Query 023576
Match_columns 280
No_of_seqs 171 out of 546
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 05:05:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023576hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5235 RFA2 Single-stranded D 100.0 3.9E-49 8.4E-54 330.3 17.4 244 13-278 13-257 (258)
2 KOG3108 Single-stranded DNA-bi 100.0 3.2E-48 6.9E-53 343.3 19.6 263 2-279 2-265 (265)
3 cd04478 RPA2_DBD_D RPA2_DBD_D: 99.9 4.6E-25 9.9E-30 168.6 12.0 94 72-165 1-95 (95)
4 cd04483 hOBFC1_like hOBFC1_lik 99.7 2.1E-17 4.6E-22 125.6 10.9 73 74-146 1-91 (92)
5 PF08784 RPA_C: Replication pr 99.7 4E-18 8.8E-23 132.1 5.8 59 213-273 44-102 (102)
6 PF10451 Stn1: Telomere regula 99.6 9.4E-14 2E-18 123.9 15.3 126 41-169 26-169 (256)
7 PF01336 tRNA_anti-codon: OB-f 99.2 1.2E-10 2.7E-15 84.0 10.2 73 73-147 1-75 (75)
8 cd04492 YhaM_OBF_like YhaM_OBF 98.9 3.5E-08 7.6E-13 72.4 10.7 76 75-153 5-82 (83)
9 PRK13480 3'-5' exoribonuclease 98.9 1.9E-08 4.1E-13 92.7 10.8 79 68-149 12-92 (314)
10 COG3390 Uncharacterized protei 98.7 1.3E-07 2.8E-12 79.3 9.5 126 43-170 11-152 (196)
11 cd03524 RPA2_OBF_family RPA2_O 98.6 3.6E-07 7.8E-12 64.4 8.9 71 74-146 1-75 (75)
12 cd04485 DnaE_OBF DnaE_OBF: A s 98.5 3.2E-07 7E-12 66.9 7.3 72 75-148 2-78 (84)
13 PRK06461 single-stranded DNA-b 98.5 1.1E-06 2.4E-11 70.9 10.2 84 44-149 4-100 (129)
14 cd04489 ExoVII_LU_OBF ExoVII_L 98.5 3.6E-06 7.7E-11 61.3 10.9 73 73-147 2-77 (78)
15 cd04491 SoSSB_OBF SoSSB_OBF: A 98.3 3.4E-06 7.5E-11 62.3 7.7 53 86-143 22-75 (82)
16 cd04482 RPA2_OBF_like RPA2_OBF 98.3 1.2E-05 2.7E-10 60.8 10.0 73 74-149 2-76 (91)
17 cd04487 RecJ_OBF2_like RecJ_OB 98.2 1.9E-05 4.1E-10 57.3 9.6 72 73-146 1-72 (73)
18 PF13742 tRNA_anti_2: OB-fold 98.1 3.3E-05 7.2E-10 59.4 10.1 75 70-146 21-99 (99)
19 cd04488 RecG_wedge_OBF RecG_we 98.0 5.7E-05 1.2E-09 53.7 9.4 63 75-140 2-68 (75)
20 cd04484 polC_OBF polC_OBF: A s 98.0 9.1E-05 2E-09 55.0 10.4 73 72-146 1-81 (82)
21 COG1107 Archaea-specific RecJ- 97.7 0.00015 3.3E-09 70.6 9.1 78 71-150 214-291 (715)
22 cd04321 ScAspRS_mt_like_N ScAs 97.6 0.00096 2.1E-08 49.7 10.3 76 72-148 1-85 (86)
23 KOG3416 Predicted nucleic acid 97.5 0.00044 9.4E-09 54.7 7.7 83 45-143 5-88 (134)
24 PF04076 BOF: Bacterial OB fol 97.5 0.0029 6.3E-08 49.0 12.2 83 43-146 21-103 (103)
25 cd04323 AsnRS_cyto_like_N AsnR 97.5 0.0021 4.6E-08 47.6 10.8 76 72-147 1-82 (84)
26 cd04100 Asp_Lys_Asn_RS_N Asp_L 97.5 0.0015 3.3E-08 48.4 10.1 76 72-147 1-83 (85)
27 COG4085 Predicted RNA-binding 97.5 0.00063 1.4E-08 57.7 8.7 84 66-149 47-138 (204)
28 PF13412 HTH_24: Winged helix- 97.5 0.00027 5.8E-09 46.6 4.7 47 214-266 1-47 (48)
29 cd04490 PolII_SU_OBF PolII_SU_ 97.4 0.0017 3.7E-08 47.7 9.3 69 73-144 2-72 (79)
30 cd04317 EcAspRS_like_N EcAspRS 97.4 0.0014 3E-08 53.0 9.7 78 72-149 16-103 (135)
31 TIGR00156 conserved hypothetic 97.3 0.007 1.5E-07 48.4 12.4 82 43-145 44-125 (126)
32 PRK00286 xseA exodeoxyribonucl 97.3 0.001 2.2E-08 64.3 9.0 112 44-167 5-119 (438)
33 cd04316 ND_PkAspRS_like_N ND_P 97.3 0.0035 7.6E-08 48.7 10.0 80 71-150 13-97 (108)
34 PRK05673 dnaE DNA polymerase I 97.3 0.00086 1.9E-08 71.6 8.6 76 72-149 979-1059(1135)
35 COG1570 XseA Exonuclease VII, 97.3 0.0036 7.7E-08 59.9 11.7 95 70-168 23-120 (440)
36 cd04320 AspRS_cyto_N AspRS_cyt 97.3 0.0035 7.6E-08 48.1 9.7 79 72-150 1-92 (102)
37 cd04322 LysRS_N LysRS_N: N-ter 97.2 0.0038 8.3E-08 48.4 9.6 77 72-148 1-81 (108)
38 cd04319 PhAsnRS_like_N PhAsnRS 97.2 0.0042 9.1E-08 47.8 9.5 79 72-150 1-83 (103)
39 PRK10053 hypothetical protein; 97.1 0.024 5.1E-07 45.7 13.2 78 43-145 48-129 (130)
40 PRK03932 asnC asparaginyl-tRNA 97.1 0.0069 1.5E-07 58.8 12.1 94 43-149 2-99 (450)
41 smart00550 Zalpha Z-DNA-bindin 97.1 0.0023 5E-08 45.6 6.4 59 215-277 5-64 (68)
42 COG3481 Predicted HD-superfami 97.0 0.00048 1E-08 62.4 3.2 63 84-149 18-80 (287)
43 cd04318 EcAsnRS_like_N EcAsnRS 97.0 0.017 3.6E-07 42.4 11.1 74 73-147 2-80 (82)
44 TIGR00237 xseA exodeoxyribonuc 97.0 0.0049 1.1E-07 59.6 10.1 94 70-167 17-113 (432)
45 PRK07373 DNA polymerase III su 97.0 0.0041 9E-08 60.2 9.2 76 72-149 282-362 (449)
46 PRK07211 replication factor A; 96.9 0.0058 1.3E-07 59.5 9.9 76 71-149 172-261 (485)
47 PRK07218 replication factor A; 96.8 0.011 2.3E-07 56.9 10.1 72 71-149 173-256 (423)
48 COG3111 Periplasmic protein wi 96.7 0.042 9.1E-07 43.5 11.4 81 42-147 43-127 (128)
49 TIGR00457 asnS asparaginyl-tRN 96.6 0.021 4.6E-07 55.5 11.2 94 44-148 1-100 (453)
50 PF13730 HTH_36: Helix-turn-he 96.5 0.01 2.2E-07 40.0 5.8 54 213-266 2-55 (55)
51 PF08220 HTH_DeoR: DeoR-like h 96.4 0.0072 1.6E-07 41.5 4.8 46 218-269 2-47 (57)
52 PF01726 LexA_DNA_bind: LexA D 96.4 0.002 4.3E-08 45.6 1.9 53 213-268 3-58 (65)
53 PF12802 MarR_2: MarR family; 96.4 0.0088 1.9E-07 41.1 5.2 57 213-273 2-58 (62)
54 PRK07217 replication factor A; 96.4 0.021 4.5E-07 52.4 8.9 74 71-149 83-160 (311)
55 PRK14699 replication factor A; 96.4 0.013 2.9E-07 57.3 8.1 77 71-148 68-157 (484)
56 PRK07211 replication factor A; 96.2 0.026 5.6E-07 55.1 9.3 77 71-149 64-151 (485)
57 TIGR01405 polC_Gram_pos DNA po 96.2 0.031 6.7E-07 60.3 10.7 78 71-148 8-92 (1213)
58 PF04703 FaeA: FaeA-like prote 96.2 0.0055 1.2E-07 42.9 3.3 46 218-268 2-47 (62)
59 PRK00448 polC DNA polymerase I 96.2 0.035 7.6E-07 60.8 10.8 80 71-150 237-323 (1437)
60 PRK08402 replication factor A; 96.2 0.027 5.8E-07 53.0 8.7 70 71-142 73-154 (355)
61 PRK07218 replication factor A; 96.2 0.037 8E-07 53.2 9.8 72 71-150 69-152 (423)
62 PRK12445 lysyl-tRNA synthetase 96.1 0.051 1.1E-06 53.5 10.8 101 45-149 44-148 (505)
63 PRK05672 dnaE2 error-prone DNA 96.1 0.022 4.8E-07 60.6 8.7 76 72-149 955-1033(1046)
64 TIGR00458 aspS_arch aspartyl-t 96.1 0.048 1E-06 52.6 10.4 79 71-149 13-96 (428)
65 PRK12366 replication factor A; 96.0 0.023 5.1E-07 57.5 8.2 74 72-150 186-270 (637)
66 PRK14699 replication factor A; 96.0 0.03 6.4E-07 54.8 8.6 75 72-149 178-265 (484)
67 PRK06920 dnaE DNA polymerase I 96.0 0.019 4.1E-07 61.4 7.7 76 72-149 945-1025(1107)
68 PF09339 HTH_IclR: IclR helix- 96.0 0.015 3.3E-07 38.9 4.7 44 220-268 7-50 (52)
69 PRK07374 dnaE DNA polymerase I 96.0 0.029 6.2E-07 60.4 9.0 77 71-149 1001-1082(1170)
70 PF01978 TrmB: Sugar-specific 96.0 0.0062 1.4E-07 43.1 2.7 52 213-270 5-56 (68)
71 PRK05159 aspC aspartyl-tRNA sy 95.9 0.063 1.4E-06 52.0 10.3 79 71-149 17-99 (437)
72 smart00346 HTH_ICLR helix_turn 95.8 0.031 6.7E-07 41.4 6.1 54 219-277 8-61 (91)
73 PRK06826 dnaE DNA polymerase I 95.8 0.04 8.7E-07 59.2 8.9 77 71-149 992-1074(1151)
74 cd04497 hPOT1_OB1_like hPOT1_O 95.7 0.11 2.4E-06 42.1 9.6 69 71-142 15-94 (138)
75 COG0017 AsnS Aspartyl/asparagi 95.7 0.076 1.7E-06 51.0 9.8 91 43-147 3-97 (435)
76 PRK00484 lysS lysyl-tRNA synth 95.7 0.083 1.8E-06 51.9 10.3 101 43-147 31-134 (491)
77 PRK15491 replication factor A; 95.7 0.069 1.5E-06 50.7 9.4 75 72-149 178-268 (374)
78 TIGR00459 aspS_bact aspartyl-t 95.7 0.077 1.7E-06 53.1 10.1 75 72-147 17-101 (583)
79 PTZ00401 aspartyl-tRNA synthet 95.6 0.16 3.4E-06 50.6 12.0 77 71-147 79-166 (550)
80 PF09012 FeoC: FeoC like trans 95.6 0.016 3.5E-07 41.2 3.7 47 219-271 3-49 (69)
81 TIGR00499 lysS_bact lysyl-tRNA 95.6 0.12 2.7E-06 50.8 10.9 99 45-147 32-134 (496)
82 smart00420 HTH_DEOR helix_turn 95.5 0.04 8.7E-07 36.1 5.3 46 218-269 2-47 (53)
83 PRK06386 replication factor A; 95.5 0.065 1.4E-06 50.4 8.4 70 71-149 118-196 (358)
84 PRK10917 ATP-dependent DNA hel 95.5 0.087 1.9E-06 53.8 10.1 66 71-139 60-129 (681)
85 PLN02903 aminoacyl-tRNA ligase 95.5 0.11 2.3E-06 52.7 10.3 78 71-148 73-161 (652)
86 PRK00476 aspS aspartyl-tRNA sy 95.4 0.12 2.6E-06 52.0 10.4 77 71-148 18-104 (588)
87 PF08279 HTH_11: HTH domain; 95.4 0.045 9.8E-07 36.8 5.2 46 218-268 2-48 (55)
88 PLN02502 lysyl-tRNA synthetase 95.4 0.16 3.5E-06 50.6 11.1 77 71-147 109-191 (553)
89 PRK07279 dnaE DNA polymerase I 95.3 0.065 1.4E-06 56.9 8.6 75 73-149 887-967 (1034)
90 smart00344 HTH_ASNC helix_turn 95.3 0.038 8.3E-07 42.4 5.2 47 215-267 2-48 (108)
91 PRK15491 replication factor A; 95.3 0.11 2.3E-06 49.4 9.2 77 71-149 68-158 (374)
92 PRK12820 bifunctional aspartyl 95.3 0.12 2.7E-06 52.7 10.1 77 71-147 19-107 (706)
93 smart00347 HTH_MARR helix_turn 95.3 0.056 1.2E-06 40.2 5.9 53 213-271 7-59 (101)
94 PLN02603 asparaginyl-tRNA synt 95.2 0.16 3.4E-06 50.7 10.3 77 71-148 108-191 (565)
95 PRK11169 leucine-responsive tr 95.1 0.041 8.9E-07 46.0 5.1 51 213-269 11-63 (164)
96 PRK08402 replication factor A; 95.1 0.11 2.3E-06 49.0 8.3 75 88-164 246-352 (355)
97 COG1200 RecG RecG-like helicas 95.1 0.18 3.9E-06 50.8 10.2 75 71-148 61-139 (677)
98 PLN02850 aspartate-tRNA ligase 95.1 0.21 4.6E-06 49.5 10.7 78 71-148 82-170 (530)
99 PF02765 POT1: Telomeric singl 95.0 0.42 9.2E-06 39.1 10.9 71 71-144 13-101 (146)
100 PLN02221 asparaginyl-tRNA synt 95.0 0.24 5.1E-06 49.6 10.9 95 43-148 31-135 (572)
101 PF13463 HTH_27: Winged helix 94.9 0.047 1E-06 38.1 4.3 53 215-272 2-54 (68)
102 COG2176 PolC DNA polymerase II 94.9 0.067 1.5E-06 56.6 7.1 79 70-148 239-324 (1444)
103 COG1571 Predicted DNA-binding 94.9 0.12 2.6E-06 49.3 8.3 75 69-147 265-341 (421)
104 COG1522 Lrp Transcriptional re 94.9 0.052 1.1E-06 44.3 5.2 48 213-266 5-52 (154)
105 PF01022 HTH_5: Bacterial regu 94.9 0.11 2.3E-06 34.0 5.7 46 216-268 2-47 (47)
106 PF00392 GntR: Bacterial regul 94.9 0.11 2.4E-06 36.1 6.2 50 218-268 6-56 (64)
107 PRK11179 DNA-binding transcrip 94.9 0.055 1.2E-06 44.6 5.3 51 213-269 6-58 (153)
108 cd04479 RPA3 RPA3: A subfamily 94.8 0.44 9.5E-06 36.6 9.8 64 71-149 16-80 (101)
109 COG3355 Predicted transcriptio 94.7 0.085 1.8E-06 42.2 5.6 51 213-268 24-74 (126)
110 PRK12366 replication factor A; 94.6 0.12 2.6E-06 52.4 8.0 75 71-148 74-162 (637)
111 TIGR00643 recG ATP-dependent D 94.6 0.26 5.6E-06 50.0 10.3 65 72-140 34-103 (630)
112 PF14947 HTH_45: Winged helix- 94.5 0.047 1E-06 39.8 3.5 55 216-279 6-60 (77)
113 PRK05813 single-stranded DNA-b 94.4 0.36 7.9E-06 42.4 9.6 80 69-152 7-105 (219)
114 cd00090 HTH_ARSR Arsenical Res 94.3 0.14 2.9E-06 35.6 5.5 50 216-272 7-56 (78)
