.|+.|+.+.. -.|.-.++|-..+|++.+++...++..
T Consensus 111 al~~L~~rer~V~~L~~---~eg~s~~EIA~~lgiS~~tVk~~l~Ra 154 (170)
T PRK06930 111 ALSVLTEREKEVYLMHR---GYGLSYSEIADYLNIKKSTVQSMIERA 154 (170)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 37889999999887754 468889999999999998877766543
No 352
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=36.59 E-value=28 Score=27.13 Aligned_cols=22 Identities=14% Similarity=0.099 Sum_probs=19.7
Q ss_pred HHhhcCCChHHHHHHHHHHhhc
Q psy7778 52 IRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 52 Ik~ktnL~~~~l~K~LK~LE~k 73 (117)
--.+.|+.|+.|++.|+.||+.
T Consensus 22 AA~~L~isq~avSr~I~~LE~~ 43 (309)
T PRK12682 22 AAKALHTSQPGVSKAIIELEEE 43 (309)
T ss_pred HHHHhcCccHHHHHHHHHHHHH
Confidence 3678999999999999999984
No 353
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=36.51 E-value=85 Score=24.30 Aligned_cols=43 Identities=7% Similarity=0.115 Sum_probs=35.7
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
+.+..||+.|+.|+.+.. -.|.-.++|-..+|++...|.+.+.
T Consensus 201 ~~l~~L~~~~r~ii~l~~---~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 201 KILPILSEREKSIIHCTF---EENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 457789999998888776 3688899999999999999876653
No 354
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=36.48 E-value=28 Score=25.41 Aligned_cols=42 Identities=12% Similarity=0.254 Sum_probs=31.7
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~ 93 (117)
.+.++-..+|++.. .|+..|..|||.+. .+-+|--+|++..+
T Consensus 3 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l 45 (140)
T PRK09514 3 RIGELAKLAEVTPD----TLRFYEKQGLMDPEVRTEGGYRLYTEQDL 45 (140)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCCeeeCHHHH
Confidence 35677888888874 56788999999986 45556678887764
No 355
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=36.46 E-value=31 Score=26.78 Aligned_cols=40 Identities=15% Similarity=0.169 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
-++..++..+-+.|+- ..=-.+.|+.|+.|++.||.||..
T Consensus 4 ~~~L~~f~~v~e~~s~----s~AA~~L~isQpavS~~I~~LE~~ 43 (300)
T PRK11074 4 EYSLEVVDAVARTGSF----SAAAQELHRVPSAVSYTVRQLEEW 43 (300)
T ss_pred HHHHHHHHHHHHhCCH----HHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3455666666666642 222567999999999999999984
No 356
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.41 E-value=28 Score=25.55 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=31.6
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
.+.++-..+|++.. .|+..|..|||++..+-+|--+|++..+
T Consensus 2 ~I~e~a~~~gvs~~----TLR~Ye~~GLl~p~r~~~g~R~Y~~~~l 43 (134)
T cd04779 2 RIGQLAHLAGVSKR----TIDYYTNLGLLTPERSDSNYRYYDETAL 43 (134)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCeeECHHHH
Confidence 35677788888875 5677899999998776666667887763
No 357
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=36.36 E-value=1.2e+02 Score=24.83 Aligned_cols=58 Identities=17% Similarity=0.133 Sum_probs=43.1
Q ss_pred ccccCCCHHHHHHH-----HHHHHhcC--CcccHHH-HHhhcC--CChHHHHHHHHHHhhcCCeeeec
Q psy7778 23 EKLKDSDNEEKVVY-----KIIEEAGN--KGIWMRD-IRFKSN--LMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 23 ~k~~~L~~eE~lVY-----~~Ie~AGn--~GIWtkd-Ik~ktn--L~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.+.+-|+.++...| ..|.+.-. .|-|.-. |-++++ ++..+++.+|.-|++-||||.-.
T Consensus 106 ~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~ 173 (271)
T TIGR02147 106 PRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE 173 (271)
T ss_pred chheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC
Confidence 35566777776644 45666553 3665444 999999 88999999999999999999753
No 358
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=36.20 E-value=28 Score=27.39 Aligned_cols=21 Identities=19% Similarity=0.156 Sum_probs=19.1
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
-.+.|+.|+.|++.||.||+.
T Consensus 23 A~~L~isQpavS~~I~~LE~~ 43 (309)
T PRK12683 23 ANALYTSQSGVSKQIKDLEDE 43 (309)
T ss_pred HHHhcCCcHHHHHHHHHHHHH
Confidence 567999999999999999984
No 359
>TIGR03184 DNA_S_dndE DNA sulfur modification protein DndE. This model describes the DndE protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=36.15 E-value=52 Score=23.53 Aligned_cols=56 Identities=20% Similarity=0.234 Sum_probs=38.5
Q ss_pred HHHHhhcCCCh-HHHHHH--HHHHhhcCCeeeecccc-CC---cccc-cCccccccchhhhhhh
Q psy7778 50 RDIRFKSNLMP-TQLNKI--LKQLETKKIIKAVKSVA-NI---EYLT-EGTVNAMVLPSRKKRE 105 (117)
Q Consensus 50 kdIk~ktnL~~-~~l~K~--LK~LE~k~LIK~VKsV~-gg---~wYt-dg~~D~~fI~~l~~~~ 105 (117)
+.|+.+||+.+ +++-|. -.+|++-...-.+.... +| .||| -|+++.-|+.-|+||.
T Consensus 12 ~~Lk~~Tgi~~~NilcR~A~~~SL~~~~~~~~~~~~~d~~~E~~~~T~~Ge~~~i~~alLkq~~ 75 (105)
T TIGR03184 12 RRLKRRTGLTPWNILCRWAFCLSLEEGSTPGVADIKLDGNVEIDWYTFAGEYGDIYLALLKQRC 75 (105)
T ss_pred HHHhcccCCCcchHHHHHHHHHHHhcCCCCCccccCCCCCeEEEeeeecCchHHHHHHHHHHHH
Confidence 46899999999 998885 57777754333332222 33 2443 2889999999999884
No 360
>PRK13824 replication initiation protein RepC; Provisional
Probab=35.85 E-value=73 Score=27.60 Aligned_cols=66 Identities=12% Similarity=0.107 Sum_probs=49.3
Q ss_pred cccccCCCHHHHHHHHHHHHhcCCccc-----------HHHHHhhc-CCChHHHHHHHHHHhhcCCeeeeccccCCcc
Q psy7778 22 NEKLKDSDNEEKVVYKIIEEAGNKGIW-----------MRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSVANIEY 87 (117)
Q Consensus 22 a~k~~~L~~eE~lVY~~Ie~AGn~GIW-----------tkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~w 87 (117)
|...-+|++-+..|.+..=.--..--| ...|-.++ ||+.++|.++|..|+.-|||.-=-|-+|.-|
T Consensus 47 a~~~lGl~~~~l~vL~aLlsf~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGLI~rrDSpNGKRy 124 (404)
T PRK13824 47 ARALLGVSDRALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIRRDSPNGKRY 124 (404)
T ss_pred HHHhcCCChhHHHHHHHHHhhCCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEeecCCCCccc
Confidence 345567777666666655443333333 56788885 8999999999999999999998888887777
No 361
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=35.84 E-value=93 Score=25.99 Aligned_cols=50 Identities=18% Similarity=0.215 Sum_probs=36.8
Q ss_pred HHHHHHHHHh--cCCcccHHHHHhh--cCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 33 KVVYKIIEEA--GNKGIWMRDIRFK--SNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 33 ~lVY~~Ie~A--Gn~GIWtkdIk~k--tnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.+++.+|++. ...-+-+++|-.+ .+....++.+-+..||..|++..+..-
T Consensus 6 ~il~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~h~s 59 (337)
T TIGR00331 6 KILKAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKPHTS 59 (337)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCCCCC
Confidence 3444444433 2244668999999 888899999999999999999775443
No 362
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=35.81 E-value=30 Score=25.27 Aligned_cols=41 Identities=15% Similarity=0.156 Sum_probs=31.3
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
.++.++...+|++..+|. ..|++|+|.+... .|.-+|++..
T Consensus 2 ysI~eVA~~~GVs~~TLR----~wE~~GLl~p~r~-~G~R~Ys~~d 42 (120)
T cd04767 2 YPIGVVAELLNIHPETLR----IWERHGLIKPARR-NGQRLYSNND 42 (120)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCcCC-CCcEEECHHH
Confidence 356788889999987654 8899999998654 6667777655
No 363
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=35.80 E-value=74 Score=23.89 Aligned_cols=37 Identities=27% Similarity=0.380 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
.+++..|+.+. .+|...++|.+.+|++.+++.|.+|.
T Consensus 159 ~~~~~~i~~~~----~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 159 TGKEEKIKKLL----DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred chhHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34445555543 56899999999999999999999984
No 364
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.22 E-value=1.1e+02 Score=20.86 Aligned_cols=70 Identities=17% Similarity=0.028 Sum_probs=48.2
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhh
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKK 103 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~ 103 (117)
+.-|+|+++ ++++.+-+.|.+...+..+.++ +.+++.+=++++...+..-...+-. ....+..++-.+.+
T Consensus 6 r~~s~EfK~--~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~~~------~~~~~~~~~~~l~~ 76 (116)
T COG2963 6 KKYSPEFKL--EAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGKGK------TVSYDAEEILRLRK 76 (116)
T ss_pred ccCCHHHHH--HHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCccc------cCCcCHHHHHHHHH
Confidence 345666552 4566667777799999999996 9999999999998766544332211 33466667766644
No 365
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=35.04 E-value=35 Score=26.18 Aligned_cols=49 Identities=12% Similarity=0.238 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc---CCeeeecccc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK---KIIKAVKSVA 83 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k---~LIK~VKsV~ 83 (117)
.+..+|..+.+.|+- ..=-.+.|+.|+.|++.|+.||.. .|+..-+.|.
T Consensus 4 ~~l~~f~~v~~~~s~----t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~r~~~ 55 (292)
T TIGR03298 4 RQLAALAAVVEEGSF----ERAAAALSVTPSAVSQRIKALEERLGQPLLVRTQPCR 55 (292)
T ss_pred HHHHHHHHHHHcCCH----HHHHHHhCCCHHHHHHHHHHHHHHhCchheecCCCCc
Confidence 344455555555542 223567899999999999999983 5555434443
No 366
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=34.77 E-value=80 Score=22.76 Aligned_cols=42 Identities=14% Similarity=0.167 Sum_probs=33.5
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+..-. |.-.++|-..+|++.++|...+
T Consensus 127 ~~l~~L~~~~r~v~~l~~~~---g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 127 RHLETLPPRQRDVVQSISVE---GASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred HHHHhCCHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHH
Confidence 46788999999888776433 8999999999999998855443
No 367
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=34.75 E-value=1.1e+02 Score=20.85 Aligned_cols=44 Identities=5% Similarity=0.122 Sum_probs=33.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
..+..|++.++.|+.+-.- .|.-.++|-..+|++.+++...+..
T Consensus 109 ~~l~~L~~~~r~il~l~~~---~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 109 KAIEKLPEQCRKIFILSRF---EGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred HHHHHCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3567888888877766332 5888999999999999996655544
No 368
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=34.74 E-value=43 Score=25.31 Aligned_cols=56 Identities=18% Similarity=0.202 Sum_probs=35.4
Q ss_pred ccccCCCHHHH--------HHHHHHHHhcCCcccHHHHHhhcC--------------CChHHHHHHHHHHhhcCCeeeec
Q psy7778 23 EKLKDSDNEEK--------VVYKIIEEAGNKGIWMRDIRFKSN--------------LMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 23 ~k~~~L~~eE~--------lVY~~Ie~AGn~GIWtkdIk~ktn--------------L~~~~l~K~LK~LE~k~LIK~VK 80 (117)
...+.|+|++- .|.-.|---|.-| ...+++..| =..+++.++|.+||.-+||....
