Query 031936
Match_columns 150
No_of_seqs 109 out of 348
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 07:24:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031936.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031936hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02853 Probable phenylalanyl 100.0 1.4E-28 2.9E-33 214.9 13.8 138 8-146 23-180 (492)
2 PTZ00326 phenylalanyl-tRNA syn 100.0 5.4E-28 1.2E-32 211.7 13.9 136 9-146 27-188 (494)
3 KOG2784 Phenylalanyl-tRNA synt 100.0 3.3E-28 7.2E-33 205.0 9.3 136 5-147 19-172 (483)
4 PRK04172 pheS phenylalanyl-tRN 99.9 6.5E-22 1.4E-26 173.8 13.2 139 5-144 22-187 (489)
5 PF03551 PadR: Transcriptional 97.2 0.0013 2.9E-08 43.6 5.7 43 13-55 27-75 (75)
6 PF14947 HTH_45: Winged helix- 96.9 0.0014 3E-08 44.2 3.9 41 11-54 27-67 (77)
7 PTZ00034 40S ribosomal protein 96.5 0.0071 1.5E-07 44.6 5.2 49 13-61 36-87 (124)
8 PF03501 S10_plectin: Plectin/ 96.4 0.0058 1.2E-07 43.2 4.3 43 13-55 33-76 (95)
9 PF13601 HTH_34: Winged helix 96.4 0.01 2.3E-07 40.3 5.4 44 11-54 22-70 (80)
10 TIGR03433 padR_acidobact trans 96.2 0.0063 1.4E-07 42.8 3.5 52 12-63 34-91 (100)
11 TIGR02337 HpaR homoprotocatech 96.2 0.0055 1.2E-07 43.8 3.2 53 9-61 48-104 (118)
12 PF13463 HTH_27: Winged helix 96.1 0.0048 1.1E-07 39.4 2.4 40 10-49 25-68 (68)
13 COG1846 MarR Transcriptional r 95.8 0.022 4.8E-07 39.4 5.0 55 9-63 42-100 (126)
14 PRK11512 DNA-binding transcrip 95.8 0.012 2.7E-07 43.4 3.8 69 8-78 59-133 (144)
15 COG5045 Ribosomal protein S10E 95.6 0.031 6.8E-07 39.4 5.1 44 12-55 34-78 (105)
16 smart00347 HTH_MARR helix_turn 95.6 0.012 2.6E-07 39.6 2.8 47 9-55 30-80 (101)
17 PRK03573 transcriptional regul 95.5 0.023 4.9E-07 41.8 4.4 52 10-61 53-108 (144)
18 TIGR02719 repress_PhaQ poly-be 95.5 0.031 6.8E-07 42.0 4.9 53 13-65 53-111 (138)
19 COG1695 Predicted transcriptio 95.4 0.024 5.2E-07 41.6 4.1 46 14-59 41-92 (138)
20 smart00529 HTH_DTXR Helix-turn 95.3 0.021 4.5E-07 39.0 3.4 48 10-59 6-53 (96)
21 PRK10870 transcriptional repre 95.3 0.027 5.8E-07 43.4 4.2 52 10-61 78-133 (176)
22 PRK09416 lstR lineage-specific 95.1 0.032 6.9E-07 41.9 3.9 43 14-56 74-118 (135)
23 PRK03902 manganese transport t 95.0 0.039 8.4E-07 40.8 4.1 53 9-63 28-80 (142)
24 PRK14165 winged helix-turn-hel 94.2 0.045 9.8E-07 44.0 3.1 56 5-60 23-79 (217)
25 COG4754 Uncharacterized conser 94.2 0.071 1.5E-06 40.6 3.9 50 11-63 36-85 (157)
26 COG3432 Predicted transcriptio 93.9 0.1 2.3E-06 36.9 4.1 43 12-54 40-83 (95)
27 TIGR01889 Staph_reg_Sar staphy 93.9 0.055 1.2E-06 38.3 2.7 53 9-61 49-105 (109)
28 PF01638 HxlR: HxlR-like helix 93.8 0.17 3.7E-06 34.6 5.0 40 14-53 30-73 (90)
29 COG1497 Predicted transcriptio 93.1 0.12 2.6E-06 42.4 3.8 52 10-63 32-83 (260)
30 KOG3344 40s ribosomal protein 93.0 0.068 1.5E-06 40.3 2.0 42 14-55 36-78 (150)
31 TIGR02277 PaaX_trns_reg phenyl 92.9 0.13 2.8E-06 42.7 3.8 52 11-64 28-80 (280)
32 PRK13777 transcriptional regul 92.6 0.13 2.8E-06 40.4 3.2 54 10-63 66-123 (185)
33 PF10771 DUF2582: Protein of u 92.1 0.11 2.4E-06 34.2 2.0 37 61-97 12-50 (65)
34 PF01978 TrmB: Sugar-specific 92.1 0.17 3.8E-06 32.6 2.9 37 10-46 29-65 (68)
35 COG1321 TroR Mn-dependent tran 91.5 0.21 4.6E-06 38.0 3.2 46 8-55 29-74 (154)
36 cd00090 HTH_ARSR Arsenical Res 91.3 0.42 9.2E-06 29.7 4.1 42 11-53 28-70 (78)
37 PF09821 AAA_assoc_C: C-termin 91.3 0.32 7E-06 35.6 3.9 51 10-63 4-54 (120)
38 PF07381 DUF1495: Winged helix 91.3 0.27 5.8E-06 34.4 3.3 44 11-54 33-88 (90)
39 PRK11050 manganese transport r 91.2 0.26 5.7E-06 37.1 3.5 55 8-64 56-110 (152)
40 PF07848 PaaX: PaaX-like prote 91.2 0.46 1E-05 31.6 4.2 40 10-49 30-70 (70)
41 PF00126 HTH_1: Bacterial regu 90.6 0.065 1.4E-06 34.0 -0.3 46 5-50 15-60 (60)
42 PF10007 DUF2250: Uncharacteri 90.4 0.43 9.4E-06 33.5 3.7 44 11-54 29-90 (92)
43 PF14277 DUF4364: Domain of un 90.2 0.49 1.1E-05 36.4 4.2 39 15-53 31-71 (163)
44 smart00418 HTH_ARSR helix_turn 89.8 0.79 1.7E-05 27.7 4.2 44 10-53 17-62 (66)
45 COG1733 Predicted transcriptio 89.7 0.79 1.7E-05 33.4 4.8 40 14-53 48-91 (120)
46 PRK11242 DNA-binding transcrip 89.7 0.25 5.4E-06 39.5 2.3 53 5-57 17-69 (296)
47 TIGR02702 SufR_cyano iron-sulf 89.0 0.3 6.4E-06 38.2 2.2 47 9-55 21-73 (203)
48 TIGR02647 DNA conserved hypoth 88.4 0.42 9.1E-06 32.5 2.3 34 18-55 34-67 (77)
49 smart00550 Zalpha Z-DNA-bindin 88.3 0.2 4.2E-06 32.8 0.6 40 9-48 28-67 (68)
50 PRK03601 transcriptional regul 87.9 0.32 6.9E-06 39.0 1.8 54 4-57 16-69 (275)
51 TIGR02036 dsdC D-serine deamin 87.3 0.35 7.7E-06 39.3 1.7 53 5-57 24-76 (302)
52 PRK11062 nhaR transcriptional 87.0 0.39 8.4E-06 38.9 1.8 54 5-58 20-73 (296)
53 TIGR03339 phn_lysR aminoethylp 86.3 0.43 9.4E-06 37.5 1.7 52 5-56 13-64 (279)
54 PF09382 RQC: RQC domain; Int 86.2 1.6 3.4E-05 30.2 4.4 43 14-56 53-97 (106)
55 COG4742 Predicted transcriptio 86.1 0.97 2.1E-05 37.4 3.7 54 12-68 35-88 (260)
56 cd00092 HTH_CRP helix_turn_hel 85.9 0.51 1.1E-05 29.6 1.6 38 8-47 30-67 (67)
57 PRK10341 DNA-binding transcrip 85.6 0.51 1.1E-05 38.5 1.9 54 4-57 22-75 (312)
58 TIGR02424 TF_pcaQ pca operon t 85.6 0.43 9.3E-06 38.4 1.4 51 5-55 19-69 (300)
59 PRK05638 threonine synthase; V 85.4 0.58 1.3E-05 40.9 2.2 41 15-55 398-440 (442)
60 PRK11233 nitrogen assimilation 84.8 0.51 1.1E-05 38.4 1.5 60 5-64 17-76 (305)
61 PRK10094 DNA-binding transcrip 84.8 0.64 1.4E-05 38.0 2.1 52 5-56 18-69 (308)
62 PRK10837 putative DNA-binding 84.8 0.53 1.2E-05 37.5 1.6 54 5-58 19-72 (290)
63 PF14338 Mrr_N: Mrr N-terminal 84.8 0.72 1.6E-05 31.6 2.0 36 19-56 56-91 (92)
64 PRK15421 DNA-binding transcrip 84.7 0.63 1.4E-05 38.3 2.0 52 5-56 18-69 (317)
65 TIGR03418 chol_sulf_TF putativ 84.6 0.3 6.4E-06 39.1 0.0 53 5-57 17-69 (291)
66 PF04458 DUF505: Protein of un 84.1 0.67 1.5E-05 42.3 2.1 42 15-56 327-370 (591)
67 COG1339 Transcriptional regula 83.8 1 2.2E-05 36.0 2.7 51 6-56 22-73 (214)
68 TIGR00637 ModE_repress ModE mo 83.7 0.82 1.8E-05 32.1 2.0 49 5-53 18-71 (99)
69 PRK14997 LysR family transcrip 83.2 0.79 1.7E-05 36.9 1.9 53 5-57 18-70 (301)
70 PRK09986 DNA-binding transcrip 83.2 0.66 1.4E-05 37.0 1.5 52 5-56 23-74 (294)
71 PRK11013 DNA-binding transcrip 82.9 0.67 1.5E-05 37.7 1.5 52 5-56 20-71 (309)
72 PRK09791 putative DNA-binding 82.7 0.72 1.6E-05 37.2 1.6 53 5-57 21-73 (302)
73 PRK09906 DNA-binding transcrip 82.6 0.69 1.5E-05 37.1 1.4 52 5-56 17-68 (296)
74 PRK10632 transcriptional regul 82.6 0.75 1.6E-05 37.5 1.6 55 4-58 17-71 (309)
75 PRK10082 cell density-dependen 82.6 0.71 1.5E-05 37.4 1.5 54 5-58 27-80 (303)
76 PRK12682 transcriptional regul 82.5 0.7 1.5E-05 37.6 1.4 54 5-58 18-72 (309)
77 PRK15092 DNA-binding transcrip 82.4 0.74 1.6E-05 37.9 1.5 53 5-57 27-79 (310)
78 PRK09801 transcriptional activ 82.2 0.7 1.5E-05 37.9 1.3 57 5-61 22-78 (310)
79 PF04458 DUF505: Protein of un 82.2 1.8 3.8E-05 39.7 3.9 61 13-75 460-536 (591)
80 PRK15243 transcriptional regul 81.5 0.85 1.8E-05 37.8 1.6 54 5-58 20-73 (297)
81 PRK10086 DNA-binding transcrip 81.3 0.85 1.9E-05 37.2 1.5 51 5-55 30-80 (311)
82 PF11313 DUF3116: Protein of u 80.7 2.3 5E-05 29.5 3.3 40 15-54 39-79 (85)
83 COG1542 Uncharacterized conser 80.6 0.88 1.9E-05 40.8 1.4 37 20-56 325-363 (593)
84 PF05158 RNA_pol_Rpc34: RNA po 80.5 3.8 8.3E-05 34.8 5.2 68 13-81 37-110 (327)
85 PRK11074 putative DNA-binding 80.4 0.9 1.9E-05 36.7 1.4 52 5-56 18-69 (300)
86 PRK11139 DNA-binding transcrip 80.3 0.96 2.1E-05 36.4 1.5 54 5-58 22-75 (297)
87 CHL00180 rbcR LysR transcripti 79.7 1.1 2.4E-05 36.4 1.6 54 5-58 21-74 (305)
88 COG0583 LysR Transcriptional r 79.6 0.99 2.2E-05 35.4 1.3 54 5-58 17-70 (297)
89 COG2345 Predicted transcriptio 79.5 1.4 3.1E-05 35.5 2.2 45 7-51 29-79 (218)
90 PRK11151 DNA-binding transcrip 79.2 0.88 1.9E-05 36.7 0.9 53 5-57 17-69 (305)
91 smart00419 HTH_CRP helix_turn_ 79.2 1.8 3.8E-05 25.2 2.1 35 9-46 14-48 (48)
92 PF12802 MarR_2: MarR family; 78.6 1.9 4.2E-05 26.6 2.2 29 10-38 28-56 (62)
93 PRK09508 leuO leucine transcri 78.1 1.2 2.7E-05 36.2 1.5 53 5-57 38-90 (314)
94 PF01325 Fe_dep_repress: Iron 78.0 1.6 3.5E-05 27.9 1.7 31 7-37 26-56 (60)
95 PRK12679 cbl transcriptional r 77.9 1.5 3.2E-05 36.0 1.9 52 5-56 18-70 (316)
96 PF09639 YjcQ: YjcQ protein; 77.8 1.3 2.9E-05 30.4 1.4 54 15-68 22-82 (88)
97 PRK12683 transcriptional regul 77.6 1.1 2.5E-05 36.6 1.1 53 5-57 18-71 (309)
98 PF13730 HTH_36: Helix-turn-he 77.4 1.4 3E-05 26.9 1.3 24 10-33 32-55 (55)
99 PRK12680 transcriptional regul 77.2 1 2.2E-05 37.4 0.8 58 4-61 17-75 (327)
100 TIGR02716 C20_methyl_CrtF C-20 76.9 1.8 4E-05 35.6 2.2 47 10-59 30-76 (306)
101 PHA00738 putative HTH transcri 76.5 4.8 0.0001 29.1 4.0 49 9-65 32-81 (108)
102 PRK12681 cysB transcriptional 76.3 1.5 3.1E-05 36.3 1.5 50 5-54 18-68 (324)
103 PRK13348 chromosome replicatio 75.3 1.3 2.9E-05 35.5 0.9 49 5-55 18-67 (294)
104 PF03444 HrcA_DNA-bdg: Winged 74.9 1.3 2.7E-05 30.3 0.6 48 8-55 28-75 (78)
105 PRK11482 putative DNA-binding 74.8 1.5 3.2E-05 36.1 1.1 54 5-58 45-98 (317)
106 PF03965 Penicillinase_R: Peni 74.2 11 0.00024 26.6 5.5 64 13-77 31-106 (115)
107 smart00346 HTH_ICLR helix_turn 74.2 3 6.5E-05 27.7 2.3 45 8-53 25-69 (91)
108 TIGR03298 argP transcriptional 72.9 1.5 3.2E-05 35.1 0.7 50 5-56 17-67 (292)
109 PF01047 MarR: MarR family; I 72.4 3.2 6.9E-05 25.5 2.0 31 9-39 23-53 (59)
110 PRK03635 chromosome replicatio 72.3 1.8 3.9E-05 34.9 1.0 50 5-56 18-68 (294)
111 TIGR02698 CopY_TcrY copper tra 71.7 21 0.00045 26.1 6.5 25 12-36 31-55 (130)
112 COG3373 Uncharacterized protei 69.9 8.3 0.00018 27.3 3.8 40 14-53 44-94 (108)
113 PF12840 HTH_20: Helix-turn-he 68.3 3.1 6.8E-05 26.1 1.3 33 6-38 27-59 (61)
114 cd07377 WHTH_GntR Winged helix 68.2 5.9 0.00013 24.2 2.6 34 11-46 33-66 (66)
115 PF13412 HTH_24: Winged helix- 68.2 3.7 8.1E-05 24.3 1.6 26 9-34 23-48 (48)
116 PRK10676 DNA-binding transcrip 67.6 4.8 0.0001 33.0 2.6 49 5-53 33-86 (263)
117 smart00345 HTH_GNTR helix_turn 67.4 5.3 0.00011 23.9 2.2 28 10-37 27-54 (60)
118 COG1378 Predicted transcriptio 67.2 3.2 7E-05 33.9 1.5 36 11-46 38-73 (247)
119 PRK11716 DNA-binding transcrip 65.6 8.4 0.00018 29.9 3.5 44 13-56 1-44 (269)
120 PRK12684 transcriptional regul 65.0 3.5 7.6E-05 33.6 1.3 50 5-54 18-68 (313)
121 PF09339 HTH_IclR: IclR helix- 63.7 2.6 5.7E-05 25.6 0.3 29 8-36 23-51 (52)
122 PRK00215 LexA repressor; Valid 62.8 5.6 0.00012 30.8 2.0 43 9-51 29-72 (205)
123 PF13814 Replic_Relax: Replica 62.6 8.5 0.00018 29.0 3.0 37 19-55 28-72 (191)
124 PF08461 HTH_12: Ribonuclease 61.4 6.1 0.00013 25.7 1.7 35 16-52 31-65 (66)
125 PF00325 Crp: Bacterial regula 61.1 5.8 0.00013 22.4 1.4 24 10-33 9-32 (32)
126 PF09012 FeoC: FeoC like trans 58.3 13 0.00028 23.9 2.9 32 8-39 19-50 (69)
127 PF09202 Rio2_N: Rio2, N-termi 57.9 21 0.00046 24.3 4.0 42 13-54 34-75 (82)
128 TIGR01610 phage_O_Nterm phage 57.5 8.7 0.00019 26.5 2.1 28 10-37 54-81 (95)
129 PF06969 HemN_C: HemN C-termin 57.4 12 0.00026 23.5 2.6 35 13-50 30-65 (66)
130 PF01726 LexA_DNA_bind: LexA D 56.8 8 0.00017 25.1 1.7 26 12-37 34-60 (65)
131 PRK09834 DNA-binding transcrip 56.3 13 0.00028 30.0 3.2 44 10-54 33-76 (263)
132 PRK10216 DNA-binding transcrip 56.1 6.3 0.00014 32.1 1.3 49 5-53 24-72 (319)
133 PF00392 GntR: Bacterial regul 55.1 9.2 0.0002 24.1 1.7 30 9-38 30-59 (64)
134 PHA02943 hypothetical protein; 54.6 22 0.00048 27.5 4.0 42 6-47 27-69 (165)
135 PF09669 Phage_pRha: Phage reg 54.3 11 0.00024 25.8 2.1 54 4-57 2-70 (93)
136 TIGR00738 rrf2_super rrf2 fami 54.2 4.8 0.0001 28.8 0.3 59 5-68 27-85 (132)
137 PF10711 DUF2513: Hypothetical 53.3 18 0.0004 25.2 3.2 45 11-55 28-79 (102)
138 COG1568 Predicted methyltransf 52.8 20 0.00044 30.6 3.8 39 13-54 44-82 (354)
139 TIGR02681 phage_pRha phage reg 52.1 5.7 0.00012 28.5 0.4 54 4-57 14-81 (108)
140 PF13545 HTH_Crp_2: Crp-like h 51.7 13 0.00029 23.6 2.2 28 11-38 36-63 (76)
141 COG2512 Predicted membrane-ass 51.7 20 0.00043 29.5 3.6 32 12-43 219-250 (258)
142 PRK06266 transcription initiat 51.5 22 0.00048 27.5 3.7 40 10-49 43-89 (178)
143 COG2512 Predicted membrane-ass 48.8 24 0.00051 29.1 3.6 15 117-132 231-245 (258)
144 PF01022 HTH_5: Bacterial regu 48.2 15 0.00032 21.8 1.8 26 10-35 22-47 (47)
145 PF08222 HTH_CodY: CodY helix- 47.6 34 0.00074 22.1 3.4 42 7-48 8-52 (61)
146 PF02082 Rrf2: Transcriptional 46.2 7 0.00015 26.0 0.1 45 5-49 27-71 (83)
147 PF01090 Ribosomal_S19e: Ribos 45.3 25 0.00055 26.5 3.0 37 16-54 93-129 (139)
148 PRK11014 transcriptional repre 45.1 11 0.00023 27.6 1.0 46 5-50 27-72 (141)
149 TIGR03697 NtcA_cyano global ni 44.9 24 0.00051 26.2 2.9 30 10-39 150-179 (193)
150 PRK04172 pheS phenylalanyl-tRN 44.8 32 0.0007 30.6 4.1 34 23-56 157-190 (489)
151 TIGR00635 ruvB Holliday juncti 43.4 7.2 0.00016 31.7 -0.2 45 8-55 260-305 (305)
152 smart00420 HTH_DEOR helix_turn 41.8 19 0.0004 20.8 1.5 27 10-36 21-47 (53)
153 COG4344 Uncharacterized protei 41.3 66 0.0014 24.8 4.7 65 13-78 41-126 (175)
154 TIGR03338 phnR_burk phosphonat 40.7 25 0.00055 26.9 2.5 35 9-43 40-74 (212)
155 PF08220 HTH_DeoR: DeoR-like h 38.7 25 0.00054 21.8 1.8 28 8-35 19-46 (57)
156 COG3327 PaaX Phenylacetic acid 37.3 35 0.00076 28.5 2.9 54 11-66 36-90 (291)
157 PF02295 z-alpha: Adenosine de 37.2 33 0.00072 22.3 2.3 36 13-48 30-65 (66)
158 PRK15090 DNA-binding transcrip 36.8 21 0.00046 28.6 1.5 51 7-58 32-86 (257)
159 PRK11523 DNA-binding transcrip 36.8 36 0.00079 27.0 2.9 35 9-43 38-72 (253)
160 PRK03837 transcriptional regul 36.6 28 0.00061 27.2 2.2 34 10-43 44-77 (241)
161 PRK10225 DNA-binding transcrip 36.5 39 0.00084 26.9 3.0 34 10-43 40-73 (257)
162 TIGR00498 lexA SOS regulatory 36.5 25 0.00054 27.0 1.9 39 9-47 31-70 (199)
163 PRK10402 DNA-binding transcrip 36.0 40 0.00086 26.2 3.0 38 10-49 176-213 (226)
164 PRK13918 CRP/FNR family transc 35.7 37 0.0008 25.5 2.7 29 10-38 156-184 (202)
165 TIGR02812 fadR_gamma fatty aci 35.5 29 0.00064 27.1 2.2 32 10-41 37-68 (235)
166 PRK04984 fatty acid metabolism 35.4 35 0.00077 26.7 2.6 34 10-43 38-71 (239)