115 smart00345 HTH_GNTR helix_turn 94.2 0.23 5.1E-06 33.2 6.3 34 236-269 19-53 (60)
116 cd07377 WHTH_GntR Winged helix 94.2 0.31 6.7E-06 33.3 7.0 38 238-276 27-64 (66)
117 PTZ00385 lysyl-tRNA synthetase 94.2 0.47 1E-05 48.1 10.9 78 72-149 109-191 (659)
118 PRK08486 single-stranded DNA-b 94.1 0.48 1E-05 40.4 9.3 78 70-149 2-107 (182)
119 PF08661 Rep_fac-A_3: Replicat 94.0 0.56 1.2E-05 36.4 8.9 69 71-149 19-88 (109)
120 cd04481 RPA1_DBD_B_like RPA1_D 94.0 0.48 1E-05 36.4 8.4 68 85-152 21-97 (106)
121 PF12840 HTH_20: Helix-turn-he 94.0 0.13 2.8E-06 35.5 4.7 48 215-268 9-56 (61)
122 cd00092 HTH_CRP helix_turn_hel 94.0 0.31 6.8E-06 33.6 6.8 44 234-278 23-66 (67)
123 PRK06386 replication factor A; 93.9 0.46 9.9E-06 44.8 9.6 65 71-142 13-86 (358)
124 PF01047 MarR: MarR family; I 93.8 0.1 2.2E-06 35.4 4.0 52 216-273 3-54 (59)
125 PRK07275 single-stranded DNA-b 93.6 0.61 1.3E-05 39.0 8.9 78 70-149 2-105 (162)
126 cd04486 YhcR_OBF_like YhcR_OBF 93.5 0.29 6.4E-06 35.7 6.1 64 75-143 2-70 (78)
127 PRK11512 DNA-binding transcrip 93.5 0.24 5.2E-06 40.2 6.3 55 213-273 37-91 (144)
128 cd04474 RPA1_DBD_A RPA1_DBD_A: 93.5 0.23 5E-06 38.2 5.8 56 71-128 10-75 (104)
129 PRK02983 lysS lysyl-tRNA synth 93.4 0.7 1.5E-05 49.8 11.2 73 72-144 653-729 (1094)
130 PRK12423 LexA repressor; Provi 93.4 0.1 2.3E-06 45.1 4.1 53 214-269 4-59 (202)
131 PF13404 HTH_AsnC-type: AsnC-t 93.3 0.17 3.7E-06 32.5 4.1 41 215-261 2-42 (42)
132 PF02082 Rrf2: Transcriptional 93.3 0.25 5.5E-06 36.2 5.5 48 219-269 11-58 (83)
133 cd04475 RPA1_DBD_B RPA1_DBD_B: 93.2 0.65 1.4E-05 35.2 7.9 64 73-141 2-78 (101)
134 smart00419 HTH_CRP helix_turn_ 93.2 0.2 4.4E-06 32.1 4.4 41 235-277 7-47 (48)
135 PF06163 DUF977: Bacterial pro 93.1 0.22 4.8E-06 39.7 5.1 48 215-268 11-58 (127)
136 TIGR00498 lexA SOS regulatory 93.0 0.13 2.8E-06 44.1 4.2 56 213-269 3-59 (199)
137 PRK06751 single-stranded DNA-b 93.0 0.81 1.7E-05 38.7 8.9 62 70-133 2-80 (173)
138 TIGR01884 cas_HTH CRISPR locus 92.9 0.31 6.8E-06 42.0 6.5 61 213-279 140-201 (203)
139 PTZ00425 asparagine-tRNA ligas 92.9 0.6 1.3E-05 46.8 9.2 62 71-133 82-147 (586)
140 PRK09834 DNA-binding transcrip 92.9 0.25 5.3E-06 44.4 6.0 55 219-278 14-68 (263)
141 PRK07459 single-stranded DNA-b 92.8 0.51 1.1E-05 37.5 7.0 61 70-132 3-76 (121)
142 COG2345 Predicted transcriptio 92.7 0.24 5.3E-06 43.4 5.5 47 216-268 11-57 (218)
143 PRK03573 transcriptional regul 92.7 0.37 7.9E-06 39.0 6.3 56 213-273 28-83 (144)
144 PRK10163 DNA-binding transcrip 92.5 0.32 6.9E-06 43.9 6.2 54 219-277 28-81 (271)
145 COG1190 LysU Lysyl-tRNA synthe 92.5 0.98 2.1E-05 44.1 9.7 99 46-148 41-143 (502)
146 TIGR01889 Staph_reg_Sar staphy 92.5 0.48 1E-05 36.6 6.4 58 213-272 22-79 (109)
147 PRK02801 primosomal replicatio 92.5 1.1 2.5E-05 34.3 8.4 33 100-134 50-82 (101)
148 PF01325 Fe_dep_repress: Iron 92.5 0.21 4.5E-06 34.7 3.8 35 234-268 20-54 (60)
149 PF00325 Crp: Bacterial regula 92.5 0.28 6.1E-06 29.6 3.9 30 237-266 3-32 (32)
150 TIGR02431 pcaR_pcaU beta-ketoa 92.4 0.32 7E-06 43.1 6.0 51 220-277 13-63 (248)
151 smart00418 HTH_ARSR helix_turn 92.3 0.32 6.9E-06 32.7 4.7 44 221-271 2-45 (66)
152 TIGR02337 HpaR homoprotocatech 92.3 0.42 9.2E-06 37.3 6.0 55 213-273 25-79 (118)
153 PF10007 DUF2250: Uncharacteri 92.3 0.32 7E-06 36.8 4.9 49 214-268 5-53 (92)
154 PRK10434 srlR DNA-bindng trans 92.3 0.24 5.3E-06 44.4 5.1 48 216-269 5-52 (256)
155 PRK10906 DNA-binding transcrip 92.0 0.28 6.1E-06 43.9 5.2 48 216-269 5-52 (252)
156 TIGR02325 C_P_lyase_phnF phosp 92.0 0.49 1.1E-05 41.4 6.6 32 238-269 34-65 (238)
157 TIGR03879 near_KaiC_dom probab 92.0 0.17 3.7E-06 36.6 3.0 49 212-266 14-62 (73)
158 TIGR02404 trehalos_R_Bsub treh 92.0 0.48 1E-05 41.5 6.6 51 217-268 5-56 (233)
159 PTZ00417 lysine-tRNA ligase; P 91.9 1 2.2E-05 45.3 9.4 101 43-148 110-217 (585)
160 PRK09764 DNA-binding transcrip 91.9 0.52 1.1E-05 41.6 6.7 51 217-268 10-61 (240)
161 TIGR02018 his_ut_repres histid 91.8 0.52 1.1E-05 41.2 6.5 51 217-268 6-57 (230)
162 PRK06752 single-stranded DNA-b 91.7 1.8 3.9E-05 33.7 8.8 77 71-149 3-105 (112)
163 PRK14999 histidine utilization 91.7 0.56 1.2E-05 41.4 6.7 51 217-268 17-68 (241)
164 PF08679 DsrD: Dissimilatory s 91.7 0.51 1.1E-05 33.3 5.0 48 217-266 2-50 (67)
165 PRK06293 single-stranded DNA-b 91.6 1.7 3.8E-05 36.3 9.1 61 71-133 2-76 (161)
166 PF03100 CcmE: CcmE; InterPro 91.6 1.5 3.3E-05 35.2 8.6 54 71-130 51-108 (131)
167 PRK06863 single-stranded DNA-b 91.6 1.6 3.6E-05 36.7 9.0 81 70-152 4-113 (168)
168 PRK10079 phosphonate metabolis 91.4 0.58 1.3E-05 41.3 6.5 31 238-268 37-67 (241)
169 PF10771 DUF2582: Protein of u 91.4 0.39 8.3E-06 34.0 4.2 48 219-272 11-58 (65)
170 PRK06958 single-stranded DNA-b 91.3 1.8 3.9E-05 36.9 9.0 62 70-133 4-85 (182)
171 COG1349 GlpR Transcriptional r 91.3 0.31 6.7E-06 43.7 4.7 46 217-268 6-51 (253)
172 PF00436 SSB: Single-strand bi 91.3 1.2 2.6E-05 33.6 7.3 62 70-133 1-81 (104)
173 COG1414 IclR Transcriptional r 91.2 0.54 1.2E-05 41.9 6.1 54 219-277 7-60 (246)
174 TIGR00621 ssb single stranded 91.2 2 4.2E-05 36.0 9.1 36 96-133 49-84 (164)
175 PF06969 HemN_C: HemN C-termin 91.0 0.25 5.4E-06 34.4 3.0 55 217-279 7-62 (66)
176 PRK11402 DNA-binding transcrip 90.9 0.74 1.6E-05 40.5 6.7 31 238-268 35-65 (241)
177 TIGR02944 suf_reg_Xantho FeS a 90.9 0.62 1.3E-05 37.1 5.6 48 219-270 12-59 (130)
178 PRK15090 DNA-binding transcrip 90.9 0.65 1.4E-05 41.5 6.3 52 220-277 18-69 (257)
179 PF08646 Rep_fac-A_C: Replicat 90.8 0.75 1.6E-05 37.4 6.1 65 88-152 55-142 (146)
180 COG2188 PhnF Transcriptional r 90.8 0.73 1.6E-05 40.7 6.5 51 217-268 12-63 (236)
181 TIGR00122 birA_repr_reg BirA b 90.5 1.1 2.5E-05 31.4 6.1 50 219-276 3-52 (69)
182 PHA02701 ORF020 dsRNA-binding 90.5 0.68 1.5E-05 39.3 5.6 51 216-272 4-54 (183)
183 PRK09954 putative kinase; Prov 90.4 0.5 1.1E-05 44.2 5.4 46 215-266 2-47 (362)
184 cd07153 Fur_like Ferric uptake 90.4 0.75 1.6E-05 35.6 5.5 49 217-270 2-55 (116)
185 PRK05813 single-stranded DNA-b 90.3 3.3 7.1E-05 36.4 10.0 81 68-151 107-211 (219)
186 PRK11569 transcriptional repre 90.3 0.69 1.5E-05 41.8 6.0 53 220-277 32-84 (274)
187 TIGR00738 rrf2_super rrf2 fami 90.2 1.2 2.6E-05 35.3 6.7 45 234-278 23-68 (132)
188 PF14394 DUF4423: Domain of un 90.2 0.84 1.8E-05 38.5 6.0 56 217-279 25-83 (171)
189 PRK08763 single-stranded DNA-b 90.1 3.1 6.8E-05 34.9 9.3 61 70-132 5-84 (164)
190 PF03444 HrcA_DNA-bdg: Winged 90.1 0.49 1.1E-05 34.6 3.9 54 214-268 2-55 (78)
191 PRK04424 fatty acid biosynthes 89.8 0.37 8.1E-06 41.1 3.6 47 217-269 8-54 (185)
192 cd04476 RPA1_DBD_C RPA1_DBD_C: 89.7 1.8 3.9E-05 35.9 7.7 72 88-161 69-164 (166)
193 cd04496 SSB_OBF SSB_OBF: A sub 89.7 2.7 5.8E-05 31.2 7.9 36 96-133 42-77 (100)
194 PF02295 z-alpha: Adenosine de 89.4 0.64 1.4E-05 32.9 4.0 49 216-268 4-52 (66)
195 PHA02943 hypothetical protein; 89.3 1.1 2.4E-05 37.0 5.8 46 216-268 11-56 (165)
196 PRK09802 DNA-binding transcrip 89.1 0.73 1.6E-05 41.7 5.2 47 216-268 17-63 (269)
197 smart00088 PINT motif in prote 89.1 0.66 1.4E-05 34.1 4.1 39 235-273 23-61 (88)
198 smart00753 PAM PCI/PINT associ 89.1 0.66 1.4E-05 34.1 4.1 39 235-273 23-61 (88)
199 COG1725 Predicted transcriptio 89.0 1.7 3.6E-05 34.9 6.5 34 237-270 36-69 (125)
200 PRK13254 cytochrome c-type bio 88.8 3.1 6.8E-05 34.3 8.2 55 71-131 52-109 (148)
201 PRK07772 single-stranded DNA-b 88.7 4.3 9.4E-05 34.7 9.3 35 97-133 52-86 (186)
202 COG0735 Fur Fe2+/Zn2+ uptake r 88.5 1.4 3.1E-05 36.0 6.0 55 214-273 19-78 (145)
203 PF10264 Stork_head: Winged he 88.5 1.3 2.8E-05 32.6 5.1 54 214-269 9-70 (80)
204 PRK13509 transcriptional repre 88.5 0.98 2.1E-05 40.4 5.5 48 216-269 5-52 (251)
205 PRK10411 DNA-binding transcrip 88.3 0.9 1.9E-05 40.4 5.1 46 216-267 4-49 (240)
206 PRK09010 single-stranded DNA-b 88.3 2.2 4.7E-05 36.3 7.2 63 69-133 5-87 (177)
207 PRK10870 transcriptional repre 88.1 2.2 4.7E-05 36.0 7.1 57 213-273 52-108 (176)
208 PRK09462 fur ferric uptake reg 88.0 1.4 3.1E-05 35.9 5.8 51 214-268 15-70 (148)
209 KOG0554 Asparaginyl-tRNA synth 87.9 1.1 2.5E-05 42.4 5.6 87 42-147 5-96 (446)
210 PF01475 FUR: Ferric uptake re 87.8 0.46 1E-05 37.2 2.7 51 215-270 7-62 (120)
211 PRK08182 single-stranded DNA-b 87.8 5.2 0.00011 32.9 9.0 61 71-133 3-87 (148)
212 PRK07274 single-stranded DNA-b 87.8 2.7 5.8E-05 33.8 7.1 62 70-133 2-80 (131)
213 TIGR03337 phnR transcriptional 87.8 1.8 4E-05 37.6 6.7 52 217-269 6-58 (231)
214 PRK13732 single-stranded DNA-b 87.8 2.3 5.1E-05 36.0 7.1 62 70-133 6-87 (175)
215 PF13601 HTH_34: Winged helix 87.7 0.73 1.6E-05 33.8 3.5 45 218-268 2-46 (80)
216 PRK05733 single-stranded DNA-b 87.5 2.7 5.8E-05 35.6 7.2 62 70-133 5-86 (172)
217 PRK11014 transcriptional repre 87.4 0.99 2.1E-05 36.6 4.5 34 236-269 25-58 (141)
218 PRK00215 LexA repressor; Valid 87.4 0.77 1.7E-05 39.5 4.0 56 214-270 2-58 (205)
219 PRK11886 bifunctional biotin-- 87.3 1.3 2.8E-05 40.9 5.7 45 218-268 6-51 (319)
220 PRK13777 transcriptional regul 86.9 2.1 4.5E-05 36.7 6.3 55 213-273 42-96 (185)
221 PRK04984 fatty acid metabolism 86.9 1.7 3.8E-05 38.0 6.1 35 234-268 28-63 (239)
222 PRK11414 colanic acid/biofilm 86.8 1.5 3.3E-05 38.0 5.6 36 233-268 31-66 (221)
223 PF04182 B-block_TFIIIC: B-blo 86.8 1.7 3.7E-05 31.3 5.0 49 216-268 2-50 (75)
224 PF14502 HTH_41: Helix-turn-he 86.8 1.4 2.9E-05 29.2 3.9 32 237-268 7-38 (48)
225 KOG0555 Asparaginyl-tRNA synth 86.7 1 2.2E-05 42.8 4.5 65 68-133 121-185 (545)
226 PRK10046 dpiA two-component re 86.5 1.6 3.5E-05 37.7 5.6 47 219-270 165-211 (225)
227 TIGR03338 phnR_burk phosphonat 86.4 1.6 3.5E-05 37.4 5.5 36 233-268 31-66 (212)
228 PF05331 DUF742: Protein of un 86.1 1.7 3.8E-05 34.2 5.0 49 212-268 39-87 (114)
229 smart00421 HTH_LUXR helix_turn 85.9 2.9 6.2E-05 27.2 5.5 41 214-262 4-44 (58)
230 TIGR01610 phage_O_Nterm phage 85.9 3 6.5E-05 31.5 6.1 35 234-268 45-79 (95)
231 TIGR02787 codY_Gpos GTP-sensin 85.7 2.1 4.6E-05 38.1 5.8 46 219-269 186-231 (251)
232 PRK03902 manganese transport t 85.7 2.3 5.1E-05 34.3 5.8 57 216-279 8-64 (142)
233 PRK06266 transcription initiat 85.7 1.8 3.9E-05 36.7 5.3 46 216-267 22-67 (178)