T Consensus 37 g~~kE~~P~~~DW~Y~RaASilRklY~~g~~G--V~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 37 GSHKELAPYDPDWWYIRAASILRKLYIRGPVG--VGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp SSS-SSTTCHHTHHHHHHHHHHHHHHHCTSB---HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred cccccCCCCCCCeeeeeHHHHHHHHHHhcCcc--hHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 35666776431 3344455556444 466675544 34468999999999999999885
No 369
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=34.70 E-value=98 Score=20.18 Aligned_cols=38 Identities=8% Similarity=0.184 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
||-.-...+....|...+..-++.....|..|.+.|..
T Consensus 50 i~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~~i~~ 87 (118)
T PF02984_consen 50 ILLARKILGKEPPWPESLEKLTGYDKEDLKECIELIQE 87 (118)
T ss_dssp HHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHhCccccCCccchhhcCCCHHHHHHHHHHHHH
Confidence 44444555555799999999999999999999999875
No 370
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=34.62 E-value=36 Score=23.08 Aligned_cols=42 Identities=10% Similarity=0.030 Sum_probs=30.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec-cccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK-SVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK-sV~gg~wYtdg~~ 93 (117)
.+.++-..+|++..+ |+..|+.|||.+.. +=+|--+|++..+
T Consensus 2 ~i~eva~~~gvs~~t----lR~ye~~Gll~p~~~~~~gyR~Y~~~~~ 44 (97)
T cd04782 2 TTGEFAKLCGISKQT----LFHYDKIGLFKPEIVKENGYRYYTLEQF 44 (97)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCccCCHHHH
Confidence 356778888888854 56779999999874 3345567877664
No 371
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=34.59 E-value=87 Score=23.95 Aligned_cols=41 Identities=10% Similarity=0.225 Sum_probs=33.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
.+..||+.++.|+.+.. -.|.-.++|-..+|++...|.+.+
T Consensus 181 ~l~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~ 221 (236)
T PRK06986 181 AIESLPEREQLVLSLYY---QEELNLKEIGAVLGVSESRVSQIH 221 (236)
T ss_pred HHHhCCHHHHHHHHhHh---ccCCCHHHHHHHHCCCHHHHHHHH
Confidence 57789998988887765 478899999999999999877443
No 372
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=34.50 E-value=89 Score=21.51 Aligned_cols=44 Identities=20% Similarity=0.200 Sum_probs=36.6
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
|=++|+.-|.. -.++|..+.++|...|.-.|..|+.+|-|-.|.
T Consensus 7 lRd~l~~~gr~--s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 7 VRDLLALRGRM--EAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHcCcc--cHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 34456555554 458999999999999999999999999999986
No 373
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=34.48 E-value=33 Score=26.10 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..++..|-+.|+ + ..--.+.++.|+.|++.|+.||..
T Consensus 4 ~~L~~f~~v~~~gs--~--s~AA~~L~isqsavS~~i~~LE~~ 42 (296)
T PRK11242 4 RHIRYFLAVAEHGN--F--TRAAEALHVSQPTLSQQIRQLEES 42 (296)
T ss_pred HHHHHHHHHHHhCC--H--HHHHHHcCCCchHHHHHHHHHHHH
Confidence 44455556666554 2 223678999999999999999984
No 374
>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=34.39 E-value=48 Score=21.85 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKII 76 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LI 76 (117)
.||+++.+ +..+-.++|++.|++++..+.-+|==|-..+=|
T Consensus 12 ~Vw~~L~~--~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI 52 (65)
T PF10771_consen 12 KVWQLLNE--NGEWSVSELKKATGLSDKEVYLAIGWLARENKI 52 (65)
T ss_dssp HHHHHHCC--SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSE
T ss_pred HHHHHHhh--CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCce
Confidence 68999887 556778999999999999999998888554434
No 375
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=34.28 E-value=97 Score=22.09 Aligned_cols=42 Identities=7% Similarity=0.086 Sum_probs=33.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.++.|+.+..- .|.-.++|-..+|++..++.+.+.
T Consensus 137 ~l~~L~~~~r~vi~l~~~---~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 137 ALAKLPEDYREVILLRHL---EGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred HHHcCCHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 467899988877766553 799999999999999998766543
No 376
>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=34.23 E-value=50 Score=19.40 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=22.3
Q ss_pred HHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 38 IIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 38 ~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.|.+-=..|+-..+|-..+|+..++|-|+|+
T Consensus 13 ~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3333445679999999999999999999875
No 377
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=34.18 E-value=57 Score=27.46 Aligned_cols=48 Identities=15% Similarity=0.204 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
++++...+=---=..|+-..+|-.+.||...+++|-|+....+|+|+=
T Consensus 11 ~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I 58 (321)
T COG2390 11 EERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKI 58 (321)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEE
Confidence 344443333334468999999999999999999999999999999984
No 378
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=33.82 E-value=1e+02 Score=18.09 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=36.8
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+-|..|..++. .|.-.++|-...++...++...++.+..|
T Consensus 3 ~~Lt~rE~~v~~l~~----~G~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 3 ADLTPREREILRLVA----QGKSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 468888888887775 45899999999999999999988887554
No 379
>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=33.71 E-value=49 Score=20.11 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=15.6
Q ss_pred HHHHHhhcCCChHHHHHHHH
Q psy7778 49 MRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK 68 (117)
.+||-..+|+..++++++|.
T Consensus 2 i~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHh
Confidence 46788888888888888774
No 380
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.43 E-value=81 Score=23.48 Aligned_cols=45 Identities=9% Similarity=0.153 Sum_probs=35.2
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~L 70 (117)
..+..||++++.|+-+..- .|.-.++|-...|++..++ .++.+.|
T Consensus 109 ~~L~~Lp~~~r~v~~L~~~---~g~s~~EIA~~LgiS~~tVk~~l~Rar~~L 157 (188)
T PRK12546 109 AAFAQLPDEQREALILVGA---SGFSYEEAAEMCGVAVGTVKSRANRARARL 157 (188)
T ss_pred HHHHhCCHHHhHHhhhHHh---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4678899999988877654 7889999999999998874 4444544
No 381
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.41 E-value=1.2e+02 Score=22.04 Aligned_cols=46 Identities=11% Similarity=0.191 Sum_probs=37.7
Q ss_pred ccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 23 EKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 23 ~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
..+..|++|+. .|-..|..+|| .+++.+..|+.-+++..-|..|-+
T Consensus 29 ~~~~~L~~E~~~Fi~~Fi~~rGn----lKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 29 PWFARLSPEQLEFIKLFIKNRGN----LKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred chhhcCCHHHHHHHHHHHHhcCC----HHHHHHHHCCCcHHHHHHHHHHHH
Confidence 36888999655 78889999998 789999999999998777776644
No 382
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=33.39 E-value=1.4e+02 Score=22.87 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=40.8
Q ss_pred cCCCHHHHHHHHHHHHhc----CCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAG----NKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AG----n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+||+-|+.|...=-.+| .+.+-.+||-++.|+..+++...|+.=|+|
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~K 205 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERK 205 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 369999988877777777 588999999999999999999888887764
No 383
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=33.35 E-value=1.4e+02 Score=24.71 Aligned_cols=52 Identities=8% Similarity=0.100 Sum_probs=42.1
Q ss_pred cCCCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChH-HHHHHHHHHhhcCCee
Q psy7778 26 KDSDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPT-QLNKILKQLETKKIIK 77 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~-~l~K~LK~LE~k~LIK 77 (117)
..||++|++...++-.-- ..||...+++.+++.... .+...+..|+..||+.
T Consensus 297 ~~l~~~~~~~~~~~~~Lr~~~gl~~~~~~~~~~~~~~~~~~~~~~~l~~~gl~~ 350 (377)
T PRK08599 297 HVLTKKEQMEEEMFLGLRKKSGVSKARFEEKFGQSFEDVFGETIQELQEQGLLE 350 (377)
T ss_pred eeCCHHHHHHHHHHHhHHhhCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEE
Confidence 347888888777776665 579999999999987544 4788899999999987
No 384
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=33.29 E-value=1.2e+02 Score=25.87 Aligned_cols=79 Identities=14% Similarity=0.062 Sum_probs=53.3
Q ss_pred cCCCHHHHHHHHHHHHh-cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc-c---cCCcccccCccccccchh
Q psy7778 26 KDSDNEEKVVYKIIEEA-GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS-V---ANIEYLTEGTVNAMVLPS 100 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs-V---~gg~wYtdg~~D~~fI~~ 100 (117)
..||++|++.-.+|..- -+.||...+++.++|......-..|..|+..||+..=.+ + .-|-++.|.-+-.=|-+.
T Consensus 340 ~~l~~~~~~~~~~~~~Lr~~~gl~~~~~~~~~g~~~~~~~~~l~~l~~~gll~~~~~~l~lT~~G~~~~d~i~~~~~~~~ 419 (430)
T PRK08208 340 YLLSEDEMKRRFIIKSLLQAQGLDLADYRQRFGSDPLRDFPELELLIDRGWLEQNGGRLRLTEEGLALSDAIGPVFISPE 419 (430)
T ss_pred eeCCHHHHHHHHHHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEECcchhhHHHHHHHHHcCHH
Confidence 34788888777777665 367999999999999765556678999999999974211 1 245555554444444444
Q ss_pred hhhh
Q psy7778 101 RKKR 104 (117)
Q Consensus 101 l~~~ 104 (117)
++.+
T Consensus 420 ~~~~ 423 (430)
T PRK08208 420 VRAL 423 (430)
T ss_pred HHHH
Confidence 4443
No 385
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.28 E-value=88 Score=21.77 Aligned_cols=44 Identities=2% Similarity=0.013 Sum_probs=34.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~L 70 (117)
.+..||+.++.|+.+-.- .|.-.++|-..+|++.+++. ++++.|
T Consensus 103 ~l~~Lp~~~r~v~~l~~~---~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 103 AIQKLPARQREAFLLRYW---EDMDVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred HHHhCCHHHHHHHHHHHH---hcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578899988888877553 68889999999999998865 445544
No 386
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=33.18 E-value=36 Score=26.61 Aligned_cols=41 Identities=20% Similarity=0.330 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
+..+..++..|.+.|+-.- --.+.++.|+.|++.|+.||..
T Consensus 8 ~~~~L~~F~av~e~gs~s~----AA~~L~iSQpavS~~I~~LE~~ 48 (312)
T PRK10341 8 KTQHLVVFQEVIRSGSIGS----AAKELGLTQPAVSKIINDIEDY 48 (312)
T ss_pred cHHHHHHHHHHHHcCCHHH----HHHHhCCChHHHHHHHHHHHHH
Confidence 4456667777777666332 2567899999999999999984
No 387
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=32.90 E-value=38 Score=26.06 Aligned_cols=39 Identities=8% Similarity=-0.026 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+..++..|-+.|+-. .--.+.++.|+.|++.||.||..
T Consensus 9 ~~l~~f~~v~~~gs~s----~AA~~L~isq~avS~~i~~LE~~ 47 (297)
T PRK11139 9 NALRAFEAAARHLSFT----RAAEELFVTQAAVSHQIKALEDF 47 (297)
T ss_pred HHHHHHHHHHHhCCHH----HHHHHhCCChHHHHHHHHHHHHH
Confidence 4555666666666522 22567899999999999999984
No 388
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=32.63 E-value=33 Score=26.98 Aligned_cols=21 Identities=14% Similarity=0.077 Sum_probs=18.9
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
-.+.|+.|+.|++.||.||+.