167 smart00344 HTH_ASNC helix_turn 35.1 20 0.00043 24.5 1.0 28 7-34 21-48 (108)
168 PRK10141 DNA-binding transcrip 34.9 34 0.00073 24.8 2.2 42 9-50 36-78 (117)
169 PRK10421 DNA-binding transcrip 34.5 42 0.00091 26.6 2.9 35 9-43 32-66 (253)
170 PF09114 MotA_activ: Transcrip 34.2 88 0.0019 22.1 4.1 38 14-54 43-80 (96)
171 COG1725 Predicted transcriptio 33.9 54 0.0012 24.2 3.2 41 9-51 41-81 (125)
172 PRK11414 colanic acid/biofilm 33.8 26 0.00056 27.2 1.6 32 9-40 40-71 (221)
173 PF04492 Phage_rep_O: Bacterio 33.7 25 0.00053 24.9 1.3 35 3-37 54-88 (100)
174 TIGR02787 codY_Gpos GTP-sensin 33.4 26 0.00056 29.0 1.5 33 5-37 200-232 (251)
175 PRK08898 coproporphyrinogen II 33.0 73 0.0016 27.4 4.3 39 13-54 348-386 (394)
176 PRK09333 30S ribosomal protein 32.2 43 0.00093 25.6 2.5 37 16-55 94-130 (150)
177 PRK09464 pdhR transcriptional 32.1 49 0.0011 26.2 2.9 32 10-41 41-72 (254)
178 PRK05660 HemN family oxidoredu 32.1 68 0.0015 27.4 4.0 38 13-53 331-368 (378)
179 PF09756 DDRGK: DDRGK domain; 32.1 22 0.00048 28.0 0.9 62 10-80 120-182 (188)
180 PRK09990 DNA-binding transcrip 32.0 47 0.001 26.2 2.9 34 10-43 38-71 (251)
181 PRK00082 hrcA heat-inducible t 31.9 26 0.00056 29.8 1.4 41 12-53 36-76 (339)
182 PRK10163 DNA-binding transcrip 31.6 41 0.00089 27.3 2.5 40 9-49 46-85 (271)
183 PF05732 RepL: Firmicute plasm 31.2 50 0.0011 25.2 2.8 47 10-61 82-128 (165)
184 TIGR02944 suf_reg_Xantho FeS a 31.1 17 0.00036 26.1 0.1 40 6-45 28-67 (130)
185 PRK11534 DNA-binding transcrip 31.0 42 0.00092 26.0 2.4 35 9-43 36-70 (224)
186 TIGR02431 pcaR_pcaU beta-ketoa 30.4 45 0.00098 26.5 2.5 38 10-50 31-68 (248)
187 COG5570 Uncharacterized small 30.2 54 0.0012 20.8 2.3 15 112-127 30-44 (57)
188 COG3355 Predicted transcriptio 29.3 49 0.0011 24.5 2.3 30 10-39 49-78 (126)
189 COG2186 FadR Transcriptional r 29.3 41 0.00088 27.0 2.1 34 10-43 41-74 (241)
190 COG1959 Predicted transcriptio 29.0 27 0.00058 26.2 0.9 50 3-52 25-74 (150)
191 PRK11569 transcriptional repre 28.7 33 0.00072 27.9 1.4 47 9-56 49-99 (274)
192 COG1414 IclR Transcriptional r 28.6 34 0.00073 27.6 1.5 43 6-49 22-64 (246)
193 PF02334 RTP: Replication term 28.5 72 0.0016 23.4 3.0 35 16-50 53-95 (122)
194 PRK11161 fumarate/nitrate redu 28.2 59 0.0013 25.1 2.8 38 10-49 191-228 (235)
195 PF04182 B-block_TFIIIC: B-blo 27.1 83 0.0018 20.5 3.0 28 11-38 26-53 (75)
196 PF04325 DUF465: Protein of un 27.0 61 0.0013 19.5 2.1 25 102-127 14-38 (49)
197 PF10771 DUF2582: Protein of u 27.0 1.1E+02 0.0024 19.9 3.5 34 11-44 30-63 (65)
198 PF02981 FokI_N: Restriction e 26.8 62 0.0014 24.6 2.5 34 20-54 109-142 (145)
199 PTZ00095 40S ribosomal protein 26.6 60 0.0013 25.3 2.5 39 16-55 118-156 (169)
200 PRK06474 hypothetical protein; 26.4 94 0.002 23.8 3.6 48 14-61 38-95 (178)
201 PRK08208 coproporphyrinogen II 26.3 92 0.002 27.1 3.9 38 13-53 371-408 (430)
202 PRK05799 coproporphyrinogen II 25.8 1E+02 0.0022 26.0 4.0 33 19-54 334-366 (374)
203 PRK11920 rirA iron-responsive 25.2 34 0.00074 25.6 0.9 48 4-51 25-72 (153)
204 PF02002 TFIIE_alpha: TFIIE al 25.2 59 0.0013 22.4 2.0 30 10-39 34-63 (105)
205 PF14502 HTH_41: Helix-turn-he 25.0 68 0.0015 19.8 2.0 29 10-38 13-41 (48)
206 TIGR02010 IscR iron-sulfur clu 24.8 42 0.0009 24.3 1.2 46 5-50 27-72 (135)
207 PRK09391 fixK transcriptional 24.6 58 0.0012 25.4 2.1 28 10-37 186-213 (230)
208 PF09972 DUF2207: Predicted me 24.5 52 0.0011 28.3 2.0 51 17-68 290-341 (511)
209 TIGR02325 C_P_lyase_phnF phosp 23.8 63 0.0014 25.1 2.2 34 10-43 39-72 (238)
210 PRK05628 coproporphyrinogen II 23.7 1.3E+02 0.0029 25.4 4.3 39 13-54 325-367 (375)
211 PF08279 HTH_11: HTH domain; 23.6 53 0.0012 19.6 1.4 28 4-31 16-43 (55)
212 PRK06294 coproporphyrinogen II 23.3 1.2E+02 0.0027 25.8 4.0 38 14-54 321-363 (370)
213 PRK12423 LexA repressor; Provi 23.1 65 0.0014 25.0 2.1 35 10-44 32-67 (202)
214 PRK11057 ATP-dependent DNA hel 23.0 1.1E+02 0.0023 28.0 3.8 43 14-56 463-505 (607)
215 PRK11402 DNA-binding transcrip 22.6 70 0.0015 25.2 2.2 34 10-43 40-73 (241)
216 PRK11179 DNA-binding transcrip 22.1 45 0.00097 24.7 1.0 31 5-35 25-55 (153)
217 PF09857 DUF2084: Uncharacteri 21.7 54 0.0012 22.7 1.2 26 113-139 47-72 (85)
218 PRK10079 phosphonate metabolis 21.5 76 0.0016 25.0 2.2 34 10-43 42-75 (241)
219 TIGR00373 conserved hypothetic 21.0 95 0.0021 23.5 2.6 29 10-38 35-63 (158)
220 cd07153 Fur_like Ferric uptake 20.8 2E+02 0.0043 19.7 4.1 34 13-46 31-66 (116)
221 TIGR02018 his_ut_repres histid 20.8 80 0.0017 24.6 2.2 35 9-43 31-65 (230)
222 PRK08599 coproporphyrinogen II 20.8 1.5E+02 0.0033 25.0 4.1 38 14-54 329-367 (377)
223 TIGR00122 birA_repr_reg BirA b 20.7 1E+02 0.0022 19.4 2.3 36 9-46 19-54 (69)
224 TIGR02404 trehalos_R_Bsub treh 20.7 79 0.0017 24.7 2.2 34 10-43 31-64 (233)
225 PRK09334 30S ribosomal protein 20.7 72 0.0016 22.1 1.7 34 3-36 41-74 (86)
226 PRK14999 histidine utilization 20.7 78 0.0017 24.9 2.2 34 10-43 43-76 (241)
227 COG0478 RIO-like serine/threon 20.4 1.1E+02 0.0023 26.1 3.0 55 13-67 41-96 (304)
228 COG2411 Uncharacterized conser 20.3 1.9E+02 0.004 22.9 4.1 22 95-127 167-188 (188)
229 PF04703 FaeA: FaeA-like prote 20.1 87 0.0019 20.2 1.9 37 9-45 21-60 (62)
230 PRK13347 coproporphyrinogen II 20.1 1.2E+02 0.0027 26.5 3.4 31 21-54 402-432 (453)
231 COG4465 CodY Pleiotropic trans 20.0 79 0.0017 26.0 2.0 34 4-37 205-238 (261)
No 1
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=99.96 E-value=1.4e-28 Score=214.90 Aligned_cols=138 Identities=49% Similarity=0.666 Sum_probs=125.1
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhcccCCCCChHHHhcCCCchhhh
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPAECSILKDELQKKPDSALFE 87 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~~g~~~~~eL~~~lg~~~~k 87 (150)
.-|...|++|++|+++++||+++|+|++++.+.+.|+||+||++|+++||||+||+++|+++|+++++||.+.+++++++
T Consensus 23 ~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~l~~~~~~~~~eL~~~l~~~~~~ 102 (492)
T PLN02853 23 QFAASHGLDHNEVVGVIKSLHGFRYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFAAVPAEGSISKDELQKKLDPAVFD 102 (492)
T ss_pred HHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHHHhhcCCccHHHHHHhhCchhHH
Confidence 34567899999999999999999999999999999999999999999999999999999874548999999989867899
Q ss_pred hHhhhhhc-------------------chHHHHHHHHHhcCCCCCHhhHHhHhhhcC-ceeeEEEEEEEEecCCCchhh
Q 031936 88 IGCSQSVE-------------------TNKFKDLLVRVQDGRAISKEDINGGLKARK-LIVNQMCKGYSVSNALKKEES 146 (150)
Q Consensus 88 Ig~g~a~K-------------------~d~~~~~L~~i~~g~~~~~~~l~~~LKKRk-Li~~~~~~~~~V~kg~~f~~~ 146 (150)
||+|||+| .|.++..|+.+..+..++++.+ ++||||| ||+.++.++|.|++|++|++.
T Consensus 103 i~~g~a~k~gwi~i~~~~~v~~~~~~~~d~~~~~L~~l~~~~~~~~~~l-~~LkkRk~Li~~~~~~~~~v~~~~~~~~~ 180 (492)
T PLN02853 103 IGFKQAMKNKWLEMGGKPQVSRKVQHVEDEVKELLLAIQEGKEVDDKDI-DALKKRRKLITLETWKGYSIKKGPNYAPE 180 (492)
T ss_pred HHHHHHHHCCcEEECCCCcEEeccCccchHHHHHHHHHhcCCCCCHHHH-HHHHhhhcceEEEEEEEEEEEECCccccc
Confidence 99999999 4667889999987766777789 9999998 999999999999999999753
No 2
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=99.95 E-value=5.4e-28 Score=211.65 Aligned_cols=136 Identities=26% Similarity=0.307 Sum_probs=122.5
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhcccCCCCChHHHhcCCCchhhhh
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPAECSILKDELQKKPDSALFEI 88 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~~g~~~~~eL~~~lg~~~~kI 88 (150)
-|..+|++|++|+++++||+++|+|++++.+.+.|+||+||++|+++||||+|||++++++| .++.++.+.+++++++|
T Consensus 27 la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~l~~~~-~~~~~l~~~~~~~~~~i 105 (494)
T PTZ00326 27 LAESLNIDHQKVVGAIKSLESANYITTEMKKSNTWTLTEEGEDYLKNGSPEYRLWQKLKEGG-ISKADDAKKLGGKVADI 105 (494)
T ss_pred HHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHHhhhcC-CCHHHHHhhhcchhHHH
Confidence 45678999999999999999999999999999999999999999999999999999999766 78888888776678999
Q ss_pred Hhhhhhc-----------------------chHHHHHHHHHhcC---CCCCHhhHHhHhhhcCceeeEEEEEEEEecCCC
Q 031936 89 GCSQSVE-----------------------TNKFKDLLVRVQDG---RAISKEDINGGLKARKLIVNQMCKGYSVSNALK 142 (150)
Q Consensus 89 g~g~a~K-----------------------~d~~~~~L~~i~~g---~~~~~~~l~~~LKKRkLi~~~~~~~~~V~kg~~ 142 (150)
|+|||+| .|.++..|+.+..+ +.++++.+ ++|||||||+.++.++|.|++|++
T Consensus 106 ~~g~~~k~~wi~i~~~~~~i~~~~~~~~~~~d~~~~~L~~i~~~~~~~~~~~~~~-~~LkkRkLi~~~~~~~~~i~~~~~ 184 (494)
T PTZ00326 106 GLGNAMKKKWIKLNKGDKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKEL-KELKKRKLATLEKIKYFVVTKGPK 184 (494)
T ss_pred HHHHHHHCCcEEEcCCCceeecccccccccccHHHHHHHHHhccCccccCCHHHH-HHHhcCCCeEEEEEEEEEEEECCc
Confidence 9999999 24467889999876 45778889 999999999999999999999999
Q ss_pred chhh
Q 031936 143 KEES 146 (150)
Q Consensus 143 f~~~ 146 (150)
|++.
T Consensus 185 ~~~~ 188 (494)
T PTZ00326 185 FAKE 188 (494)
T ss_pred cccc
Confidence 9754
No 3
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.3e-28 Score=205.04 Aligned_cols=136 Identities=30% Similarity=0.370 Sum_probs=125.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhcccCCCCChHHHhcCCCch
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPAECSILKDELQKKPDSA 84 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~~g~~~~~eL~~~lg~~ 84 (150)
.|+--++..+.+|+.++++++||++.|+|+++..+++.|.||+||++++.+||||++||.+++++| +.++||++.+
T Consensus 19 ~s~~l~a~~~~~h~~~v~al~SL~a~~~i~~~~~~~~~~~LT~EG~~i~~eGS~E~~v~~~i~~~g-l~~~el~~k~--- 94 (483)
T KOG2784|consen 19 DSSDLAAPFNEDHQQVVGALKSLQAGGVIEVKDVETKTYELTAEGEEIAREGSHEALVFESIPEEG-LAIAELMKKL--- 94 (483)
T ss_pred ChhhhcCchhhhhHHHHHHHHHHhhcCceEEEeeeeEEEeeChhHHHHHhcCCcceeeeeccCccc-cCHHHHHhhh---
Confidence 345566778899999999999999999999999999999999999999999999999999999988 9999999985
Q ss_pred hhhhHhhhhhc------------------chHHHHHHHHHhcCCCCCHhhHHhHhhhcCceeeEEEEEEEEecCCCchhh
Q 031936 85 LFEIGCSQSVE------------------TNKFKDLLVRVQDGRAISKEDINGGLKARKLIVNQMCKGYSVSNALKKEES 146 (150)
Q Consensus 85 ~~kIg~g~a~K------------------~d~~~~~L~~i~~g~~~~~~~l~~~LKKRkLi~~~~~~~~~V~kg~~f~~~ 146 (150)
. .||+++||| .|.++.+|..|..|... .+++ ++|||||||.+.++++|.|+|||+|+|+
T Consensus 95 ~-giG~~~A~~nkWI~~d~~~~~r~v~~itD~v~~~l~~ik~g~~~-ake~-~dlkKrKLi~~~~~~~f~v~KGp~Fst~ 171 (483)
T KOG2784|consen 95 V-GIGQSKAFKNKWIRVDKSRVVRDVDSITDEVRNQLQQIKRGSAD-AKEV-EDLKKRKLISEVKIKVFSVTKGPNFSTS 171 (483)
T ss_pred h-ccchhhhhccceEEecCcccccchhhhhHHHHHHHHHHHcCcch-HHHH-HHHHhhhhhccceeEEEEEecCCcccch
Confidence 3 399999999 68899999999988754 7789 9999999999999999999999999998
Q ss_pred h
Q 031936 147 L 147 (150)
Q Consensus 147 ~ 147 (150)
+
T Consensus 172 l 172 (483)
T KOG2784|consen 172 L 172 (483)
T ss_pred H
Confidence 6
No 4
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=99.87 E-value=6.5e-22 Score=173.75 Aligned_cols=139 Identities=22% Similarity=0.190 Sum_probs=121.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhcccCCCCChHHHhcC-CCc
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPAECSILKDELQKK-PDS 83 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~~g~~~~~eL~~~-lg~ 83 (150)
+++.-|..+++++++|.+++++|+++|+|+.+......+.||+||++|+++|+||+|+++++.+.++++++||.+. ++.
T Consensus 22 s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l~~~~g~~~~el~~~aL~~ 101 (489)
T PRK04172 22 TLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGLPERRLLNALKDGGEVSLDELKEALLDK 101 (489)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcCHHHHHHHhhHhcCCcCHHHHHHhhccc
Confidence 3444566789999999999999999999999998899999999999999999999999999996333899999988 776
Q ss_pred hhhhhHhhhhhc------------------chHHHHHHHHHhcCCC-----CCHhhHHhHhhhcCceeeEEEEEEEEe--
Q 031936 84 ALFEIGCSQSVE------------------TNKFKDLLVRVQDGRA-----ISKEDINGGLKARKLIVNQMCKGYSVS-- 138 (150)
Q Consensus 84 ~~~kIg~g~a~K------------------~d~~~~~L~~i~~g~~-----~~~~~l~~~LKKRkLi~~~~~~~~~V~-- 138 (150)
+++++|+|||+| .|.++..|+.+..|+. ++.+.+ ++|+|||||+.++.+.|.|+
T Consensus 102 ~~~~i~~~~l~k~g~i~i~~G~~i~~~~~~~d~~~~~L~~l~~g~~~~~~~~~~~~l-~~LkkRkL~~~~~~~~~~~~~~ 180 (489)
T PRK04172 102 KEVGIALGNLARKGWAKIEKGKVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVL-KELKKRKLVEEKERTERSVELT 180 (489)
T ss_pred hhHHHHHHHHHHCCCeecCCCceeecCcccCcHHHHHHHHHhccCccccccCCHHHH-HHHHhcCCeEEEEEEEEEEEEc
Confidence 789999999999 4678889999987753 677889 99999999999999999977
Q ss_pred -cCCCch
Q 031936 139 -NALKKE 144 (150)
Q Consensus 139 -kg~~f~ 144 (150)
+|++|+
T Consensus 181 ~~~~~~~ 187 (489)
T PRK04172 181 DAGLELL 187 (489)
T ss_pred cchhhhh
Confidence 555554
No 5
>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=97.18 E-value=0.0013 Score=43.58 Aligned_cols=43 Identities=12% Similarity=0.047 Sum_probs=38.6
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEe------eeEEEcCHhHHHHHHc
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIK------RETRVLTDEGKKYAAE 55 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~------~~~~~LTeEG~~yl~~ 55 (150)
..+++..|..+++.|+.+|+|+..... ++.|.+|+.|++++++
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 467899999999999999999997776 8999999999998864
No 6
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.91 E-value=0.0014 Score=44.17 Aligned_cols=41 Identities=15% Similarity=0.140 Sum_probs=33.8
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
...++++..+...+++|..+|+| ......|.||+.|+++++
T Consensus 27 ~~~~L~~~~~~~yL~~L~~~gLI---~~~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 27 YKANLNYSTLKKYLKELEEKGLI---KKKDGKYRLTEKGKEFLE 67 (77)
T ss_dssp TTST--HHHHHHHHHHHHHTTSE---EEETTEEEE-HHHHHHHH
T ss_pred HHhCcCHHHHHHHHHHHHHCcCe---eCCCCEEEECccHHHHHH
Confidence 34689999999999999999999 447899999999999985
No 7
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=96.47 E-value=0.0071 Score=44.63 Aligned_cols=49 Identities=16% Similarity=0.011 Sum_probs=38.7
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHc--CChHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAE--GSSEIQ 61 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~--GsPE~r 61 (150)
++++---|+.+++||.++|+|+-.-. ..-.|.||+||.+|+.+ ++|+..