234 PRK03837 transcriptional regul 85.5 2.3 5.1E-05 37.1 6.2 35 234-268 34-69 (241)
235 PRK11534 DNA-binding transcrip 85.5 1.9 4.1E-05 37.4 5.6 36 233-268 27-62 (224)
236 PRK07217 replication factor A; 85.4 2.8 6.1E-05 38.7 6.7 58 87-148 217-296 (311)
237 PRK06642 single-stranded DNA-b 85.3 4 8.7E-05 33.7 7.1 62 70-133 5-87 (152)
238 PRK09990 DNA-binding transcrip 85.2 2.2 4.7E-05 37.7 5.9 37 232-268 26-63 (251)
239 PF04545 Sigma70_r4: Sigma-70, 85.1 3.6 7.9E-05 26.8 5.5 41 213-260 4-44 (50)
240 PF15072 DUF4539: Domain of un 85.1 2.6 5.6E-05 31.5 5.2 65 74-141 6-73 (86)
241 PF08281 Sigma70_r4_2: Sigma-7 85.0 2.3 4.9E-05 28.1 4.6 40 213-259 10-49 (54)
242 PRK10681 DNA-binding transcrip 84.8 1.8 3.9E-05 38.6 5.2 46 216-267 7-52 (252)
243 PRK13165 cytochrome c-type bio 84.6 7.4 0.00016 32.5 8.3 55 71-131 58-116 (160)
244 PF00196 GerE: Bacterial regul 84.4 2.3 5E-05 28.7 4.5 41 213-261 3-43 (58)
245 PRK07135 dnaE DNA polymerase I 84.1 3.7 8.1E-05 43.7 7.8 59 72-133 899-961 (973)
246 PF13545 HTH_Crp_2: Crp-like h 84.1 2 4.3E-05 30.4 4.2 34 235-268 27-60 (76)
247 PRK14165 winged helix-turn-hel 84.1 2.1 4.6E-05 37.5 5.1 40 233-272 18-57 (217)
248 PF02760 HIN: HIN-200/IF120x d 84.0 5.9 0.00013 33.0 7.3 41 82-127 125-165 (170)
249 COG3888 Predicted transcriptio 83.8 2.3 5E-05 38.3 5.2 46 217-266 5-50 (321)
250 PF02002 TFIIE_alpha: TFIIE al 83.8 0.94 2E-05 34.7 2.5 44 217-266 14-57 (105)
251 PF02796 HTH_7: Helix-turn-hel 83.7 2.2 4.9E-05 27.4 3.9 33 218-258 11-43 (45)
252 PRK13150 cytochrome c-type bio 83.5 8.6 0.00019 32.1 8.2 55 71-131 58-116 (159)
253 PRK09464 pdhR transcriptional 83.5 2.9 6.2E-05 37.0 5.9 35 234-268 31-66 (254)
254 PRK10225 DNA-binding transcrip 83.5 3.1 6.7E-05 36.9 6.1 36 233-268 29-65 (257)
255 TIGR00617 rpa1 replication fac 83.5 4.6 9.9E-05 40.9 7.9 73 89-162 512-607 (608)
256 PRK11639 zinc uptake transcrip 83.4 2.4 5.1E-05 35.6 5.0 51 214-269 24-79 (169)
257 TIGR00617 rpa1 replication fac 83.3 6.5 0.00014 39.8 8.9 65 72-141 312-389 (608)
258 cd06170 LuxR_C_like C-terminal 83.2 4 8.7E-05 26.5 5.2 40 215-262 2-41 (57)
259 PF13936 HTH_38: Helix-turn-he 83.1 2.2 4.7E-05 27.4 3.7 38 214-258 5-42 (44)
260 PTZ00111 DNA replication licen 83.0 2.7 5.9E-05 44.2 6.2 42 234-276 857-910 (915)
261 COG2512 Predicted membrane-ass 82.8 2.3 4.9E-05 38.4 4.9 49 212-266 191-240 (258)
262 COG4742 Predicted transcriptio 82.8 2.8 6.1E-05 37.7 5.5 57 214-279 11-67 (260)
263 PF09106 SelB-wing_2: Elongati 82.3 2 4.3E-05 29.4 3.4 37 233-269 14-53 (59)
264 PF07106 TBPIP: Tat binding pr 82.2 2.6 5.7E-05 35.2 4.8 45 218-267 3-49 (169)
265 PF12869 tRNA_anti-like: tRNA_ 82.1 5.6 0.00012 31.9 6.7 87 44-134 44-133 (144)
266 PRK11523 DNA-binding transcrip 82.1 4 8.7E-05 36.1 6.3 36 233-268 28-64 (253)
267 PRK10141 DNA-binding transcrip 82.1 3.7 7.9E-05 32.5 5.3 49 215-269 15-63 (117)
268 PRK04036 DNA polymerase II sma 81.9 5.4 0.00012 39.4 7.6 61 71-132 154-216 (504)
269 PF05158 RNA_pol_Rpc34: RNA po 81.9 1.8 3.9E-05 40.4 4.0 53 212-268 80-132 (327)
270 TIGR02010 IscR iron-sulfur clu 81.9 4.1 8.8E-05 32.7 5.7 47 220-269 12-58 (135)
271 PF05491 RuvB_C: Holliday junc 81.8 3.2 6.9E-05 30.2 4.5 55 212-269 4-59 (76)
272 TIGR00373 conserved hypothetic 81.8 3 6.6E-05 34.6 5.0 42 219-266 17-58 (158)
273 COG1654 BirA Biotin operon rep 81.8 7.3 0.00016 28.6 6.4 57 217-277 4-60 (79)
274 TIGR02147 Fsuc_second hypothet 81.8 4.4 9.4E-05 36.8 6.4 43 236-279 136-181 (271)
275 PF04255 DUF433: Protein of un 81.5 3 6.6E-05 28.3 4.1 33 219-259 22-55 (56)
276 PRK10421 DNA-binding transcrip 81.3 3.7 8E-05 36.4 5.8 36 233-268 22-58 (253)
277 TIGR02812 fadR_gamma fatty aci 81.2 4.2 9.1E-05 35.5 6.0 36 233-268 26-62 (235)
278 COG2996 Predicted RNA-bindinin 81.1 4.6 0.0001 36.5 6.1 61 214-276 223-284 (287)
279 COG1497 Predicted transcriptio 81.1 3.8 8.3E-05 36.4 5.5 57 217-279 11-67 (260)
280 COG1846 MarR Transcriptional r 80.9 4.9 0.00011 30.5 5.7 55 214-274 20-74 (126)
281 PRK15481 transcriptional regul 80.7 3.9 8.4E-05 39.1 6.1 34 235-268 27-61 (431)
282 PHA00738 putative HTH transcri 80.7 4.5 9.7E-05 31.5 5.2 49 215-269 11-59 (108)
283 PRK11050 manganese transport r 80.5 4.2 9.2E-05 33.4 5.4 35 235-269 50-84 (152)
284 PF04492 Phage_rep_O: Bacterio 80.1 5.6 0.00012 30.5 5.6 56 213-268 29-86 (100)
285 PRK13159 cytochrome c-type bio 79.9 11 0.00024 31.2 7.6 64 71-144 52-119 (155)
286 COG4189 Predicted transcriptio 79.9 3 6.4E-05 37.0 4.4 48 215-268 22-69 (308)
287 COG0587 DnaE DNA polymerase II 79.7 2.4 5.3E-05 45.7 4.6 63 72-136 978-1046(1139)
288 PRK04172 pheS phenylalanyl-tRN 79.5 3.8 8.3E-05 40.3 5.7 51 213-269 3-53 (489)
289 TIGR00635 ruvB Holliday juncti 79.4 2.9 6.3E-05 37.9 4.6 54 213-270 235-290 (305)
290 COG0173 AspS Aspartyl-tRNA syn 79.0 5.8 0.00012 39.4 6.6 63 71-133 16-79 (585)
291 PF01399 PCI: PCI domain; Int 78.9 2.5 5.4E-05 31.5 3.3 39 234-272 58-96 (105)
292 COG1802 GntR Transcriptional r 78.7 4.6 0.0001 35.2 5.5 52 217-268 17-71 (230)
293 PF04967 HTH_10: HTH DNA bindi 78.6 8.3 0.00018 26.0 5.4 45 214-258 1-45 (53)
294 PRK11920 rirA iron-responsive 78.5 5.5 0.00012 32.8 5.5 35 235-269 23-57 (153)
295 PF05584 Sulfolobus_pRN: Sulfo 78.4 7.6 0.00016 28.0 5.4 46 217-269 6-51 (72)
296 COG4190 Predicted transcriptio 78.4 6.2 0.00013 31.8 5.4 51 213-269 61-111 (144)
297 PF00538 Linker_histone: linke 78.3 7.6 0.00017 28.0 5.6 51 216-269 4-64 (77)
298 PF08221 HTH_9: RNA polymerase 78.2 5 0.00011 27.9 4.4 47 216-268 13-59 (62)
299 COG1339 Transcriptional regula 78.0 3.6 7.8E-05 35.5 4.3 50 220-270 4-53 (214)
300 PRK11753 DNA-binding transcrip 78.0 3.4 7.3E-05 35.0 4.3 41 237-279 169-209 (211)
301 PRK10430 DNA-binding transcrip 77.9 5.7 0.00012 34.5 5.8 54 214-271 159-213 (239)
302 PRK10857 DNA-binding transcrip 77.6 6.6 0.00014 32.8 5.8 36 234-269 23-58 (164)
303 COG2442 Uncharacterized conser 76.9 5.3 0.00011 29.3 4.4 35 220-262 35-70 (79)
304 PHA03103 double-strand RNA-bin 76.8 6.9 0.00015 33.4 5.7 38 234-272 25-62 (183)
305 PRK15201 fimbriae regulatory p 76.7 7 0.00015 33.3 5.6 42 213-262 133-174 (198)
306 PF08280 HTH_Mga: M protein tr 76.6 4.4 9.6E-05 27.7 3.7 39 218-262 7-45 (59)
307 PRK06341 single-stranded DNA-b 76.5 13 0.00027 31.3 7.1 62 70-132 5-86 (166)
308 PF04157 EAP30: EAP30/Vps36 fa 76.4 5.2 0.00011 35.0 5.1 50 214-267 172-221 (223)
309 smart00526 H15 Domain in histo 76.0 11 0.00024 26.1 5.8 51 216-269 6-64 (66)
310 smart00529 HTH_DTXR Helix-turn 75.9 5.2 0.00011 29.6 4.3 39 239-278 2-40 (96)
311 PRK15411 rcsA colanic acid cap 75.9 5.8 0.00013 34.2 5.2 42 213-262 137-178 (207)
312 PF13518 HTH_28: Helix-turn-he 75.2 9.6 0.00021 24.6 5.0 30 236-265 12-41 (52)
313 COG2332 CcmE Cytochrome c-type 74.8 21 0.00045 29.4 7.7 56 71-132 52-111 (153)
314 PRK09334 30S ribosomal protein 74.3 5.3 0.00011 29.8 3.8 34 234-267 39-72 (86)
315 PF08461 HTH_12: Ribonuclease 74.2 6.6 0.00014 27.6 4.2 40 220-264 2-46 (66)
316 PF05158 RNA_pol_Rpc34: RNA po 73.9 2.7 5.9E-05 39.2 2.8 51 213-266 6-57 (327)
317 TIGR01714 phage_rep_org_N phag 73.8 7.2 0.00016 30.9 4.7 42 236-278 51-92 (119)
318 PHA02591 hypothetical protein; 73.3 2.8 6.1E-05 30.6 2.1 25 234-258 57-81 (83)
319 KOG1885 Lysyl-tRNA synthetase 73.1 12 0.00027 36.4 6.9 75 72-146 106-186 (560)
320 PRK13719 conjugal transfer tra 72.7 9.3 0.0002 33.5 5.6 43 212-262 142-184 (217)
321 PF01638 HxlR: HxlR-like helix 72.6 4.3 9.3E-05 30.1 3.1 49 218-273 7-56 (90)
322 PF13384 HTH_23: Homeodomain-l 72.4 3.9 8.5E-05 26.5 2.6 29 236-264 17-45 (50)
323 PRK10840 transcriptional regul 72.3 8.3 0.00018 32.8 5.3 42 213-262 150-191 (216)
324 PF11994 DUF3489: Protein of u 72.2 14 0.00031 26.6 5.5 47 216-268 10-58 (72)
325 COG1321 TroR Mn-dependent tran 72.1 8.6 0.00019 31.8 5.1 34 235-268 23-56 (154)
326 COG4901 Ribosomal protein S25 71.6 8 0.00017 29.7 4.3 50 217-268 42-91 (107)
327 PRK11475 DNA-binding transcrip 71.6 9 0.00019 33.1 5.3 42 213-262 134-175 (207)
328 PRK06474 hypothetical protein; 71.3 11 0.00023 31.9 5.6 50 215-269 10-60 (178)
329 TIGR00721 tfx DNA-binding prot 71.2 10 0.00022 30.8 5.2 37 213-257 6-42 (137)
330 PRK04217 hypothetical protein; 71.1 9.9 0.00021 29.7 4.9 40 212-258 41-80 (110)
331 PF09397 Ftsk_gamma: Ftsk gamm 70.8 14 0.00031 26.0 5.2 48 215-268 5-52 (65)
332 COG2197 CitB Response regulato 70.4 9.1 0.0002 33.1 5.1 42 213-262 148-189 (211)
333 PRK04214 rbn ribonuclease BN/u 70.2 8 0.00017 37.1 5.1 55 221-278 297-351 (412)
334 PRK15320 transcriptional activ 70.1 11 0.00023 32.9 5.3 43 212-262 163-205 (251)
335 PRK15466 carboxysome structura 69.8 6.4 0.00014 32.9 3.7 46 218-268 111-156 (166)
336 PRK00082 hrcA heat-inducible t 69.4 9.8 0.00021 35.6 5.4 50 214-269 4-60 (339)
337 PF08222 HTH_CodY: CodY helix- 69.1 10 0.00022 26.1 3.9 31 238-268 6-36 (61)
338 PF07381 DUF1495: Winged helix 69.0 9.2 0.0002 28.8 4.1 48 215-266 8-65 (90)
339 COG3432 Predicted transcriptio 68.2 4.1 9E-05 31.0 2.1 56 219-279 18-76 (95)
340 PRK05638 threonine synthase; V 68.1 10 0.00023 36.6 5.5 48 214-268 369-418 (442)
341 cd00131 PAX Paired Box domain 67.5 13 0.00028 29.7 5.0 44 216-267 21-64 (128)
342 PF09202 Rio2_N: Rio2, N-termi 67.4 18 0.00038 26.7 5.3 54 214-269 4-57 (82)
343 TIGR03882 cyclo_dehyd_2 bacter 67.1 14 0.00031 31.6 5.6 33 236-268 42-76 (193)
344 PRK10100 DNA-binding transcrip 67.0 12 0.00027 32.4 5.3 42 213-262 155-196 (216)
345 PF14493 HTH_40: Helix-turn-he 67.0 9.2 0.0002 28.4 3.9 31 235-265 12-42 (91)
346 PRK10402 DNA-binding transcrip 66.5 15 0.00032 31.8 5.7 52 216-268 150-201 (226)
347 TIGR03697 NtcA_cyano global ni 66.4 8.7 0.00019 31.9 4.1 32 237-268 144-175 (193)
348 PRK13918 CRP/FNR family transc 66.2 8.5 0.00019 32.3 4.0 40 236-277 149-188 (202)
349 PF10557 Cullin_Nedd8: Cullin 65.7 12 0.00026 26.3 4.0 47 216-268 8-62 (68)
350 PRK15431 ferrous iron transpor 65.5 12 0.00026 27.4 4.1 44 220-269 6-49 (78)
351 PRK00080 ruvB Holliday junctio 65.5 8.8 0.00019 35.4 4.2 55 212-269 255-310 (328)
352 smart00531 TFIIE Transcription 65.1 8.8 0.00019 31.3 3.7 31 236-266 15-45 (147)
353 KOG2411 Aspartyl-tRNA syntheta 65.0 19 0.00041 35.5 6.3 63 71-133 48-111 (628)