T Consensus 23 A~~L~isQpavS~~ik~LE~~ 43 (313)
T PRK12684 23 AKALYTSQPGVSKAIIELEDE 43 (313)
T ss_pred HHHhcCCChHHHHHHHHHHHH
Confidence 567899999999999999983
No 389
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=32.45 E-value=1e+02 Score=23.97 Aligned_cols=42 Identities=14% Similarity=0.223 Sum_probs=34.1
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.|+.|+.+..- +|.-.++|-..+|++...|.++.+
T Consensus 206 ~l~~L~~~er~vi~~~~~---~~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 206 AMKKLNDREKLILNLRFF---QGKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred HHHcCCHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 466899999888877652 578899999999999999776544
No 390
>PRK01381 Trp operon repressor; Provisional
Probab=32.43 E-value=66 Score=23.06 Aligned_cols=46 Identities=17% Similarity=0.170 Sum_probs=34.3
Q ss_pred ccC-CCHHHHHH----HHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 25 LKD-SDNEEKVV----YKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 25 ~~~-L~~eE~lV----Y~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
+.. ||++|+.. |+++..--..++--|+|..++|+..++|+|+=+.|
T Consensus 29 l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~L 79 (99)
T PRK01381 29 LTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSL 79 (99)
T ss_pred HHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHh
Confidence 444 78888744 34444444667999999999999999988876666
No 391
>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=32.25 E-value=47 Score=19.40 Aligned_cols=26 Identities=15% Similarity=0.307 Sum_probs=20.2
Q ss_pred CCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 44 NKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 44 n~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
..|+-.+++-..+|++.+.+++.++.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 46888899999999999999988754
No 392
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=32.02 E-value=37 Score=23.51 Aligned_cols=39 Identities=15% Similarity=0.032 Sum_probs=31.0
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K 65 (117)
.+..||+.++.|+.+-. -+|.-.++|-..+|++.++|.|
T Consensus 104 ~l~~Lp~~~r~v~~l~~---~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 104 LISILPNKQKKIIYMKF---FEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHhhcC
Confidence 47788888888776633 3688899999999999988764
No 393
>KOG0081|consensus
Probab=31.97 E-value=15 Score=29.39 Aligned_cols=14 Identities=21% Similarity=0.434 Sum_probs=12.7
Q ss_pred cccCccccccchhh
Q psy7778 88 LTEGTVNAMVLPSR 101 (117)
Q Consensus 88 Ytdg~~D~~fI~~l 101 (117)
||||+|++.||..+
T Consensus 29 YTD~~F~~qFIsTV 42 (219)
T KOG0081|consen 29 YTDGKFNTQFISTV 42 (219)
T ss_pred ecCCcccceeEEEe
Confidence 99999999999764
No 394
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=31.83 E-value=68 Score=25.66 Aligned_cols=48 Identities=10% Similarity=0.254 Sum_probs=41.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
+.+..||+-|+.|+++|-+..++= .-+++|-.++|.++++|.|--+.|
T Consensus 11 ~~~~~Lt~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kL 60 (281)
T COG1737 11 ERYDSLTKSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKL 60 (281)
T ss_pred HHHhcCCHHHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 457789999999999998877743 467999999999999999999988
No 395
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=31.25 E-value=38 Score=24.97 Aligned_cols=42 Identities=5% Similarity=0.011 Sum_probs=30.0
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC-cccccCc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI-EYLTEGT 92 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg-~wYtdg~ 92 (117)
..+.++-+.+|++. +.|+..|+.|||.+...-.+| -+|++..
T Consensus 8 ~~IgevAk~~Gvs~----~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~ 50 (144)
T PRK13752 8 LTIGVFAKAAGVNV----ETIRFYQRKGLLPEPDKPYGSIRRYGEAD 50 (144)
T ss_pred ccHHHHHHHHCcCH----HHHHHHHHCCCCCCCccCCCCCeecCHHH
Confidence 56778888888887 457889999999865443343 6666554
No 396
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=31.19 E-value=1.5e+02 Score=22.19 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=23.3
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
.|.-..+|-..+|+....|++.|+-+.
T Consensus 119 ~g~s~~~iA~~lg~s~~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIGKSRAHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHc
Confidence 466678899999999999999999864
No 397
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=31.18 E-value=1.4e+02 Score=20.72 Aligned_cols=43 Identities=14% Similarity=0.119 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.|++-|..|..++. +|.-.++|..+.++...++...++.+..|
T Consensus 149 ~lt~re~~vl~~l~----~g~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 149 VLSNREVTILRYLV----SGLSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred cCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 58888888877764 45899999999999999999998888665
No 398
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=31.17 E-value=60 Score=17.17 Aligned_cols=23 Identities=22% Similarity=0.303 Sum_probs=18.6
Q ss_pred CcccHHHHHhhcCCChHHHHHHH
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
.|+-.+++...+|++...+.+.+
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 57788899999999988887654
No 399
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=31.11 E-value=93 Score=22.52 Aligned_cols=42 Identities=10% Similarity=0.101 Sum_probs=32.8
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+.. -.|.-..+|-..+|++..+|...+
T Consensus 124 ~~l~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l 165 (186)
T PRK05602 124 QALAALPERQREAIVLQY---YQGLSNIEAAAVMDISVDALESLL 165 (186)
T ss_pred HHHHhCCHHHHHHhhHHH---hcCCCHHHHHHHhCcCHHHHHHHH
Confidence 356788998888776654 468999999999999999865443
No 400
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=31.09 E-value=38 Score=27.14 Aligned_cols=21 Identities=33% Similarity=0.351 Sum_probs=19.2
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
-.+.|+.|+.|++.|+.||+.
T Consensus 23 A~~L~isQpavS~~I~~LE~~ 43 (327)
T PRK12680 23 AARVHATQPGLSKQLKQLEDE 43 (327)
T ss_pred HHHhcCCchHHHHHHHHHHHH
Confidence 678999999999999999984
No 401
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.06 E-value=53 Score=23.42 Aligned_cols=44 Identities=20% Similarity=0.123 Sum_probs=33.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~L 70 (117)
-+..||+.++.|+.+..- .|.-.++|-..+|++.+.+ .++++.|
T Consensus 123 ~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 123 ALSKLDPEFRAPVILKHY---YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred HHHcCCHHHhheeeehhh---cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 577889988887766443 4899999999999999965 5555554
No 402
>smart00526 H15 Domain in histone families 1 and 5.
Probab=30.96 E-value=1.4e+02 Score=18.67 Aligned_cols=52 Identities=19% Similarity=0.233 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhcC-CcccHHHHHh----hcCC----ChHHHHHHHHHHhhcCCeeeecc
Q psy7778 30 NEEKVVYKIIEEAGN-KGIWMRDIRF----KSNL----MPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 30 ~eE~lVY~~Ie~AGn-~GIWtkdIk~----ktnL----~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
+-..+|...|.+..+ .|.....|++ +.++ +...|+++|+.+..+|.+..+|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecCC
Confidence 344577777777776 6666555554 2332 13458999999999999887764
No 403
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=30.72 E-value=52 Score=24.23 Aligned_cols=52 Identities=15% Similarity=0.335 Sum_probs=43.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
.-+|-..|-+||++.=+-+ .||=.+.|..+.++.+..+.-+++.|=.+||.+
T Consensus 16 ~~glk~~eI~IY~lLve~~-~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~ 67 (113)
T COG5625 16 AIGLKKNEIRIYSLLVEKG-RGMRIREIQRELGISERTVRAAVAVLLRRGLLA 67 (113)
T ss_pred HcCCCcchhhhhhHHHHhc-CCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHH
Confidence 3456667899999887765 589899999999999999999999998888776
No 404
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=30.71 E-value=44 Score=25.94 Aligned_cols=42 Identities=14% Similarity=0.128 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|+-.+..++..|.+.|+-.- --.+.++.|+.|++.|+.||+.
T Consensus 4 m~l~~L~~F~~v~e~gs~s~----AA~~L~isqpavS~~I~~LE~~ 45 (296)
T PRK11062 4 INYNHLYYFWMVCKEGSVVG----AAEALFLTPQTITGQIKALEER 45 (296)
T ss_pred cCHHHHHHHHHHHhcCCHHH----HHHHhCCChHHHHHHHHHHHHH
Confidence 55566667777777666332 2567899999999999999984
No 405
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=30.66 E-value=1.2e+02 Score=22.76 Aligned_cols=61 Identities=13% Similarity=0.248 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHH-HHhhc----CCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRD-IRFKS----NLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkd-Ik~kt----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
.+++-..+|..++... .-|--... |...+ .++..+|-.+|+.||..|+|.+-..-.+-.+|
T Consensus 40 ~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y 105 (135)
T PRK09416 40 KEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYY 105 (135)
T ss_pred ccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEE
Confidence 3555667788888766 66665544 34443 35688999999999999999875432233444
No 406
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.63 E-value=42 Score=23.81 Aligned_cols=43 Identities=5% Similarity=0.148 Sum_probs=31.5
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTVN 94 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~D 94 (117)
.+.++-..+|++.. .|+..|..|||.+. .+-+|--+|++..+.
T Consensus 2 ~I~e~a~~~gvs~~----tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~ 45 (126)
T cd04785 2 SIGELARRTGVNVE----TIRYYESIGLLPEPARTAGGYRLYGAAHVE 45 (126)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCccccCHHHHH
Confidence 35677788888875 46789999999875 444566788877643
No 407
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.62 E-value=27 Score=28.12 Aligned_cols=28 Identities=21% Similarity=0.444 Sum_probs=25.2
Q ss_pred cCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778 56 SNLMPTQLNKILKQLETKKIIKAVKSVA 83 (117)
Q Consensus 56 tnL~~~~l~K~LK~LE~k~LIK~VKsV~ 83 (117)
.||.++.+...|+.|+.|+||..|.+-.
T Consensus 48 mnLse~eVq~~l~~L~~r~lvr~~sgsR 75 (215)
T COG3132 48 MNLSESEVQEQLDNLEKRHLVRTVSGSR 75 (215)
T ss_pred hcCCHHHHHHHHHHHHHhhhHHHhhcch
Confidence 5799999999999999999999988554
No 408
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.61 E-value=1.3e+02 Score=21.15 Aligned_cols=41 Identities=15% Similarity=0.186 Sum_probs=32.0
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..||+.++.|+.+-. .|.-.++|-...|++.+++.+.+
T Consensus 108 ~~l~~L~~~~r~il~l~~----~g~s~~eIA~~lgis~~tV~~~i 148 (166)
T PRK09639 108 EVLAKMTERDRTVLLLRF----SGYSYKEIAEALGIKESSVGTTL 148 (166)
T ss_pred HHHHcCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence 357788988887765533 78999999999999999866554
No 409
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=30.50 E-value=45 Score=30.48 Aligned_cols=55 Identities=22% Similarity=0.165 Sum_probs=44.5
Q ss_pred CCCHHHHHH-HHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 27 DSDNEEKVV-YKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 27 ~L~~eE~lV-Y~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
-||..|..| |.+=..+=..|....||-.+.+.....+-++|-.||+||+|+...+
T Consensus 422 ~LT~~e~kvl~kiP~~~ikrg~liedi~~~~g~~eeev~~sl~kleskgfveeL~n 477 (593)
T COG1542 422 YLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDEEEVIKSLGKLESKGFVEELPN 477 (593)
T ss_pred ccchhHHHHHHhccccccchhhHHHHHHhhcCccHHHHHHHHHHHhhcchHHHhcc
Confidence 467766644 4443445578999999999999999999999999999999998754
No 410
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=30.35 E-value=1.5e+02 Score=23.30 Aligned_cols=44 Identities=7% Similarity=0.205 Sum_probs=35.7
Q ss_pred CCHHHH--HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEK--VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~--lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|..+|| .|.+++..-|. +-..+|-..+|....++.|=|+.||..