T Consensus 36 l~vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL~LP~ei 87 (124)
T PTZ00034 36 LNVPNLHVMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPPDV 87 (124)
T ss_pred cCCccHHHHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHhCCCccc
Confidence 45666689999999999999987655 45667999999999976 455543
No 8
>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=96.41 E-value=0.0058 Score=43.23 Aligned_cols=43 Identities=19% Similarity=0.088 Sum_probs=34.9
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHc
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAE 55 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~ 55 (150)
++++--.|+.+++||.++|+|+-.-. ..-.|.||+||.+|+.+
T Consensus 33 l~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~ 76 (95)
T PF03501_consen 33 LNVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLRE 76 (95)
T ss_dssp TSSBHHHHHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHH
T ss_pred cCCCcHHHHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHH
Confidence 46777789999999999999987554 45567999999999965
No 9
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=96.39 E-value=0.01 Score=40.27 Aligned_cols=44 Identities=16% Similarity=0.034 Sum_probs=34.6
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEe-----eeEEEcCHhHHHHHH
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIK-----RETRVLTDEGKKYAA 54 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~-----~~~~~LTeEG~~yl~ 54 (150)
..+|++...+-..++.|+..|||++++.. .+.|.||++|++..+
T Consensus 22 ~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~ 70 (80)
T PF13601_consen 22 EELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE 70 (80)
T ss_dssp HHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred HHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence 34789999999999999999999997654 567999999999874
No 10
>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=96.18 E-value=0.0063 Score=42.76 Aligned_cols=52 Identities=13% Similarity=0.049 Sum_probs=43.1
Q ss_pred ccCCChHHHHHHHHhhccCCceEEee------EeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQD------IKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~------~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
...+++..+..+++.|+.+|+|+... .....|.||+.|++++++-.++.+-+
T Consensus 34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~~~~ 91 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESWARL 91 (100)
T ss_pred ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHHH
Confidence 35678899999999999999999842 22588999999999998877776655
No 11
>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=96.16 E-value=0.0055 Score=43.78 Aligned_cols=53 Identities=13% Similarity=0.026 Sum_probs=43.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEee----EeeeEEEcCHhHHHHHHcCChHHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQD----IKRETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~----~~~~~~~LTeEG~~yl~~GsPE~r 61 (150)
-+..+++++..+.+.++.|+.+|+|.-.. .-...+.||++|+++++.-.|..+
T Consensus 48 la~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~ 104 (118)
T TIGR02337 48 LANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQIE 104 (118)
T ss_pred HHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHH
Confidence 34557899999999999999999999864 345689999999999988777554
No 12
>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=96.10 E-value=0.0048 Score=39.45 Aligned_cols=40 Identities=15% Similarity=0.063 Sum_probs=30.9
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEG 49 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG 49 (150)
+..++++...+.+.++.|..+|+|.-.... ...|.||++|
T Consensus 25 ~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 25 AERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 445799999999999999999999665544 3689999998
No 13
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=95.81 E-value=0.022 Score=39.41 Aligned_cols=55 Identities=11% Similarity=0.003 Sum_probs=45.8
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhHHHHHHcCChHHHHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
-+..++++...|-+.++.|+.+|+|.-.... ...+.||++|++.+..-.|..+-+
T Consensus 42 la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~~~~~ 100 (126)
T COG1846 42 LAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLPAAQEL 100 (126)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhccHHHHH
Confidence 3556899999999999999999999987664 457899999999998888844433
No 14
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=95.79 E-value=0.012 Score=43.41 Aligned_cols=69 Identities=12% Similarity=0.058 Sum_probs=50.3
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEee----EeeeEEEcCHhHHHHHHcCChHH--HHHhhcccCCCCChHHHh
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQD----IKRETRVLTDEGKKYAAEGSSEI--QLFLAVPAECSILKDELQ 78 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~----~~~~~~~LTeEG~~yl~~GsPE~--rl~~~l~~~g~~~~~eL~ 78 (150)
.-+..+++++..|.+.++.|+.+|||.-+. .-...+.||++|+..++...++. .+...+-+ + ++-+|+.
T Consensus 59 eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~~~~~l~~-~-ls~ee~~ 133 (144)
T PRK11512 59 ELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQELTK-N-LTADEVA 133 (144)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHHHHHHHHHHHHHHc-c-CCHHHHH
Confidence 335567999999999999999999999754 45667799999999988877664 24433332 3 5544443
No 15
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=95.65 E-value=0.031 Score=39.39 Aligned_cols=44 Identities=14% Similarity=0.164 Sum_probs=35.6
Q ss_pred ccCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHc
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAE 55 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~ 55 (150)
+++++---|+.++++|-++|||+..-. .-..|.||+||.+|+.+
T Consensus 34 el~ipNL~vika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLRE 78 (105)
T COG5045 34 ELEIPNLHVIKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLRE 78 (105)
T ss_pred ccCCCchHHHHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHH
Confidence 456666679999999999999988554 45567999999999864
No 16
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.56 E-value=0.012 Score=39.63 Aligned_cols=47 Identities=15% Similarity=0.109 Sum_probs=39.6
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeE----eeeEEEcCHhHHHHHHc
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDI----KRETRVLTDEGKKYAAE 55 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~----~~~~~~LTeEG~~yl~~ 55 (150)
-+..+++++..+.+.++.|+..|+|..... ....|.||+.|..++..
T Consensus 30 la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 30 LAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 345678999999999999999999987654 45688999999998765
No 17
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=95.54 E-value=0.023 Score=41.82 Aligned_cols=52 Identities=10% Similarity=0.070 Sum_probs=43.1
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEee----EeeeEEEcCHhHHHHHHcCChHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQD----IKRETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~----~~~~~~~LTeEG~~yl~~GsPE~r 61 (150)
+..+++++..|.+.++.|+.+|+|+-.. .-...+.||++|+.+++...|-..
T Consensus 53 a~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~ 108 (144)
T PRK03573 53 AKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVIN 108 (144)
T ss_pred HHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHHH
Confidence 4457999999999999999999999864 345678999999999987766544
No 18
>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=95.45 E-value=0.031 Score=41.98 Aligned_cols=53 Identities=17% Similarity=0.154 Sum_probs=43.6
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEe------eeEEEcCHhHHHHHHcCChHHHHHhh
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIK------RETRVLTDEGKKYAAEGSSEIQLFLA 65 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~------~~~~~LTeEG~~yl~~GsPE~rl~~~ 65 (150)
..+++..|..+++.|+..|+|...... .+.|.||+.|++++..-..+.+-+..
T Consensus 53 ~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~~ 111 (138)
T TIGR02719 53 SSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQN 111 (138)
T ss_pred CCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHHH
Confidence 356788999999999999999975322 58899999999999888877776644
No 19
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=95.40 E-value=0.024 Score=41.56 Aligned_cols=46 Identities=20% Similarity=0.079 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHhhccCCceEEeeEe------eeEEEcCHhHHHHHHcCChH
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDIK------RETRVLTDEGKKYAAEGSSE 59 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~~------~~~~~LTeEG~~yl~~GsPE 59 (150)
..++..|...++.|+..|+|+..... .+.|.||+.|++++..-..+
T Consensus 41 ~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~ 92 (138)
T COG1695 41 EPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREE 92 (138)
T ss_pred cCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHH
Confidence 46888999999999999999986443 58999999999999765533
No 20
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.34 E-value=0.021 Score=38.99 Aligned_cols=48 Identities=15% Similarity=0.103 Sum_probs=39.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSE 59 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE 59 (150)
+..+++++..+.+++..|+.+|+|..... ..|.||+.|+.....=.+.
T Consensus 6 a~~l~is~stvs~~l~~L~~~glI~r~~~--~~~~lT~~g~~~~~~~~~~ 53 (96)
T smart00529 6 AERLNVSPPTVTQMLKKLEKDGLVEYEPY--RGITLTEKGRRLARRLLRK 53 (96)
T ss_pred HHHhCCChHHHHHHHHHHHHCCCEEEcCC--CceEechhHHHHHHHHHHH
Confidence 45579999999999999999999999774 3799999999987444343
No 21
>PRK10870 transcriptional repressor MprA; Provisional
Probab=95.30 E-value=0.027 Score=43.44 Aligned_cols=52 Identities=8% Similarity=0.043 Sum_probs=44.0
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhHHHHHHcCChHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG~~yl~~GsPE~r 61 (150)
+..+++++..+-+.++.|+.+|+|.-.... ...+.||++|+.+++.-.|...
T Consensus 78 a~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~~ 133 (176)
T PRK10870 78 SCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQH 133 (176)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence 455799999999999999999999986554 4678999999999988877554
No 22
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=95.07 E-value=0.032 Score=41.87 Aligned_cols=43 Identities=12% Similarity=0.016 Sum_probs=36.8
Q ss_pred CCChHHHHHHHHhhccCCceEEee--EeeeEEEcCHhHHHHHHcC
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQD--IKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~--~~~~~~~LTeEG~~yl~~G 56 (150)
.+++..|...+..|+..|+|+... ..++.|.||+.|+++++.=
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~ 118 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKA 118 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHH
Confidence 457889999999999999999853 4578999999999988654
No 23
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=94.97 E-value=0.039 Score=40.82 Aligned_cols=53 Identities=19% Similarity=0.120 Sum_probs=41.3
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
-+..+++++.+|.+.++.|+.+|+|..+. ...+.||+.|+..+..=..-.+++
T Consensus 28 la~~l~vs~~svs~~l~~L~~~Gli~~~~--~~~i~LT~~G~~~a~~~~~~h~~~ 80 (142)
T PRK03902 28 IAEALSVHPSSVTKMVQKLDKDEYLIYEK--YRGLVLTPKGKKIGKRLVYRHELL 80 (142)
T ss_pred HHHHhCCChhHHHHHHHHHHHCCCEEEec--CceEEECHHHHHHHHHHHHHHHHH
Confidence 35568999999999999999999998653 356999999999876533344444
No 24
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=94.20 E-value=0.045 Score=44.03 Aligned_cols=56 Identities=11% Similarity=0.035 Sum_probs=44.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEee-EeeeEEEcCHhHHHHHHcCChHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQD-IKRETRVLTDEGKKYAAEGSSEI 60 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~-~~~~~~~LTeEG~~yl~~GsPE~ 60 (150)
|++.-+..++++++.+.+.++.|+.+|+|+-+. .....+.||+.|++.++.-..++
T Consensus 23 S~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~ 79 (217)
T PRK14165 23 SSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADY 79 (217)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHH
Confidence 344445668999999999999999999997754 24577899999999996655554
No 25
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=94.16 E-value=0.071 Score=40.62 Aligned_cols=50 Identities=24% Similarity=0.258 Sum_probs=44.3
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
.+.++|.++++-++.-++.-|+|+.+.- -..+|++|++|++.+.||++.+
T Consensus 36 ~e~~vdidDL~piv~ta~~Lglv~~e~G---DiilT~~Gk~~v~~~~~erK~l 85 (157)
T COG4754 36 KEMEVDIDDLMPIVETASLLGLVTAESG---DIILTDEGKEYVESPIRERKEL 85 (157)
T ss_pred HHhCCChhhHHHHHHHHHhcCceeccCC---CEEEehhhHHHHhCChHHHHHH
Confidence 3568899999999999999999998754 5789999999999999999865
No 26
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=93.89 E-value=0.1 Score=36.87 Aligned_cols=43 Identities=19% Similarity=0.184 Sum_probs=35.4
Q ss_pred ccCCChHHHHHHHHhhccCCceEEeeEe-eeEEEcCHhHHHHHH
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQDIK-RETRVLTDEGKKYAA 54 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~~~-~~~~~LTeEG~~yl~ 54 (150)
..++++......+..|.+.|++...... ...|.||+.|+..++
T Consensus 40 ~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle 83 (95)
T COG3432 40 GANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLE 83 (95)
T ss_pred ecCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHH
Confidence 3588999999999999999966665555 559999999999854
No 27
>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=93.85 E-value=0.055 Score=38.33 Aligned_cols=53 Identities=15% Similarity=0.078 Sum_probs=42.7
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhHHHHHHcCChHHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG~~yl~~GsPE~r 61 (150)
-+...+++...|-+.++.|+.+|+|.-.... ...+.||++|+..++.-.+|..
T Consensus 49 L~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~ 105 (109)
T TIGR01889 49 IIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEIE 105 (109)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHHH
Confidence 3455789999999999999999999964433 5567899999999887666654
No 28
>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=93.80 E-value=0.17 Score=34.63 Aligned_cols=40 Identities=15% Similarity=0.129 Sum_probs=32.6
Q ss_pred CCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhHHHHH
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEGKKYA 53 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG~~yl 53 (150)
++++..+...++.|++.|+|.-.... ...|.||+.|++..
T Consensus 30 ~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 30 GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred hhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 78899999999999999999876543 46899999999865
No 29
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=93.13 E-value=0.12 Score=42.44 Aligned_cols=52 Identities=17% Similarity=0.140 Sum_probs=47.0
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
|..+|+.+|.|.-.++.|-..|+|.. .-.-.|++|++|.+.+.+-.-|.|-|
T Consensus 32 A~~lgiT~QaVsehiK~Lv~eG~i~~--~gR~~Y~iTkkG~e~l~~~~~dlr~f 83 (260)
T COG1497 32 AKKLGITLQAVSEHIKELVKEGLIEK--EGRGEYEITKKGAEWLLEQLSDLRRF 83 (260)
T ss_pred HHHcCCCHHHHHHHHHHHHhccceee--cCCeeEEEehhHHHHHHHHHHHHHHH
Confidence 45689999999999999999999998 56678999999999999999888877
No 30
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=92.97 E-value=0.068 Score=40.29 Aligned_cols=42 Identities=19% Similarity=0.062 Sum_probs=33.7
Q ss_pred CCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHc
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAE 55 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~ 55 (150)
.++--.|+.+++||.|+|||+-.-. -.-.|.||.||.+|+.+
T Consensus 36 ~vpNL~vikaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~ 78 (150)
T KOG3344|consen 36 EVPNLHVIKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLRE 78 (150)
T ss_pred CCccHHHHHHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHH
Confidence 3555578999999999999987554 34567999999999965
No 31
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=92.90 E-value=0.13 Score=42.65 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=43.5
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHcCChHHHHHh
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAEGSSEIQLFL 64 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~GsPE~rl~~ 64 (150)
..+|++...|..++..|+..|+|+.+.. ....|.||+.|+++++.+. .|+|.
T Consensus 28 ~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~--~rIy~ 80 (280)
T TIGR02277 28 AGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAA--QRIYD 80 (280)
T ss_pred HhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHh--hhhcC
Confidence 4479999999999999999999988643 3589999999999999754 56664
No 32
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=92.59 E-value=0.13 Score=40.39 Aligned_cols=54 Identities=17% Similarity=0.004 Sum_probs=43.5
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEe----eEeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQ----DIKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e----~~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
+...+++...+.+.++.|+.+|+|.-. ..-.....||++|++.+++=.|...-+
T Consensus 66 a~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~~~~~ 123 (185)
T PRK13777 66 AKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEEYDPE 123 (185)
T ss_pred HHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHHHH
Confidence 344678889999999999999999965 355677899999999998776655544
No 33
>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=92.13 E-value=0.11 Score=34.21 Aligned_cols=37 Identities=11% Similarity=0.076 Sum_probs=30.7
Q ss_pred HHHhhcccCCCCChHHHhcCC--CchhhhhHhhhhhcch
Q 031936 61 QLFLAVPAECSILKDELQKKP--DSALFEIGCSQSVETN 97 (150)
Q Consensus 61 rl~~~l~~~g~~~~~eL~~~l--g~~~~kIg~g~a~K~d 97 (150)
.||++|.++++.++.+|.+.. ...+...|+||+.|+|
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTT
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccC
Confidence 689999986679999999774 4667888999999955
No 34
>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=92.12 E-value=0.17 Score=32.56 Aligned_cols=37 Identities=3% Similarity=-0.100 Sum_probs=32.3
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcC
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLT 46 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LT 46 (150)
+..+|++...|.+++++|+.+|+|.........|...
T Consensus 29 a~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 29 AEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 4557999999999999999999999998887777654
No 35
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=91.53 E-value=0.21 Score=38.02 Aligned_cols=46 Identities=15% Similarity=0.159 Sum_probs=38.7
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
.-|..+++.+.+|-..++.|+..|||.+++. .-+.||+.|++.+..
T Consensus 29 diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y--~gi~LT~~G~~~a~~ 74 (154)
T COG1321 29 DIAERLKVSPPSVTEMLKRLERLGLVEYEPY--GGVTLTEKGREKAKE 74 (154)
T ss_pred HHHHHhCCCcHHHHHHHHHHHHCCCeEEecC--CCeEEChhhHHHHHH
Confidence 3456789999999999999999999998654 568999999987743
No 36
>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=91.33 E-value=0.42 Score=29.74 Aligned_cols=42 Identities=14% Similarity=0.044 Sum_probs=34.2
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEe-eeEEEcCHhHHHHH
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIK-RETRVLTDEGKKYA 53 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~-~~~~~LTeEG~~yl 53 (150)
..++++...+-+++..|.+.|+|...... ...|.+|+ |+++.
T Consensus 28 ~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~ 70 (78)
T cd00090 28 ERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLL 70 (78)
T ss_pred HHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHH
Confidence 44688999999999999999999975433 67889997 77654
No 37
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=91.30 E-value=0.32 Score=35.57 Aligned_cols=51 Identities=12% Similarity=0.105 Sum_probs=44.8
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLF 63 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~ 63 (150)
|..++++.+++...+.-++--|++++.. -...||+.|+.+++.+..|++-+
T Consensus 4 a~~l~~eiDdL~p~~eAaelLgf~~~~~---Gdi~LT~~G~~f~~a~~~~rK~i 54 (120)
T PF09821_consen 4 ADELHLEIDDLLPIVEAAELLGFAEVEE---GDIRLTPLGRRFAEADIDERKEI 54 (120)
T ss_pred HHHhCCcHHHHHHHHHHHHHcCCeeecC---CcEEeccchHHHHHCChHHHHHH
Confidence 4567889999999999999999999975 57899999999999998888744
No 38
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=91.29 E-value=0.27 Score=34.42 Aligned_cols=44 Identities=18% Similarity=0.046 Sum_probs=35.4
Q ss_pred cccCCChHHHHHHHH----------hhccCCce--EEeeEeeeEEEcCHhHHHHHH
Q 031936 11 VSVTVDAQLNESVIK----------KFGLFVGL--PAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~----------sL~~kglI--~~e~~~~~~~~LTeEG~~yl~ 54 (150)
-..+.+++.|.|++. ||-..|+| ..+..-.+.|.||++|+.+++
T Consensus 33 r~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~ 88 (90)
T PF07381_consen 33 RSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEKGKRIAE 88 (90)
T ss_pred HHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChhhhhHHh
Confidence 346889999999985 89999999 334456679999999998864
No 39
>PRK11050 manganese transport regulator MntR; Provisional
Probab=91.20 E-value=0.26 Score=37.05 Aligned_cols=55 Identities=18% Similarity=0.137 Sum_probs=44.8
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHh
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFL 64 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~ 64 (150)
.-+..+++++..|.+++..|+..|+|.... ...+.||+.|+.++....+-.+.+.
T Consensus 56 eLA~~l~is~stVsr~l~~Le~~GlI~r~~--~~~v~LT~~G~~l~~~~~~~~~~le 110 (152)
T PRK11050 56 DIAARLGVSQPTVAKMLKRLARDGLVEMRP--YRGVFLTPEGEKLAQESRERHQIVE 110 (152)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEec--CCceEECchHHHHHHHHHHHHHHHH
Confidence 345668999999999999999999987644 3468999999999887777666664
No 40
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=91.16 E-value=0.46 Score=31.56 Aligned_cols=40 Identities=15% Similarity=0.095 Sum_probs=32.0
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe-eeEEEcCHhH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK-RETRVLTDEG 49 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~-~~~~~LTeEG 49 (150)
...+|++.+.+..++..|..+|+++.+..- ...|.||+.|
T Consensus 30 l~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 30 LAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp HCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred HHHcCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 346799999999999999999999887665 7788999987
No 41
>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=90.65 E-value=0.065 Score=33.97 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=33.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGK 50 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~ 50 (150)
|-++.|..+++++..|-+.++.|+..==+..-......+.||++|+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~~lT~~G~ 60 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELGVPLFERSGRGLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSSEEE-HHHH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEECCCCeeEChhhC
Confidence 3456778899999999999999999633333334445699999996
No 42
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=90.36 E-value=0.43 Score=33.50 Aligned_cols=44 Identities=16% Similarity=0.071 Sum_probs=35.7
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEe------------------eeEEEcCHhHHHHHH
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIK------------------RETRVLTDEGKKYAA 54 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~------------------~~~~~LTeEG~~yl~ 54 (150)
..+++|.+.|...+..|+..|+|+-..-. .+.|.||.+|+.++.
T Consensus 29 ~~l~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~G~~llR 90 (92)
T PF10007_consen 29 RRLKIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTREGELLLR 90 (92)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHhHHHHHh
Confidence 34689999999999999999998754322 357899999998875
No 43
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=90.17 E-value=0.49 Score=36.40 Aligned_cols=39 Identities=8% Similarity=0.021 Sum_probs=33.5
Q ss_pred CChHHHHHHHHhhccCCceEEe--eEeeeEEEcCHhHHHHH
Q 031936 15 VDAQLNESVIKKFGLFVGLPAQ--DIKRETRVLTDEGKKYA 53 (150)
Q Consensus 15 ~~~~~v~~~l~sL~~kglI~~e--~~~~~~~~LTeEG~~yl 53 (150)
++.=.+-+++..|.+.|+|..+ ......|.+|++|++.+
T Consensus 31 ~nYF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl 71 (163)
T PF14277_consen 31 TNYFTLQQALSELVESGLITLETDSDNKTRYSITEKGKETL 71 (163)
T ss_pred ccHHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHH
Confidence 3556788999999999999986 56789999999999865
No 44
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=89.77 E-value=0.79 Score=27.67 Aligned_cols=44 Identities=16% Similarity=0.004 Sum_probs=35.5
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEee-EeeeEEEcCH-hHHHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQD-IKRETRVLTD-EGKKYA 53 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~-~~~~~~~LTe-EG~~yl 53 (150)
+..++++...+.+.++.|...|+|.... .....|.+|+ .|.+.+
T Consensus 17 ~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~ 62 (66)
T smart00418 17 AEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLL 62 (66)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHH
Confidence 3456899999999999999999999766 5567788998 666544
No 45
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=89.75 E-value=0.79 Score=33.43 Aligned_cols=40 Identities=13% Similarity=0.072 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHhhccCCceEEeeEe----eeEEEcCHhHHHHH
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDIK----RETRVLTDEGKKYA 53 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~~----~~~~~LTeEG~~yl 53 (150)
++.+..+-+-++.|+..|+|.-+... +..|.||+-|+...
T Consensus 48 ~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 48 GISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred ccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHH
Confidence 48889999999999999999987775 89999999998754
No 46
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=89.70 E-value=0.25 Score=39.51 Aligned_cols=53 Identities=19% Similarity=0.195 Sum_probs=44.9
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+..+....