354 cd06171 Sigma70_r4 Sigma70, re 64.9 23 0.00051 22.1 5.2 41 214-261 11-51 (55)
355 PF03965 Penicillinase_R: Peni 64.7 10 0.00022 29.4 3.9 52 214-271 1-56 (115)
356 smart00351 PAX Paired Box doma 64.7 16 0.00035 28.9 5.1 44 216-267 21-64 (125)
357 PF07848 PaaX: PaaX-like prote 64.6 24 0.00052 25.2 5.4 39 234-272 18-59 (70)
358 cd00073 H15 linker histone 1 a 64.5 29 0.00063 25.7 6.1 53 215-270 5-65 (88)
359 PF12324 HTH_15: Helix-turn-he 64.4 19 0.00041 26.3 4.8 42 215-262 23-64 (77)
360 PF09104 BRCA-2_OB3: BRCA2, ol 64.4 33 0.00072 28.1 6.8 58 69-127 17-76 (143)
361 COG1959 Predicted transcriptio 64.3 19 0.00041 29.5 5.6 46 220-268 12-57 (150)
362 TIGR00644 recJ single-stranded 64.1 66 0.0014 32.0 10.4 70 60-141 463-534 (539)
363 TIGR02952 Sig70_famx2 RNA poly 63.9 16 0.00035 29.6 5.2 41 213-260 122-162 (170)
364 TIGR02063 RNase_R ribonuclease 63.8 18 0.00039 37.3 6.5 54 217-275 3-60 (709)
365 PF09681 Phage_rep_org_N: N-te 63.8 15 0.00033 29.1 4.7 41 236-277 53-93 (121)
366 KOG3341 RNA polymerase II tran 63.7 15 0.00032 32.2 4.9 51 212-268 172-222 (249)
367 PF13542 HTH_Tnp_ISL3: Helix-t 63.3 19 0.00042 23.3 4.5 38 215-260 14-51 (52)
368 TIGR02716 C20_methyl_CrtF C-20 63.1 12 0.00027 34.0 4.7 53 217-278 11-63 (306)
369 PF07638 Sigma70_ECF: ECF sigm 63.1 14 0.0003 31.1 4.7 40 214-260 136-175 (185)
370 PRK00118 putative DNA-binding 63.0 18 0.00038 28.0 4.8 40 213-259 17-56 (104)
371 PRK09047 RNA polymerase factor 62.7 13 0.00027 30.0 4.3 39 213-258 106-144 (161)
372 PF10668 Phage_terminase: Phag 62.7 14 0.00031 25.6 3.8 35 216-255 7-41 (60)
373 PRK09642 RNA polymerase sigma 62.7 12 0.00026 30.3 4.1 39 213-258 106-144 (160)
374 TIGR00331 hrcA heat shock gene 62.5 16 0.00034 34.2 5.4 46 218-269 4-56 (337)
375 PRK09483 response regulator; P 62.4 18 0.00038 30.1 5.3 41 213-261 148-188 (217)
376 PRK11642 exoribonuclease R; Pr 62.1 20 0.00042 37.7 6.4 53 218-276 21-77 (813)
377 TIGR00594 polc DNA-directed DN 62.0 16 0.00035 39.4 5.9 35 71-105 982-1022(1022)
378 TIGR02999 Sig-70_X6 RNA polyme 62.0 13 0.00028 30.7 4.3 40 213-259 134-173 (183)
379 TIGR02937 sigma70-ECF RNA poly 61.8 18 0.00039 28.0 5.0 42 213-261 110-151 (158)
380 PRK12547 RNA polymerase sigma 61.8 15 0.00033 29.9 4.6 41 213-260 112-152 (164)
381 PRK05472 redox-sensing transcr 61.7 15 0.00033 31.7 4.8 46 216-265 16-61 (213)
382 PF09756 DDRGK: DDRGK domain; 61.7 7.9 0.00017 33.2 2.9 50 217-272 100-149 (188)
383 COG5625 Predicted transcriptio 61.6 12 0.00026 28.7 3.6 52 215-271 20-84 (113)
384 PF03297 Ribosomal_S25: S25 ri 61.4 9.5 0.00021 29.6 3.0 35 234-268 57-91 (105)
385 COG2390 DeoR Transcriptional r 61.4 16 0.00035 34.0 5.1 42 235-276 25-66 (321)
386 COG4565 CitB Response regulato 61.3 22 0.00048 31.2 5.6 53 212-269 153-206 (224)
387 PRK06759 RNA polymerase factor 60.4 18 0.00039 28.9 4.8 40 213-259 106-145 (154)
388 PRK03975 tfx putative transcri 60.4 23 0.0005 28.9 5.3 37 213-257 6-42 (141)
389 PRK12529 RNA polymerase sigma 60.3 13 0.00029 30.8 4.1 39 213-258 127-165 (178)
390 PRK12539 RNA polymerase sigma 59.7 14 0.00031 30.8 4.1 40 213-259 131-170 (184)
391 PF13567 DUF4131: Domain of un 59.3 43 0.00092 26.6 6.9 60 71-135 76-146 (176)
392 PRK10736 hypothetical protein; 59.2 28 0.00062 33.1 6.4 41 235-276 320-360 (374)
393 TIGR02698 CopY_TcrY copper tra 59.1 30 0.00065 27.6 5.7 49 214-268 2-54 (130)
394 PF11662 DUF3263: Protein of u 59.0 33 0.00071 25.1 5.3 49 213-264 2-50 (77)
395 PF04297 UPF0122: Putative hel 58.7 22 0.00049 27.3 4.7 40 213-259 17-56 (101)
396 PRK11924 RNA polymerase sigma 58.7 17 0.00036 29.6 4.4 40 213-259 125-164 (179)
397 PRK09391 fixK transcriptional 58.7 14 0.00031 32.1 4.1 32 236-267 179-210 (230)
398 KOG3818 DNA polymerase epsilon 57.9 34 0.00073 33.3 6.6 78 67-155 173-250 (525)
399 PRK12523 RNA polymerase sigma 57.7 17 0.00036 29.9 4.2 40 213-259 119-158 (172)
400 COG5071 RPN5 26S proteasome re 57.7 16 0.00034 34.0 4.2 54 213-271 331-388 (439)
401 PF04218 CENP-B_N: CENP-B N-te 57.6 4.1 8.9E-05 27.3 0.4 24 235-258 21-44 (53)
402 TIGR03209 P21_Cbot clostridium 57.4 9.3 0.0002 30.3 2.5 36 213-255 107-142 (142)
403 PRK00135 scpB segregation and 57.1 13 0.00029 31.8 3.6 30 234-263 18-47 (188)
404 PRK12520 RNA polymerase sigma 57.0 17 0.00037 30.4 4.2 39 213-258 131-169 (191)
405 PF10078 DUF2316: Uncharacteri 56.9 13 0.00027 28.0 2.9 24 235-258 22-45 (89)
406 cd04438 DEP_dishevelled DEP (D 56.8 27 0.00058 25.8 4.7 39 238-276 35-75 (84)
407 PRK09645 RNA polymerase sigma 56.4 18 0.00038 29.6 4.2 38 213-257 118-155 (173)
408 TIGR02985 Sig70_bacteroi1 RNA 56.4 24 0.00053 27.9 4.9 41 213-260 113-153 (161)
409 COG3398 Uncharacterized protei 56.4 23 0.00051 31.2 4.9 49 214-268 99-147 (240)
410 PRK12546 RNA polymerase sigma 56.4 19 0.00042 30.3 4.5 40 213-259 113-152 (188)
411 PRK15369 two component system 56.4 25 0.00053 28.5 5.1 42 213-262 149-190 (211)
412 PRK12516 RNA polymerase sigma 56.0 21 0.00046 30.0 4.6 38 213-257 116-153 (187)
413 COG2771 CsgD DNA-binding HTH d 56.0 41 0.00089 22.3 5.4 41 213-261 4-44 (65)
414 PRK13919 putative RNA polymera 55.6 21 0.00045 29.6 4.5 39 213-258 135-173 (186)
415 PRK09652 RNA polymerase sigma 55.6 22 0.00047 29.0 4.6 40 213-259 128-167 (182)
416 PLN02532 asparagine-tRNA synth 55.5 52 0.0011 33.6 7.9 64 82-148 129-199 (633)
417 PF04057 Rep-A_N: Replication 55.4 90 0.002 23.7 8.5 79 68-147 18-99 (101)
418 PRK10360 DNA-binding transcrip 55.2 29 0.00063 28.2 5.3 42 213-262 137-178 (196)
419 PRK14136 recX recombination re 55.1 26 0.00055 32.4 5.2 52 213-275 160-214 (309)
420 TIGR02948 SigW_bacill RNA poly 54.7 20 0.00044 29.5 4.3 41 213-260 136-176 (187)
421 PRK12536 RNA polymerase sigma 54.4 20 0.00042 29.8 4.1 40 213-259 129-168 (181)
422 PF07223 DUF1421: Protein of u 54.4 16 0.00035 34.5 3.9 33 233-265 315-350 (358)
423 PRK09637 RNA polymerase sigma 54.4 23 0.0005 29.5 4.6 39 213-258 106-144 (181)
424 PRK09649 RNA polymerase sigma 54.3 22 0.00047 29.8 4.4 39 213-258 130-168 (185)
425 PRK09415 RNA polymerase factor 54.2 21 0.00045 29.6 4.3 40 213-259 127-166 (179)
426 PRK13239 alkylmercury lyase; P 54.2 24 0.00051 30.7 4.6 41 215-261 21-61 (206)
427 PF04760 IF2_N: Translation in 54.1 8.1 0.00018 25.7 1.4 38 236-273 3-42 (54)
428 PRK12542 RNA polymerase sigma 54.1 20 0.00042 29.9 4.1 39 213-258 122-160 (185)
429 PRK12545 RNA polymerase sigma 53.7 21 0.00045 30.3 4.3 39 213-258 139-177 (201)
430 COG2186 FadR Transcriptional r 53.5 38 0.00083 29.9 6.0 51 217-268 15-66 (241)
431 PRK09647 RNA polymerase sigma 53.5 23 0.0005 30.3 4.5 40 213-259 138-177 (203)
432 TIGR02989 Sig-70_gvs1 RNA poly 53.3 29 0.00062 27.8 4.9 41 213-260 111-151 (159)
433 PRK12531 RNA polymerase sigma 53.0 20 0.00043 30.2 4.0 40 213-259 141-180 (194)
434 PF09860 DUF2087: Uncharacteri 52.8 34 0.00074 24.5 4.6 57 217-276 12-69 (71)
435 PRK12512 RNA polymerase sigma 52.8 24 0.00052 29.2 4.4 40 213-259 131-170 (184)
436 PRK11161 fumarate/nitrate redu 52.7 19 0.00042 31.0 4.0 34 236-269 184-217 (235)
437 PF12793 SgrR_N: Sugar transpo 52.7 22 0.00048 27.9 3.9 34 234-267 17-50 (115)
438 smart00843 Ftsk_gamma This dom 52.7 38 0.00081 23.7 4.6 48 215-268 4-51 (63)
439 PF13551 HTH_29: Winged helix- 52.5 31 0.00067 25.8 4.7 30 235-264 10-40 (112)
440 PRK12524 RNA polymerase sigma 52.5 26 0.00056 29.5 4.6 40 213-259 136-175 (196)
441 PRK07037 extracytoplasmic-func 52.4 24 0.00051 28.5 4.3 39 213-258 109-147 (163)
442 PRK12543 RNA polymerase sigma 52.4 25 0.00054 29.1 4.5 39 213-258 117-155 (179)
443 PF12658 Ten1: Telomere cappin 52.2 1.2E+02 0.0026 24.1 11.0 78 71-150 26-114 (124)
444 TIGR02983 SigE-fam_strep RNA p 52.0 28 0.00062 28.0 4.7 41 213-260 110-150 (162)
445 PRK12527 RNA polymerase sigma 51.8 27 0.00059 28.1 4.5 39 213-258 105-143 (159)
446 PRK12528 RNA polymerase sigma 51.8 25 0.00053 28.4 4.3 40 213-259 113-152 (161)
447 PRK12511 RNA polymerase sigma 51.7 23 0.0005 29.7 4.2 38 213-257 111-148 (182)
448 PRK10188 DNA-binding transcrip 51.5 33 0.00071 30.3 5.3 41 213-261 179-219 (240)
449 PF04539 Sigma70_r3: Sigma-70 51.4 21 0.00046 25.2 3.4 25 237-261 21-45 (78)
450 PRK09651 RNA polymerase sigma 51.3 25 0.00055 28.9 4.3 40 213-259 119-158 (172)
451 PRK12533 RNA polymerase sigma 51.0 22 0.00048 30.8 4.0 40 213-259 134-173 (216)
452 PRK05660 HemN family oxidoredu 50.9 24 0.00052 33.4 4.6 43 235-279 320-362 (378)
453 KOG1767 40S ribosomal protein 50.9 15 0.00032 28.4 2.4 33 235-267 59-91 (110)
454 PRK11923 algU RNA polymerase s 50.9 27 0.00059 29.1 4.5 40 213-259 138-177 (193)
455 TIGR02844 spore_III_D sporulat 50.8 29 0.00062 25.5 4.0 35 217-258 7-41 (80)
456 PF04079 DUF387: Putative tran 50.8 18 0.0004 30.1 3.3 27 235-262 12-38 (159)
457 PRK12530 RNA polymerase sigma 50.7 24 0.00052 29.6 4.1 39 213-258 134-172 (189)
458 PRK06811 RNA polymerase factor 50.5 26 0.00057 29.3 4.3 40 213-259 131-170 (189)
459 PRK12540 RNA polymerase sigma 50.5 28 0.00061 29.1 4.5 39 213-258 111-149 (182)
460 TIGR02959 SigZ RNA polymerase 50.1 30 0.00066 28.4 4.6 38 213-257 100-137 (170)
461 PF15490 Ten1_2: Telomere-capp 50.0 1.3E+02 0.0027 23.8 11.8 78 71-156 22-105 (118)
462 cd04448 DEP_PIKfyve DEP (Dishe 50.0 37 0.0008 24.8 4.5 38 239-276 35-73 (81)
463 PRK12514 RNA polymerase sigma 49.9 27 0.00058 28.8 4.3 40 213-259 129-168 (179)
464 PRK10651 transcriptional regul 49.8 38 0.00081 27.8 5.2 42 213-262 155-196 (216)
465 PRK09643 RNA polymerase sigma 49.8 29 0.00063 29.1 4.5 39 213-258 134-172 (192)
466 PRK12532 RNA polymerase sigma 49.7 26 0.00057 29.3 4.3 39 213-258 136-174 (195)
467 PRK12522 RNA polymerase sigma 49.6 29 0.00062 28.5 4.4 38 214-258 120-157 (173)
468 COG0629 Ssb Single-stranded DN 49.6 86 0.0019 26.0 7.3 35 97-133 50-84 (167)
469 PRK09646 RNA polymerase sigma 49.5 26 0.00056 29.5 4.1 40 213-259 142-181 (194)
470 PRK12526 RNA polymerase sigma 49.3 29 0.00064 29.5 4.5 40 213-259 153-192 (206)
471 PRK12525 RNA polymerase sigma 49.3 26 0.00056 28.6 4.1 39 213-258 118-156 (168)
472 PRK12541 RNA polymerase sigma 49.2 27 0.00058 28.2 4.1 40 213-259 112-151 (161)