T Consensus 3 m~~~eR~~~I~~~l~~~~~--v~v~eLa~~~~VS~~TIRRDL~~Le~~ 48 (252)
T PRK10681 3 TRRDERIGQLLQALKRSDK--LHLKDAAALLGVSEMTIRRDLNAHSAP 48 (252)
T ss_pred CCHHHHHHHHHHHHHHcCC--CcHHHHHHHhCCCHHHHHHHHHHhhcC
Confidence 334444 77888877544 889999999999999999999999953
No 411
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=30.34 E-value=1.2e+02 Score=24.53 Aligned_cols=42 Identities=10% Similarity=0.113 Sum_probs=34.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
+..|++.|+.|+.+..- +.+|.-.++|-...|++...|.+++
T Consensus 225 l~~L~~rer~vl~lr~~-~~~~~t~~EIa~~lgvs~~~V~q~~ 266 (289)
T PRK07500 225 LQTLNERELRIIRERRL-REDGATLEALGEELGISKERVRQIE 266 (289)
T ss_pred HhcCCHHHHHHHHHHhc-CCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 46899999999888762 3589999999999999999866544
No 412
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=30.27 E-value=43 Score=24.83 Aligned_cols=18 Identities=22% Similarity=0.547 Sum_probs=15.4
Q ss_pred cCCChHHHHHHHHHHhhc
Q psy7778 56 SNLMPTQLNKILKQLETK 73 (117)
Q Consensus 56 tnL~~~~l~K~LK~LE~k 73 (117)
.++.|+.|++.|+.||..
T Consensus 1 L~isQpavS~~I~~LE~~ 18 (269)
T PRK11716 1 MHVSPSTLSRQIQRLEEE 18 (269)
T ss_pred CCcChHHHHHHHHHHHHH
Confidence 368899999999999874
No 413
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=30.23 E-value=1.1e+02 Score=21.83 Aligned_cols=46 Identities=9% Similarity=0.078 Sum_probs=33.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~LE 71 (117)
+.+..|++.++.|+.+-. -.|.-.++|-..+|++.+++ .++.+.|.
T Consensus 134 ~~l~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 134 RAVEALPEDLRTAITLRE---LEGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred HHHHcCCHHHhhhhhhhh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 367788888888776654 36788899999999998875 44555553
No 414
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.20 E-value=1e+02 Score=22.34 Aligned_cols=46 Identities=13% Similarity=0.161 Sum_probs=35.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHhh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLET 72 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE~ 72 (117)
.+..|+++++.|+.+-. -.|.-.++|-..+|++.++|. |+++.|..
T Consensus 138 ~l~~L~~~~~~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 138 ALAQLPESQRQVLELAY---YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred HHHhCCHHHhhhhhhhh---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 56778888887776654 358899999999999999866 66666643
No 415
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=30.18 E-value=44 Score=26.98 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.+...+..|.+.|+-. .=-.+.++.|+.|++.||.||..
T Consensus 7 rqL~~F~aVae~gSfs----~AA~~L~isQpavS~~Ik~LE~e 45 (297)
T PRK15243 7 KKLKIFITLMETGSFS----IATSVLYITRTPLSRVISDLERE 45 (297)
T ss_pred HHHHHHHHHHHcCCHH----HHHHHHCcCHHHHHHHHHHHHHH
Confidence 3445566666666522 22567899999999999999983
No 416
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=30.18 E-value=64 Score=25.33 Aligned_cols=69 Identities=14% Similarity=0.044 Sum_probs=48.9
Q ss_pred HHHHHHHHhcCCcccH--------HHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc--------------CCcccccC
Q psy7778 34 VVYKIIEEAGNKGIWM--------RDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA--------------NIEYLTEG 91 (117)
Q Consensus 34 lVY~~Ie~AGn~GIWt--------kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~--------------gg~wYtdg 91 (117)
.|+.-|.+.=..|.|. ++|-.+.|..-++|.=+|+.|+.+|||-.=.+.- ..+|..+.
T Consensus 14 ~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V~~~~~~~~~~~~~~~~~~~ 93 (241)
T COG2186 14 EVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFVRPRSEWNLDPLVLPLRLLL 93 (241)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEecCCccCccchhhhHHHHHc
Confidence 3455555555666665 8999999999999999999999999997655432 12455555
Q ss_pred ccccccchhhh
Q psy7778 92 TVNAMVLPSRK 102 (117)
Q Consensus 92 ~~D~~fI~~l~ 102 (117)
.+|..++..+-
T Consensus 94 ~~~~~~~~~ll 104 (241)
T COG2186 94 EDDPDSIFDLL 104 (241)
T ss_pred ccChhhHHHHH
Confidence 55666655554
No 417
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.15 E-value=1.3e+02 Score=20.83 Aligned_cols=43 Identities=19% Similarity=0.128 Sum_probs=32.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.-+..||+.++.|+.+-. =+|.-.++|-..+|++.++|...+.
T Consensus 102 ~~l~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 102 DFMSVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHHhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 356789998887765433 2478899999999999998655443
No 418
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=30.03 E-value=1.4e+02 Score=21.20 Aligned_cols=53 Identities=11% Similarity=0.100 Sum_probs=30.3
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec--ccc-CCcccc---cCccccccchh
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK--SVA-NIEYLT---EGTVNAMVLPS 100 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK--sV~-gg~wYt---dg~~D~~fI~~ 100 (117)
-..+|-..||||..++..+|++|..-++.=.+. ++. +.-+|. =|-||.+-|+.
T Consensus 23 nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~WG~id~~wi~~ 81 (90)
T PF09904_consen 23 NVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISDWGPIDRKWIAD 81 (90)
T ss_dssp -HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-TTB-HHHHHH
T ss_pred cHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeeecCCCCHHHHHH
Confidence 778999999999999999999998766654432 221 111232 25567666654
No 419
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=29.98 E-value=1.2e+02 Score=24.33 Aligned_cols=46 Identities=9% Similarity=0.134 Sum_probs=36.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
..+..|++.|+.|..+-.-. .+|.-.++|-...|++...|.++.+.
T Consensus 226 ~al~~L~~rEr~VL~lry~~-~~~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 226 DALEGLDERSRDIIEARWLD-DDKSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred HHHhcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 35778999999888776532 27888999999999999988765543
No 420
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=29.96 E-value=45 Score=26.51 Aligned_cols=43 Identities=7% Similarity=0.061 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
.|+-.+..++..+.+.|+=. .=-.+.++.|+.|++.||.||+.
T Consensus 10 ~m~l~~L~~F~~v~e~gs~s----~AA~~L~iSQpavS~~I~~LE~~ 52 (310)
T PRK15092 10 NLDLDLLRTFVAVADLNTFA----AAAAAVCRTQSAVSQQMQRLEQL 52 (310)
T ss_pred cCCHHHHHHHHHHHHcCCHH----HHHHHhCCChHHHHHHHHHHHHH
Confidence 57777778888888887732 22678999999999999999984
No 421
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=29.86 E-value=43 Score=24.88 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=19.0
Q ss_pred HhhcCCChHHHHHHHHHHhhc
Q psy7778 53 RFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 53 k~ktnL~~~~l~K~LK~LE~k 73 (117)
..+.++.|+.|++.|+.||..
T Consensus 22 A~~L~isqsavS~~I~~LE~~ 42 (297)
T COG0583 22 AERLGLSQSAVSRQIKRLEEE 42 (297)
T ss_pred HHHhCCCChHHHHHHHHHHHH
Confidence 567899999999999999983
No 422
>PRK15482 transcriptional regulator MurR; Provisional
Probab=29.78 E-value=87 Score=24.68 Aligned_cols=47 Identities=11% Similarity=0.172 Sum_probs=39.6
Q ss_pred cccCCCHHHHHHHHHHHHhcC--CcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGN--KGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
.+..||+-|+.|.+.|-+-.. .-+-.++|-.+++..+++|.|--|.|
T Consensus 10 ~~~~Lt~~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkL 58 (285)
T PRK15482 10 AESEFTENEQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKL 58 (285)
T ss_pred HHhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHh
Confidence 466799999988888876554 34667999999999999999999998
No 423
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=29.64 E-value=45 Score=24.16 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=33.7
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec-cccCCcccccCccc-cccchhhh
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK-SVANIEYLTEGTVN-AMVLPSRK 102 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK-sV~gg~wYtdg~~D-~~fI~~l~ 102 (117)
.+.++-+.+|++. +.|+..|+.|||.+.. +-+|--.|++..++ ..||-.++
T Consensus 2 ~Ige~a~~~gvs~----~tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr 54 (131)
T cd04786 2 KIGELAKRSGMAA----SRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQ 54 (131)
T ss_pred CHHHHHHHHCcCH----HHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHH
Confidence 4667788888887 4578899999998754 33444567766533 34444443
No 424
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=29.47 E-value=1.1e+02 Score=22.00 Aligned_cols=41 Identities=7% Similarity=0.088 Sum_probs=31.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
.+..|++.++.|+.+-. =.|.-.++|-..+|++..++...|
T Consensus 134 ~l~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~~v~~~l 174 (187)
T PRK12534 134 CLAELEPPRSELIRTAF---FEGITYEELAARTDTPIGTVKSWI 174 (187)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChhHHHHHH
Confidence 56788888776665544 389999999999999998855444
No 425
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.36 E-value=45 Score=23.91 Aligned_cols=41 Identities=12% Similarity=0.202 Sum_probs=30.8
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~ 92 (117)
.+.++-..+|++.. .|+..|..|||.+. .+-+|--+|++..
T Consensus 3 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~ 44 (131)
T TIGR02043 3 QIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDED 44 (131)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHH
Confidence 45677888888875 56788999999986 4555557777665
No 426
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=29.12 E-value=1.9e+02 Score=24.77 Aligned_cols=53 Identities=13% Similarity=0.174 Sum_probs=42.9
Q ss_pred cCCCHHHHHHHHHHHHh-cCCcccHHHHHhhcCCChHHH---HHHHHHHhhcCCeee
Q psy7778 26 KDSDNEEKVVYKIIEEA-GNKGIWMRDIRFKSNLMPTQL---NKILKQLETKKIIKA 78 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~ktnL~~~~l---~K~LK~LE~k~LIK~ 78 (117)
..|+++|++...+|..- -+.|+...+++.++|...... -..|+.|+..|||..
T Consensus 360 ~~l~~~~~~~~~~~~~L~~~~~ld~~~~~~~~g~~~~~~~~~~~~l~~l~~~gl~~~ 416 (453)
T PRK13347 360 YALSDDDRLRRAIIETLMCNFPVDLAAIAARHGFFARYFLDELARLEPLAADGLVTI 416 (453)
T ss_pred ecCCHHHHHHHHHHHHHHhhCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEE
Confidence 45788898888888887 478999999999999875433 367899999999884
No 427
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.03 E-value=48 Score=23.63 Aligned_cols=49 Identities=12% Similarity=0.211 Sum_probs=33.7
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCccc-cccchhh
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTVN-AMVLPSR 101 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~D-~~fI~~l 101 (117)
+.++-+.+|++.. .|+..|..|||.+. .+-+|--+|++..+. ..||-.+
T Consensus 3 I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~l 53 (127)
T TIGR02047 3 IGELAQKTGVSVE----TIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNC 53 (127)
T ss_pred HHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHH
Confidence 4567778888874 57888999999864 555666788876633 3444444
No 428
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=28.82 E-value=1.4e+02 Score=23.68 Aligned_cols=45 Identities=22% Similarity=0.391 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCC-cccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 34 VVYKIIEEAGNK-GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 34 lVY~~Ie~AGn~-GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.|...+.+..++ .|-.++|..+|++...-| +.+|+.-++|+..++
T Consensus 137 ~i~~~L~~~~~~~~isi~~is~~Tgi~~~DI---i~tL~~l~~l~~~~~ 182 (188)
T PF01853_consen 137 VILEYLLEFKGKKSISIKDISQETGIRPEDI---ISTLQQLGMLKYYKG 182 (188)
T ss_dssp HHHHHHHHTSSE--EEHHHHHHHH-BTHHHH---HHHHHHTT-EEEETT
T ss_pred HHHHHHHhcCCCCeEEHHHHHHHHCCCHHHH---HHHHHHCCCEEEECC
Confidence 344556666554 899999999999998765 555666677776654
No 429
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=28.76 E-value=1.3e+02 Score=21.91 Aligned_cols=41 Identities=17% Similarity=0.106 Sum_probs=33.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+..|++.++.|+.+ .- .|.-.++|-..+|++.+++...+..