T Consensus 17 s~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~~~ 69 (296)
T PRK11242 17 NFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYAR 69 (296)
T ss_pred CHHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEcCCceeechhHHHHHHHHH
Confidence 45778889999999999999999998666666677899999999999876543
No 47
>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=89.03 E-value=0.3 Score=38.24 Aligned_cols=47 Identities=9% Similarity=0.041 Sum_probs=38.8
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEee------EeeeEEEcCHhHHHHHHc
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQD------IKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~------~~~~~~~LTeEG~~yl~~ 55 (150)
-|..+|+++..|.+.++.|+.+|+|.... .....|.||+.|...+.+
T Consensus 21 LA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 21 LAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 35568999999999999999999998763 245668999999987654
No 48
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=88.41 E-value=0.42 Score=32.48 Aligned_cols=34 Identities=15% Similarity=-0.068 Sum_probs=28.9
Q ss_pred HHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 18 QLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 18 ~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
.+++.++++|-+||+|+-..-. .||+||.+.+++
T Consensus 34 p~~i~a~~RLheKGLI~~pdGg----yLT~~G~~~aEh 67 (77)
T TIGR02647 34 PAAVAAAARLHEKGLTTQPDGG----YLTSLGLEAAEH 67 (77)
T ss_pred HHHHHHHHHHHHcCCccCCCCC----EecHHHHHHHHH
Confidence 4688999999999999876555 899999988764
No 49
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.26 E-value=0.2 Score=32.82 Aligned_cols=40 Identities=13% Similarity=-0.039 Sum_probs=33.4
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHh
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDE 48 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeE 48 (150)
-|..+|++...|.+.+..|+..|+|.........|.++.+
T Consensus 28 La~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~~ 67 (68)
T smart00550 28 LAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTDK 67 (68)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEeecC
Confidence 3566899999999999999999999887665578888753
No 50
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=87.94 E-value=0.32 Score=39.02 Aligned_cols=54 Identities=13% Similarity=0.087 Sum_probs=44.8
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
.|-++.|..+++.+.+|-+.++.||+.==+..-.+....+.||++|+.+++.--
T Consensus 16 gs~s~AA~~L~isqpavS~~I~~LE~~lG~~LF~R~~r~~~lT~~G~~l~~~a~ 69 (275)
T PRK03601 16 RHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAE 69 (275)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCCceEEECCCceEECHhHHHHHHHHH
Confidence 355678888999999999999999997666666677788999999999776543
No 51
>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=87.28 E-value=0.35 Score=39.30 Aligned_cols=53 Identities=17% Similarity=0.079 Sum_probs=45.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||+.==+..-.+....+.||++|+.++..-.
T Consensus 24 s~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~ 76 (302)
T TIGR02036 24 SFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALK 76 (302)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCceEEECCCceeECHhHHHHHHHHH
Confidence 55677888999999999999999998666666788899999999999886554
No 52
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=87.01 E-value=0.39 Score=38.88 Aligned_cols=54 Identities=13% Similarity=-0.056 Sum_probs=45.1
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++.--+
T Consensus 20 s~s~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~ 73 (296)
T PRK11062 20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADK 73 (296)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHcCccceeecCCceeECHhHHHHHHHHHH
Confidence 557788899999999999999999986666666678889999999988755443
No 53
>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=86.31 E-value=0.43 Score=37.54 Aligned_cols=52 Identities=13% Similarity=0.087 Sum_probs=43.7
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+..++.-
T Consensus 13 s~~~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a 64 (279)
T TIGR03339 13 SFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIV 64 (279)
T ss_pred CHHHHHHHhcCCchHHHHHHHHHHHHhCCccEEEcCCeEEEChhHHHHHHHH
Confidence 4567788899999999999999999866666666788899999999887544
No 54
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=86.20 E-value=1.6 Score=30.23 Aligned_cols=43 Identities=19% Similarity=0.063 Sum_probs=36.0
Q ss_pred CCChHHHHHHHHhhccCCceEEeeE--eeeEEEcCHhHHHHHHcC
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDI--KRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~--~~~~~~LTeEG~~yl~~G 56 (150)
+++...+.+.+..|...|++..... ....+.+|+.|++++.+.
T Consensus 53 ~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~ 97 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGK 97 (106)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTT
T ss_pred cCCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCCC
Confidence 5688899999999999999977777 777999999999998754
No 55
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=86.15 E-value=0.97 Score=37.41 Aligned_cols=54 Identities=13% Similarity=0.023 Sum_probs=48.3
Q ss_pred ccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhccc
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPA 68 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~ 68 (150)
.++++..+++..++.|...|+|.-+ ...|.||+-|+-++++-.|=...++++.+
T Consensus 35 ~l~vs~~ai~pqiKkL~~~~LV~~~---~~~Y~LS~~G~iiv~km~~ll~tl~v~e~ 88 (260)
T COG4742 35 ELNVSSSAILPQIKKLKDKGLVVQE---GDRYSLSSLGKIIVEKMEPLLDTLEVFEE 88 (260)
T ss_pred HhCCCcHHHHHHHHHHhhCCCEEec---CCEEEecchHHHHHHHHHHHHHHHHHHHh
Confidence 3688899999999999999999766 78999999999999999998888888864
No 56
>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=85.86 E-value=0.51 Score=29.60 Aligned_cols=38 Identities=5% Similarity=-0.049 Sum_probs=30.8
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCH
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTD 47 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTe 47 (150)
.-+..+|+++..|.+.+..|+..|+|.... ...|.+++
T Consensus 30 ela~~~g~s~~tv~r~l~~L~~~g~i~~~~--~~~~~l~~ 67 (67)
T cd00092 30 EIADYLGLTRETVSRTLKELEEEGLISRRG--RGKYRVNP 67 (67)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEecC--CCeEEeCC
Confidence 345568999999999999999999999876 44677653
No 57
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=85.58 E-value=0.51 Score=38.47 Aligned_cols=54 Identities=13% Similarity=0.127 Sum_probs=45.3
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
.|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++.--
T Consensus 22 gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~a~ 75 (312)
T PRK10341 22 GSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSE 75 (312)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceEChhHHHHHHHHH
Confidence 356788889999999999999999998656666677788999999999986543
No 58
>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=85.56 E-value=0.43 Score=38.36 Aligned_cols=51 Identities=14% Similarity=0.218 Sum_probs=43.0
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
|-+..|..+++.+..|-+.++.||..==+..-.+....+.||+.|+.++..
T Consensus 19 S~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~~lT~~G~~l~~~ 69 (300)
T TIGR02424 19 SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRH 69 (300)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCccccHhHHHHHHH
Confidence 556778889999999999999999986566666678889999999998843
No 59
>PRK05638 threonine synthase; Validated
Probab=85.38 E-value=0.58 Score=40.95 Aligned_cols=41 Identities=17% Similarity=0.135 Sum_probs=34.3
Q ss_pred CChHHHHHHHHhhccCCceEEe--eEeeeEEEcCHhHHHHHHc
Q 031936 15 VDAQLNESVIKKFGLFVGLPAQ--DIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 15 ~~~~~v~~~l~sL~~kglI~~e--~~~~~~~~LTeEG~~yl~~ 55 (150)
++...|...|+.|+..|+|+.. +-....|.||+.|++++.+
T Consensus 398 ~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 398 LKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred CCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 6788999999999999999874 3346679999999998753
No 60
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=84.85 E-value=0.51 Score=38.37 Aligned_cols=60 Identities=7% Similarity=-0.035 Sum_probs=47.4
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFL 64 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~ 64 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+....-+=.+.++
T Consensus 17 S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R~~r~v~lT~~G~~l~~~a~~~l~~~~ 76 (305)
T PRK11233 17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCE 76 (305)
T ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEeCCCCceECHhHHHHHHHHHHHHHHHH
Confidence 556788889999999999999999975555555567889999999999877665444443
No 61
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=84.83 E-value=0.64 Score=38.00 Aligned_cols=52 Identities=15% Similarity=0.053 Sum_probs=45.0
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++..
T Consensus 18 s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a 69 (308)
T PRK10094 18 SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQA 69 (308)
T ss_pred CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCceeECHhHHHHHHHH
Confidence 5577888999999999999999999866777777888899999999987554
No 62
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=84.78 E-value=0.53 Score=37.45 Aligned_cols=54 Identities=11% Similarity=0.178 Sum_probs=44.3
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+.+|-+.++.||+.==+..-.+....+.||+.|+.+......
T Consensus 19 s~t~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~ 72 (290)
T PRK10837 19 STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALA 72 (290)
T ss_pred CHHHHHHHhCCCccHHHHHHHHHHHHhCCccEeecCCeEEECHhHHHHHHHHHH
Confidence 446778889999999999999999975555556677789999999998876544
No 63
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=84.77 E-value=0.72 Score=31.64 Aligned_cols=36 Identities=19% Similarity=0.016 Sum_probs=27.5
Q ss_pred HHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 19 LNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 19 ~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
.+-=++..|...|+|.- ...-.|.||++|++++.++
T Consensus 56 ri~Wa~~~L~~aGli~~--~~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 56 RIRWARSYLKKAGLIER--PKRGIWRITEKGRKALAEH 91 (92)
T ss_pred hHHHHHHHHHHCCCccC--CCCCceEECHhHHHHHhhC
Confidence 34446677888999944 3477999999999998764
No 64
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=84.68 E-value=0.63 Score=38.34 Aligned_cols=52 Identities=12% Similarity=0.052 Sum_probs=43.1
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++..
T Consensus 18 s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~~r~v~lT~~G~~l~~~a 69 (317)
T PRK15421 18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLA 69 (317)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEecCCCceECHhHHHHHHHH
Confidence 5567888999999999999999999755555555678899999999987544
No 65
>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=84.61 E-value=0.3 Score=39.11 Aligned_cols=53 Identities=15% Similarity=0.154 Sum_probs=44.3
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||+.==+..-.+....+.||+.|+.+.+.-.
T Consensus 17 s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~a~ 69 (291)
T TIGR03418 17 SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQRLFEAVR 69 (291)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCceeEcHhHHHHHHHHH
Confidence 45778889999999999999999998656666667888999999999875443
No 66
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=84.15 E-value=0.67 Score=42.32 Aligned_cols=42 Identities=14% Similarity=0.094 Sum_probs=35.1
Q ss_pred CChHHHHHHHHhhccCCceEEee-Ee-eeEEEcCHhHHHHHHcC
Q 031936 15 VDAQLNESVIKKFGLFVGLPAQD-IK-RETRVLTDEGKKYAAEG 56 (150)
Q Consensus 15 ~~~~~v~~~l~sL~~kglI~~e~-~~-~~~~~LTeEG~~yl~~G 56 (150)
.+.+.+-.++.+|+++++|..+. .. +..|.||+.|+.+++.-
T Consensus 327 ~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 327 KNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred cchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 35566888999999999999876 44 78999999999999744
No 67
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=83.75 E-value=1 Score=36.01 Aligned_cols=51 Identities=14% Similarity=0.044 Sum_probs=41.6
Q ss_pred CcccccccCCChHHHHHHHHhhccCCceEEee-EeeeEEEcCHhHHHHHHcC
Q 031936 6 SSASTVSVTVDAQLNESVIKKFGLFVGLPAQD-IKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 6 ~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~-~~~~~~~LTeEG~~yl~~G 56 (150)
|+--+-.++.+.|...+.+++|+..|+|+-+. ..-+...+||.|.+.+.+=
T Consensus 22 ~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~ 73 (214)
T COG1339 22 SSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKE 73 (214)
T ss_pred HHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHH
Confidence 34445568999999999999999999999777 5556679999999998553
No 68
>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=83.68 E-value=0.82 Score=32.14 Aligned_cols=49 Identities=14% Similarity=0.093 Sum_probs=38.8
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeEe----eeEEEcCHhHHHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDIK----RETRVLTDEGKKYA 53 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~~----~~~~~LTeEG~~yl 53 (150)
|-+..|..+|+++..|-+.++.|+.. |.--++... ..-+.||+.|+.++
T Consensus 18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 18 SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 44567788999999999999999996 544444443 45899999999987
No 69
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=83.17 E-value=0.79 Score=36.90 Aligned_cols=53 Identities=9% Similarity=0.045 Sum_probs=43.9
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||+.==+..-.+....++||+.|+.++..-.
T Consensus 18 s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~~~lT~~G~~l~~~a~ 70 (301)
T PRK14997 18 GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCK 70 (301)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeeccCcceEcHhHHHHHHHHH
Confidence 44677888999999999999999998656666667888999999998875543
No 70
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=83.16 E-value=0.66 Score=37.00 Aligned_cols=52 Identities=19% Similarity=0.158 Sum_probs=43.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....++||+.|+.++..-
T Consensus 23 s~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a 74 (294)
T PRK09986 23 HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEES 74 (294)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCceeECHhHHHHHHHH
Confidence 5567788899999999999999999866666666788899999999887543
No 71
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=82.93 E-value=0.67 Score=37.72 Aligned_cols=52 Identities=15% Similarity=0.107 Sum_probs=42.8
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+..|..+++.+..|-+.++.||+.==+..-.+....+.||++|+.+++.-
T Consensus 20 S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R~~~~v~LT~~G~~l~~~a 71 (309)
T PRK11013 20 SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEV 71 (309)
T ss_pred cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeeecCCCcccCHHHHHHHHHH
Confidence 5577888899999999999999999755555556677799999999987644
No 72
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=82.73 E-value=0.72 Score=37.21 Aligned_cols=53 Identities=13% Similarity=0.092 Sum_probs=42.8
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-++.|..+++.+.+|-+.++.||+.==+..-.+....+.||++|+.++..-.
T Consensus 21 s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R~~r~~~lT~~G~~l~~~a~ 73 (302)
T PRK09791 21 SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAS 73 (302)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceECccHHHHHHHHH
Confidence 45677888999999999999999997444454567788999999999876543
No 73
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=82.62 E-value=0.69 Score=37.08 Aligned_cols=52 Identities=15% Similarity=0.201 Sum_probs=44.7
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+..++.-
T Consensus 17 s~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a 68 (296)
T PRK09906 17 NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDA 68 (296)
T ss_pred CHHHHHHHhCCCCcHHHHHHHHHHHHhCCeeeeeCCCcceEcHhHHHHHHHH
Confidence 4467788899999999999999999876777777889999999999988544
No 74
>PRK10632 transcriptional regulator; Provisional
Probab=82.58 E-value=0.75 Score=37.51 Aligned_cols=55 Identities=13% Similarity=0.080 Sum_probs=46.0
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
.|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++.-.+
T Consensus 17 gS~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~i~lT~~G~~l~~~a~~ 71 (309)
T PRK10632 17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRR 71 (309)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeecccCCCceechhHHHHHHHHHH
Confidence 4567788889999999999999999986667777778889999999998755443
No 75
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=82.55 E-value=0.71 Score=37.38 Aligned_cols=54 Identities=17% Similarity=0.183 Sum_probs=44.3
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+......||++|+.+++..-+
T Consensus 27 S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R~~r~~~lT~~G~~l~~~a~~ 80 (303)
T PRK10082 27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRH 80 (303)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEecCCCCccCHHHHHHHHHHHH
Confidence 456778889999999999999999975555666667789999999999876543
No 76
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=82.51 E-value=0.7 Score=37.56 Aligned_cols=54 Identities=11% Similarity=0.001 Sum_probs=42.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEE-EcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR-VLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~-~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+ .||+.|+.++.....
T Consensus 18 s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~~~~~ 72 (309)
T PRK12682 18 NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIER 72 (309)
T ss_pred CHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEECCCCcCccCHhHHHHHHHHHH
Confidence 557788899999999999999999974445545555555 899999998866543
No 77
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=82.35 E-value=0.74 Score=37.90 Aligned_cols=53 Identities=13% Similarity=0.179 Sum_probs=44.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||+.|+.++....
T Consensus 27 s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~~~~~LT~~G~~l~~~a~ 79 (310)
T PRK15092 27 TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYAR 79 (310)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEECCCCceECHhHHHHHHHHH
Confidence 45678888999999999999999998666666667778899999999876654
No 78
>PRK09801 transcriptional activator TtdR; Provisional
Probab=82.24 E-value=0.7 Score=37.87 Aligned_cols=57 Identities=12% Similarity=0.092 Sum_probs=46.5
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~r 61 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.++.....=..
T Consensus 22 s~t~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~r~~~lT~~G~~l~~~a~~il~ 78 (310)
T PRK09801 22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILT 78 (310)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHhCCEeeeecCCCCcccHhHHHHHHHHHHHHH
Confidence 446678889999999999999999986666666678899999999999866654333
No 79
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=82.18 E-value=1.8 Score=39.65 Aligned_cols=61 Identities=15% Similarity=0.127 Sum_probs=47.3
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHH--HHcCChH--------------HHHHhhcccCCCCChH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKY--AAEGSSE--------------IQLFLAVPAECSILKD 75 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~y--l~~GsPE--------------~rl~~~l~~~g~~~~~ 75 (150)
.+.+...+..++.+|+++|+|..- ....++||+-|+.+ +-.|-|+ +||++++.+.|+.-.+
T Consensus 460 ~~~ee~~i~~AL~kLEArGfI~~L--p~g~iilTeaG~~ik~Alsg~p~~e~~g~~~PVtP~~~rVL~Ai~~~g~lyvK 536 (591)
T PF04458_consen 460 VGKEEEEIIEALEKLEARGFIEIL--PNGMIILTEAGELIKRALSGVPEQEILGFGFPVTPTIYRVLKAIREVGTLYVK 536 (591)
T ss_pred cccchHHHHHHHHHHHhcchHHHc--CCCcEEEehhhHHHHHHHhcCCcccccccCCCCCHHHHHHHHHHHHhhhhhhh
Confidence 345667788999999999999764 45678999999876 6689999 8999998865534333
No 80
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=81.51 E-value=0.85 Score=37.82 Aligned_cols=54 Identities=17% Similarity=-0.030 Sum_probs=45.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-+..|..+++...+|-..++.||..==+..-.+....+.||++|+.++..-..
T Consensus 20 Sfs~AA~~L~isQpavS~~Ik~LE~eLG~~LF~R~~r~~~LT~aG~~ll~~a~~ 73 (297)
T PRK15243 20 SFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKS 73 (297)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHhCCccEEeCCCCeeECHHHHHHHHHHHH
Confidence 456778889999999999999999986666677788999999999999865544
No 81
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=81.26 E-value=0.85 Score=37.20 Aligned_cols=51 Identities=16% Similarity=0.109 Sum_probs=44.8
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||+.|+.++..
T Consensus 30 s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~LT~~G~~l~~~ 80 (311)
T PRK10086 30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80 (311)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCeeEEEcCCCcccCHhHHHHHHH
Confidence 446778889999999999999999987777778888999999999998864
No 82
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=80.75 E-value=2.3 Score=29.48 Aligned_cols=40 Identities=13% Similarity=-0.031 Sum_probs=32.7
Q ss_pred CChHHHHHHHHhhccCCceEE-eeEeeeEEEcCHhHHHHHH
Q 031936 15 VDAQLNESVIKKFGLFVGLPA-QDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 15 ~~~~~v~~~l~sL~~kglI~~-e~~~~~~~~LTeEG~~yl~ 54 (150)
....++.-.+.|||..|+|.- .....++|.+|+.|...++
T Consensus 39 ~TKNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~ 79 (85)
T PF11313_consen 39 FTKNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLA 79 (85)
T ss_pred ccHHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHH
Confidence 356789999999999998765 4556678999999998765
No 83
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=80.57 E-value=0.88 Score=40.82 Aligned_cols=37 Identities=22% Similarity=0.170 Sum_probs=31.3
Q ss_pred HHHHHHhhccCCceEEeeEee--eEEEcCHhHHHHHHcC
Q 031936 20 NESVIKKFGLFVGLPAQDIKR--ETRVLTDEGKKYAAEG 56 (150)
Q Consensus 20 v~~~l~sL~~kglI~~e~~~~--~~~~LTeEG~~yl~~G 56 (150)
+-.++.+|+++|+|+.+..+. -+|+||+.|+++++.+
T Consensus 325 vt~aL~~LEs~glik~ev~k~g~l~yvlTe~Gekvle~l 363 (593)
T COG1542 325 VTAALYTLESFGLIKREVVKNGDLTYVLTEFGEKVLEDL 363 (593)
T ss_pred HHHHHHhhhhccchhhhhhhcCceEEEehhhhHHHHhcc
Confidence 678999999999999865544 4799999999988765
No 84
>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=80.47 E-value=3.8 Score=34.81 Aligned_cols=68 Identities=16% Similarity=0.071 Sum_probs=45.1
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcC--HhHHHHHHcCChHHHHHhhccc---CCCCChHHHhcCC
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLT--DEGKKYAAEGSSEIQLFLAVPA---ECSILKDELQKKP 81 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LT--eEG~~yl~~GsPE~rl~~~l~~---~g~~~~~eL~~~l 81 (150)
.+++.+.++.++..|.+.|++.+-.. ....|.+- ++...+..--..|+.||+.+.+ .| |-..+|+...
T Consensus 37 ~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag~~G-Iw~~~i~~~t 110 (327)
T PF05158_consen 37 PGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAGNKG-IWTKDIKKKT 110 (327)
T ss_dssp TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE--SSS-----SSSCCHHHHHHHHHHHTTT--EEHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCC-CcHHHHHHHc
Confidence 47899999999999999998888654 33466665 4444444333448888899874 45 8889998774
No 85
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=80.43 E-value=0.9 Score=36.75 Aligned_cols=52 Identities=15% Similarity=0.211 Sum_probs=44.1
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.+++.-
T Consensus 18 s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~~ 69 (300)
T PRK11074 18 SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEA 69 (300)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEEeCCCCceECccHHHHHHHH
Confidence 4567788899999999999999999866677677788899999999987443
No 86
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=80.29 E-value=0.96 Score=36.40 Aligned_cols=54 Identities=22% Similarity=0.279 Sum_probs=44.7
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+......||++|+.++...-.