473 PRK15418 transcriptional regul 49.2 21 0.00046 33.1 3.8 41 235-275 28-68 (318)
474 PRK12534 RNA polymerase sigma 49.0 25 0.00055 29.1 4.0 41 213-260 137-177 (187)
475 PRK08898 coproporphyrinogen II 49.0 32 0.00069 32.8 5.1 53 219-279 327-379 (394)
476 PRK09648 RNA polymerase sigma 48.8 28 0.0006 29.0 4.2 39 213-258 139-177 (189)
477 PF01853 MOZ_SAS: MOZ/SAS fami 48.5 19 0.00041 30.9 3.1 41 217-260 134-174 (188)
478 PRK12538 RNA polymerase sigma 48.3 27 0.00059 30.6 4.2 39 213-258 171-209 (233)
479 TIGR02392 rpoH_proteo alternat 48.2 40 0.00087 30.2 5.4 44 213-261 218-265 (270)
480 cd04449 DEP_DEPDC5-like DEP (D 48.2 44 0.00094 24.4 4.7 39 238-276 35-75 (83)
481 PRK08295 RNA polymerase factor 47.9 33 0.00072 28.9 4.6 40 213-260 155-194 (208)
482 TIGR03020 EpsA transcriptional 47.8 42 0.00092 30.0 5.4 42 213-262 190-231 (247)
483 PRK09958 DNA-binding transcrip 47.4 44 0.00095 27.4 5.2 42 213-262 143-184 (204)
484 PRK12513 RNA polymerase sigma 47.0 20 0.00043 30.1 3.0 24 235-258 154-177 (194)
485 TIGR02943 Sig70_famx1 RNA poly 46.8 30 0.00065 29.0 4.1 40 213-259 131-170 (188)
486 cd05694 S1_Rrp5_repeat_hs2_sc2 46.7 84 0.0018 22.3 5.9 48 74-128 7-54 (74)
487 TIGR02939 RpoE_Sigma70 RNA pol 46.2 29 0.00064 28.6 4.0 25 235-259 153-177 (190)
488 PRK09639 RNA polymerase sigma 46.0 43 0.00093 27.0 4.9 39 213-259 112-150 (166)
489 TIGR02954 Sig70_famx3 RNA poly 46.0 35 0.00077 27.7 4.4 40 213-259 119-158 (169)
490 PF12651 RHH_3: Ribbon-helix-h 45.8 37 0.00081 21.7 3.5 23 240-262 18-41 (44)
491 PRK12515 RNA polymerase sigma 45.6 35 0.00077 28.4 4.4 39 213-258 131-169 (189)
492 PRK05602 RNA polymerase sigma 45.4 32 0.00069 28.5 4.1 39 213-258 128-166 (186)
493 PHA03068 DNA-binding phosphopr 45.3 56 0.0012 29.3 5.5 49 121-170 73-127 (270)
494 PF06971 Put_DNA-bind_N: Putat 45.2 34 0.00073 22.8 3.3 34 220-257 16-49 (50)
495 PF11948 DUF3465: Protein of u 45.1 1.6E+02 0.0035 23.7 8.3 62 73-138 39-105 (131)
496 COG3398 Uncharacterized protei 45.0 47 0.001 29.3 5.0 48 216-269 174-221 (240)
497 PF00292 PAX: 'Paired box' dom 44.8 41 0.0009 26.9 4.3 44 215-266 20-63 (125)
498 PRK12537 RNA polymerase sigma 44.8 31 0.00068 28.6 3.9 40 213-259 133-172 (182)
499 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 44.7 24 0.00052 23.5 2.5 42 214-262 5-46 (50)
500 TIGR02960 SigX5 RNA polymerase 44.3 33 0.00071 31.3 4.3 24 235-258 157-180 (324)
No 1
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.9e-49 Score=330.32 Aligned_cols=244 Identities=24% Similarity=0.451 Sum_probs=190.9
Q ss_pred cCccccCCCCCCCCCCCCCCcccCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEE
Q 023576 13 FSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFT 92 (280)
Q Consensus 13 ~~ggGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~ 92 (280)
..+|||.+.+++.+ ...+....+.++|+|||||||+++.+.. .++.|.+++.++.+|++||+||++....++..|+
T Consensus 13 it~g~~~~~~s~p~---~drseg~~~vntLrpvTIKQIl~~~qd~-~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~ 88 (258)
T COG5235 13 ITRGQIFGTGSPPP---MDRSEGGYIVNTLRPVTIKQILSCDQDE-TDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFV 88 (258)
T ss_pred eeccceecCCCCCC---CCccccCceeeeeeeeEHHHhhcccccc-cCCceeecceEEeeEEEEEEEEeeeecccceEEE
Confidence 45889986655421 2233445678999999999999999976 6789999999999999999999999999999999
Q ss_pred EEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcCCCC
Q 023576 93 LDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQV 172 (280)
Q Consensus 93 LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~~~~ 172 (280)
|+||||.|+|++|...+.+.+.+....++.||||+|.||.|+||+.|.+..|++|+|+||+++|+||||+.||.+++...
T Consensus 89 iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~~I~d~NeV~~HfLe~I~~Hl~~t~~~~ 168 (258)
T COG5235 89 IEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQ 168 (258)
T ss_pred EecCCceEEEEecCCCchHHHhccccccccEEEEecceeeeCCeeEEehhheeeccccchhHHHHHHHHHHHHHHHHHhc
Confidence 99999999999998777666777888999999999999999999999999999999999999999999999999988654
Q ss_pred CCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCchhHHHHHHhcCCC-CCCCCCccCHHHHHHHhCCCHH
Q 023576 173 QGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPS-SSERERGVHVNELSEQLKIPQK 251 (280)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Vl~~i~~~~-~~~~e~Gv~v~~I~~~l~~~~~ 251 (280)
. |..+. .+.++.+.+..+.+. + +.+...||+.++.++|... ......+|++..|++.++.+
T Consensus 169 ~------ple~~--~~n~GqSlf~k~dNd-----t---Ssgss~lq~~~~~c~~~~~~~~~~~~~V~I~~lsqs~~~d-- 230 (258)
T COG5235 169 R------PLEEE--VKNDGQSLFAKLDND-----T---SSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQSYSED-- 230 (258)
T ss_pred c------hhhhh--cCCCccceeeeccCc-----c---ccccccccHHHHHHHHHhcCCCCcccceeehHhhhhcCcc--
Confidence 3 21110 001111101112211 0 1234679999999988752 22334677777777777755
Q ss_pred HHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 252 KIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 252 ~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
+.+..++.|..+|+||.|+|++|||++
T Consensus 231 et~v~~d~L~~~g~iYpTvD~n~fkt~ 257 (258)
T COG5235 231 ETRVNIDVLLRDGHIYPTVDGNEFKTT 257 (258)
T ss_pred ceeeeeeeehhCceEEeeecCcceeec
Confidence 444459999999999999999999986
No 2
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=100.00 E-value=3.2e-48 Score=343.26 Aligned_cols=263 Identities=35% Similarity=0.561 Sum_probs=202.7
Q ss_pred CCCCcCCCCCCcCccccCCCCCCCCCCCCCCcccCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEE
Q 023576 2 FSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYN 81 (280)
Q Consensus 2 ~~~~~~~~~~~~~ggGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~ 81 (280)
+.+..|....++.+|++++++.......+....+.++..+++|+||+||.++....+ ..|.+++.++.+|.+||+|++
T Consensus 2 f~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~v~~~ti~qi~s~~~~~~--~~~~i~~~~v~~v~~VGivr~ 79 (265)
T KOG3108|consen 2 FSSYTFEDYNGQSSGGQGPGQFTTSRPPSSQSITNRRVQGVVPLTIKQILSSTQDDD--SVFKIGGVEVSAVSIVGIVRN 79 (265)
T ss_pred cccccceecccccccccCCCcccccCCccccccccceeccccccceeeecccccccc--ccEEEccEEEEEEEEEEEEEe
Confidence 344455555566777776555332211222233456889999999999999988652 299999999999999999999
Q ss_pred eeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHH
Q 023576 82 KEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECI 161 (280)
Q Consensus 82 ~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i 161 (280)
+++..+.+.|+|+|+||.|+|++|...+.+..+...+++|.||||.|.|+.|+|+++|.+++|+||.|+||+++|+|||+
T Consensus 80 ~e~~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~pv~D~Nevt~h~LE~i 159 (265)
T KOG3108|consen 80 IEKSATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRPVEDFNEVTTHFLEVI 159 (265)
T ss_pred ceecCcceEEEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecccCCCCceeEEEEeeeeeecCCceeEEeehhh
Confidence 99999999999999999999999998776666678999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCchhHHHHHHhcCCCCCCCCCccCHHH
Q 023576 162 YFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNE 241 (280)
Q Consensus 162 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~ 241 (280)
++|+.+++.+.. +..... +.+.+..+ .+.-... ++++ ..+..|..+++.|++.+++..+ .+|+|+.+
T Consensus 160 ~~hl~~s~~~~~---~sa~~~---~~~~~~~s-~~~~~~~--~~~s-~~~~~l~~i~~~v~~~~~~~~h---~eGv~~~~ 226 (265)
T KOG3108|consen 160 NAHLSLSKSPSQ---SSAGND---PVGFPGMS-EAADSGY--SQES-GQSSQLERIQQRVLQAIESGLH---IEGVHIKE 226 (265)
T ss_pred HHHHHhhhcccc---cccccC---CCCCcccc-ccccccc--Cccc-ccchhhhHHHHHHHHhhhcCcc---cccccHHH
Confidence 999999987654 111000 00000000 0000000 0111 1112378899999999999753 47999999
Q ss_pred HHHHhC-CCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 242 LSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 242 I~~~l~-~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
|+++|+ .....+++++++|++|||||+|+||+|||+|+
T Consensus 227 i~~~l~~~~~~~~~~~~~~l~~eG~iy~TvD~~hFks~~ 265 (265)
T KOG3108|consen 227 IAAQLREPSVSELREAVDFLLNEGHIYSTVDEEHFKSTN 265 (265)
T ss_pred HHHHhcccchhhHHHHHHHHhcCCeEEEeechhheeecC
Confidence 999997 66778999999999999999999999999985
No 3
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=99.93 E-value=4.6e-25 Score=168.64 Aligned_cols=94 Identities=55% Similarity=0.986 Sum_probs=86.2
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCc
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNF 150 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~ 150 (280)
+|++||+|++++..++++.|+|+|+||+|+|++|.+.+.+ ....+.+++|+||+|.|+++.|++++||+++.++|++|+
T Consensus 1 ~v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~~v~d~ 80 (95)
T cd04478 1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDF 80 (95)
T ss_pred CEEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEEEeCCc
Confidence 4899999999999999999999999999999999876531 123678999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHH
Q 023576 151 DEVTCHYIECIYFHL 165 (280)
Q Consensus 151 Nei~~H~Le~i~~~l 165 (280)
||+++|+|||+++||
T Consensus 81 ne~~~h~l~~~~~~l 95 (95)
T cd04478 81 NEVTYHLLEVIYVHL 95 (95)
T ss_pred cHHHHhHhhhhhhhC
Confidence 999999999999985
No 4
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=99.74 E-value=2.1e-17 Score=125.59 Aligned_cols=73 Identities=27% Similarity=0.578 Sum_probs=64.5
Q ss_pred EEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh------------------hhhccCCCCCEEEEEEEEeeeCC
Q 023576 74 TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT------------------REMEAIQDGMYVRLIGNLKSFQG 135 (280)
Q Consensus 74 ~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~------------------~~~~~~~~G~yVrV~G~l~~f~~ 135 (280)
.|||+|+++++.++|+.|+|||+||+|+|++|.+...+. ...+.+++|+||||.|+|+.|++
T Consensus 1 ~ivG~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg 80 (92)
T cd04483 1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRG 80 (92)
T ss_pred CeEEEEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCC
Confidence 389999999999999999999999999999998754221 34567999999999999999999
Q ss_pred eeEEEEEEEee
Q 023576 136 KKQIVAFSVRP 146 (280)
Q Consensus 136 ~~~i~~~~ir~ 146 (280)
++||++..|..