T Consensus 153 ~~~L~~~~r~vl~l-~~---e~~s~~EIA~~lgis~~tV~~~l~r 193 (208)
T PRK08295 153 EELLSELEKEVLEL-YL---DGKSYQEIAEELNRHVKSIDNALQR 193 (208)
T ss_pred HHhCCHHHHHHHHH-HH---ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46899999988876 43 5899999999999999987655544
No 430
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=28.70 E-value=2.7e+02 Score=21.25 Aligned_cols=55 Identities=15% Similarity=0.205 Sum_probs=46.2
Q ss_pred ccccCCCH--HHHHHHHHHHHhcCCcc--cHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 23 EKLKDSDN--EEKVVYKIIEEAGNKGI--WMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 23 ~k~~~L~~--eE~lVY~~Ie~AGn~GI--WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
.-+.++|+ +-..+|..|..-++--+ .-..|.+..|++...|.-+|+....-++|+
T Consensus 89 ~y~~~~P~Re~F~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVt 147 (195)
T PF10141_consen 89 AYFEGMPTREQFKKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVT 147 (195)
T ss_pred hhhcCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEE
Confidence 34788998 34499999999888543 558899999999999999999998888877
No 431
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.66 E-value=98 Score=22.47 Aligned_cols=46 Identities=9% Similarity=0.113 Sum_probs=34.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~LE 71 (117)
..+..|+++++.|+.+-. =.|.-.++|-..+|++..++ .||.+.|-
T Consensus 134 ~~l~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 134 RTIQQLPEDLRTALTLRE---FDGLSYEDIASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred HHHHhCCHHHhHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 357889998887776654 37888999999999998874 44555553
No 432
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=28.56 E-value=1.8e+02 Score=19.38 Aligned_cols=55 Identities=20% Similarity=0.165 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHHHHhcC-CcccHHHHHhh----cCC----ChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 28 SDNEEKVVYKIIEEAGN-KGIWMRDIRFK----SNL----MPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn-~GIWtkdIk~k----tnL----~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
-++-..||...|.+..+ .|.....|++- ... +...+.++|+.+..+|.+..++..
T Consensus 4 hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~ 67 (88)
T cd00073 4 HPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGT 67 (88)
T ss_pred CCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCC
Confidence 34556677777777665 78777777653 211 245689999999999999999864
No 433
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.55 E-value=47 Score=18.23 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=24.9
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV 93 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~ 93 (117)
..++...+|++.++|.+-.+ .+.+.+.+...+...|+..++
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~----~g~~~~~~~~~~~~~~~~~ei 43 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVK----EGKLKAIRTPGGHRRFPEEDL 43 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH----cCCCCceeCCCCceecCHHHH
Confidence 35667778888877766554 577776554433333554443
No 434
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=28.49 E-value=1.6e+02 Score=24.67 Aligned_cols=51 Identities=8% Similarity=0.102 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHh-cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 27 DSDNEEKVVYKIIEEA-GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
-||++|++..-++..- -..||...+++.+++.+...+...|+.|+..||+.
T Consensus 318 ~ls~~~~~~~~~~l~LR~~~Gld~~~f~~~~g~~~~~~~~~l~~l~~~gll~ 369 (394)
T PRK08898 318 EVGARDLPFEFMLNALRLTDGVPAHLFQERTGLPLAAIEPQLAAAEQRGLLE 369 (394)
T ss_pred ecCHhhHHHHHHHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4677776543333221 57899999999999988777788999999999986
No 435
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=28.25 E-value=48 Score=23.15 Aligned_cols=40 Identities=5% Similarity=0.222 Sum_probs=29.7
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeec-cccCCcccccCc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVK-SVANIEYLTEGT 92 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK-sV~gg~wYtdg~ 92 (117)
+.++-..+|++.. .|+..|..|||.++. +-+|--.|++-.
T Consensus 3 Ige~A~~~gvs~~----tlR~ye~~GLl~p~~r~~~g~R~Y~~~~ 43 (107)
T cd01111 3 ISQLALDAGVSVH----IVRDYLLRGLLHPVARTEGGYGLFDDCA 43 (107)
T ss_pred HHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHH
Confidence 5677888888875 467889999999874 445666676655
No 436
>PRK13749 transcriptional regulator MerD; Provisional
Probab=28.17 E-value=73 Score=23.13 Aligned_cols=42 Identities=5% Similarity=0.221 Sum_probs=32.3
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCcc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTV 93 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~ 93 (117)
-+.++-.++|+.. +.|+..|.+||+.++ .+-+|--+|++..+
T Consensus 5 tIgelA~~~gvS~----~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l 47 (121)
T PRK13749 5 TVSRLALDAGVSV----HIVRDYLLRGLLRPVACTTGGYGLFDDAAL 47 (121)
T ss_pred cHHHHHHHHCCCH----HHHHHHHHCCCCCCCCcCCCCCccCCHHHH
Confidence 4567788888887 457889999999997 55577778877653
No 437
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=28.16 E-value=1.6e+02 Score=21.00 Aligned_cols=40 Identities=13% Similarity=0.072 Sum_probs=31.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
+..||+.++.|+.+..- +|.-.++|-..+|++.++|...|
T Consensus 132 l~~Lp~~~r~v~~l~~~---~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 132 LAQVDPRQAEVVELRFF---AGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred hhcCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHH
Confidence 55599988888776643 68899999999999998855433
No 438
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=28.04 E-value=1.2e+02 Score=19.82 Aligned_cols=38 Identities=16% Similarity=0.165 Sum_probs=29.7
Q ss_pred CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV 82 (117)
.-+.+--|.++..+.-+.-.+++-.||..|+|.+-.+.
T Consensus 19 ~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~ 56 (65)
T PF09397_consen 19 GKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGS 56 (65)
T ss_dssp TCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TT
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCC
Confidence 45788889999999999999999999999999887654
No 439
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=28.04 E-value=1.4e+02 Score=20.81 Aligned_cols=43 Identities=7% Similarity=0.030 Sum_probs=33.0
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
..+..||+.++.|+.+-. -.|.-.++|-..+|++..+|...+.
T Consensus 106 ~~l~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 106 RALRRLPARQRAVVVLRY---YEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred HHHHhCCHHHHHHhhhHH---HhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 356788998888876644 2389999999999999998655443
No 440
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=28.02 E-value=45 Score=25.92 Aligned_cols=42 Identities=14% Similarity=0.117 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
|+-.+..++..+.+.|+-- .--.+.++.|+.|++.|+.||..
T Consensus 5 ~~l~~L~~f~~v~e~gs~s----~AA~~L~isqpavS~~i~~LE~~ 46 (305)
T CHL00180 5 FTLDQLRILKAIATEGSFK----KAAESLYISQPAVSLQIKNLEKQ 46 (305)
T ss_pred ccHHHHHHHHHHHHcCCHH----HHHHHhcCCChHHHHHHHHHHHH
Confidence 4445666777777777533 23567899999999999999984
No 441
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=27.64 E-value=1.1e+02 Score=17.74 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
...++.+-|=.++-.++|-.++|++.+.+-+...
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 3567889999999999999999999998876544
No 442
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=27.55 E-value=65 Score=23.52 Aligned_cols=45 Identities=16% Similarity=0.257 Sum_probs=33.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHHh
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQLE 71 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~LE 71 (117)
-+..||+.++.|+.+.. -.|.-.++|-..+|++..+|. ++++.|.
T Consensus 136 ~l~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 136 ALETLPDEQREVFLLRE---HGDLELEEIAELTGVPEETVKSRLRYALQKLR 184 (194)
T ss_pred HHHhCCHhHhhheeeeh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36677777776665443 578999999999999999874 6666663
No 443
>KOG3233|consensus
Probab=27.51 E-value=2e+02 Score=24.42 Aligned_cols=62 Identities=13% Similarity=0.149 Sum_probs=51.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcC-CChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN-LMPTQLNKILKQLETKKIIKAVKSVANIEYL 88 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn-L~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY 88 (117)
.|+.+-.-+|..|-.+-..||-..+|-..++ ++.+.+..+|..|=++++|+-+++=.+..++
T Consensus 7 ~~~~e~~~~~~~~~~~~p~git~q~L~~~~p~~~~~~~~salN~lLs~~~l~llr~~~~l~yr 69 (297)
T KOG3233|consen 7 ALPVEIENILIQIVKQIPEGITQQELQSEMPQISATDRASALNILLSRGLLDLLRQNTGLVYR 69 (297)
T ss_pred cChHHHHHHHHHHHHhccccccHHHHHHHcCCCcHHHHHHHHHHHHhcCcchhhccCCcceEe
Confidence 3556555666666688889999999999987 8999999999999999999999887666555
No 444
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.31 E-value=1.2e+02 Score=21.96 Aligned_cols=45 Identities=13% Similarity=0.035 Sum_probs=33.0
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHH----HHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQ----LNKILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~----l~K~LK~L 70 (117)
..+..||+.++.|+.+-. =.|.-.++|-..+|++..+ +.++++.|
T Consensus 113 ~~l~~Lp~~~r~i~~l~~---~e~~s~~EIA~~lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 113 ELIHKLPYKLRQVIILRY---LHDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred HHHHhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 357788998887776632 2578899999999999988 44455544
No 445
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=27.27 E-value=82 Score=25.12 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=25.8
Q ss_pred HHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 52 IRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 52 Ik~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
|..+|||..+.|-|+|-.|.+-|+|.=.++
T Consensus 166 Iq~RT~LSRS~ImkILs~LKkGgYIei~rG 195 (207)
T PRK11832 166 IHQRTRISRSVVAEVLAALRKGGYIEMNKG 195 (207)
T ss_pred HHHhccccHHHHHHHHHHHhcCCCEEEecC
Confidence 456799999999999999999999976554
No 446
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=27.27 E-value=1.9e+02 Score=20.45 Aligned_cols=53 Identities=19% Similarity=0.282 Sum_probs=39.6
Q ss_pred ccccCCCHHHHHHHHHHHHhcC---CcccHHHHH-hhcCCChHHHHHHHHHHhhcCC
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGN---KGIWMRDIR-FKSNLMPTQLNKILKQLETKKI 75 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn---~GIWtkdIk-~ktnL~~~~l~K~LK~LE~k~L 75 (117)
.+.+-|+++|..+|.+-+.||- -++..--+- -+.|.++..+-..||+|+++.-
T Consensus 18 ~rk~~Ls~eE~EL~ELa~~AGv~~dp~VFriildLL~~nVsP~AI~qmLK~m~s~~~ 74 (88)
T PF12926_consen 18 RRKKVLSAEEVELYELAQLAGVPMDPEVFRIILDLLRLNVSPDAIFQMLKSMCSGSR 74 (88)
T ss_pred HHHhccCHHHHHHHHHHHHhCCCcChHHHHHHHHHHHcCCCHHHHHHHHHHHHcccc
Confidence 4567799999999999988884 233322221 3689999999999999998643
No 447
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=26.64 E-value=48 Score=24.16 Aligned_cols=40 Identities=15% Similarity=0.216 Sum_probs=30.2
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
+.++-+.+|++.. .|+..|..|||.+..+-+|--+|++..
T Consensus 4 I~EvA~~~Gvs~~----tLRyYE~~GLl~p~r~~~g~R~Y~~~d 43 (139)
T cd01110 4 VGEVAKRSGVAVS----ALHFYEQKGLIASWRNAGNQRRYPRDV 43 (139)
T ss_pred HHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeEECHHH
Confidence 5677788888874 567899999999887765666776644
No 448
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=26.39 E-value=1.5e+02 Score=23.40 Aligned_cols=42 Identities=10% Similarity=0.177 Sum_probs=35.1
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.|+.|+.+.. -+|.-.++|-..+|++...|.+.++
T Consensus 202 al~~L~~~er~vi~l~y---~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 202 AILALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 56789999998888876 3688899999999999998776644
No 449
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=26.28 E-value=1.6e+02 Score=22.91 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=35.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
..+..|++.|+.|+.+-. -+|.-.++|-..+|+++..|.++.+
T Consensus 202 ~~l~~L~~rer~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 202 EAMKRLNEREKMILNMRF---FEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHHcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356789999998888765 3578899999999999999876654
No 450
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=26.27 E-value=2e+02 Score=20.31 Aligned_cols=31 Identities=10% Similarity=-0.093 Sum_probs=23.1
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhh
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFK 55 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k 55 (117)
.-.||+-|+.|..++-...++=+-..+|-..