T Consensus 22 s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~r~l~lT~~G~~l~~~~~~ 75 (297)
T PRK11139 22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIRE 75 (297)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCchheEecCCceeECHhHHHHHHHHHH
Confidence 446778889999999999999999985555557777889999999998866533
No 87
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=79.73 E-value=1.1 Score=36.35 Aligned_cols=54 Identities=19% Similarity=0.205 Sum_probs=44.1
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+..|-+.++.||..==+..-.+....+.||+.|+.+++..-.
T Consensus 21 s~s~AA~~L~isqpavS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~ 74 (305)
T CHL00180 21 SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNR 74 (305)
T ss_pred CHHHHHHHhcCCChHHHHHHHHHHHHhCCEEEEecCCCceECHhHHHHHHHHHH
Confidence 456778889999999999999999975555555667789999999999765543
No 88
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=79.58 E-value=0.99 Score=35.40 Aligned_cols=54 Identities=15% Similarity=0.198 Sum_probs=40.7
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-++.|..+++.+.+|-..++.||..==+..-.+....+.||++|+.+...-..
T Consensus 17 s~t~AA~~L~isqsavS~~I~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~ 70 (297)
T COG0583 17 SFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVRLTEAGERLLERARR 70 (297)
T ss_pred cHHHHHHHhCCCChHHHHHHHHHHHHhCchheeecCCceeeCHhHHHHHHHHHH
Confidence 446678889999999999999999964344444443449999999998865443
No 89
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=79.47 E-value=1.4 Score=35.53 Aligned_cols=45 Identities=7% Similarity=0.049 Sum_probs=38.5
Q ss_pred cccccccCCChHHHHHHHHhhccCCceEEeeEee------eEEEcCHhHHH
Q 031936 7 SASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKR------ETRVLTDEGKK 51 (150)
Q Consensus 7 ~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~------~~~~LTeEG~~ 51 (150)
..-|..+|++...|.+-+..|+.+|+|.++.... ..|.||+-|..
T Consensus 29 ~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 29 DELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 3446678999999999999999999999985443 78999999987
No 90
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=79.17 E-value=0.88 Score=36.75 Aligned_cols=53 Identities=13% Similarity=0.087 Sum_probs=44.9
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+....+.||+.|+.+++.-.
T Consensus 17 S~s~AA~~L~itQpavS~~i~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~a~ 69 (305)
T PRK11151 17 HFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQAR 69 (305)
T ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHhCchheeeCCCceeECccHHHHHHHHH
Confidence 55678889999999999999999998656666668999999999999886543
No 91
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=79.16 E-value=1.8 Score=25.18 Aligned_cols=35 Identities=6% Similarity=-0.026 Sum_probs=27.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcC
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLT 46 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LT 46 (150)
-+..+|+++..+.+.+..|+..|+|.... ..|.+|
T Consensus 14 la~~l~~s~~tv~~~l~~L~~~g~l~~~~---~~~~i~ 48 (48)
T smart00419 14 IAELLGLTRETVSRTLKRLEKEGLISREG---GRIVIL 48 (48)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeC---CEEEEC
Confidence 35568999999999999999999998653 345554
No 92
>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=78.61 E-value=1.9 Score=26.59 Aligned_cols=29 Identities=3% Similarity=-0.025 Sum_probs=24.0
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
+..++++++.|-+.++.|+.+|||..+..
T Consensus 28 a~~l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 28 AERLGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45679999999999999999999987754
No 93
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=78.09 E-value=1.2 Score=36.24 Aligned_cols=53 Identities=2% Similarity=-0.067 Sum_probs=44.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+.||++|+.++..--
T Consensus 38 s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~~~ 90 (314)
T PRK09508 38 NITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVR 90 (314)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHhhCCCcEEEcCCCCcCcHHHHHHHHHHH
Confidence 45677888999999999999999998666677777888999999999876543
No 94
>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=77.97 E-value=1.6 Score=27.85 Aligned_cols=31 Identities=6% Similarity=-0.031 Sum_probs=25.9
Q ss_pred cccccccCCChHHHHHHHHhhccCCceEEee
Q 031936 7 SASTVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 7 ~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
+.-|..+|+.+.+|-..++.|+.+|||..++
T Consensus 26 ~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 26 KDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 3346678999999999999999999999875
No 95
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=77.92 E-value=1.5 Score=35.97 Aligned_cols=52 Identities=8% Similarity=-0.140 Sum_probs=39.9
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-++.|..+++.+.+|-+.++.||.. |.-=+++.....+.||+.|+.++...
T Consensus 18 s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~~a 70 (316)
T PRK12679 18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIA 70 (316)
T ss_pred CHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECCCcccccCHhHHHHHHHH
Confidence 55778888999999999999999997 44444443334468999999876544
No 96
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=77.77 E-value=1.3 Score=30.37 Aligned_cols=54 Identities=9% Similarity=0.057 Sum_probs=31.1
Q ss_pred CChHHHHHHHHhhccCCceE-------EeeEeeeEEEcCHhHHHHHHcCChHHHHHhhccc
Q 031936 15 VDAQLNESVIKKFGLFVGLP-------AQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPA 68 (150)
Q Consensus 15 ~~~~~v~~~l~sL~~kglI~-------~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~ 68 (150)
+.......++..|...|||. .-........+|.+|.+|+++-|-=.++++.+++
T Consensus 22 ~~~~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~ENS~mkKa~k~lKe 82 (88)
T PF09639_consen 22 ITDSYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEENSMMKKAYKFLKE 82 (88)
T ss_dssp S-HHHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHHHT-S---------
T ss_pred hhHHHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHHHHHHHHHHHHHHH
Confidence 33366788999999999996 3334556778999999999988877777777764
No 97
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=77.58 E-value=1.1 Score=36.55 Aligned_cols=53 Identities=13% Similarity=0.016 Sum_probs=41.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEE-EcCHhHHHHHHcCC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR-VLTDEGKKYAAEGS 57 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~-~LTeEG~~yl~~Gs 57 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+..... .||++|+.+.+..-
T Consensus 18 S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~ 71 (309)
T PRK12683 18 NLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVE 71 (309)
T ss_pred CHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEeeCCCCcCCcCHHHHHHHHHHH
Confidence 556778889999999999999999974444444556665 89999999875543
No 98
>PF13730 HTH_36: Helix-turn-helix domain
Probab=77.43 E-value=1.4 Score=26.88 Aligned_cols=24 Identities=13% Similarity=0.025 Sum_probs=21.2
Q ss_pred ccccCCChHHHHHHHHhhccCCce
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGL 33 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI 33 (150)
+...|+....|.++++.|+.+|+|
T Consensus 32 a~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 32 AKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHCcCHHHHHHHHHHHHHCcCC
Confidence 445799999999999999999986
No 99
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=77.23 E-value=1 Score=37.35 Aligned_cols=58 Identities=10% Similarity=0.051 Sum_probs=45.8
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEE-cCHhHHHHHHcCChHHH
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRV-LTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~-LTeEG~~yl~~GsPE~r 61 (150)
.|-++.|..+++.+.+|-+.++.||..==+..-.+....+. ||++|+.+++....=..
T Consensus 17 gS~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v~~LT~~G~~l~~~a~~il~ 75 (327)
T PRK12680 17 LNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLS 75 (327)
T ss_pred CCHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEECCCcCCccCccHHHHHHHHHHHHH
Confidence 35677888999999999999999999755566666666774 99999998876654333
No 100
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=76.94 E-value=1.8 Score=35.55 Aligned_cols=47 Identities=9% Similarity=-0.004 Sum_probs=41.4
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSE 59 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE 59 (150)
|...|+++..+.+.+..|.+.|+++.+ ...|.+|+.+..++..++|.
T Consensus 30 A~~~~~~~~~~~~lL~~L~~lgll~~~---~~~y~~t~~~~~~l~~~~~~ 76 (306)
T TIGR02716 30 AADTGSVPPRLEMLLETLRQMRVINLE---DGKWSLTEFADYMFSPTPKE 76 (306)
T ss_pred HHHcCCChHHHHHHHHHHHhCCCeEec---CCcEecchhHHhhccCCccc
Confidence 456799999999999999999999864 36899999999999888875
No 101
>PHA00738 putative HTH transcription regulator
Probab=76.50 E-value=4.8 Score=29.12 Aligned_cols=49 Identities=14% Similarity=0.022 Sum_probs=39.0
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE-EcCHhHHHHHHcCChHHHHHhh
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR-VLTDEGKKYAAEGSSEIQLFLA 65 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~-~LTeEG~~yl~~GsPE~rl~~~ 65 (150)
-+..+++....|.+-++-|+..|+|..+..-+..| .|. .+.|++++++.
T Consensus 32 Lae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln--------~~~~~~~l~~~ 81 (108)
T PHA00738 32 ISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIR--------ENSKEIQILNS 81 (108)
T ss_pred HHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEEC--------CCccHHHHHhh
Confidence 34567899999999999999999999987766554 666 55777777755
No 102
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=76.35 E-value=1.5 Score=36.34 Aligned_cols=50 Identities=10% Similarity=0.043 Sum_probs=41.3
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEE-EcCHhHHHHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR-VLTDEGKKYAA 54 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~-~LTeEG~~yl~ 54 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+....+ .||++|+.++.
T Consensus 18 S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~ 68 (324)
T PRK12681 18 NVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIR 68 (324)
T ss_pred CHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHH
Confidence 557788889999999999999999986566666666666 69999999873
No 103
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=75.31 E-value=1.3 Score=35.46 Aligned_cols=49 Identities=14% Similarity=-0.012 Sum_probs=39.3
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
|-++.|..+++.+.+|-+.++.||.. |.-=+++ .. .+.||++|+.+++.
T Consensus 18 s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R-~r-~i~lT~~G~~l~~~ 67 (294)
T PRK13348 18 SFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GR-PCRPTPAGQRLLRH 67 (294)
T ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeec-CC-CCccChhHHHHHHH
Confidence 44677888999999999999999996 6555555 44 79999999988743
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=74.90 E-value=1.3 Score=30.32 Aligned_cols=48 Identities=8% Similarity=-0.006 Sum_probs=41.9
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
.-+..+++++..|...+..|++.|||.......-=++.|+.|-+++..
T Consensus 28 ~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 28 TIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred HHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence 345568899999999999999999999999999999999999887754
No 105
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=74.77 E-value=1.5 Score=36.12 Aligned_cols=54 Identities=11% Similarity=-0.036 Sum_probs=42.8
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCCh
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSS 58 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsP 58 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+......||++|+.+.+....
T Consensus 45 s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v~lT~~G~~l~~~~~~ 98 (317)
T PRK11482 45 GIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQ 98 (317)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCCcceEecCCCccCCHHHHHHHHHHHH
Confidence 456778889999999999999999964344444567789999999988766443
No 106
>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=74.21 E-value=11 Score=26.57 Aligned_cols=64 Identities=17% Similarity=0.096 Sum_probs=37.1
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeee-EEEcCHhHHHHHH-----------cCChHHHHHhhcccCCCCChHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRE-TRVLTDEGKKYAA-----------EGSSEIQLFLAVPAECSILKDEL 77 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~-~~~LTeEG~~yl~-----------~GsPE~rl~~~l~~~g~~~~~eL 77 (150)
.++....|.-.+..|..||+|+.+..-.. .|..+=.=++|.. .|++..-+..++.... ++.+|+
T Consensus 31 ~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~~-ls~~el 106 (115)
T PF03965_consen 31 RSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQELRQFLDRLFDGSIPQLVAALVESEE-LSPEEL 106 (115)
T ss_dssp SS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHCT--S-HHHH
T ss_pred cccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCC-CCHHHH
Confidence 57889999999999999999999875432 3443222222222 4555555555554332 554443
No 107
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=74.17 E-value=3 Score=27.67 Aligned_cols=45 Identities=2% Similarity=-0.034 Sum_probs=35.0
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHH
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYA 53 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl 53 (150)
.-+..+|++...|.+.+..|+..|+|.... ....|.++...-.+.
T Consensus 25 ~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~-~~~~y~l~~~~~~~~ 69 (91)
T smart00346 25 ELAERLGLSKSTAHRLLNTLQELGYVEQDG-QNGRYRLGPKVLELG 69 (91)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHCCCeeecC-CCCceeecHHHHHHH
Confidence 345567999999999999999999998754 245788887665543
No 108
>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=72.92 E-value=1.5 Score=35.10 Aligned_cols=50 Identities=12% Similarity=0.041 Sum_probs=39.2
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+..|..+++.+.+|-+.++.||.. |.-=+++ . ..++||++|+.+++.-
T Consensus 17 s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~-r~~~lT~~G~~l~~~~ 67 (292)
T TIGR03298 17 SFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-T-QPCRATEAGQRLLRHA 67 (292)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCchheec-C-CCCcCCHhHHHHHHHH
Confidence 44567788999999999999999996 4433344 4 5899999999987543
No 109
>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=72.44 E-value=3.2 Score=25.46 Aligned_cols=31 Identities=6% Similarity=-0.034 Sum_probs=25.7
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEe
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIK 39 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~ 39 (150)
-+..+++++..+-+.++.|+.+|+|.-+...
T Consensus 23 la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 23 LAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 3556789999999999999999999987654
No 110
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=72.30 E-value=1.8 Score=34.85 Aligned_cols=50 Identities=10% Similarity=0.026 Sum_probs=40.2
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
|-+.+|..+++.+.+|-+.++.||.. |.-=+++ . ..++||+.|+.+++.-
T Consensus 18 s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R-~-~~~~lT~~G~~l~~~a 68 (294)
T PRK03635 18 SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-T-QPCRPTEAGQRLLRHA 68 (294)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeec-C-CCCccCHHHHHHHHHH
Confidence 45677888999999999999999996 5544555 4 4899999999987443
No 111
>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=71.69 E-value=21 Score=26.09 Aligned_cols=25 Identities=4% Similarity=-0.084 Sum_probs=22.5
Q ss_pred ccCCChHHHHHHHHhhccCCceEEe
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQ 36 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e 36 (150)
..++++..|...+..|..||+|...
T Consensus 31 ~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 31 KKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred ccCCcHHHHHHHHHHHHHCCceeee
Confidence 3578999999999999999999876
No 112
>COG3373 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.91 E-value=8.3 Score=27.31 Aligned_cols=40 Identities=15% Similarity=0.038 Sum_probs=30.6
Q ss_pred CCChHHHHHHHH----------hhccCCceEEee-EeeeEEEcCHhHHHHH
Q 031936 14 TVDAQLNESVIK----------KFGLFVGLPAQD-IKRETRVLTDEGKKYA 53 (150)
Q Consensus 14 ~~~~~~v~~~l~----------sL~~kglI~~e~-~~~~~~~LTeEG~~yl 53 (150)
+-|++.|.|.+. ||-..|+|.+++ .-.+.|.|||+|+...
T Consensus 44 ~SDPSNV~GcL~Glg~RYnGe~SLi~LGLVe~~~~nGfKyykltdygkk~v 94 (108)
T COG3373 44 KSDPSNVKGCLEGLGVRYNGEESLIGLGLVEVEQKNGFKYYKLTEYGKKMV 94 (108)
T ss_pred cCCchHHHHHHHhcCCcccCchhhhhcceeEeeecCCEEEEehhHHHHHHH
Confidence 457888888875 566678888754 4578899999999765
No 113
>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=68.33 E-value=3.1 Score=26.09 Aligned_cols=33 Identities=9% Similarity=-0.060 Sum_probs=26.6
Q ss_pred CcccccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 6 SSASTVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 6 ~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
.+.-+..+|++.+.+...++.|+..|+|+..+.
T Consensus 27 ~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 27 VSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 334456689999999999999999999998764
No 114
>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=68.22 E-value=5.9 Score=24.23 Aligned_cols=34 Identities=3% Similarity=-0.030 Sum_probs=26.2
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcC
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLT 46 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LT 46 (150)
...+++...|-.+++.|+..|+|+... ...|.||
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~--~~~~~l~ 66 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRP--GRGTFVA 66 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecC--CCeEEeC
Confidence 447899999999999999999987654 2344443
No 115
>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=68.21 E-value=3.7 Score=24.32 Aligned_cols=26 Identities=8% Similarity=-0.054 Sum_probs=21.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLP 34 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~ 34 (150)
-|..+|++...|-+.++.|..+|+|+
T Consensus 23 la~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 23 LAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 35567999999999999999999985
No 116
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=67.60 E-value=4.8 Score=33.00 Aligned_cols=49 Identities=14% Similarity=0.096 Sum_probs=39.4
Q ss_pred cCcccccccCCChHHHHHHHHhhccC-CceEEeeE----eeeEEEcCHhHHHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLF-VGLPAQDI----KRETRVLTDEGKKYA 53 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~k-glI~~e~~----~~~~~~LTeEG~~yl 53 (150)
|-++.|..+++.+.++-..++.|+.. |+--++.. ......||++|+..+
T Consensus 33 S~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~lT~~G~~l~ 86 (263)
T PRK10676 33 SISQGAKLAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGERLI 86 (263)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCcEECHHHHHHH
Confidence 45677888999999999999999995 65444444 255699999999988
No 117
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.38 E-value=5.3 Score=23.93 Aligned_cols=28 Identities=4% Similarity=-0.022 Sum_probs=24.4
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEee
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
+..++++...|..+++.|+..|+|....
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 5568999999999999999999987654
No 118
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=67.25 E-value=3.2 Score=33.86 Aligned_cols=36 Identities=6% Similarity=-0.132 Sum_probs=31.9
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcC
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLT 46 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LT 46 (150)
...|+|...|..++.+|+.||+|.+..-....|..-
T Consensus 38 ~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av 73 (247)
T COG1378 38 EASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAV 73 (247)
T ss_pred HHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeC
Confidence 447999999999999999999999988888888765
No 119
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=65.59 E-value=8.4 Score=29.88 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=35.6
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
+++...+|-+.++.||..==+..-.+....+.||+.|+.++..-
T Consensus 1 L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a 44 (269)
T PRK11716 1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFA 44 (269)
T ss_pred CCcChHHHHHHHHHHHHHhCCeeEEecCCceeECHhHHHHHHHH
Confidence 35678889999999999865666666788899999999887543
No 120
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=65.00 E-value=3.5 Score=33.65 Aligned_cols=50 Identities=14% Similarity=0.095 Sum_probs=39.9
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeE-EEcCHhHHHHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRET-RVLTDEGKKYAA 54 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~-~~LTeEG~~yl~ 54 (150)
|-+++|..+++.+.+|-+.++.||..==+..-.+.... +.||+.|+.++.
T Consensus 18 S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~ 68 (313)
T PRK12684 18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILA 68 (313)
T ss_pred CHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHH
Confidence 55778888999999999999999997444554455555 479999999875
No 121
>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=63.72 E-value=2.6 Score=25.62 Aligned_cols=29 Identities=0% Similarity=-0.127 Sum_probs=23.7
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEe
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQ 36 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e 36 (150)
.-+...|++...+.+.+..|...|||.-+
T Consensus 23 eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 23 EIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 33566799999999999999999999754
No 122
>PRK00215 LexA repressor; Validated
Probab=62.75 E-value=5.6 Score=30.81 Aligned_cols=43 Identities=2% Similarity=-0.104 Sum_probs=37.1
Q ss_pred cccccCC-ChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHH
Q 031936 9 STVSVTV-DAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKK 51 (150)
Q Consensus 9 ~~~~~~~-~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~ 51 (150)
-+..+|+ ++..+.+.+..|+.+|+|+-.......+.|+++|.-
T Consensus 29 la~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~ 72 (205)
T PRK00215 29 IADALGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQL 72 (205)
T ss_pred HHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcceEEecccccc
Confidence 4556899 999999999999999999998888888899877653
No 123
>PF13814 Replic_Relax: Replication-relaxation
Probab=62.57 E-value=8.5 Score=29.05 Aligned_cols=37 Identities=14% Similarity=0.062 Sum_probs=32.4
Q ss_pred HHHHHHHhhccCCceEEeeE--------eeeEEEcCHhHHHHHHc
Q 031936 19 LNESVIKKFGLFVGLPAQDI--------KRETRVLTDEGKKYAAE 55 (150)
Q Consensus 19 ~v~~~l~sL~~kglI~~e~~--------~~~~~~LTeEG~~yl~~ 55 (150)
.+.+.++.|...|+|..... ....|.||+.|.+++..
T Consensus 28 ~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 28 TARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred HHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 79999999999999988765 55789999999999873
No 124
>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=61.43 E-value=6.1 Score=25.67 Aligned_cols=35 Identities=11% Similarity=0.130 Sum_probs=27.5
Q ss_pred ChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHH
Q 031936 16 DAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKY 52 (150)
Q Consensus 16 ~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~y 52 (150)
..++|-+-++.|+..|++. ..-..-..||+.|.+.
T Consensus 31 se~avRrrLr~me~~Glt~--~~g~~G~~iT~~G~~~ 65 (66)
T PF08461_consen 31 SEEAVRRRLRAMERDGLTR--KVGRQGRIITEKGLDE 65 (66)
T ss_pred hHHHHHHHHHHHHHCCCcc--ccCCcccccCHHHHhh
Confidence 3489999999999999766 3344466899999875
No 125
>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=61.14 E-value=5.8 Score=22.45 Aligned_cols=24 Identities=8% Similarity=-0.002 Sum_probs=20.3
Q ss_pred ccccCCChHHHHHHHHhhccCCce
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGL 33 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI 33 (150)
|..+|+..+.|-+.++.|+..|+|
T Consensus 9 A~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 9 ADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHhCCcHHHHHHHHHHHHHcCCC
Confidence 455789999999999999999986
No 126
>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=58.32 E-value=13 Score=23.92 Aligned_cols=32 Identities=6% Similarity=0.020 Sum_probs=24.6
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEEeeEe
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPAQDIK 39 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~ 39 (150)
.-|..++++++.|.+.+.-|..+|+|.-....