T Consensus 81 ~~ql~i~~~~~ 91 (92)
T cd04483 81 EREINASVVYK 91 (92)
T ss_pred eeEEEEEEEEe
Confidence 99999998864
No 5
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=99.73 E-value=4e-18 Score=132.06 Aligned_cols=59 Identities=37% Similarity=0.682 Sum_probs=50.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
++++++++||++|++. +..++|||+++|+++|++++++|++||++|++||+||+|||||
T Consensus 44 ~~~~~~~~Vl~~i~~~--~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 102 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQ--PNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDDD 102 (102)
T ss_dssp -S-HHHHHHHHHHHC------TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSSTT
T ss_pred CCCHHHHHHHHHHHhc--CCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCCC
Confidence 6899999999999992 3578899999999999999999999999999999999999996
No 6
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=99.56 E-value=9.4e-14 Score=123.94 Aligned_cols=126 Identities=19% Similarity=0.313 Sum_probs=95.4
Q ss_pred cee-eeeHHHHhhcccC----------CCCCCCeEECCEEEeeEEEEEEEEEeeec----CCeeEEEEEcCCc--eEEEE
Q 023576 41 GLV-PVTVKMISEASHS----------GDDKSNFMINGLEITNVTLVGLVYNKEER----ASDVNFTLDDGTG--RVVCK 103 (280)
Q Consensus 41 ~~~-PvtIkqi~~a~~~----------~~~~~~~~i~g~~i~~V~iVG~V~~~~~~----~t~~~~~LdDgTG--~I~~~ 103 (280)
.+. ||+|+||+..... ....+.|.+.++||..|+|||.|+.+... ..++.|+|||+|| .|+|+
T Consensus 26 ~~~~PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~ 105 (256)
T PF10451_consen 26 KVTVPLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECK 105 (256)
T ss_dssp SEE-E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEE
T ss_pred cccCcEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEE
Confidence 344 9999999982211 01256889999999999999999999865 7899999999999 89999
Q ss_pred EecccccC-hhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcC
Q 023576 104 RWASEVFD-TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK 169 (280)
Q Consensus 104 ~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~ 169 (280)
.|.+.... .-....+ .|+.|+|.|.++ ++.++|.+..|..+.+++++..||.+++..+-.|.+
T Consensus 106 ~~~~~~~~~~l~~~~~-~G~~V~VkG~vs--r~~~ql~ve~i~~~~~l~~Ei~fW~~~~~~R~~L~~ 169 (256)
T PF10451_consen 106 CSKSSYLSMGLPINDL-IGKVVEVKGTVS--RNERQLDVERIELVRDLNAEIEFWKERMRFRKELSK 169 (256)
T ss_dssp EEHHHHHCCCHHCTT--TT-EEEEEEEEE--SSSEEEEEEEEEEETSCCHHHHHHHHHHHHHHHCCC
T ss_pred EEcccccccCCCccCC-CCcEEEEEEEEc--cCcEEEEEEEEEccCChHHHHHHHHHHHHHHHHcCC
Confidence 99763211 1112344 999999999999 899999999999999999999999999998755543
No 7
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=99.23 E-value=1.2e-10 Score=84.01 Aligned_cols=73 Identities=29% Similarity=0.430 Sum_probs=63.5
Q ss_pred EEEEEEEEEe-eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe-eEEEEEEEeeC
Q 023576 73 VTLVGLVYNK-EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK-KQIVAFSVRPV 147 (280)
Q Consensus 73 V~iVG~V~~~-~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~-~~i~~~~ir~v 147 (280)
|+|.|+|.++ .....++.|+|+|+||.|+|++|.+.. ......+++|+.|+|.|+++.+++. .+|.+.+++++
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~--~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~~~i~~l 75 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEY--ERFREKLKEGDIVRVRGKVKRYNGGELELIVPKIEIL 75 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHH--HHHHHTS-TTSEEEEEEEEEEETTSSEEEEEEEEEEE
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHh--hHHhhcCCCCeEEEEEEEEEEECCccEEEEECEEEEC
Confidence 7899999999 778899999999999999999998321 2346789999999999999999987 99999999864
No 8
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=98.87 E-value=3.5e-08 Score=72.44 Aligned_cols=76 Identities=25% Similarity=0.390 Sum_probs=61.7
Q ss_pred EEEEEEEee--ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchH
Q 023576 75 LVGLVYNKE--ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDE 152 (280)
Q Consensus 75 iVG~V~~~~--~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Ne 152 (280)
+|-.++... .+..++.++|+|.||.|+|++|.+.. .....+++|.+|.|.|+++.|++..++.+..|.+++++|+
T Consensus 5 ~v~~~~~~~tk~g~~~~~~~l~D~tg~i~~~~f~~~~---~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~l~~~~~ 81 (83)
T cd04492 5 LIKSKELRTAKNGKPYLALTLQDKTGEIEAKLWDASE---EDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTEEDG 81 (83)
T ss_pred EEEEeeeecccCCCcEEEEEEEcCCCeEEEEEcCCCh---hhHhhCCCCCEEEEEEEEEEeCCceeEEEEEEEECCcccC
Confidence 444444432 23368999999999999999997543 2246799999999999999999999999999999999886
Q ss_pred H
Q 023576 153 V 153 (280)
Q Consensus 153 i 153 (280)
.
T Consensus 82 ~ 82 (83)
T cd04492 82 V 82 (83)
T ss_pred C
Confidence 4
No 9
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=98.85 E-value=1.9e-08 Score=92.66 Aligned_cols=79 Identities=16% Similarity=0.311 Sum_probs=63.8
Q ss_pred EEEeeEEEEEEEEEe--eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576 68 LEITNVTLVGLVYNK--EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR 145 (280)
Q Consensus 68 ~~i~~V~iVG~V~~~--~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir 145 (280)
..|..+.+|-.+.-. +.+.+|+.++|.|.||.|+|++|...+ +....+++|++|+|.|++..|+++.|+++..|+
T Consensus 12 ~~v~~~~lv~~~~~~~~knG~~yl~l~l~D~tG~I~ak~W~~~~---~~~~~~~~g~vv~v~G~v~~y~g~~Ql~i~~i~ 88 (314)
T PRK13480 12 EQVDHFLLIKSATKGVASNGKPFLTLILQDKSGDIEAKLWDVSP---EDEATYVPETIVHVKGDIINYRGRKQLKVNQIR 88 (314)
T ss_pred CEeeEEEEEEEceeeecCCCCeEEEEEEEcCCcEEEEEeCCCCh---hhHhhcCCCCEEEEEEEEEEECCcceEEEEEeE
Confidence 445666655555432 234579999999999999999998754 236779999999999999999999999999999
Q ss_pred eCCC
Q 023576 146 PVTN 149 (280)
Q Consensus 146 ~v~d 149 (280)
+++.
T Consensus 89 ~~~~ 92 (314)
T PRK13480 89 LATE 92 (314)
T ss_pred ECCC
Confidence 8754
No 10
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.68 E-value=1.3e-07 Score=79.35 Aligned_cols=126 Identities=22% Similarity=0.332 Sum_probs=93.4
Q ss_pred eeeeHHHHhhcccCCC--C---CCCeE--ECCEEEeeEEEEEEEEEeee---cCCeeEEEEEcCCceEEEEEeccccc--
Q 023576 43 VPVTVKMISEASHSGD--D---KSNFM--INGLEITNVTLVGLVYNKEE---RASDVNFTLDDGTGRVVCKRWASEVF-- 110 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~--~---~~~~~--i~g~~i~~V~iVG~V~~~~~---~~t~~~~~LdDgTG~I~~~~w~~~~~-- 110 (280)
+-|+++.|.++..+.. + ...+. -=|..+++|.|||.+.+... +.++..+++.|.||.+.+ |...-.
T Consensus 11 ~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~V--yag~yqPE 88 (196)
T COG3390 11 YRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYV--YAGQYQPE 88 (196)
T ss_pred HHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEE--EcCCCChH
Confidence 3477889988766541 1 12333 46899999999999999764 457999999999999888 322111
Q ss_pred ChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee----CCCchHHHHHHHHHHHHHHHhcCC
Q 023576 111 DTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP----VTNFDEVTCHYIECIYFHLQNSKS 170 (280)
Q Consensus 111 ~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~----v~d~Nei~~H~Le~i~~~l~~~~~ 170 (280)
+....+.++.+++|.|.|++++|+..--...++||| ..|++-..+|-+++.+..+..-+.
T Consensus 89 a~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siRpE~vs~vde~~r~~Wv~eta~~tl~Ri~a 152 (196)
T COG3390 89 AKAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKVDEEARDLWVLETAEQTLERIKA 152 (196)
T ss_pred HHHHHHhccCCceEEEecccceeecCCCceEEEechhhhhhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 123457789999999999999999876666667766 345677789999999988776554
No 11
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=98.61 E-value=3.6e-07 Score=64.44 Aligned_cols=71 Identities=30% Similarity=0.446 Sum_probs=58.6
Q ss_pred EEEEEEEEeeecC---CeeEEEEEcCC-ceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 74 TLVGLVYNKEERA---SDVNFTLDDGT-GRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 74 ~iVG~V~~~~~~~---t~~~~~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
+++|.|.++.... .+..++|+|+| |.|+|.+|.+... .....+++|++|.|.|+++.+++++++.+..++|
T Consensus 1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~--~~~~~~~~g~~v~v~g~v~~~~~~~~l~~~~~~~ 75 (75)
T cd03524 1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAE--ELENLLKEGQVVYIKGKVKKFRGRLQLIVESIEL 75 (75)
T ss_pred CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHH--HHHhhccCCCEEEEEEEEEecCCeEEEEeeeecC
Confidence 3789999987654 68999999999 9999999986532 1235689999999999999999999999876653
No 12
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=98.54 E-value=3.2e-07 Score=66.88 Aligned_cols=72 Identities=15% Similarity=0.223 Sum_probs=57.0
Q ss_pred EEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCC
Q 023576 75 LVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVT 148 (280)
Q Consensus 75 iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~ 148 (280)
++|.|.++.. ...++.++|+|+||.++|++|.+.-. .....+++|.+|.|.|+++.|++..++.+..+.++.
T Consensus 2 i~g~v~~~~~~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~--~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~~~ 78 (84)
T cd04485 2 VAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYE--KYRDLLKEDALLLVEGKVERRDGGLRLIAERIEDLE 78 (84)
T ss_pred EEEEEEEeEEEEcCCCCEEEEEEEEeCCCeEEEEECHHHHH--HHHHHhcCCCEEEEEEEEEecCCceEEEeeccccHH
Confidence 5677766532 22479999999999999999964311 124578999999999999999999999998887775
No 13
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.51 E-value=1.1e-06 Score=70.86 Aligned_cols=84 Identities=19% Similarity=0.268 Sum_probs=65.2
Q ss_pred eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeee-------c--CCeeEEEEEcCCceEEEEEecccccChhh
Q 023576 44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEE-------R--ASDVNFTLDDGTGRVVCKRWASEVFDTRE 114 (280)
Q Consensus 44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~-------~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~ 114 (280)
++.|++|... ...|.+++.|.++.. . ..+..++|.|.||+|.+++|.+..
T Consensus 4 ~~kI~dL~~g----------------~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a----- 62 (129)
T PRK06461 4 ITKIKDLKPG----------------MERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQA----- 62 (129)
T ss_pred ceEHHHcCCC----------------CCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCcc-----
Confidence 5678888532 134566667765421 1 238889999999999999998642
Q ss_pred hccCCCCCEEEEE-EEEeeeCCeeEEEEE---EEeeCCC
Q 023576 115 MEAIQDGMYVRLI-GNLKSFQGKKQIVAF---SVRPVTN 149 (280)
Q Consensus 115 ~~~~~~G~yVrV~-G~l~~f~~~~~i~~~---~ir~v~d 149 (280)
..|++|+.|+|. |.++.|+++.+|++. .|+++.+
T Consensus 63 -~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 63 -GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred -ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 468999999999 888999999999998 6888875
No 14
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=98.45 E-value=3.6e-06 Score=61.32 Aligned_cols=73 Identities=25% Similarity=0.434 Sum_probs=59.5
Q ss_pred EEEEEEEEEeee-cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC--CeeEEEEEEEeeC
Q 023576 73 VTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVRPV 147 (280)
Q Consensus 73 V~iVG~V~~~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir~v 147 (280)
+++.|.|.+++. +.....++|+|.||.|+|.+|.+... .....+++|+.|.|.|++..+. ++.+|.+..|.|.