T Consensus 145 ~~~Lt~~E~~il~~l~~~~g~~~s~~~i~~~ 175 (223)
T PRK11517 145 SITLTRKEFQLLWLLASRAGEIIPRTVIASE 175 (223)
T ss_pred EEeCCHHHHHHHHHHHhCCCccCCHHHHHHH
Confidence 4469999999998888877765656655555
No 451
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=26.14 E-value=2.2e+02 Score=24.23 Aligned_cols=60 Identities=15% Similarity=0.186 Sum_probs=48.5
Q ss_pred cCCCHHHHHHH-HHHH--HhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778 26 KDSDNEEKVVY-KIIE--EAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI 85 (117)
Q Consensus 26 ~~L~~eE~lVY-~~Ie--~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg 85 (117)
+.||+-++-|. .+|. .-.+.-|=.++|-...|-++-++...+.+|.+-||+.+|.+=+||
T Consensus 2 ~~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGG 64 (294)
T COG2524 2 KELTSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGG 64 (294)
T ss_pred ccccHHHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCC
Confidence 46888777444 4443 234447888999999999999999999999999999999998876
No 452
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=26.09 E-value=2.2e+02 Score=19.69 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=30.9
Q ss_pred CCHHHH-HHHHHHHHhc---CCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 28 SDNEEK-VVYKIIEEAG---NKGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 28 L~~eE~-lVY~~Ie~AG---n~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
||+.|+ .+=+-++-|. ..|.--++|..+||...++|+|+=+.|.
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455444 3333344443 5899999999999999999888766664
No 453
>PRK07157 acetate kinase; Provisional
Probab=25.99 E-value=58 Score=28.45 Aligned_cols=46 Identities=15% Similarity=0.260 Sum_probs=36.4
Q ss_pred ChHHHHHHHHHHhhcCCeeeecc--------ccCCcccccCc-cccccchhhhhh
Q psy7778 59 MPTQLNKILKQLETKKIIKAVKS--------VANIEYLTEGT-VNAMVLPSRKKR 104 (117)
Q Consensus 59 ~~~~l~K~LK~LE~k~LIK~VKs--------V~gg~wYtdg~-~D~~fI~~l~~~ 104 (117)
|...+..+++.|...++++.... |+||+.|+... .|.+.++.|++-
T Consensus 61 h~~al~~il~~l~~~~~~~~~~~i~aVGHRVVHGG~~f~~~v~I~~~v~~~i~~l 115 (400)
T PRK07157 61 HKVAVAVLIEIWEENKLIEDLEEIELIGFRVVHGGDYFNGPTKLDDKEISKIEKV 115 (400)
T ss_pred HHHHHHHHHHHHHhcCccCcccceeEEEEeeecCCCCCCCCEEECHHHHHHHHhc
Confidence 67789999999987776654433 35999999888 899999888763
No 454
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=25.93 E-value=93 Score=25.95 Aligned_cols=47 Identities=13% Similarity=0.115 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778 33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK 80 (117)
..|...|-.-+. -+=.+||-.+.++....++-.+|.|...|||.+=.
T Consensus 13 fqIL~ei~~~qp-~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~g 59 (260)
T COG1497 13 FQILSEIAVRQP-RVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEG 59 (260)
T ss_pred HHHHHHHHHhCC-CCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecC
Confidence 344444433322 35678999999999999999999999999999833
No 455
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=25.80 E-value=98 Score=27.66 Aligned_cols=49 Identities=12% Similarity=0.059 Sum_probs=42.4
Q ss_pred ccccCCCHHHHHHHHHHHHhcC--CcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGN--KGIWMRDIRFKSNLMPTQLNKILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~LE 71 (117)
+.+.+||+-|+.|.++|-+-.+ .-+-+++|-.+++...++|.|-.|.|-
T Consensus 349 ~~~~~Lt~~E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLG 399 (638)
T PRK14101 349 QMRDALTPAERRVADLALNHPRSIINDPIVDIARKADVSQPTVIRFCRSLG 399 (638)
T ss_pred HHHhhcCHHHHHHHHHHHhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4577899999999999987765 356789999999999999999999993
No 456
>PRK05660 HemN family oxidoreductase; Provisional
Probab=25.69 E-value=2.1e+02 Score=23.91 Aligned_cols=51 Identities=8% Similarity=0.046 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778 27 DSDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK 77 (117)
.|+.+|++...++-.-. .+||....+..++|.........|+.|+..||+.
T Consensus 301 ~l~~~~~~~e~~~~~Lr~~~G~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~ 352 (378)
T PRK05660 301 DVEAADRPFEFFMNRFRLLEAAPRADFEAYTGLPESVIRPQLDEALAQGYLT 352 (378)
T ss_pred cCChhhHHHHHHHHhchhccCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 36776666555555444 4799999999999988777778999999999987
No 457
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=25.65 E-value=94 Score=21.12 Aligned_cols=40 Identities=13% Similarity=0.221 Sum_probs=30.7
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCc
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGT 92 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~ 92 (117)
+.++...+|++. +.|+..|..|||.+...-. |=--|++..
T Consensus 3 I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~d 43 (124)
T COG0789 3 IGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPED 43 (124)
T ss_pred HHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHHH
Confidence 456677788887 4578899999999998885 666777655
No 458
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.64 E-value=60 Score=22.37 Aligned_cols=41 Identities=15% Similarity=0.148 Sum_probs=29.8
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc--cCCcccccCc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV--ANIEYLTEGT 92 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV--~gg~wYtdg~ 92 (117)
.+.++-..+|++.. .|+..|.+|||.+...- +|--+|++..
T Consensus 2 ~i~eva~~~gis~~----tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~ 44 (108)
T cd01107 2 TIGEFAKLSNLSIK----ALRYYDKIGLLKPAYVDPDTGYRYYSAEQ 44 (108)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHcCCCCCCcCCCCCCccccCHHH
Confidence 46778888999985 56789999999886532 3446666655
No 459
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.56 E-value=1.7e+02 Score=21.51 Aligned_cols=41 Identities=7% Similarity=-0.003 Sum_probs=32.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
-+..||+.++.|+.+..- +|.-.++|-..+|++.+++...|
T Consensus 138 ~l~~Lp~~~r~v~~l~~~---eg~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 138 FLDRLPKAQRDVLQAVYL---EELPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHhCcCHHHHHHHH
Confidence 577888888888776543 68889999999999998865444
No 460
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=25.50 E-value=93 Score=19.52 Aligned_cols=31 Identities=26% Similarity=0.218 Sum_probs=25.2
Q ss_pred HHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 38 IIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 38 ~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
+++.|- +|...||.-+-.++..+++-+.||.
T Consensus 14 Ivema~-nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 14 IVEMAF-NGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred HHHHHh-cCCcchhhHhHhcchHHHHHHHHhc
Confidence 455554 6778899999999999999998884
No 461
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=25.49 E-value=90 Score=25.40 Aligned_cols=36 Identities=14% Similarity=0.312 Sum_probs=29.7
Q ss_pred ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee-eccc
Q psy7778 47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA-VKSV 82 (117)
Q Consensus 47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~-VKsV 82 (117)
=..-.|....|+.|..|=++|+.||.-|||-+ +--+
T Consensus 29 ~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~ 65 (217)
T COG1777 29 CYVSEISRELGVSQKAVLKHLRILERAGLVESRIEKI 65 (217)
T ss_pred hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhcccc
Confidence 34456778899999999999999999999998 4444
No 462
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=25.41 E-value=2.7e+02 Score=20.18 Aligned_cols=70 Identities=7% Similarity=0.096 Sum_probs=55.7
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhh
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSR 101 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l 101 (117)
..+|++|.+.|+.+-.. -....+|-...+||-.++.=.+--|...|+|-.-..... -..+.-|.++++.+
T Consensus 38 ~~~l~pE~~~Il~lC~~----~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~p~~~---~~~~~pd~~lLe~V 107 (114)
T PF05331_consen 38 PAGLGPEHRAILELCRR----PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRAPAPP---DAADRPDRDLLERV 107 (114)
T ss_pred CCCCCHHHHHHHHHHCC----CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeCCCCC---ccCCCCCHHHHHHH
Confidence 57899999999988766 789999999999999999999999999999976544433 12344677766654
No 463
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.40 E-value=1.4e+02 Score=21.21 Aligned_cols=41 Identities=7% Similarity=0.047 Sum_probs=32.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
-+..||+.++.|+.+..- .|.-.++|-...|++...+...+
T Consensus 133 ~l~~L~~~~r~il~l~~~---~~~s~~eIA~~lgis~~~v~~~l 173 (187)
T PRK09641 133 AILQLPEKYRTVIVLKYI---EDLSLKEISEILDLPVGTVKTRI 173 (187)
T ss_pred HHHhCCHHHHHHhhhHHh---hCCCHHHHHHHHCCCHHHHHHHH
Confidence 577899988888766543 68999999999999998865544
No 464
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=25.02 E-value=1.6e+02 Score=20.81 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=33.7
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~L 70 (117)
..+..|++.++.|+.+..- .|.-.++|...+|++.+++. ++++.|
T Consensus 115 ~~l~~L~~~~r~i~~l~~~---~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 115 KAIDTLNDKYQTAIILRYY---HDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred HHHHhCCHHHhHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3567899988877766553 37889999999999998754 444444
No 465
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.99 E-value=1.3e+02 Score=23.34 Aligned_cols=46 Identities=7% Similarity=0.075 Sum_probs=34.2
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHH----HHHHHHHh
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQL----NKILKQLE 71 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l----~K~LK~LE 71 (117)
.-+..|++.++.|+.+-. -.|.-.++|-..+|++.++| .|+++.|.
T Consensus 167 ~~L~~Lp~~~R~v~~L~~---~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 167 AAMQRLPEQQRIAVILSY---HENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred HHHHhCCHHHHHHhhhHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 356778888887765543 57899999999999999874 45555553
No 466
>PRK12440 acetate kinase; Reviewed
Probab=24.84 E-value=63 Score=28.21 Aligned_cols=46 Identities=11% Similarity=0.107 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHHhhcCCeeeeccc-----cCCcccccCc-cccccchhhhhh
Q psy7778 59 MPTQLNKILKQLETKKIIKAVKSV-----ANIEYLTEGT-VNAMVLPSRKKR 104 (117)
Q Consensus 59 ~~~~l~K~LK~LE~k~LIK~VKsV-----~gg~wYtdg~-~D~~fI~~l~~~ 104 (117)
|...+..++..|...+.+..+..| +||+.|++.. .|.+.++.|++-
T Consensus 64 h~~al~~il~~l~~~~~~~~I~aVGHRVVHGG~~f~~~v~I~~~v~~~i~~l 115 (397)
T PRK12440 64 HKIAIGRLVGLTEELGFTQDIVAVGHRIVHGGEKFTSTVRIDEEVTAEIESL 115 (397)
T ss_pred HHHHHHHHHHHHHhcCCccceeEEEEEeecCCCccCCCEEECHHHHHHHHhc
Confidence 566899999999766544555555 6999999998 899999888763
No 467
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=24.71 E-value=1.7e+02 Score=23.28 Aligned_cols=42 Identities=12% Similarity=0.134 Sum_probs=34.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
-+..|++.|+.|..+.. -.|.-.++|-..+|++...|.+.++
T Consensus 212 ~l~~L~~rer~vl~l~y---~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 212 LLAALPERERTVLVLRF---FESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHcCCHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46788998888877765 3588899999999999999887554
No 468
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.59 E-value=1.6e+02 Score=21.68 Aligned_cols=45 Identities=7% Similarity=0.130 Sum_probs=34.7
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHH----HHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLN----KILKQL 70 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~----K~LK~L 70 (117)
..+..||+.++.|+.+-.- .|.-.++|-..+|++..++. ++++.|
T Consensus 112 ~~L~~Lp~~~r~i~~L~~~---~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 112 AALDQLPDDQREAIILVGA---SGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3577889988888877544 68899999999999998754 455555
No 469
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=24.54 E-value=1.1e+02 Score=25.56 Aligned_cols=53 Identities=21% Similarity=0.235 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
.|..-|+++...++.+ +=|-++|.+.-.++..+++.+++-.||.||++-.|+.