T Consensus 19 eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 19 ELAREFGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 34567899999999999999999999865443
No 127
>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=57.87 E-value=21 Score=24.27 Aligned_cols=42 Identities=17% Similarity=0.073 Sum_probs=33.2
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
.++++..+...+..|-..++|......-.-|.||-.|-+++.
T Consensus 34 s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 34 SGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp HT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHHH
T ss_pred hCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHHH
Confidence 477889999999999999999997777788999999999874
No 128
>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=57.47 E-value=8.7 Score=26.48 Aligned_cols=28 Identities=11% Similarity=-0.081 Sum_probs=24.2
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEee
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
|..+|++++.|-++++.|+.+|+|..+.
T Consensus 54 a~~~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 54 AELTGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence 4457999999999999999999998654
No 129
>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=57.40 E-value=12 Score=23.46 Aligned_cols=35 Identities=14% Similarity=0.114 Sum_probs=23.8
Q ss_pred cCCChHHH-HHHHHhhccCCceEEeeEeeeEEEcCHhHH
Q 031936 13 VTVDAQLN-ESVIKKFGLFVGLPAQDIKRETRVLTDEGK 50 (150)
Q Consensus 13 ~~~~~~~v-~~~l~sL~~kglI~~e~~~~~~~~LTeEG~ 50 (150)
.|.+.... ...+..+...|+|+.+. ..+.||++|.
T Consensus 30 ~g~~~~~~~~~~l~~l~~~Gll~~~~---~~l~lT~~G~ 65 (66)
T PF06969_consen 30 FGIDFAEEFQKELEELQEDGLLEIDG---GRLRLTEKGR 65 (66)
T ss_dssp TT--THHH-HHHHHHHHHTTSEEE-S---SEEEE-TTTG
T ss_pred HCcCHHHHHHHHHHHHHHCCCEEEeC---CEEEECcccC
Confidence 45554444 66799999999996654 7899999984
No 130
>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=56.81 E-value=8 Score=25.08 Aligned_cols=26 Identities=4% Similarity=-0.043 Sum_probs=22.2
Q ss_pred ccCCC-hHHHHHHHHhhccCCceEEee
Q 031936 12 SVTVD-AQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 12 ~~~~~-~~~v~~~l~sL~~kglI~~e~ 37 (150)
.+|+. +..|...++.|+.+|+|+-..
T Consensus 34 ~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 34 ALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 45775 899999999999999998654
No 131
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=56.31 E-value=13 Score=30.04 Aligned_cols=44 Identities=5% Similarity=-0.077 Sum_probs=36.1
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
+..+|++...+.+.+..|+..|||..... ...|.||....++..
T Consensus 33 a~~lgl~kstv~RlL~tL~~~g~v~~~~~-~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 33 AELTGLHRTTVRRLLETLQEEGYVRRSAS-DDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEEecC-CCcEEEcHHHHHHHH
Confidence 45579999999999999999999987553 347999988876654
No 132
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=56.10 E-value=6.3 Score=32.13 Aligned_cols=49 Identities=10% Similarity=-0.060 Sum_probs=41.1
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYA 53 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl 53 (150)
|-++.|..+++.+.+|-+.++.||..==+..-.+......||+.|+...
T Consensus 24 s~t~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~ 72 (319)
T PRK10216 24 SVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSME 72 (319)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEEecCCCcccCHHHHHHH
Confidence 4567788899999999999999999766666667788899999998653
No 133
>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=55.08 E-value=9.2 Score=24.07 Aligned_cols=30 Identities=3% Similarity=-0.116 Sum_probs=24.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
-+..++++...|..++..|++.|+|.....
T Consensus 30 la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 30 LAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 355679999999999999999999988654
No 134
>PHA02943 hypothetical protein; Provisional
Probab=54.65 E-value=22 Score=27.45 Aligned_cols=42 Identities=10% Similarity=0.086 Sum_probs=34.6
Q ss_pred CcccccccCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCH
Q 031936 6 SSASTVSVTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTD 47 (150)
Q Consensus 6 ~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTe 47 (150)
.+--|..+|++|..+...+.-|+..|+|.-.++ ....|+|.+
T Consensus 27 tseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~ 69 (165)
T PHA02943 27 TSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDE 69 (165)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEECh
Confidence 334466789999999999999999998876555 478889998
No 135
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=54.27 E-value=11 Score=25.83 Aligned_cols=54 Identities=15% Similarity=-0.011 Sum_probs=39.6
Q ss_pred ccCcccccccCCChHHHHHHHHhhccC------Cce----EEe-----eEeeeEEEcCHhHHHHHHcCC
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLF------VGL----PAQ-----DIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~k------glI----~~e-----~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|+|---|...|..|..|++.|..+... +.. .+. ......|.||+.|-..+-.|.
T Consensus 2 ~tS~~IAe~~gk~H~~Vlr~I~~~~~~~~~~~~~~~~f~~~~~y~~~~gr~~~~y~Ltk~g~~lL~~~~ 70 (93)
T PF09669_consen 2 TTSREIAEMFGKRHKNVLRDIRKLIEKECSPEFGQLNFFIESKYKDGQGRSYPCYLLTKDGFTLLVMGY 70 (93)
T ss_pred CCHHHHHHHHCccHHHHHHHHHHHHhhhcchhhhhccCcceeeeECCCCcEeEEEEEccChhheehhhh
Confidence 556666778899999999999999855 222 222 224668999999988887774
No 136
>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=54.19 E-value=4.8 Score=28.78 Aligned_cols=59 Identities=8% Similarity=-0.048 Sum_probs=42.2
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHHHHhhccc
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQLFLAVPA 68 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~ 68 (150)
++..-+...++++..|.+.+..|...|+|....-...-|.|+...+++ .=..|++++.+
T Consensus 27 s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i-----tl~~I~~~~e~ 85 (132)
T TIGR00738 27 SVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI-----TVGDVVRAVEG 85 (132)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC-----CHHHHHHHHcC
Confidence 344445678999999999999999999998754444568887766653 22346666654
No 137
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=53.31 E-value=18 Score=25.21 Aligned_cols=45 Identities=9% Similarity=-0.116 Sum_probs=36.9
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEee-------eEEEcCHhHHHHHHc
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKR-------ETRVLTDEGKKYAAE 55 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~-------~~~~LTeEG~~yl~~ 55 (150)
.-.+.+.+.|.-.+..|...|+|....... ....||-+|-+++..
T Consensus 28 ~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~ 79 (102)
T PF10711_consen 28 EIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDA 79 (102)
T ss_pred cccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHH
Confidence 345778899999999999999999987666 345899999887743
No 138
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=52.76 E-value=20 Score=30.56 Aligned_cols=39 Identities=15% Similarity=0.090 Sum_probs=33.7
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
...+.-.+.+.+..|+..|+|++++.. ..||+-|++.++
T Consensus 44 s~~plp~v~~i~~~l~~egiv~~~~g~---v~~TekG~E~~e 82 (354)
T COG1568 44 SDLPLPLVASILEILEDEGIVKIEEGG---VELTEKGEELAE 82 (354)
T ss_pred ccCCchHHHHHHHHHHhcCcEEEecCc---EeehhhhHHHHH
Confidence 345667899999999999999998776 889999999886
No 139
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=52.10 E-value=5.7 Score=28.46 Aligned_cols=54 Identities=19% Similarity=-0.048 Sum_probs=36.0
Q ss_pred ccCcccccccCCChHHHHHHHHhhccC------C---ceE--E---eeEeeeEEEcCHhHHHHHHcCC
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLF------V---GLP--A---QDIKRETRVLTDEGKKYAAEGS 57 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~k------g---lI~--~---e~~~~~~~~LTeEG~~yl~~Gs 57 (150)
|+|-.-|...|-.|..|++.|..|... + +.. + .......|.||.+|-..+-.|.
T Consensus 14 ttS~~IAe~fgK~H~~VlR~Ir~l~~~~~~~~f~~~~F~~~~y~~~~g~~~~~Y~ltkdgf~lLvmg~ 81 (108)
T TIGR02681 14 TDSLTMAQMFGKRHDNVIRDIKVLLIEANETEFGQLNFEETQYQDEQNKKQPMFNLTEDGFTIVAMGY 81 (108)
T ss_pred EeHHHHHHHHCcchHHHHHHHHHHHhhhccccccccCceeeEEEcCCCcEEEEEEEcCCceEEEEecC
Confidence 566667888999999999999999532 1 111 1 1223456778887766665664
No 140
>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=51.74 E-value=13 Score=23.63 Aligned_cols=28 Identities=7% Similarity=-0.069 Sum_probs=24.3
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
...|+..+.|.+.++.|+..|+|.++..
T Consensus 36 ~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 36 DMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 4468999999999999999999997654
No 141
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=51.67 E-value=20 Score=29.55 Aligned_cols=32 Identities=3% Similarity=0.037 Sum_probs=28.4
Q ss_pred ccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
++|.+...|-+.++.||.+|+|+.++.-.+.+
T Consensus 219 ~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~ 250 (258)
T COG2512 219 ALGLSKTTVSRILRRLEKRGLIEKEKKGRTNI 250 (258)
T ss_pred hhCCChHHHHHHHHHHHhCCceEEEEeCCeeE
Confidence 46889999999999999999999988877665
No 142
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.54 E-value=22 Score=27.54 Aligned_cols=40 Identities=10% Similarity=-0.163 Sum_probs=31.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEee-------eEEEcCHhH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKR-------ETRVLTDEG 49 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~-------~~~~LTeEG 49 (150)
|..+|+....|.+.+..|...|+|.+..... ..|.||.+-
T Consensus 43 A~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~ 89 (178)
T PRK06266 43 AEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEK 89 (178)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHH
Confidence 4557999999999999999999999765333 367777554
No 143
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=48.78 E-value=24 Score=29.11 Aligned_cols=15 Identities=27% Similarity=0.304 Sum_probs=12.3
Q ss_pred HHhHhhhcCceeeEEE
Q 031936 117 INGGLKARKLIVNQMC 132 (150)
Q Consensus 117 l~~~LKKRkLi~~~~~ 132 (150)
+ ..|-|||||+..+.
T Consensus 231 L-~~LEk~GlIe~~K~ 245 (258)
T COG2512 231 L-RRLEKRGLIEKEKK 245 (258)
T ss_pred H-HHHHhCCceEEEEe
Confidence 6 88889999987754
No 144
>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=48.19 E-value=15 Score=21.76 Aligned_cols=26 Identities=8% Similarity=-0.065 Sum_probs=21.9
Q ss_pred ccccCCChHHHHHHHHhhccCCceEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPA 35 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~ 35 (150)
+..+|+++..|-..++.|+..|+|+.
T Consensus 22 ~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 22 AEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHhccccchHHHHHHHHHHHCcCeeC
Confidence 45579999999999999999999963
No 145
>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=47.57 E-value=34 Score=22.14 Aligned_cols=42 Identities=14% Similarity=0.127 Sum_probs=27.5
Q ss_pred cccccccCCChHHHHHHHHhhccCCceEEeeE---eeeEEEcCHh
Q 031936 7 SASTVSVTVDAQLNESVIKKFGLFVGLPAQDI---KRETRVLTDE 48 (150)
Q Consensus 7 ~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~---~~~~~~LTeE 48 (150)
|--|...|+...-++.+++.|++.|+|..... -+..-.+.+.
T Consensus 8 s~iAd~~GiTRSvIVNALRKleSaGvIesrSlGmKGT~ikvlN~~ 52 (61)
T PF08222_consen 8 SKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDY 52 (61)
T ss_dssp HHHHHHHT--HHHHHHHHHHHHHTTSEEEEETTSS-EEEEE--TH
T ss_pred HHHHHHhCccHHHHHHHHHHHHhcCceeecccCCCceeeeeecHH
Confidence 33456689999999999999999999996544 3333344443
No 146
>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=46.17 E-value=7 Score=26.03 Aligned_cols=45 Identities=9% Similarity=0.002 Sum_probs=34.4
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEG 49 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG 49 (150)
++..-|...++++..+...+..|...|+|...+-..--|.|+...
T Consensus 27 s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 27 SSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 334446678999999999999999999999887767777776543
No 147
>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=45.32 E-value=25 Score=26.47 Aligned_cols=37 Identities=11% Similarity=0.162 Sum_probs=28.6
Q ss_pred ChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 16 DAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 16 ~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
+-.-+..++..||..|+|+..+ ..--.||++|+..+.
T Consensus 93 sg~iiR~~LqqLE~~glv~k~~--~~GR~lT~~G~~~lD 129 (139)
T PF01090_consen 93 SGSIIRKILQQLEKAGLVEKDP--KGGRRLTPKGQRDLD 129 (139)
T ss_dssp HHHHHHHHHHHHHHTTSEEEET--TTEEEE-HHHHHHHH
T ss_pred CcHHHHHHHHHHHHCCCEEecC--CCCCEECHHHHHHHH
Confidence 3456778899999999999886 444589999998765
No 148
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=45.10 E-value=11 Score=27.65 Aligned_cols=46 Identities=17% Similarity=-0.028 Sum_probs=38.2
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGK 50 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~ 50 (150)
|...-|...|++..-|..++..|...|+|...+-..--|.|+..-+
T Consensus 27 s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~~~ 72 (141)
T PRK11014 27 SISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPAS 72 (141)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCCHH
Confidence 3345567789999999999999999999999998888888875443
No 149
>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=44.90 E-value=24 Score=26.21 Aligned_cols=30 Identities=3% Similarity=-0.075 Sum_probs=25.5
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK 39 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~ 39 (150)
|..+|+.++.|-++++.|+..|+|.+....
T Consensus 150 A~~lG~tretvsR~l~~l~~~g~I~~~~~~ 179 (193)
T TIGR03697 150 AEAIGSTRVTITRLLGDLRKKKLISIHKKK 179 (193)
T ss_pred HHHhCCcHHHHHHHHHHHHHCCCEEecCCE
Confidence 344689999999999999999999987643
No 150
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=44.82 E-value=32 Score=30.61 Aligned_cols=34 Identities=24% Similarity=0.268 Sum_probs=31.3
Q ss_pred HHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 23 VIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 23 ~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
.++.|..+++|+..+.....+.+|+.|.+++++|
T Consensus 157 ~l~~LkkRkL~~~~~~~~~~~~~~~~~~~~~~~~ 190 (489)
T PRK04172 157 VLKELKKRKLVEEKERTERSVELTDAGLELLKEG 190 (489)
T ss_pred HHHHHHhcCCeEEEEEEEEEEEEccchhhhhhcc
Confidence 5788888999999999999999999999999887
No 151
>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=43.44 E-value=7.2 Score=31.67 Aligned_cols=45 Identities=16% Similarity=0.004 Sum_probs=37.1
Q ss_pred ccccccCCChHHHHHHHH-hhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 8 ASTVSVTVDAQLNESVIK-KFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~-sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
.-|..+|+++..+.+.+. .|-.+|+|. ....-.+.|++|.+|+++
T Consensus 260 ~ia~~lg~~~~~~~~~~e~~Li~~~li~---~~~~g~~~~~~~~~~~~~ 305 (305)
T TIGR00635 260 TLAAALGEDADTIEDVYEPYLLQIGFLQ---RTPRGRIATELAYEHLGL 305 (305)
T ss_pred HHHHHhCCCcchHHHhhhHHHHHcCCcc---cCCchhhhhHHHHHHhCC
Confidence 345568999999999999 699999994 666677899999999864
No 152
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.76 E-value=19 Score=20.80 Aligned_cols=27 Identities=11% Similarity=-0.117 Sum_probs=23.2
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEe
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQ 36 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e 36 (150)
+..+++++..+.+.++.|..+|+|...
T Consensus 21 ~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 21 AELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 445799999999999999999998754
No 153
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.27 E-value=66 Score=24.84 Aligned_cols=65 Identities=12% Similarity=0.023 Sum_probs=47.6
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEe------------------eeEEEcCHhHHHHHHcCChHH--HHH-hhcccCCC
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIK------------------RETRVLTDEGKKYAAEGSSEI--QLF-LAVPAECS 71 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~------------------~~~~~LTeEG~~yl~~GsPE~--rl~-~~l~~~g~ 71 (150)
..+|.-.|..+++.|..-|+|..-... .+.|.||.||+-.+++=.||. .+| ..++. +-
T Consensus 41 tkiPl~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~rege~~lr~i~~~~l~~~y~~~l~n-~~ 119 (175)
T COG4344 41 TKIPLPRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREGEAVLREITPEWLGKLYVRLLKN-GW 119 (175)
T ss_pred ccCChHHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechhHHHHHHhcCHHHHHHHHHHHcCc-ch
Confidence 456778899999999999999864432 367899999999999999986 344 44443 32
Q ss_pred CChHHHh
Q 031936 72 ILKDELQ 78 (150)
Q Consensus 72 ~~~~eL~ 78 (150)
..+..+.
T Consensus 120 l~l~ilr 126 (175)
T COG4344 120 LVLLILR 126 (175)
T ss_pred HHHHHHH
Confidence 4444444
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=40.67 E-value=25 Score=26.93 Aligned_cols=35 Identities=3% Similarity=-0.138 Sum_probs=29.0
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
-+..+|++...|..++..|+..|+|++.+..-...
T Consensus 40 La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V 74 (212)
T TIGR03338 40 IAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFV 74 (212)
T ss_pred HHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEE
Confidence 35668999999999999999999999877654333
No 155
>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=38.70 E-value=25 Score=21.84 Aligned_cols=28 Identities=7% Similarity=-0.127 Sum_probs=23.7
Q ss_pred ccccccCCChHHHHHHHHhhccCCceEE
Q 031936 8 ASTVSVTVDAQLNESVIKKFGLFVGLPA 35 (150)
Q Consensus 8 ~~~~~~~~~~~~v~~~l~sL~~kglI~~ 35 (150)
.-+..+++++..+.+.+..|+..|+|.-
T Consensus 19 ela~~~~VS~~TiRRDl~~L~~~g~i~r 46 (57)
T PF08220_consen 19 ELAEEFGVSEMTIRRDLNKLEKQGLIKR 46 (57)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3455689999999999999999998754
No 156
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=37.34 E-value=35 Score=28.54 Aligned_cols=54 Identities=9% Similarity=0.095 Sum_probs=42.4
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeE-EEcCHhHHHHHHcCChHHHHHhhc
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRET-RVLTDEGKKYAAEGSSEIQLFLAV 66 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~-~~LTeEG~~yl~~GsPE~rl~~~l 66 (150)
+..|+....|..++..+...|.+..+.+-... |.|||-|..-...+ +.++|..-
T Consensus 36 ~~fG~sE~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a--~~riy~~~ 90 (291)
T COG3327 36 AEFGISETTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRA--ARRIYPRT 90 (291)
T ss_pred HHcCccHHHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHH--hhhhcCCC
Confidence 45789999999999999999988887765555 99999998776665 45555433
No 157
>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=37.24 E-value=33 Score=22.26 Aligned_cols=36 Identities=11% Similarity=0.039 Sum_probs=29.1
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHh
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDE 48 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeE 48 (150)
++++..+|-+++.+|+..|.|..+...--.|.||++
T Consensus 30 L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~l~~~ 65 (66)
T PF02295_consen 30 LSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWSLTEK 65 (66)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEECSSSTEEEE-HC
T ss_pred cchhHHHHHHHHHHHHHCCCEeeCCCCCCceEeccC
Confidence 345578999999999999999988878888888864
No 158
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=36.82 E-value=21 Score=28.60 Aligned_cols=51 Identities=12% Similarity=0.018 Sum_probs=37.7
Q ss_pred cccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHh----HHHHHHcCCh
Q 031936 7 SASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDE----GKKYAAEGSS 58 (150)
Q Consensus 7 ~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeE----G~~yl~~GsP 58 (150)
+.-+..+|++...+.+.+..|...|||.-. .....|.|+.. |..|..+...
T Consensus 32 ~eia~~lgl~kstv~Rll~tL~~~G~l~~~-~~~~~Y~lG~~~~~lg~~~~~~~~l 86 (257)
T PRK15090 32 TELSQRVMMSKSTVYRFLQTMKTLGYVAQE-GESEKYSLTLKLFELGAKALQNVDL 86 (257)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCcEEecHHHHHHHHHHHhhCcH
Confidence 334566899999999999999999999775 33467888754 5666655443
No 159
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=36.76 E-value=36 Score=27.00 Aligned_cols=35 Identities=6% Similarity=-0.151 Sum_probs=29.4
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
-+..+|++...|.-++..|+..|+|++.+..-..+
T Consensus 38 Lae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 72 (253)
T PRK11523 38 IADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHV 72 (253)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeeEE
Confidence 35568999999999999999999999987765444
No 160
>PRK03837 transcriptional regulator NanR; Provisional
Probab=36.65 E-value=28 Score=27.17 Aligned_cols=34 Identities=6% Similarity=-0.116 Sum_probs=28.4
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+..+|++...|..|+..|+..|+|++.+..-...