T Consensus 2 ~~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~--~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i~~~ 77 (78)
T cd04489 2 VWVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNAR--RLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEIEPA 77 (78)
T ss_pred EEEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhh--hCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEEC
Confidence 578899988764 33478999999999999999986431 1236789999999999999874 7899999998774
No 15
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=98.30 E-value=3.4e-06 Score=62.33 Aligned_cols=53 Identities=17% Similarity=0.330 Sum_probs=47.3
Q ss_pred CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEEEE
Q 023576 86 ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVAFS 143 (280)
Q Consensus 86 ~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~~~ 143 (280)
..+..++|.|.||+|.+++|.+.+ ...+++|+.|++. |.++.|++..+|.+..
T Consensus 22 ~~~~~~~l~D~TG~i~~~~W~~~~-----~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 22 GKVQSGLVGDETGTIRFTLWDEKA-----ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred eEEEEEEEECCCCEEEEEEECchh-----cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 468999999999999999998753 4679999999999 9999999999998764
No 16
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=98.25 E-value=1.2e-05 Score=60.83 Aligned_cols=73 Identities=18% Similarity=0.275 Sum_probs=59.4
Q ss_pred EEEEEEEEeee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576 74 TLVGLVYNKEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN 149 (280)
Q Consensus 74 ~iVG~V~~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d 149 (280)
+|.|.|.+... .+..+-|+|.|.++.|.|.+|............+++||-|.|.|.++.|. ||.+.+++++.-
T Consensus 2 ~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~y~---ql~ve~l~~~gl 76 (91)
T cd04482 2 RVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT---TLNLEKLRVIRL 76 (91)
T ss_pred EEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEecCC---EEEEEEEEECCC
Confidence 67899988765 45679999999999999999976521112346789999999999999998 899999998754
No 17
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=98.20 E-value=1.9e-05 Score=57.32 Aligned_cols=72 Identities=25% Similarity=0.314 Sum_probs=59.5
Q ss_pred EEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 73 VTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 73 V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
|++-|.|.+....+..+-|+|.|.++.|.|.+|...... ....+++|+-|.|.|++...+++-|+.+..|+.
T Consensus 1 v~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~~--~~~~l~~Gd~V~v~G~v~~~~G~~ql~v~~i~~ 72 (73)
T cd04487 1 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVR--AYPEVEVGDIVRVTGEVEPRDGQLQIEVESLEV 72 (73)
T ss_pred CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccC--CcCCCCCCCEEEEEEEEecCCeEEEEEEeeEEE
Confidence 467898887655556799999999999999999765421 245789999999999999988899999998875
No 18
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=98.13 E-value=3.3e-05 Score=59.36 Aligned_cols=75 Identities=24% Similarity=0.385 Sum_probs=64.3
Q ss_pred EeeEEEEEEEEEeee-cCCeeEEEEEcCCceEEEEEecccccChhhh-ccCCCCCEEEEEEEEeeeC--CeeEEEEEEEe
Q 023576 70 ITNVTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREM-EAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVR 145 (280)
Q Consensus 70 i~~V~iVG~V~~~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~-~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir 145 (280)
+..|+|.|.|.++.. ....+=|+|-|+...|.|.+|..... .-. ..+++|+-|.|.|++..|. |+.++.+..|+
T Consensus 21 ~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~--~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~i~ 98 (99)
T PF13742_consen 21 LPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRAR--RIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVEDID 98 (99)
T ss_pred cCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHh--hCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEEeE
Confidence 589999999999987 67788899999999999999986542 112 4689999999999999995 78999999998
Q ss_pred e
Q 023576 146 P 146 (280)
Q Consensus 146 ~ 146 (280)
|
T Consensus 99 P 99 (99)
T PF13742_consen 99 P 99 (99)
T ss_pred C
Confidence 7
No 19
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=98.04 E-value=5.7e-05 Score=53.70 Aligned_cols=63 Identities=30% Similarity=0.400 Sum_probs=49.1
Q ss_pred EEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576 75 LVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV 140 (280)
Q Consensus 75 iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~ 140 (280)
+.|.|.++.. ...++.++|.|+||.|+|+.|.... .....+++|+.+.|.|+++.|++..++.
T Consensus 2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~---~~~~~~~~G~~~~v~Gkv~~~~~~~qi~ 68 (75)
T cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQP---YLKKQLPPGTRVRVSGKVKRFRGGLQIV 68 (75)
T ss_pred EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCH---HHHhcCCCCCEEEEEEEEeecCCeeEEe
Confidence 4566665432 2358999999999999999996321 2346799999999999999999887775
No 20
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=98.02 E-value=9.1e-05 Score=54.96 Aligned_cols=73 Identities=23% Similarity=0.447 Sum_probs=56.6
Q ss_pred eEEEEEEEEEeeecC-----CeeEEEEEcCCceEEEEEecccccChhhhccCC-CCCEEEEEEEEe--eeCCeeEEEEEE
Q 023576 72 NVTLVGLVYNKEERA-----SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ-DGMYVRLIGNLK--SFQGKKQIVAFS 143 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~-----t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~G~yVrV~G~l~--~f~~~~~i~~~~ 143 (280)
.|.|-|.|-.++.+. .-++|.|.|.|.+|.|+.|.. + +......++ +|++|+|.|++. .|.....+.+..
T Consensus 1 ~v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~-~-~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~~i~~ 78 (82)
T cd04484 1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLR-K-DEKDKEELKSKGDWVRVRGKVQYDTFSKELVLMIND 78 (82)
T ss_pred CEEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEecc-C-ChhHHhhcccCCCEEEEEEEEEEccCCCceEEEeee
Confidence 367889997775422 356899999999999999985 2 223456789 999999999987 577888888877
Q ss_pred Eee
Q 023576 144 VRP 146 (280)
Q Consensus 144 ir~ 146 (280)
|.+
T Consensus 79 i~~ 81 (82)
T cd04484 79 IEE 81 (82)
T ss_pred EEE
Confidence 765
No 21
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.73 E-value=0.00015 Score=70.63 Aligned_cols=78 Identities=24% Similarity=0.312 Sum_probs=68.9
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCc
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNF 150 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~ 150 (280)
..|.|.|.|..+...+.-..|+|.|+||.|+|--|....- ...+.+++|++|+|+|.++.-.++.||-+..+.+++-.
T Consensus 214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv--RAyP~IevGdiV~ViG~V~~r~g~lQiE~~~me~L~G~ 291 (715)
T COG1107 214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV--RAYPEIEVGDIVEVIGEVTRRDGRLQIEIEAMEKLTGD 291 (715)
T ss_pred ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc--ccCCCCCCCceEEEEEEEeecCCcEEEeehhhHHhhCc
Confidence 6899999999999888889999999999999998875431 23578999999999999999999999999999888763
No 22
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=97.62 E-value=0.00096 Score=49.74 Aligned_cols=76 Identities=17% Similarity=0.143 Sum_probs=54.8
Q ss_pred eEEEEEEEEEeee-cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC-------CeeEEEEE
Q 023576 72 NVTLVGLVYNKEE-RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ-------GKKQIVAF 142 (280)
Q Consensus 72 ~V~iVG~V~~~~~-~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~-------~~~~i~~~ 142 (280)
.|+|.|+|.+++. .....-+.|.|+|| .|.|.. ......-.....+..|+.|.|.|.+..-. +...|.+.
T Consensus 1 ~V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~-~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~ 79 (86)
T cd04321 1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVS-TAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVD 79 (86)
T ss_pred CEEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEE-CCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEE
Confidence 3789999999987 55666669999999 588754 32211112235689999999999998743 55678887
Q ss_pred EEeeCC
Q 023576 143 SVRPVT 148 (280)
Q Consensus 143 ~ir~v~ 148 (280)
.+..+.
T Consensus 80 ~i~il~ 85 (86)
T cd04321 80 DIQTLN 85 (86)
T ss_pred EEEEec
Confidence 776653
No 23
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=97.55 E-value=0.00044 Score=54.67 Aligned_cols=83 Identities=23% Similarity=0.207 Sum_probs=62.4
Q ss_pred eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEE
Q 023576 45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYV 124 (280)
Q Consensus 45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yV 124 (280)
..||||..+.+.- ..+..|...|.++...+......+.+-|.||+|.+-+|.+. ...|++||.|
T Consensus 5 i~ikdi~P~~kN~----------~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~------~~~~~PGDIi 68 (134)
T KOG3416|consen 5 IFIKDIKPGLKNI----------NVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEE------GCLIQPGDII 68 (134)
T ss_pred hhHhhcChhhhcc----------eEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCc------CcccCCccEE
Confidence 4588887775532 22344555666666666668999999999999999999854 3679999999
Q ss_pred EEEEEEee-eCCeeEEEEEE
Q 023576 125 RLIGNLKS-FQGKKQIVAFS 143 (280)
Q Consensus 125 rV~G~l~~-f~~~~~i~~~~ 143 (280)
|..|...+ |++.+.|.+-+
T Consensus 69 rLt~Gy~Si~qg~LtL~~GK 88 (134)
T KOG3416|consen 69 RLTGGYASIFQGCLTLYVGK 88 (134)
T ss_pred EecccchhhhcCceEEEecC
Confidence 99988875 67877776543
No 24
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=97.54 E-value=0.0029 Score=48.98 Aligned_cols=83 Identities=20% Similarity=0.201 Sum_probs=56.7
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM 122 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~ 122 (280)
...|++|++++. ++ ..|.|-|.|+..-..+ .|...|.||+|.+.+=.+. ..-..+.+++
T Consensus 21 ~~~TV~~a~~~~----Dd----------~~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~g~~vt~~~ 79 (103)
T PF04076_consen 21 TVTTVAQAKNAK----DD----------TPVTLEGNIVKQLGDD---KYLFRDATGEIEVEIDDDV----WRGQTVTPDD 79 (103)
T ss_dssp ----HHHHTTS-----SS----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEE--GGG----STT----TTS
T ss_pred CeEeHHHHhhCc----CC----------CeEEEEEEEEEEecCC---EEEEECCCCcEEEEEChhh----cCCcccCCCC
Confidence 447899998762 12 6889999998877666 6789999999998752221 1124578889
Q ss_pred EEEEEEEEeeeCCeeEEEEEEEee
Q 023576 123 YVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 123 yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
.|+|.|.+..--.+..|-+.+|++
T Consensus 80 ~Vri~GeVDk~~~~~~IdV~~I~K 103 (103)
T PF04076_consen 80 KVRISGEVDKDWNKTEIDVDRIEK 103 (103)
T ss_dssp EEEEEEEEEEETTEEEEEEEEEEE
T ss_pred EEEEEEEEeCCCCceEEEEEEEEC
Confidence 999999999766788899888864
No 25
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=97.51 E-value=0.0021 Score=47.56 Aligned_cols=76 Identities=17% Similarity=0.197 Sum_probs=55.0
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe------eEEEEEEEe
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK------KQIVAFSVR 145 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~------~~i~~~~ir 145 (280)
.|+|.|+|.+++......-+.|.|+||.|.|..-.+...+......+..|+.|.|.|.+..-... ..|.+..+.
T Consensus 1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~Ei~~~~i~ 80 (84)
T cd04323 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPRAKQAPGGYELQVDYLE 80 (84)
T ss_pred CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEECCcccCCCCCEEEEEEEEE
Confidence 47899999999887777777999999999986533321111234578999999999999975433 456666665
Q ss_pred eC
Q 023576 146 PV 147 (280)
Q Consensus 146 ~v 147 (280)
.+
T Consensus 81 vl 82 (84)
T cd04323 81 II 82 (84)
T ss_pred EE
Confidence 44
No 26
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=97.51 E-value=0.0015 Score=48.37 Aligned_cols=76 Identities=22% Similarity=0.281 Sum_probs=56.1
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeee------CCeeEEEEEEE
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSF------QGKKQIVAFSV 144 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f------~~~~~i~~~~i 144 (280)
.|+|.|+|.+++......-+.|.|+||.+.|..-.+...+ ......+..|++|.|.|.+..- .+...|.+..+
T Consensus 1 ~V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~i 80 (85)
T cd04100 1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEEL 80 (85)
T ss_pred CEEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeEE
Confidence 3789999999988777666799999999999764332211 1234679999999999999863 34466777766
Q ss_pred eeC
Q 023576 145 RPV 147 (280)
Q Consensus 145 r~v 147 (280)
+.+
T Consensus 81 ~il 83 (85)
T cd04100 81 EVL 83 (85)
T ss_pred EEE
Confidence 654
No 27
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=97.50 E-value=0.00063 Score=57.67 Aligned_cols=84 Identities=21% Similarity=0.334 Sum_probs=63.8
Q ss_pred CCEEEeeEEEEEEEEEeee--cCCeeEEEEEcCCceEEEEEecccccC---hhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576 66 NGLEITNVTLVGLVYNKEE--RASDVNFTLDDGTGRVVCKRWASEVFD---TREMEAIQDGMYVRLIGNLKSFQGKKQIV 140 (280)
Q Consensus 66 ~g~~i~~V~iVG~V~~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~G~yVrV~G~l~~f~~~~~i~ 140 (280)
+|.-+.-|.+=|.|.+.+. ...-..+.|+|+||.|++..+...+.. ..-++.+.+|++|.|.|+++.|+++.+|.
T Consensus 47 ~G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~yrG~~eVk 126 (204)
T COG4085 47 DGRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEYRGSSEVK 126 (204)
T ss_pred CceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccCcEEEEEEEEEEeCCCceee
Confidence 3455667888888888763 446778899999999999999765431 11234678999999999999999999998
Q ss_pred EEE---EeeCCC
Q 023576 141 AFS---VRPVTN 149 (280)
Q Consensus 141 ~~~---ir~v~d 149 (280)
+.. +||+.-
T Consensus 127 vnq~~d~~~l~k 138 (204)
T COG4085 127 VNQPNDSRPLPK 138 (204)
T ss_pred ccCccccccccc
Confidence 654 455544
No 28
>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=97.45 E-value=0.00027 Score=46.65 Aligned_cols=47 Identities=32% Similarity=0.572 Sum_probs=39.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
|+..+.+||++|.+. .+++..+|++.++++...|...|..|.++|.|
T Consensus 1 l~~~~~~Il~~l~~~------~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 1 LDETQRKILNYLREN------PRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp --HHHHHHHHHHHHC------TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHHHc------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 356788999999974 37999999999999999999999999999987
No 29
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=97.43 E-value=0.0017 Score=47.74 Aligned_cols=69 Identities=22% Similarity=0.278 Sum_probs=49.1
Q ss_pred EEEEEEEEEee--ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEE
Q 023576 73 VTLVGLVYNKE--ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSV 144 (280)
Q Consensus 73 V~iVG~V~~~~--~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~i 144 (280)
|.++|.|.+++ ..... .++|+|.||+++|.+|.+.-.--.....+.++..|-|.|++.. ++. .+.+..|
T Consensus 2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~-~~~-~l~~~~I 72 (79)
T cd04490 2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSK-DGG-LIFADEI 72 (79)
T ss_pred EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEec-CCC-EEEEEEe
Confidence 57888888775 22234 9999999999999999765320012357899999999999966 444 5555544
No 30
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=97.43 E-value=0.0014 Score=52.99 Aligned_cols=78 Identities=19% Similarity=0.265 Sum_probs=57.1
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee----------CCeeEEEE
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF----------QGKKQIVA 141 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i~~ 141 (280)
.|+|.|+|.+++......-+.|.|++|.+.|.+-.....+......+..|++|.|.|.+..- .+...|.+
T Consensus 16 ~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~ 95 (135)
T cd04317 16 EVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVA 95 (135)
T ss_pred EEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEE
Confidence 49999999999887766667999999999987643322111234579999999999998852 23466777
Q ss_pred EEEeeCCC
Q 023576 142 FSVRPVTN 149 (280)
Q Consensus 142 ~~ir~v~d 149 (280)
..+..+..