T Consensus 13 ~m~~~e~l~~laae~h--kiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~r 65 (269)
T COG5340 13 SMRESELLSHLAAEGH--KIITIRDVAETLEVAPNTLRELASRLEKKGWLERILR 65 (269)
T ss_pred hHHHHHHHHHHHHHhC--ceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhcC
Confidence 3445677777666644 5678899999999999999999999999999987764
No 470
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.46 E-value=1.7e+02 Score=22.66 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=34.1
Q ss_pred ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
..+..|++.++.|+.+-. -.|.-.++|-..+|++...|...+
T Consensus 197 ~~l~~L~~~~r~vl~l~~---~~~~s~~EIA~~lgis~~tV~~~~ 238 (251)
T PRK07670 197 EKIKQLSEKEQLVISLFY---KEELTLTEIGQVLNLSTSRISQIH 238 (251)
T ss_pred HHHhcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHH
Confidence 357789999998887765 488889999999999999876544
No 471
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=24.34 E-value=1.1e+02 Score=22.92 Aligned_cols=42 Identities=14% Similarity=0.152 Sum_probs=35.1
Q ss_pred HHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778 37 KIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA 78 (117)
Q Consensus 37 ~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~ 78 (117)
.+.--|...-+-+++|-..|||-|+-++=+.+-|..++.|..
T Consensus 32 tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~ 73 (124)
T COG4738 32 TLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDE 73 (124)
T ss_pred HHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccch
Confidence 334445566789999999999999999999999999998863
No 472
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.29 E-value=1.8e+02 Score=20.35 Aligned_cols=43 Identities=12% Similarity=0.149 Sum_probs=33.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~ 69 (117)
-+..||++++.|+.+-.- .|.-.++|...+|++.+++...|..
T Consensus 110 ~l~~L~~~~r~v~~L~~~---~g~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 110 LLDGLPPLVKRAFLLAQV---DGLGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred HHHHCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 477888888877755432 6788999999999999998776654
No 473
>PRK04841 transcriptional regulator MalT; Provisional
Probab=24.25 E-value=1.7e+02 Score=26.25 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=39.0
Q ss_pred cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73 (117)
Q Consensus 26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k 73 (117)
..||+-|..|..++. +|.-.++|-.+.++..++|...|+.+=.|
T Consensus 837 ~~lt~~e~~v~~~~~----~g~~~~~ia~~l~~s~~tv~~h~~~~~~k 880 (903)
T PRK04841 837 SPLTQREWQVLGLIY----SGYSNEQIAGELDVAATTIKTHIRNLYQK 880 (903)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 459999999999886 79999999999999999999999987544
No 474
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.24 E-value=1.7e+02 Score=21.21 Aligned_cols=40 Identities=3% Similarity=0.011 Sum_probs=30.9
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKI 66 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~ 66 (117)
-+..||++++.|+-+-. -.|.-.++|-...|++.+++...
T Consensus 128 ~l~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~ 167 (189)
T PRK12515 128 CLAKLSPAHREIIDLVY---YHEKSVEEVGEIVGIPESTVKTR 167 (189)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHH
Confidence 47788888887764433 37999999999999999875443
No 475
>PF13814 Replic_Relax: Replication-relaxation
Probab=24.04 E-value=1.1e+02 Score=22.31 Aligned_cols=33 Identities=12% Similarity=0.076 Sum_probs=24.8
Q ss_pred HHHHHhhcCCChH---HHHHHHHHHhhcCCeeeecc
Q psy7778 49 MRDIRFKSNLMPT---QLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 49 tkdIk~ktnL~~~---~l~K~LK~LE~k~LIK~VKs 81 (117)
+..|..-.+.... .+.+.|+.|+..++|+.+..
T Consensus 12 ~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~ 47 (191)
T PF13814_consen 12 TDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRR 47 (191)
T ss_pred HHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecc
Confidence 3444444444444 79999999999999999987
No 476
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=23.92 E-value=1.8e+02 Score=20.90 Aligned_cols=40 Identities=18% Similarity=0.193 Sum_probs=31.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKI 66 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~ 66 (117)
-+..|++.++.|+.+-. -.|.-.++|...+|++..++...
T Consensus 97 ~l~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~ 136 (170)
T TIGR02959 97 MIKELPDEYREAIRLTE---LEGLSQQEIAEKLGLSLSGAKSR 136 (170)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHH
Confidence 45789999888877654 47888999999999999875443
No 477
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=23.85 E-value=2.2e+02 Score=24.29 Aligned_cols=74 Identities=16% Similarity=0.278 Sum_probs=52.7
Q ss_pred CCCHHHHHHHHHH-HH--hcCCcccHHHHHhhc--CCChHHHHHHHHHHhhcCCeee-------eccccCCcccccCccc
Q psy7778 27 DSDNEEKVVYKII-EE--AGNKGIWMRDIRFKS--NLMPTQLNKILKQLETKKIIKA-------VKSVANIEYLTEGTVN 94 (117)
Q Consensus 27 ~L~~eE~lVY~~I-e~--AGn~GIWtkdIk~kt--nL~~~~l~K~LK~LE~k~LIK~-------VKsV~gg~wYtdg~~D 94 (117)
.|++-++.|+..| +. +..+=|=+|.|..+. ++..++|..-++.||..|||.+ |+|..|=-+|-|.-.+
T Consensus 3 ~l~~Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr~YVd~ll~ 82 (346)
T COG1420 3 KLDERQRLILRAIVEDYLATGEPVGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYRYYVDHLLE 82 (346)
T ss_pred CchHHHHHHHHHHHHHHHhcCCccchHHHHHHhCCCCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHHHHHHHhcc
Confidence 4666555555444 32 555667899999998 5777899999999999999985 5555676777776655
Q ss_pred cccchh
Q psy7778 95 AMVLPS 100 (117)
Q Consensus 95 ~~fI~~ 100 (117)
.+-.+.
T Consensus 83 ~~~~~~ 88 (346)
T COG1420 83 VEDLSE 88 (346)
T ss_pred cCCCCh
Confidence 444433
No 478
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.81 E-value=1.9e+02 Score=20.66 Aligned_cols=41 Identities=10% Similarity=0.142 Sum_probs=32.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
.+..||++++.|+.+-.- .|.-.++|-..+|++.++|...|
T Consensus 116 ~l~~Lp~~~r~v~~L~~~---~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 116 LLGKLSSKARAAFLYNRL---DGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHH
Confidence 577889988888876543 57889999999999998865444
No 479
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=23.74 E-value=1.7e+02 Score=24.07 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=35.5
Q ss_pred ccccCCCHHHHHHHHHHH-HhcCCcccHHHHHhhcCCChHHHHHHH
Q psy7778 23 EKLKDSDNEEKVVYKIIE-EAGNKGIWMRDIRFKSNLMPTQLNKIL 67 (117)
Q Consensus 23 ~k~~~L~~eE~lVY~~Ie-~AGn~GIWtkdIk~ktnL~~~~l~K~L 67 (117)
.-+..|++.++.|+.+-. -.+-+|.-.++|-..+|++...|.+++
T Consensus 258 ~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~ 303 (325)
T PRK05657 258 KWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQ 303 (325)
T ss_pred HHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 357789999998887544 244589999999999999999866553
No 480
>PRK12397 propionate kinase; Reviewed
Probab=23.74 E-value=69 Score=28.07 Aligned_cols=47 Identities=19% Similarity=0.283 Sum_probs=36.5
Q ss_pred ChHHHHHHHHHHhhcCCeeee---ccc-----cCCcccccCc-cccccchhhhhhh
Q psy7778 59 MPTQLNKILKQLETKKIIKAV---KSV-----ANIEYLTEGT-VNAMVLPSRKKRE 105 (117)
Q Consensus 59 ~~~~l~K~LK~LE~k~LIK~V---KsV-----~gg~wYtdg~-~D~~fI~~l~~~~ 105 (117)
|+..+..+++.|...++++.. ..| |||+.|+... +|.+.++.|++-.
T Consensus 61 h~~al~~il~~l~~~~~~~~~~~i~aVGHRVVHGG~~f~~~v~I~~~v~~~i~~l~ 116 (404)
T PRK12397 61 HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLA 116 (404)
T ss_pred HHHHHHHHHHHHHhcCccCCccceeEEEEeeccCCCCCCCCEEECHHHHHHHHHHH
Confidence 677899999999877765543 333 5999999998 8999999887643
No 481
>KOG2593|consensus
Probab=23.69 E-value=66 Score=28.66 Aligned_cols=57 Identities=19% Similarity=0.277 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778 31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT 92 (117)
Q Consensus 31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~ 92 (117)
+..+|..+|-..+ =+---||+....++..+|.++|..|+..+||+-.+-+..++ ||.
T Consensus 30 ~~~lild~llr~~--~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~---nGr 86 (436)
T KOG2593|consen 30 EHVLILDALLRRQ--CVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAE---NGR 86 (436)
T ss_pred hhHHHHHHHHHhh--hcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCC---CCc
Confidence 4555555554333 23345899999999999999999999999999988887666 555
No 482
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=23.65 E-value=1.5e+02 Score=22.83 Aligned_cols=42 Identities=17% Similarity=0.087 Sum_probs=32.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.++.|+.+-.- .|.-.++|-..+|++.+.|.+.|.
T Consensus 131 al~~Lp~~~R~v~~L~y~---eg~s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 131 ALAKLPVEYREVLVLREL---EDMSYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred HHHcCCHHHHhHhhhHHh---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567788888877766443 689999999999999998665543
No 483
>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=23.60 E-value=1.7e+02 Score=17.38 Aligned_cols=36 Identities=22% Similarity=0.221 Sum_probs=24.7
Q ss_pred HHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 37 KIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 37 ~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
..|++--+.++-.+..-.+.|+|.++|.+.++--.+
T Consensus 7 ~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 7 KAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp HHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHHTTT
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 345554455599999999999999999988876543
No 484
>KOG2313|consensus
Probab=23.59 E-value=1.2e+02 Score=21.90 Aligned_cols=41 Identities=20% Similarity=0.364 Sum_probs=27.3
Q ss_pred CeEEEEEeCccccccccCCCH--HHHHHHHHHHHhcCC-cccHHHH
Q psy7778 10 GNLLYKVKDPVTNEKLKDSDN--EEKVVYKIIEEAGNK-GIWMRDI 52 (117)
Q Consensus 10 ~~l~yk~~~~e~a~k~~~L~~--eE~lVY~~Ie~AGn~-GIWtkdI 52 (117)
++--|++. -..+++.+|+. -.||||+++.+.... |+--=+|
T Consensus 49 ~EtHFrv~--vVS~~FeG~s~v~RHRlVy~~L~eEl~~~gvHAL~i 92 (100)
T KOG2313|consen 49 AETHFRVE--VVSSAFEGLSLVKRHRLVYKALKEELAGTGVHALSI 92 (100)
T ss_pred CccEEEEE--EechhhCCccHHHHHHHHHHHHHHHhhccceeEEEe
Confidence 44445543 34456888887 577999999888776 7644333
No 485
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=23.54 E-value=1.5e+02 Score=20.01 Aligned_cols=44 Identities=9% Similarity=0.140 Sum_probs=30.3
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCcccc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGTVNA 95 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~~D~ 95 (117)
.++++-..+|++.++|. ..|..|++.+...-. |--+|++..++.