T Consensus 44 ae~~gVSRt~VREAL~~L~~eGlv~~~~~~G~~V 77 (241)
T PRK03837 44 MAFFGVGRPAVREALQALKRKGLVQISHGERARV 77 (241)
T ss_pred HHHhCCCHHHHHHHHHHHHHCCCEEEecCCceeE
Confidence 4568999999999999999999999976654433
No 161
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=36.54 E-value=39 Score=26.86 Aligned_cols=34 Identities=3% Similarity=-0.148 Sum_probs=28.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+..+|++...|..++..|++.|+|++.+..-..+
T Consensus 40 a~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 73 (257)
T PRK10225 40 AEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYV 73 (257)
T ss_pred HHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 5568999999999999999999999887654433
No 162
>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=36.52 E-value=25 Score=26.96 Aligned_cols=39 Identities=13% Similarity=-0.006 Sum_probs=31.8
Q ss_pred cccccCCC-hHHHHHHHHhhccCCceEEeeEeeeEEEcCH
Q 031936 9 STVSVTVD-AQLNESVIKKFGLFVGLPAQDIKRETRVLTD 47 (150)
Q Consensus 9 ~~~~~~~~-~~~v~~~l~sL~~kglI~~e~~~~~~~~LTe 47 (150)
-|..+|++ +..|.+.+..|+.+|+|..+........+++
T Consensus 31 la~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~~~ 70 (199)
T TIGR00498 31 IARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRILD 70 (199)
T ss_pred HHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeEEeCC
Confidence 35678998 9999999999999999998776655566654
No 163
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=35.97 E-value=40 Score=26.19 Aligned_cols=38 Identities=11% Similarity=-0.126 Sum_probs=29.8
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEG 49 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG 49 (150)
|..+|+.++.|-+.++.|+..|+|..... ....+..++
T Consensus 176 A~~lG~sretvsR~L~~L~~~G~I~~~~~--~i~I~d~~~ 213 (226)
T PRK10402 176 AEYLGVSYRHLLYVLAQFIQDGYLKKSKR--GYLIKNRKQ 213 (226)
T ss_pred HHHHCCcHHHHHHHHHHHHHCCCEEeeCC--EEEEeCHHH
Confidence 45679999999999999999999998764 344454444
No 164
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=35.74 E-value=37 Score=25.48 Aligned_cols=29 Identities=10% Similarity=-0.123 Sum_probs=24.5
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
|..+|+.++.|-+.++.|+..|+|.....
T Consensus 156 A~~lG~tretvsR~l~~l~~~g~I~~~~~ 184 (202)
T PRK13918 156 AAAVGSVRETVTKVIGELSREGYIRSGYG 184 (202)
T ss_pred HHHhCccHHHHHHHHHHHHHCCCEEcCCC
Confidence 34568999999999999999999986543
No 165
>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=35.53 E-value=29 Score=27.12 Aligned_cols=32 Identities=16% Similarity=0.019 Sum_probs=27.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeee
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRE 41 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~ 41 (150)
+..+|++...|..|+..|+..|+|++.+..-.
T Consensus 37 a~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~ 68 (235)
T TIGR02812 37 SELIGVTRTTLREVLQRLARDGWLTIQHGKPT 68 (235)
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEEeCCCcc
Confidence 45689999999999999999999999876543
No 166
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=35.41 E-value=35 Score=26.67 Aligned_cols=34 Identities=15% Similarity=-0.000 Sum_probs=28.7
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
++.+|++...|..|+..|+..|+|...+..-..+
T Consensus 38 ae~~gVSRt~VReAL~~L~~eGlv~~~~g~G~~V 71 (239)
T PRK04984 38 SELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV 71 (239)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEe
Confidence 4568999999999999999999999987755444
No 167
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=35.10 E-value=20 Score=24.54 Aligned_cols=28 Identities=7% Similarity=-0.021 Sum_probs=24.4
Q ss_pred cccccccCCChHHHHHHHHhhccCCceE
Q 031936 7 SASTVSVTVDAQLNESVIKKFGLFVGLP 34 (150)
Q Consensus 7 ~~~~~~~~~~~~~v~~~l~sL~~kglI~ 34 (150)
+.-+..+|+++..+.+.++.|+..|+|.
T Consensus 21 ~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 21 AELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 3445668999999999999999999998
No 168
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=34.85 E-value=34 Score=24.80 Aligned_cols=42 Identities=5% Similarity=-0.197 Sum_probs=33.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeee-EEEcCHhHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRE-TRVLTDEGK 50 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~-~~~LTeEG~ 50 (150)
-+..+++++..|-..++-|+..|+|+.+..-.. .|.|.++..
T Consensus 36 la~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~ 78 (117)
T PRK10141 36 LCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIP 78 (117)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHH
Confidence 345689999999999999999999998776554 568876543
No 169
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=34.49 E-value=42 Score=26.63 Aligned_cols=35 Identities=9% Similarity=-0.140 Sum_probs=28.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
-+..+|++...|..++..|+..|+|++.+..-..+
T Consensus 32 Lae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~~V 66 (253)
T PRK10421 32 LAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 66 (253)
T ss_pred HHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeEEE
Confidence 35568999999999999999999999987654433
No 170
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=34.19 E-value=88 Score=22.06 Aligned_cols=38 Identities=16% Similarity=0.039 Sum_probs=29.2
Q ss_pred CCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
.+....|-+-+.-|--+|||+-. -.-|++|++|..++.
T Consensus 43 ~~~~~~V~SNIGvLIKkglIEKS---GDGlv~T~~g~~Ii~ 80 (96)
T PF09114_consen 43 EMNKASVNSNIGVLIKKGLIEKS---GDGLVITEEGMDIII 80 (96)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEE---TTEEEE-HHHHHHHH
T ss_pred HhhhhHHHHhHHHHHHcCccccc---CCceEEechHHHHHH
Confidence 56677888889999999999654 445999999999874
No 171
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=33.85 E-value=54 Score=24.21 Aligned_cols=41 Identities=10% Similarity=0.044 Sum_probs=32.6
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKK 51 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~ 51 (150)
-|..+++++..|-++-..|+..|+|.+..-.-.. .|+.|.+
T Consensus 41 lA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~f--V~~~~~~ 81 (125)
T COG1725 41 LAKDLGVNPNTVQRAYQELEREGIVETKRGKGTF--VTEDAKE 81 (125)
T ss_pred HHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEE--EcCCchh
Confidence 4667899999999999999999999987766544 4555543
No 172
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=33.83 E-value=26 Score=27.20 Aligned_cols=32 Identities=3% Similarity=-0.028 Sum_probs=27.5
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEee
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKR 40 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~ 40 (150)
-+..+|++...|..|+..|+..|+|++.+..-
T Consensus 40 La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g 71 (221)
T PRK11414 40 LAEQLGMSITPVREALLRLVSVNALSVAPAQA 71 (221)
T ss_pred HHHHHCCCchhHHHHHHHHHHCCCEEecCCCc
Confidence 35568999999999999999999999876654
No 173
>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=33.70 E-value=25 Score=24.86 Aligned_cols=35 Identities=6% Similarity=-0.096 Sum_probs=28.7
Q ss_pred cccCcccccccCCChHHHHHHHHhhccCCceEEee
Q 031936 3 LMSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 3 ~~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
.+|-+.-+...|++++.|-.+++.|...++|..+.
T Consensus 54 ~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 54 RISNSQIAEMTGLSRDHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred eeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence 34556666778999999999999999999996655
No 174
>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=33.36 E-value=26 Score=28.97 Aligned_cols=33 Identities=9% Similarity=0.053 Sum_probs=28.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEee
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
+.+.-|...|+....+..+++.|++.|+|....
T Consensus 200 se~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 200 VASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 334456778999999999999999999999988
No 175
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=33.01 E-value=73 Score=27.40 Aligned_cols=39 Identities=10% Similarity=-0.046 Sum_probs=30.0
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
.|.+.+.+...+..|...|++..+ ...+.||++|...+.
T Consensus 348 ~g~~~~~~~~~l~~l~~~gll~~~---~~~~~LT~~G~~~~d 386 (394)
T PRK08898 348 TGLPLAAIEPQLAAAEQRGLLERD---HTRIRPTPLGQRFLN 386 (394)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEE---CCEEEEChhHhHHHH
Confidence 355556677788899999998854 357999999987653
No 176
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=32.16 E-value=43 Score=25.56 Aligned_cols=37 Identities=11% Similarity=0.217 Sum_probs=29.8
Q ss_pred ChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 16 DAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 16 ~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
+-.-+..++..||..|+|+-.. .--+||+.|+..+.+
T Consensus 94 sg~iiR~~LqqLE~~glVek~~---~GR~lT~~G~~~LD~ 130 (150)
T PRK09333 94 SGSIIRKILQQLEKAGLVEKTK---KGRVITPKGRSLLDN 130 (150)
T ss_pred ccHHHHHHHHHHHHCCCeeeCC---CCCEeCHHHHHHHHH
Confidence 3345788999999999999766 566799999987754
No 177
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=32.13 E-value=49 Score=26.19 Aligned_cols=32 Identities=9% Similarity=-0.082 Sum_probs=27.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeee
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRE 41 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~ 41 (150)
+..+|++...|.-++..|+..|+|++.+..-.
T Consensus 41 a~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~ 72 (254)
T PRK09464 41 AKQFDVSRPSLREAIQRLEAKGLLLRRQGGGT 72 (254)
T ss_pred HHHhCCCHHHHHHHHHHHHHCCCEEEecCcee
Confidence 45689999999999999999999999876543
No 178
>PRK05660 HemN family oxidoreductase; Provisional
Probab=32.11 E-value=68 Score=27.41 Aligned_cols=38 Identities=11% Similarity=0.073 Sum_probs=29.3
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYA 53 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl 53 (150)
.|.+..+....+..|.+.|++..+ ...+.||++|.-++
T Consensus 331 ~g~~~~~~~~~l~~l~~~gl~~~~---~~~~~lt~~G~~~~ 368 (378)
T PRK05660 331 TGLPESVIRPQLDEALAQGYLTET---ADHWQITEHGKLFL 368 (378)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEe---CCEEEECcchhHHH
Confidence 355555566788999999998864 45899999998765
No 179
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=32.06 E-value=22 Score=28.01 Aligned_cols=62 Identities=10% Similarity=0.005 Sum_probs=22.2
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeE-eeeEEEcCHhHHHHHHcCChHHHHHhhcccCCCCChHHHhcC
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDI-KRETRVLTDEGKKYAAEGSSEIQLFLAVPAECSILKDELQKK 80 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~-~~~~~~LTeEG~~yl~~GsPE~rl~~~l~~~g~~~~~eL~~~ 80 (150)
|..+|+..++++.-|..|+..|.|+--.- .-.++-+|++--. .|.++|...|.+++.+|.+.
T Consensus 120 a~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~---------~va~fi~~rGRvsi~el~~~ 182 (188)
T PF09756_consen 120 AAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEME---------AVAKFIKQRGRVSISELAQE 182 (188)
T ss_dssp HHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE------------------------------------
T ss_pred HHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHH---------HHHHHHHHcCCccHHHHHHH
Confidence 45679999999999999999997764222 2344455655432 34567776677999988764
No 180
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=32.01 E-value=47 Score=26.20 Aligned_cols=34 Identities=0% Similarity=-0.239 Sum_probs=28.8
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+..+|+....|.-++..|+..|+|++.+..-..+
T Consensus 38 a~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 71 (251)
T PRK09990 38 CEKLGFSRSALREGLTVLRGRGIIETAQGRGSFV 71 (251)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEE
Confidence 4568999999999999999999999987754443
No 181
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=31.91 E-value=26 Score=29.81 Aligned_cols=41 Identities=17% Similarity=0.191 Sum_probs=36.9
Q ss_pred ccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHH
Q 031936 12 SVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYA 53 (150)
Q Consensus 12 ~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl 53 (150)
.+++++..|.+.+..|+..|++. ..+..--.+.|+.|-+|-
T Consensus 36 ~l~~S~aTIR~dm~~Le~~G~l~-~~h~sagrIPT~kGYR~Y 76 (339)
T PRK00082 36 GLGVSSATIRNDMADLEELGLLE-KPHTSSGRIPTDKGYRYF 76 (339)
T ss_pred CCCCChHHHHHHHHHHHhCCCcC-CCcCCCCCCcCHHHHHHH
Confidence 48899999999999999999998 788888889999998873
No 182
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=31.57 E-value=41 Score=27.30 Aligned_cols=40 Identities=3% Similarity=-0.165 Sum_probs=32.3
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhH
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEG 49 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG 49 (150)
-+..+|++...+.+.+..|...|||.... ....|.|+..-
T Consensus 46 Ia~~lglpkStv~RlL~tL~~~G~l~~~~-~~~~Y~lG~~l 85 (271)
T PRK10163 46 ISLNLDLPLSTTFRLLKVLQAADFVYQDS-QLGWWHIGLGV 85 (271)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCEEEcC-CCCeEEecHHH
Confidence 35567999999999999999999997654 45678887653
No 183
>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=31.16 E-value=50 Score=25.23 Aligned_cols=47 Identities=6% Similarity=0.019 Sum_probs=35.9
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcCChHHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEGSSEIQ 61 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~GsPE~r 61 (150)
+..+|++...|.++++.|+.+++|.-. ..-.|.+.+.= +=+|+.-.+
T Consensus 82 a~~l~iS~~Tv~r~ik~L~e~~iI~k~--~~G~Y~iNP~~---~~kG~~~~~ 128 (165)
T PF05732_consen 82 AEKLGISKPTVSRAIKELEEKNIIKKI--RNGAYMINPNF---FFKGDRDKR 128 (165)
T ss_pred HHHhCCCHHHHHHHHHHHHhCCcEEEc--cCCeEEECcHH---heeCcHHHH
Confidence 456899999999999999999988643 44678888863 446776443
No 184
>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=31.05 E-value=17 Score=26.08 Aligned_cols=40 Identities=10% Similarity=0.059 Sum_probs=29.8
Q ss_pred CcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEc
Q 031936 6 SSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVL 45 (150)
Q Consensus 6 ~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~L 45 (150)
...-+..+++++..|...+..|+..|+|....-...-|.|
T Consensus 28 ~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l 67 (130)
T TIGR02944 28 AAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTL 67 (130)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhh
Confidence 3334566899999999999999999999775433334444
No 185
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=30.99 E-value=42 Score=25.99 Aligned_cols=35 Identities=6% Similarity=-0.142 Sum_probs=28.9
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
-+..+|++...|..++..|+..|+|.+.+..-..+
T Consensus 36 Lae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V 70 (224)
T PRK11534 36 LTSRYALGVGPLREALSQLVAERLVTVVNQKGYRV 70 (224)
T ss_pred HHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEe
Confidence 34567999999999999999999999887665443
No 186
>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=30.40 E-value=45 Score=26.45 Aligned_cols=38 Identities=5% Similarity=-0.112 Sum_probs=31.2
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGK 50 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~ 50 (150)
+..+|++...+.+.+..|+..||+.-+ ...|.|+..=-
T Consensus 31 a~~lglpksT~~RlL~tL~~~G~l~~~---~~~Y~lG~~~~ 68 (248)
T TIGR02431 31 AEATGLTRAAARRFLLTLVELGYVTSD---GRLFWLTPRVL 68 (248)
T ss_pred HHHHCcCHHHHHHHHHHHHHCCCEEeC---CCEEEecHHHH
Confidence 455799999999999999999999753 46799986543
No 187
>COG5570 Uncharacterized small protein [Function unknown]
Probab=30.25 E-value=54 Score=20.81 Aligned_cols=15 Identities=40% Similarity=0.321 Sum_probs=12.1
Q ss_pred CCHhhHHhHhhhcCce
Q 031936 112 ISKEDINGGLKARKLI 127 (150)
Q Consensus 112 ~~~~~l~~~LKKRkLi 127 (150)
.++-.+ .+||||||.
T Consensus 30 ~dd~~i-~eLKRrKL~ 44 (57)
T COG5570 30 SDDLAI-RELKRRKLR 44 (57)
T ss_pred cchHHH-HHHHHHHHH
Confidence 466678 999999986
No 188
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=29.33 E-value=49 Score=24.52 Aligned_cols=30 Identities=0% Similarity=-0.146 Sum_probs=25.5
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK 39 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~ 39 (150)
|..++.+...|-++++.|...|+|.-+...
T Consensus 49 ae~lnr~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 49 AEILNRSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence 445788999999999999999999876654
No 189
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=29.30 E-value=41 Score=26.97 Aligned_cols=34 Identities=6% Similarity=-0.076 Sum_probs=29.1
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
++.+|+....|.-+++.|+.+|+|.+..-.-.++
T Consensus 41 ae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V 74 (241)
T COG2186 41 AERFGVSRTVVREALKRLEAKGLVEIRQGSGTFV 74 (241)
T ss_pred HHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEe
Confidence 4568999999999999999999999987665554
No 190
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=28.99 E-value=27 Score=26.18 Aligned_cols=50 Identities=12% Similarity=-0.009 Sum_probs=43.1
Q ss_pred cccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHH
Q 031936 3 LMSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKY 52 (150)
Q Consensus 3 ~~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~y 52 (150)
.+++..-|+..++++.=+.+.+..|...|+|+..+=..==|.|.....++
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~I 74 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEEI 74 (150)
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCChHHC
Confidence 34556667889999999999999999999999999999999998777654
No 191
>PRK11569 transcriptional repressor IclR; Provisional
Probab=28.65 E-value=33 Score=27.85 Aligned_cols=47 Identities=2% Similarity=-0.055 Sum_probs=35.7
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHh----HHHHHHcC
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDE----GKKYAAEG 56 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeE----G~~yl~~G 56 (150)
-+..+|++...+.+.+..|...||+... .....|.|... |..|..+.
T Consensus 49 ia~~lglpksTv~RlL~tL~~~G~l~~~-~~~~~Y~lG~~l~~Lg~~~~~~~ 99 (274)
T PRK11569 49 LAQQAGLPNSTTHRLLTTMQQQGFVRQV-GELGHWAIGAHAFIVGSSFLQSR 99 (274)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCeEecCHHHHHHHHHHHhhC
Confidence 3556799999999999999999999753 33667888765 55565433
No 192
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=28.57 E-value=34 Score=27.58 Aligned_cols=43 Identities=2% Similarity=-0.135 Sum_probs=34.3
Q ss_pred CcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhH
Q 031936 6 SSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEG 49 (150)
Q Consensus 6 ~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG 49 (150)
.+.-+...|++...+.+.+..|...|||..... ...|.|+..=
T Consensus 22 l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~-~g~Y~Lg~~~ 64 (246)
T COG1414 22 LAELAERLGLPKSTVHRLLQTLVELGYVEQDPE-DGRYRLGPRL 64 (246)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCC-CCcEeehHHH
Confidence 344466789999999999999999999998775 4467777653
No 193
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=28.52 E-value=72 Score=23.38 Aligned_cols=35 Identities=14% Similarity=-0.110 Sum_probs=26.5
Q ss_pred ChHHHHHHHHhhccCCceEEee--------EeeeEEEcCHhHH
Q 031936 16 DAQLNESVIKKFGLFVGLPAQD--------IKRETRVLTDEGK 50 (150)
Q Consensus 16 ~~~~v~~~l~sL~~kglI~~e~--------~~~~~~~LTeEG~ 50 (150)
+|++|.+++..|...|+++-.. .+...|.+|++++
T Consensus 53 ~hsEvYraLHeL~~dGilk~~K~k~~~~k~QEiv~Y~f~d~ek 95 (122)
T PF02334_consen 53 NHSEVYRALHELVDDGILKQVKRKEEGVKFQEIVLYHFTDEEK 95 (122)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESSHHH
T ss_pred CHHHHHHHHHHHHhhhHHHHHhccccCCcceEEEEEEeccHHH
Confidence 7899999999999999984332 3456788898644
No 194
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=28.22 E-value=59 Score=25.06 Aligned_cols=38 Identities=5% Similarity=0.026 Sum_probs=29.7
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhH
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEG 49 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG 49 (150)
|..+|+.++.|-+.++.|+..|+|...... ..++-.++
T Consensus 191 A~~lG~sr~tvsR~l~~l~~~g~I~~~~~~--i~i~d~~~ 228 (235)
T PRK11161 191 GNYLGLTVETISRLLGRFQKSGMLAVKGKY--ITIENNDA 228 (235)
T ss_pred HHHhCCcHHHHHHHHHHHHHCCCEEecCCE--EEEcCHHH
Confidence 556799999999999999999999988753 34444443
No 195
>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=27.09 E-value=83 Score=20.51 Aligned_cols=28 Identities=14% Similarity=-0.021 Sum_probs=24.5
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
...|.|+..+-..++.|+.+|+|.-...
T Consensus 26 ~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 26 KLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 3467899999999999999999988766
No 196
>PF04325 DUF465: Protein of unknown function (DUF465); InterPro: IPR007420 Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C-terminal of the motor domain. Members of this family may form coiled coil structures.; PDB: 1ZHC_A.
Probab=27.00 E-value=61 Score=19.54 Aligned_cols=25 Identities=24% Similarity=0.302 Sum_probs=14.7
Q ss_pred HHHHHhcCCCCCHhhHHhHhhhcCce
Q 031936 102 LLVRVQDGRAISKEDINGGLKARKLI 127 (150)
Q Consensus 102 ~L~~i~~g~~~~~~~l~~~LKKRkLi 127 (150)
.+..+..+...++..+ ..|||+||-
T Consensus 14 ~I~~~e~~~~~~d~~l-~~LKk~kL~ 38 (49)
T PF04325_consen 14 EIHRLEKRPEPDDEEL-ERLKKEKLR 38 (49)
T ss_dssp HHHHHHTT--S-HHHH-HHHHHHHHH
T ss_pred HHHHHHhCCCCCHHHH-HHHHHHHHH
Confidence 3344444444667778 999998874
No 197
>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=26.97 E-value=1.1e+02 Score=19.90 Aligned_cols=34 Identities=9% Similarity=-0.089 Sum_probs=27.4
Q ss_pred cccCCChHHHHHHHHhhccCCceEEeeEeeeEEE
Q 031936 11 VSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRV 44 (150)
Q Consensus 11 ~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~ 44 (150)
...+.+..++..++-||.-.+=|.+++.....|+
T Consensus 30 k~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~~v 63 (65)
T PF10771_consen 30 KATGLSDKEVYLAIGWLARENKIEFEEKNGELYV 63 (65)
T ss_dssp HHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEEE
T ss_pred HHhCcCHHHHHHHHHHHhccCceeEEeeCCEEEE
Confidence 3467889999999999999999999877766553
No 198
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=26.78 E-value=62 Score=24.57 Aligned_cols=34 Identities=21% Similarity=0.199 Sum_probs=27.5
Q ss_pred HHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 20 NESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 20 v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
--+.+.|--+.|+|.+.. +..++.+|+-|++|++
T Consensus 109 Ad~flrwAvslgfl~~~~-~~Dtf~IT~lG~~~~~ 142 (145)
T PF02981_consen 109 ADGFLRWAVSLGFLDYDR-ETDTFSITELGKKYVK 142 (145)
T ss_dssp HHHHHHHHHHTTSEEEET-TTTEEEE-HHHHHHHH
T ss_pred ccceeeeeeeeCceeecc-CCCEEEeehhHHHHhh
Confidence 446788888999999976 4678999999999986
No 199
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=26.61 E-value=60 Score=25.28 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=29.7
Q ss_pred ChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHc
Q 031936 16 DAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAE 55 (150)
Q Consensus 16 ~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~ 55 (150)
+-.-+..++..||..|+|+-.+. ..--.||+.|+.-+.+
T Consensus 118 Sg~iiR~~LQqLE~~glVek~~~-~~GR~lT~~Gr~~LD~ 156 (169)
T PTZ00095 118 SGKILRWICQQLEKLGLVEQGPK-KKGRRLTRKGCNFANA 156 (169)
T ss_pred chHHHHHHHHHHHHCCCEEecCC-CCCCEECHhHHHHHHH
Confidence 44567788999999999996543 2345999999987754
No 200
>PRK06474 hypothetical protein; Provisional
Probab=26.45 E-value=94 Score=23.84 Aligned_cols=48 Identities=10% Similarity=-0.092 Sum_probs=35.8
Q ss_pred CCChHHHHHHHHhhccCCceEEeeE------eeeEEEcCHhHHHH----HHcCChHHH
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDI------KRETRVLTDEGKKY----AAEGSSEIQ 61 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~------~~~~~~LTeEG~~y----l~~GsPE~r 61 (150)
+++...|.+.++.|+..|+|..... ....|.+++++-.. +..-+||..
T Consensus 38 ~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~~~~~~~~~~~e~~ 95 (178)
T PRK06474 38 DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKIEGSEWTGLSDDEK 95 (178)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeeeCHHHHHHhCHHHH
Confidence 6888999999999999999998553 34788999887553 223356653
No 201
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=26.30 E-value=92 Score=27.11 Aligned_cols=38 Identities=16% Similarity=-0.026 Sum_probs=29.4
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHH
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYA 53 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl 53 (150)
.|.+.......+..|...|++..+ ...+.||++|..+.
T Consensus 371 ~g~~~~~~~~~l~~l~~~gll~~~---~~~l~lT~~G~~~~ 408 (430)
T PRK08208 371 FGSDPLRDFPELELLIDRGWLEQN---GGRLRLTEEGLALS 408 (430)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEE---CCEEEECcchhhHH
Confidence 455655566788899999999874 45799999998754
No 202
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=25.79 E-value=1e+02 Score=26.04 Aligned_cols=33 Identities=18% Similarity=0.172 Sum_probs=25.8
Q ss_pred HHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 19 LNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 19 ~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
.+...+..|...|++..+ ...+.||++|..++.
T Consensus 334 ~~~~~l~~l~~~gl~~~~---~~~~~lT~~G~~~~~ 366 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEK---EGRIYLSERGIEVSN 366 (374)
T ss_pred HHHHHHHHHHHCCCEEEE---CCEEEEChhHHHHHH
Confidence 345578899999998864 357999999987664
No 203
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=25.20 E-value=34 Score=25.61 Aligned_cols=48 Identities=4% Similarity=-0.148 Sum_probs=40.6
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHH
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKK 51 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~ 51 (150)
+++..-|...++++.-+...+..|...|+|...+-..-=|.|+..-++
T Consensus 25 ~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~e 72 (153)
T PRK11920 25 SRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAAD 72 (153)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHH
Confidence 455566778899999999999999999999999988888888866554
No 204
>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=25.19 E-value=59 Score=22.41 Aligned_cols=30 Identities=7% Similarity=-0.094 Sum_probs=22.6
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEe
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIK 39 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~ 39 (150)
|...++++..+...+..|...++|.+....
T Consensus 34 a~~~~l~~~~vRkiL~~L~~~~lv~~~~~~ 63 (105)
T PF02002_consen 34 AKKLGLKPKEVRKILYKLYEDGLVSYRRRK 63 (105)
T ss_dssp HHTT-S-HHHHHHHHHHHHHHSS-EEEEE-
T ss_pred HHHhCCCHHHHHHHHHHHHHCCCeEEEEEE
Confidence 456799999999999999999999887543
No 205
>PF14502 HTH_41: Helix-turn-helix domain
Probab=24.99 E-value=68 Score=19.85 Aligned_cols=29 Identities=7% Similarity=-0.048 Sum_probs=24.3
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
+..+++..-.|-.+++.|++.|-|..+.+
T Consensus 13 ~~~~~vs~GtiQ~Alk~Le~~gaI~Le~r 41 (48)
T PF14502_consen 13 SEKFGVSRGTIQNALKFLEENGAIKLESR 41 (48)
T ss_pred HHHhCcchhHHHHHHHHHHHCCcEEeeec
Confidence 34567888899999999999999998764
No 206
>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=24.78 E-value=42 Score=24.33 Aligned_cols=46 Identities=7% Similarity=-0.098 Sum_probs=35.2
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHH
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGK 50 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~ 50 (150)
++..-+...+++..-+...+..|...|+|....-..--|.|+..-+
T Consensus 27 s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~~ 72 (135)
T TIGR02010 27 TLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAE 72 (135)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCHH
Confidence 4444566789999999999999999999987655555677775444
No 207
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.59 E-value=58 Score=25.44 Aligned_cols=28 Identities=0% Similarity=-0.156 Sum_probs=24.2
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEee
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
|..+|+.++.|-+.++.|+..|+|.+..
T Consensus 186 A~~lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 186 ADYLGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence 4457999999999999999999997654
No 208
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=24.46 E-value=52 Score=28.27 Aligned_cols=51 Identities=8% Similarity=-0.094 Sum_probs=35.9
Q ss_pred hHHHHHHHHhhccCCceEEeeEe-eeEEEcCHhHHHHHHcCChHHHHHhhccc
Q 031936 17 AQLNESVIKKFGLFVGLPAQDIK-RETRVLTDEGKKYAAEGSSEIQLFLAVPA 68 (150)
Q Consensus 17 ~~~v~~~l~sL~~kglI~~e~~~-~~~~~LTeEG~~yl~~GsPE~rl~~~l~~ 68 (150)
++.+.+.+-.|..+|+|++++.. ...|.++-.... ..--.+|..+++.|-.
T Consensus 290 ~~~l~Atll~La~kg~l~i~~~~~~~~~~i~~~~~~-~~l~~~E~~ll~~l~~ 341 (511)
T PF09972_consen 290 DRDLTATLLDLARKGYLTIEEEEPKKDYRIRLLNKP-SDLSPYERALLDWLFN 341 (511)
T ss_pred hhhHHHHHHHHHHCCCEEEeeccCCccEEEEEcCCC-cCCCHHHHHHHHHHhc
Confidence 78999999999999999999875 344444433333 2222348888888874
No 209
>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=23.84 E-value=63 Score=25.11 Aligned_cols=34 Identities=12% Similarity=-0.098 Sum_probs=28.4
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+...|+....|.+|+..|...|+|....-.-+..
T Consensus 39 a~~~~VSR~TvR~Al~~L~~eGli~r~~G~GtfV 72 (238)
T TIGR02325 39 AERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72 (238)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 5567999999999999999999999877655444
No 210
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=23.67 E-value=1.3e+02 Score=25.41 Aligned_cols=39 Identities=21% Similarity=0.038 Sum_probs=28.7
Q ss_pred cCCChHHHH----HHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 13 VTVDAQLNE----SVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 13 ~~~~~~~v~----~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
.|+|...+. ..+..|...|++..+ ...+.||++|...+.
T Consensus 325 ~g~~~~~~~~~~~~~l~~l~~~gl~~~~---~~~~~lT~~G~~~~~ 367 (375)
T PRK05628 325 EGLPLALLDAAERARAARVVADGLLAAE---GGRLVLTLRGRLLAD 367 (375)
T ss_pred cCCCHHHHHHHHHHHHHHHHHCCCEEEE---CCEEEEChhhhHHHH
Confidence 366655543 467889999998864 457999999987653
No 211
>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=23.60 E-value=53 Score=19.58 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=22.4
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCC
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFV 31 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kg 31 (150)
+++..-|..++++...|.+.++.|...|
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3444556778999999999999999999
No 212
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=23.35 E-value=1.2e+02 Score=25.76 Aligned_cols=38 Identities=8% Similarity=0.024 Sum_probs=28.2
Q ss_pred CCChHHH-----HHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 14 TVDAQLN-----ESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 14 ~~~~~~v-----~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
|++...+ ...+..|++.|++..+ ...+.||++|..++.
T Consensus 321 Gi~~~~~~~~~~~~~l~~~~~~gll~~~---~~~i~lT~~G~~~~~ 363 (370)
T PRK06294 321 GIPLADFPSELTSELIMHPIIQELFTKN---DQALSLNKKGRLFHD 363 (370)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCEEEE---CCEEEECcchhhHHH
Confidence 5554443 3678899999998864 457999999987654
No 213
>PRK12423 LexA repressor; Provisional
Probab=23.05 E-value=65 Score=25.02 Aligned_cols=35 Identities=0% Similarity=-0.126 Sum_probs=27.5
Q ss_pred ccccC-CChHHHHHHHHhhccCCceEEeeEeeeEEE
Q 031936 10 TVSVT-VDAQLNESVIKKFGLFVGLPAQDIKRETRV 44 (150)
Q Consensus 10 ~~~~~-~~~~~v~~~l~sL~~kglI~~e~~~~~~~~ 44 (150)
|..+| .....|..++..|+.+|+|+..........
T Consensus 32 a~~~g~~s~~~v~~~l~~L~~~G~l~~~~~~~~~~~ 67 (202)
T PRK12423 32 AQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIR 67 (202)
T ss_pred HHHhCCCChHHHHHHHHHHHHCCCEEecCCCcceee
Confidence 44578 478899999999999999999877543333
No 214
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=23.00 E-value=1.1e+02 Score=27.96 Aligned_cols=43 Identities=12% Similarity=0.005 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHHcC
Q 031936 14 TVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAAEG 56 (150)
Q Consensus 14 ~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~~G 56 (150)
+.+...+.+.+..|.+.||+...........||+.|+.+++.-
T Consensus 463 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~l~~~ 505 (607)
T PRK11057 463 DKSHEHWVSVIRQLIHLGLVTQNIAQHSALQLTEAARPVLRGE 505 (607)
T ss_pred cCCHHHHHHHHHHHHHcCCceeccCccceEEECHHHHHHhcCC
Confidence 3467789999999999999999888888999999999988654
No 215
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=22.56 E-value=70 Score=25.16 Aligned_cols=34 Identities=12% Similarity=-0.189 Sum_probs=28.4
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
++..|+....|.+|+..|...|+|.-..-.=+.+
T Consensus 40 a~~~~VSR~TvR~Al~~L~~eGli~r~~G~GTfV 73 (241)
T PRK11402 40 CTQYNVSRITIRKAISDLVADGVLIRWQGKGTFV 73 (241)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecCceeEE
Confidence 4567999999999999999999999876655544
No 216
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.11 E-value=45 Score=24.65 Aligned_cols=31 Identities=6% Similarity=-0.085 Sum_probs=26.6
Q ss_pred cCcccccccCCChHHHHHHHHhhccCCceEE
Q 031936 5 SSSASTVSVTVDAQLNESVIKKFGLFVGLPA 35 (150)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~ 35 (150)
|.+.-|..+|+++..|.+-++.|++.|+|..
T Consensus 25 s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 25 PYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 4445577789999999999999999999974
No 217
>PF09857 DUF2084: Uncharacterized protein conserved in bacteria (DUF2084); InterPro: IPR018654 This domain is found in various hypothetical bacterial proteins that have no known function.
Probab=21.72 E-value=54 Score=22.68 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=21.6
Q ss_pred CHhhHHhHhhhcCceeeEEEEEEEEec
Q 031936 113 SKEDINGGLKARKLIVNQMCKGYSVSN 139 (150)
Q Consensus 113 ~~~~l~~~LKKRkLi~~~~~~~~~V~k 139 (150)
+-.++ .-||+|+||..+.-.-|.|+.
T Consensus 47 tl~vF-~kLK~krlI~S~~g~PYrIt~ 72 (85)
T PF09857_consen 47 TLAVF-RKLKRKRLIASKNGGPYRITR 72 (85)
T ss_pred CHHHH-HHHhhccceeccCCCCeEEcH
Confidence 56678 999999999998888787754
No 218
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=21.51 E-value=76 Score=24.99 Aligned_cols=34 Identities=6% Similarity=-0.156 Sum_probs=28.0
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
++..|+....|.+|+..|...|+|....-.=+..
T Consensus 42 a~~~~VSR~TVR~Al~~L~~eGli~r~~G~GtfV 75 (241)
T PRK10079 42 AARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLV 75 (241)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 5567999999999999999999998766555443
No 219
>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=20.99 E-value=95 Score=23.45 Aligned_cols=29 Identities=0% Similarity=-0.205 Sum_probs=25.1
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDI 38 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~ 38 (150)
|..+|++...|.+.+..|..+|+|...+.
T Consensus 35 a~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~ 63 (158)
T TIGR00373 35 SLELGIKLNEVRKALYALYDAGLADYKRR 63 (158)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCceeeee
Confidence 45679999999999999999999976653
No 220
>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=20.84 E-value=2e+02 Score=19.68 Aligned_cols=34 Identities=3% Similarity=-0.071 Sum_probs=26.7
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEe--eeEEEcC
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIK--RETRVLT 46 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~--~~~~~LT 46 (150)
.+++...|.+.++.|.+.|+|.--... ...|.++
T Consensus 31 ~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 31 PSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 367899999999999999999875443 3566665
No 221
>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=20.82 E-value=80 Score=24.62 Aligned_cols=35 Identities=3% Similarity=-0.191 Sum_probs=29.3
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
-++..|++...|.+|+..|+..|+|....-.-++.
T Consensus 31 La~~~~VSR~TVR~Al~~L~~eGli~r~~G~GtfV 65 (230)
T TIGR02018 31 LVAQYGCSRMTVNRALRELTDAGLLERRQGVGTFV 65 (230)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 35668999999999999999999998877665554
No 222
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=20.82 E-value=1.5e+02 Score=25.00 Aligned_cols=38 Identities=16% Similarity=0.017 Sum_probs=27.7
Q ss_pred CCChHH-HHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 14 TVDAQL-NESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 14 ~~~~~~-v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
|.+..+ +...+..|...|++..+ ...+.||++|..+..
T Consensus 329 ~~~~~~~~~~~~~~l~~~gl~~~~---~~~~~lt~~G~~~~~ 367 (377)
T PRK08599 329 GQSFEDVFGETIQELQEQGLLEED---DDHVRLTKKGKFLGN 367 (377)
T ss_pred CcCHHHHHHHHHHHHHHCCCEEEE---CCEEEECccHhHHHH
Confidence 444333 45578899999999864 457999999987653
No 223
>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=20.73 E-value=1e+02 Score=19.41 Aligned_cols=36 Identities=6% Similarity=-0.144 Sum_probs=27.6
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeEeeeEEEcC
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLT 46 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LT 46 (150)
-+..+|+....|.+.++.|++.|+..... ..-|.+.
T Consensus 19 La~~l~vS~~tv~~~l~~L~~~g~~i~~~--~~g~~l~ 54 (69)
T TIGR00122 19 LGEALGMSRTAVNKHIQTLREWGVDVLTV--GKGYRLP 54 (69)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEEec--CCceEec
Confidence 35568999999999999999999866554 4455553
No 224
>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=20.72 E-value=79 Score=24.67 Aligned_cols=34 Identities=3% Similarity=-0.195 Sum_probs=28.3
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+...|++...|.+|+..|...|+|.-..-.=+..
T Consensus 31 a~~~gVSR~TVR~Al~~L~~eGli~r~~G~GTfV 64 (233)
T TIGR02404 31 MDQYGASRETVRKALNLLTEAGYIQKIQGKGSIV 64 (233)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEeCCceEEE
Confidence 4567999999999999999999998877555544
No 225
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=20.71 E-value=72 Score=22.06 Aligned_cols=34 Identities=6% Similarity=0.050 Sum_probs=25.6
Q ss_pred cccCcccccccCCChHHHHHHHHhhccCCceEEe
Q 031936 3 LMSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQ 36 (150)
Q Consensus 3 ~~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e 36 (150)
+.+.|.-+..+++.-+-...+|..|+.+|+|..-
T Consensus 41 ~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 41 IVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred EEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 3344445566788888889999999999988553
No 226
>PRK14999 histidine utilization repressor; Provisional
Probab=20.69 E-value=78 Score=24.92 Aligned_cols=34 Identities=3% Similarity=-0.236 Sum_probs=28.3
Q ss_pred ccccCCChHHHHHHHHhhccCCceEEeeEeeeEE
Q 031936 10 TVSVTVDAQLNESVIKKFGLFVGLPAQDIKRETR 43 (150)
Q Consensus 10 ~~~~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~ 43 (150)
+...|+....|.+|+..|...|+|....-.-+.+
T Consensus 43 a~~~gVSR~TVR~Al~~L~~eGli~r~~GkGTfV 76 (241)
T PRK14999 43 VAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76 (241)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecCcEEEE
Confidence 5567999999999999999999998777655543
No 227
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=20.40 E-value=1.1e+02 Score=26.06 Aligned_cols=55 Identities=16% Similarity=0.065 Sum_probs=43.1
Q ss_pred cCCChHHHHHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH-cCChHHHHHhhcc
Q 031936 13 VTVDAQLNESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA-EGSSEIQLFLAVP 67 (150)
Q Consensus 13 ~~~~~~~v~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~-~GsPE~rl~~~l~ 67 (150)
.+++.+.+...++.|...++|.-......-|.||-.|-+++. +-+-...++.++.
T Consensus 41 ar~~~~~~~~~L~~L~~l~lv~r~~~~y~Gy~lT~~GyD~LAL~~l~~r~~ve~iG 96 (304)
T COG0478 41 ARMDEEELLYRLKRLDKLKLVSRRTISYEGYQLTFSGYDALALHALVKRGIVEAIG 96 (304)
T ss_pred cCCCHHHHHHHHHHHHhcCceeccCCcceeEEEEecchhHHHHHHHHHcChHHhhc
Confidence 578889999999999999999998889999999999999863 2233333444443
No 228
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=20.30 E-value=1.9e+02 Score=22.89 Aligned_cols=22 Identities=27% Similarity=0.449 Sum_probs=15.7
Q ss_pred cchHHHHHHHHHhcCCCCCHhhHHhHhhhcCce
Q 031936 95 ETNKFKDLLVRVQDGRAISKEDINGGLKARKLI 127 (150)
Q Consensus 95 K~d~~~~~L~~i~~g~~~~~~~l~~~LKKRkLi 127 (150)
|-+.++..|... . .+|++||++
T Consensus 167 kr~~ir~vLrKa----------y-~~L~~rGli 188 (188)
T COG2411 167 KRGRIRRVLRKA----------Y-HELKKRGLI 188 (188)
T ss_pred hhhHHHHHHHHH----------H-HHHHhccCC
Confidence 356677776544 6 889999985
No 229
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=20.11 E-value=87 Score=20.15 Aligned_cols=37 Identities=8% Similarity=-0.036 Sum_probs=26.7
Q ss_pred cccccCCChHHHHHHHHhhccCCceEEeeE---eeeEEEc
Q 031936 9 STVSVTVDAQLNESVIKKFGLFVGLPAQDI---KRETRVL 45 (150)
Q Consensus 9 ~~~~~~~~~~~v~~~l~sL~~kglI~~e~~---~~~~~~L 45 (150)
-|..+|+++-.+...+..|+..|.|...+. ....|.|
T Consensus 21 iA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l 60 (62)
T PF04703_consen 21 IADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWRL 60 (62)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEEE
T ss_pred HHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeeee
Confidence 355689999999999999999999976443 2245555
No 230
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=20.06 E-value=1.2e+02 Score=26.52 Aligned_cols=31 Identities=10% Similarity=-0.019 Sum_probs=25.2
Q ss_pred HHHHHhhccCCceEEeeEeeeEEEcCHhHHHHHH
Q 031936 21 ESVIKKFGLFVGLPAQDIKRETRVLTDEGKKYAA 54 (150)
Q Consensus 21 ~~~l~sL~~kglI~~e~~~~~~~~LTeEG~~yl~ 54 (150)
...+..|+..|+|..+ ...+.||+.|.-++.
T Consensus 402 ~~~l~~l~~~gl~~~~---~~~~~lT~~G~~~~~ 432 (453)
T PRK13347 402 LARLEPLAADGLVTID---GGGIRVTPEGRPLIR 432 (453)
T ss_pred HHHHHHHHHCCCEEEE---CCEEEECcchhHHHH
Confidence 4677899999999875 347999999987764
No 231
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=20.02 E-value=79 Score=25.96 Aligned_cols=34 Identities=9% Similarity=0.079 Sum_probs=27.9
Q ss_pred ccCcccccccCCChHHHHHHHHhhccCCceEEee
Q 031936 4 MSSSASTVSVTVDAQLNESVIKKFGLFVGLPAQD 37 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~v~~~l~sL~~kglI~~e~ 37 (150)
..+|--|-..|+..+-++.|+..|++.|+|....
T Consensus 205 lvASkiADrvGITRSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 205 LVASKIADRVGITRSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred eeehhhhhhhCchHHHHHHHHHHhhhcCceeecc
Confidence 3345556678999999999999999999998753
Done!