T Consensus 2 ti~eva~~~gvs~~tlR----~ye~~Gll~~~~~~~~g~R~y~~~di~~ 46 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH----YYDEIGLLKPSRRTENGYRLYTEEDLER 46 (103)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCceeeCHHHHHH
Confidence 46788889999997765 567799998754333 445566655443
No 486
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=23.50 E-value=95 Score=21.75 Aligned_cols=33 Identities=24% Similarity=0.438 Sum_probs=27.8
Q ss_pred cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778 48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81 (117)
Q Consensus 48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs 81 (117)
|-.. |.+.+|.-..++|+|+.-..++.|..|.+
T Consensus 43 WG~~-Knk~~M~YeklSRaLRyyy~~~il~Kv~g 75 (87)
T smart00413 43 WGQR-KNKPNMNYEKLSRALRYYYKKNILRKVPG 75 (87)
T ss_pred Hhhh-cCCCCCCHHHHHHHHHHHHhcCcEEecCC
Confidence 5433 57788999999999999999999998854
No 487
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=23.39 E-value=73 Score=21.75 Aligned_cols=50 Identities=12% Similarity=0.177 Sum_probs=34.8
Q ss_pred HHHHHhhcCCChHHHHHHHHHHhhcCCeeee-ccccCCcccccCcc-ccccchhhh
Q psy7778 49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAV-KSVANIEYLTEGTV-NAMVLPSRK 102 (117)
Q Consensus 49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V-KsV~gg~wYtdg~~-D~~fI~~l~ 102 (117)
+.++-..+|++.++ |+..|..|+|.++ .+-+|--+|++..+ ...||-.++
T Consensus 3 i~e~A~~~gvs~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~ 54 (99)
T cd04772 3 TVDLARAIGLSPQT----VRNYESLGLIPPAERTANGYRIYTDKHIAALRAYRALL 54 (99)
T ss_pred HHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHh
Confidence 45677788888865 4577999999985 45567788888774 334554443
No 488
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=23.33 E-value=85 Score=19.49 Aligned_cols=28 Identities=11% Similarity=0.376 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHH-HHhcCCc-ccHHHHHhh
Q psy7778 28 SDNEEKVVYKII-EEAGNKG-IWMRDIRFK 55 (117)
Q Consensus 28 L~~eE~lVY~~I-e~AGn~G-IWtkdIk~k 55 (117)
++.-..+|.++| ..+++.| ||..++...
T Consensus 3 ~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~ 32 (74)
T PF12872_consen 3 LEELKKLLRELLESQKGEDGWVSLSQLGQE 32 (74)
T ss_dssp -HHHHHHHHHHHHHTCTTTSSEEHHHHHHH
T ss_pred HHHHHHHHHHHHHhCcCCCceEEHHHHHHH
Confidence 344567899999 4455455 998887755
No 489
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=1.8e+02 Score=20.76 Aligned_cols=42 Identities=7% Similarity=0.181 Sum_probs=32.9
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..||+.++.|+.+-. -+|.-.++|-..+|++.+++...|+
T Consensus 115 ~l~~L~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 115 LLDGLSGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46679998888876653 4688899999999999998665543
No 490
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=23.10 E-value=1.1e+02 Score=16.17 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=18.9
Q ss_pred CcccHHHHHhhcCCChHHHHHHHH
Q psy7778 45 KGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 45 ~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.|+-..++...++++...+++.++
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHc
Confidence 578888888999998888877543
No 491
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=23.08 E-value=14 Score=21.56 Aligned_cols=12 Identities=8% Similarity=0.227 Sum_probs=10.3
Q ss_pred CCcccccCcccc
Q psy7778 84 NIEYLTEGTVNA 95 (117)
Q Consensus 84 gg~wYtdg~~D~ 95 (117)
+|.|++.|+|+.
T Consensus 26 ~G~W~d~~el~~ 37 (41)
T PF13453_consen 26 GGIWFDAGELEK 37 (41)
T ss_pred CeEEccHHHHHH
Confidence 999999998864
No 492
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=23.05 E-value=79 Score=24.75 Aligned_cols=22 Identities=23% Similarity=0.157 Sum_probs=19.0
Q ss_pred ChHHHHHHHHHHhhcCCeeeec
Q psy7778 59 MPTQLNKILKQLETKKIIKAVK 80 (117)
Q Consensus 59 ~~~~l~K~LK~LE~k~LIK~VK 80 (117)
.-+++.++|.+||.-|||...+
T Consensus 118 Sg~iiR~~LQqLE~~glVek~~ 139 (169)
T PTZ00095 118 SGKILRWICQQLEKLGLVEQGP 139 (169)
T ss_pred chHHHHHHHHHHHHCCCEEecC
Confidence 3468999999999999999764
No 493
>cd07287 PX_RPK118_like The phosphoinositide binding Phox Homology domain of RPK118-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily bear similarity to human RPK118, which contains an N-terminal PX domain, a Microtubule Interacting and Trafficking (MIT) domain, and a kinase domain. RPK118 binds sphingosine kinase, a key enzyme in the synthesis of sphingosine 1-phosphate (SPP), a lipid messenger involved in many cellular events. RPK118 may be involved in transmitting SPP-mediated signaling. It also binds the antioxidant peroxiredoxin-3 (PRDX3) and may be involved in the transport of PRDX3 from the cytoplasm to its site of function in the mitochondria. Members of this subfamily also show similarity to sorting nexin 15 (SNX15), which contains PX and MIT domains but does not contain a kinase doma
Probab=22.89 E-value=83 Score=22.57 Aligned_cols=26 Identities=19% Similarity=0.355 Sum_probs=18.7
Q ss_pred ccccCCcccccCccccccchhhhhhhhh
Q psy7778 80 KSVANIEYLTEGTVNAMVLPSRKKREER 107 (117)
Q Consensus 80 KsV~gg~wYtdg~~D~~fI~~l~~~~~~ 107 (117)
+...++.|+ |.||.+||+..++--|+
T Consensus 69 Pp~p~k~~~--g~~d~~fIe~RR~~Le~ 94 (118)
T cd07287 69 PPFAKAKVF--GRFDESVIEERRQCAED 94 (118)
T ss_pred CCCCCceee--cCCCHHHHHHHHHHHHH
Confidence 333466666 57999999998877664
No 494
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=22.77 E-value=1.4e+02 Score=19.26 Aligned_cols=41 Identities=15% Similarity=0.233 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778 32 EKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLET 72 (117)
Q Consensus 32 E~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~ 72 (117)
|...|.++..-= ++.+-..++..+.++..+++.+.++.+..
T Consensus 15 ~s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 15 ESLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp GSHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 445555555444 78899999999999999999999999865
No 495
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=22.69 E-value=3.7e+02 Score=20.86 Aligned_cols=69 Identities=20% Similarity=0.172 Sum_probs=0.0
Q ss_pred EEEEeCcccc---------ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee--cc
Q psy7778 13 LYKVKDPVTN---------EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV--KS 81 (117)
Q Consensus 13 ~yk~~~~e~a---------~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V--Ks 81 (117)
.|++....+- .+.+.||.-...+..+| |=++.|-..+|-.--|-. -..+|++|..++||+++ +.
T Consensus 61 ~y~l~tk~e~~~~i~~~~~~~~~~LS~aaLEtLAII--AY~QPITr~eIe~IRGv~---s~~~l~~L~ergLI~~~Gr~~ 135 (186)
T TIGR00281 61 SYSLVTKPAFADYIHRFLPAKLKNLNSASLEVLAII--AYKQPITRARINEIRGVK---SYQIVDDLVEKGLVVELGRKD 135 (186)
T ss_pred EEEEEEhHHHHHHHHHHhccccccCCHHHHHHHHHH--HHcCCcCHHHHHHHcCCC---HHHHHHHHHHCCCeEecCcCC
Q ss_pred ccCCc
Q psy7778 82 VANIE 86 (117)
Q Consensus 82 V~gg~ 86 (117)
+.|-+
T Consensus 136 ~~Grp 140 (186)
T TIGR00281 136 TPGRS 140 (186)
T ss_pred CCCCC
No 496
>PF13551 HTH_29: Winged helix-turn helix
Probab=22.69 E-value=1.3e+02 Score=19.56 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=27.8
Q ss_pred CCccc-HHHHHhhcCCChHHHHHHHHHHhhcCC
Q psy7778 44 NKGIW-MRDIRFKSNLMPTQLNKILKQLETKKI 75 (117)
Q Consensus 44 n~GIW-tkdIk~ktnL~~~~l~K~LK~LE~k~L 75 (117)
.+|.. ..++-..+|++..++.+.++..+..|+
T Consensus 9 ~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 9 AEGVSTIAEIARRLGISRRTVYRWLKRYREGGI 41 (112)
T ss_pred HcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccH
Confidence 45775 889999999999999999999998883
No 497
>PRK12379 propionate/acetate kinase; Provisional
Probab=22.63 E-value=75 Score=27.73 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=36.9
Q ss_pred ChHHHHHHHHHHhhcCCeeeeccc-----cCCcccccCc-cccccchhhhhhh
Q psy7778 59 MPTQLNKILKQLETKKIIKAVKSV-----ANIEYLTEGT-VNAMVLPSRKKRE 105 (117)
Q Consensus 59 ~~~~l~K~LK~LE~k~LIK~VKsV-----~gg~wYtdg~-~D~~fI~~l~~~~ 105 (117)
|...+..+++.|...+...++..| |||+.|++.. .|.+.++.|++..
T Consensus 60 h~~a~~~i~~~l~~~~~~~~i~aVGHRVVHGG~~f~~~v~V~~~v~~~l~~~~ 112 (396)
T PRK12379 60 YEGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESVIITDEVIDNIRRVS 112 (396)
T ss_pred HHHHHHHHHHHHHhcCCccceeEEEEeeeCCCCCCCCCEEECHHHHHHHHhcC
Confidence 566799999999766545565555 6999999988 9999999988754
No 498
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=22.62 E-value=2.4e+02 Score=19.65 Aligned_cols=58 Identities=9% Similarity=0.117 Sum_probs=38.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhc---------CCChHHHHHHHHHHhhc---CCeeeeccc
Q psy7778 25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKS---------NLMPTQLNKILKQLETK---KIIKAVKSV 82 (117)
Q Consensus 25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt---------nL~~~~l~K~LK~LE~k---~LIK~VKsV 82 (117)
...||+-|+.|+.++-...++=.-..+|-... +.=...|+++-|.|+.. .+|+.|.++
T Consensus 145 ~~~Lt~~E~~il~~l~~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~~~~~~~i~t~~g~ 214 (218)
T TIGR01387 145 RITLTRKEFQLLWLLMRRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDDPFEEKLIHTIRGM 214 (218)
T ss_pred EEeCCHHHHHHHHHHHhCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcCCCCCCcEEEeCCc
Confidence 44699999999999988877766666666554 22234566666677532 356665543
No 499
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=22.60 E-value=1.8e+02 Score=22.77 Aligned_cols=42 Identities=10% Similarity=0.207 Sum_probs=33.9
Q ss_pred cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68 (117)
Q Consensus 24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK 68 (117)
.+..|++.++.|+.+..- .|.-.++|-..+|++...|.+.++
T Consensus 200 ~l~~L~~~~r~vl~l~y~---~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 200 ALAQLEERTREVLEFVFL---HDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHcCCHHHHHHHHHHHH---CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 467899988888776653 588999999999999998766554
No 500
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=22.60 E-value=1.3e+02 Score=21.94 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=34.8
Q ss_pred CCHHHH----HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778 28 SDNEEK----VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL 70 (117)
Q Consensus 28 L~~eE~----lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L 70 (117)
||++|| .=|++|++-=+.-.-.|.|..+.|-..++|||-=.+|
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~L 84 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSL 84 (103)
T ss_pred cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhh
Confidence 677776 3478899988888999999999999999998854444
Done!