T Consensus 96 ~~i~vl~~ 103 (135)
T cd04317 96 SELEVLNK 103 (135)
T ss_pred eEEEEEEC
Confidence 77766654
No 31
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=97.34 E-value=0.007 Score=48.45 Aligned_cols=82 Identities=17% Similarity=0.202 Sum_probs=58.5
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM 122 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~ 122 (280)
...|++|++++. ++ ..|.|-|.|+..-..+ .|...|+||.|.+.+=.+. ..-..+.+++
T Consensus 44 ~~~tV~~a~~~~----Dd----------t~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~G~~v~p~d 102 (126)
T TIGR00156 44 KKMTVDFAKSMH----DG----------ASVTLRGNIISHIGDD---RYVFRDKSGEINVVIPAAV----WNGREVQPKD 102 (126)
T ss_pred ceEeHHHHhhCC----CC----------CEEEEEEEEEEEeCCc---eEEEECCCCCEEEEECHHH----cCCCcCCCCC
Confidence 368999998862 23 5788888888766554 6789999999888751110 1123578899
Q ss_pred EEEEEEEEeeeCCeeEEEEEEEe
Q 023576 123 YVRLIGNLKSFQGKKQIVAFSVR 145 (280)
Q Consensus 123 yVrV~G~l~~f~~~~~i~~~~ir 145 (280)
-|||.|.|..--....|-+.+|+
T Consensus 103 ~V~I~GeVDk~~~~~~IdV~~I~ 125 (126)
T TIGR00156 103 MVNISGSLDKKSAPAEVDVTHIQ 125 (126)
T ss_pred EEEEEEEECCCCCCeEEEEEEEE
Confidence 99999999854345677777765
No 32
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=97.32 E-value=0.001 Score=64.25 Aligned_cols=112 Identities=17% Similarity=0.216 Sum_probs=83.0
Q ss_pred eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576 44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM 122 (280)
Q Consensus 44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~ 122 (280)
|+++++|...-+.- ++.. +..|+|.|.|.+.... +..+=|+|-|.+..|.|.+|...... -...+++|+
T Consensus 5 ~~svsel~~~ik~~-------le~~-~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~--~~~~~~~G~ 74 (438)
T PRK00286 5 ILSVSELNRYVKSL-------LERD-LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARR--LKFKPEEGM 74 (438)
T ss_pred cCcHHHHHHHHHHH-------HHhh-CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhc--CCCCCCCCC
Confidence 57888887654321 1222 6899999999998765 45788999999999999999865321 124579999
Q ss_pred EEEEEEEEeeeC--CeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHh
Q 023576 123 YVRLIGNLKSFQ--GKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQN 167 (280)
Q Consensus 123 yVrV~G~l~~f~--~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~ 167 (280)
-|.|.|++..|. |.-||.|..|.|.-- -++ +--+|-+...|..
T Consensus 75 ~v~v~g~~~~y~~~g~~ql~v~~i~~~g~-G~l-~~~~~~lk~~L~~ 119 (438)
T PRK00286 75 KVLVRGKVSLYEPRGDYQLIVEEIEPAGI-GAL-AAAFEQLKEKLAA 119 (438)
T ss_pred EEEEEEEEEEECCCCCEEEEEEEeeeCCc-cHH-HHHHHHHHHHHHH
Confidence 999999999985 679999999998764 454 4445555555543
No 33
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=97.28 E-value=0.0035 Score=48.69 Aligned_cols=80 Identities=15% Similarity=0.148 Sum_probs=58.6
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEe
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVR 145 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir 145 (280)
..|+|.|+|.+++......-+.|.|+||.|.|.+-...... ......+..|+.|.|.|.+..-.. ...|.+..++
T Consensus 13 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~i~ 92 (108)
T cd04316 13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEEIE 92 (108)
T ss_pred CEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeEEE
Confidence 35899999999988777777799999999998664322111 123456899999999999887432 3667778777
Q ss_pred eCCCc
Q 023576 146 PVTNF 150 (280)
Q Consensus 146 ~v~d~ 150 (280)
.+...
T Consensus 93 il~~~ 97 (108)
T cd04316 93 VLSEA 97 (108)
T ss_pred EEeCC
Confidence 76654
No 34
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=97.28 E-value=0.00086 Score=71.64 Aligned_cols=76 Identities=20% Similarity=0.237 Sum_probs=61.8
Q ss_pred eEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 72 NVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 72 ~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
.|.++|.|.+++. +..+..++|+|.||.|++++|.+.-. .....+.+|..|.|.|++..++++.+|.+..|.+
T Consensus 979 ~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye--~~~~~L~~g~iV~V~GkVe~~~~~~qlii~~I~~ 1056 (1135)
T PRK05673 979 VVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALE--KYRDLLEEDRIVVVKGQVSFDDGGLRLTAREVMD 1056 (1135)
T ss_pred eEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeccc
Confidence 5788888888754 23578899999999999999975421 2235689999999999999988889999999988
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+.+
T Consensus 1057 L~~ 1059 (1135)
T PRK05673 1057 LEE 1059 (1135)
T ss_pred HHH
Confidence 854
No 35
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=97.26 E-value=0.0036 Score=59.91 Aligned_cols=95 Identities=23% Similarity=0.270 Sum_probs=77.0
Q ss_pred EeeEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee--CCeeEEEEEEEee
Q 023576 70 ITNVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--QGKKQIVAFSVRP 146 (280)
Q Consensus 70 i~~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~~~~~i~~~~ir~ 146 (280)
+.+|+|-|.|.+++... ..+=|+|-|....|.|.+|.....- -...+++|+.|-|.|+|..| +|+-||.+..|+|
T Consensus 23 ~~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~--l~f~p~eG~~V~v~G~is~Y~~rG~YQi~~~~~~p 100 (440)
T COG1570 23 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRR--LKFRPEEGMQVLVRGKISLYEPRGDYQIVAESMEP 100 (440)
T ss_pred CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccc--cCCCccCCCEEEEEEEEEEEcCCCceEEEEecCCc
Confidence 78999999999998544 3788999999999999999876421 12457999999999999999 5789999999998
Q ss_pred CCCchHHHHHHHHHHHHHHHhc
Q 023576 147 VTNFDEVTCHYIECIYFHLQNS 168 (280)
Q Consensus 147 v~d~Nei~~H~Le~i~~~l~~~ 168 (280)
.-. -. .+--+|.++..|...
T Consensus 101 ~G~-G~-L~~~~E~lK~kL~aE 120 (440)
T COG1570 101 AGL-GA-LYLAFEQLKAKLAAE 120 (440)
T ss_pred CCh-hH-HHHHHHHHHHHHHhC
Confidence 765 33 366778888887654
No 36
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=97.26 E-value=0.0035 Score=48.11 Aligned_cols=79 Identities=11% Similarity=0.010 Sum_probs=58.4
Q ss_pred eEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccc--cCh--hhhccCCCCCEEEEEEEEeeeC--------CeeE
Q 023576 72 NVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEV--FDT--REMEAIQDGMYVRLIGNLKSFQ--------GKKQ 138 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~--~~~--~~~~~~~~G~yVrV~G~l~~f~--------~~~~ 138 (280)
.|+|.|+|.+++... ...-+.|.|+||.|.|.+-.+.. .+. .....+..|+.|.|.|.+..-. +...
T Consensus 1 ~V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~E 80 (102)
T cd04320 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVE 80 (102)
T ss_pred CEEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEE
Confidence 378999999998876 66777999999999999864421 111 1235689999999999998631 3467
Q ss_pred EEEEEEeeCCCc
Q 023576 139 IVAFSVRPVTNF 150 (280)
Q Consensus 139 i~~~~ir~v~d~ 150 (280)
|.+..++.+...
T Consensus 81 l~~~~i~il~~~ 92 (102)
T cd04320 81 LHIEKIYVVSEA 92 (102)
T ss_pred EEEEEEEEEecC
Confidence 788887777543
No 37
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=97.21 E-value=0.0038 Score=48.44 Aligned_cols=77 Identities=13% Similarity=0.188 Sum_probs=54.2
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhcc-CCCCCEEEEEEEEeee-CCeeEEEEEEEeeC
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEA-IQDGMYVRLIGNLKSF-QGKKQIVAFSVRPV 147 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~-~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~v 147 (280)
.|+|.|+|.+++.....+-+.|-|+||.|.|.+-.....+. ..... +..|+.|.|.|.+..- .+...|.+..+.-+
T Consensus 1 ~v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~il 80 (108)
T cd04322 1 EVSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLL 80 (108)
T ss_pred CEEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEe
Confidence 47899999999988777778999999999997643321111 11234 8999999999998854 34455555555444
Q ss_pred C
Q 023576 148 T 148 (280)
Q Consensus 148 ~ 148 (280)
.
T Consensus 81 s 81 (108)
T cd04322 81 S 81 (108)
T ss_pred e
Confidence 3
No 38
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=97.18 E-value=0.0042 Score=47.82 Aligned_cols=79 Identities=24% Similarity=0.205 Sum_probs=56.6
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEeeC
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVRPV 147 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir~v 147 (280)
.|+|.|+|.+++......-+.|.|+||.+.|.+-.+...+ ......+..|+.|.|.|.+..-.. ...|.+..+..+
T Consensus 1 ~V~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl 80 (103)
T cd04319 1 KVTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEII 80 (103)
T ss_pred CEEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEE
Confidence 3789999999988777777799999999998764331111 122356899999999999986432 245677777666
Q ss_pred CCc
Q 023576 148 TNF 150 (280)
Q Consensus 148 ~d~ 150 (280)
...
T Consensus 81 ~~a 83 (103)
T cd04319 81 QNV 83 (103)
T ss_pred ecC
Confidence 554
No 39
>PRK10053 hypothetical protein; Provisional
Probab=97.10 E-value=0.024 Score=45.67 Aligned_cols=78 Identities=14% Similarity=0.251 Sum_probs=57.0
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEE----ecccccChhhhccC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKR----WASEVFDTREMEAI 118 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~----w~~~~~~~~~~~~~ 118 (280)
...|++|.+++. ++ ..|.|-|.|+..-..+ .|...|+||.|.+.+ |.. ..+
T Consensus 48 ~~~tV~~a~~~~----Dd----------~~V~L~G~Iv~~lg~d---~Y~F~D~tG~I~VeID~~~w~G--------~~v 102 (130)
T PRK10053 48 RKMTVEQAKTMH----DG----------ATVSLRGNLIDHKGDD---RYVFRDKSGEINVIIPAAVFDG--------REV 102 (130)
T ss_pred ceEEHHHhhcCc----CC----------CeEEEEEEEEEEeCCc---eEEEECCCCcEEEEeCHHHcCC--------CcC
Confidence 357999988752 23 5677788887765554 678999999988875 532 357
Q ss_pred CCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576 119 QDGMYVRLIGNLKSFQGKKQIVAFSVR 145 (280)
Q Consensus 119 ~~G~yVrV~G~l~~f~~~~~i~~~~ir 145 (280)
.+.+.|||.|.+..=.....|-+.+|+
T Consensus 103 ~p~~kV~I~GevDk~~~~~~IdV~~i~ 129 (130)
T PRK10053 103 QPDQMININGSLDKKSAPPVVRVTHLQ 129 (130)
T ss_pred CCCCEEEEEEEECCCCCCeEEEEEEEe
Confidence 889999999999864445677777765
No 40
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=97.09 E-value=0.0069 Score=58.80 Aligned_cols=94 Identities=18% Similarity=0.193 Sum_probs=67.8
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDG 121 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G 121 (280)
.+++|++|+..... | ..|+|.|+|.+++......-+.|.|+||.|.+.+-.+...+ -.....+..|
T Consensus 2 ~~~~~~~~~~~~~~----------~---~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~ 68 (450)
T PRK03932 2 MRVSIKDILKGKYV----------G---QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTG 68 (450)
T ss_pred CcEEHHHhcccccC----------C---CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCC
Confidence 46789998732111 1 67999999999988776667799999998877764433111 1234568999
Q ss_pred CEEEEEEEEeeeC---CeeEEEEEEEeeCCC
Q 023576 122 MYVRLIGNLKSFQ---GKKQIVAFSVRPVTN 149 (280)
Q Consensus 122 ~yVrV~G~l~~f~---~~~~i~~~~ir~v~d 149 (280)
+.|.|.|.+..-. +...|.+..++.+..
T Consensus 69 s~v~v~G~v~~~~~~~~~~el~~~~i~vl~~ 99 (450)
T PRK03932 69 SSVIVTGTVVESPRAGQGYELQATKIEVIGE 99 (450)
T ss_pred cEEEEEEEEEcCCCCCCCEEEEEEEEEEccC
Confidence 9999999999743 356788888877664
No 41
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.06 E-value=0.0023 Score=45.63 Aligned_cols=59 Identities=20% Similarity=0.394 Sum_probs=48.5
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC-ccccc
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE-FHYKF 277 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd-~hfk~ 277 (280)
...+++||.+|+..+ +.|++..+|++.++++...|+..|..|.++|.|...-+. -.|..
T Consensus 5 ~~~~~~IL~~L~~~g----~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i 64 (68)
T smart00550 5 DSLEEKILEFLENSG----DETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKL 64 (68)
T ss_pred hHHHHHHHHHHHHCC----CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEe
Confidence 357889999999852 337999999999999999999999999999999875433 34443
No 42
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=97.03 E-value=0.00048 Score=62.41 Aligned_cols=63 Identities=29% Similarity=0.481 Sum_probs=56.3
Q ss_pred ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576 84 ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN 149 (280)
Q Consensus 84 ~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d 149 (280)
....++.++++|.||.|+++.|+-... ....+..|..|++.|....|++.+|+.+..+|++++
T Consensus 18 ~~~~~l~l~~~d~~gei~~~~wd~~~~---~~~~~~~~~Vv~~~g~~~~~~~~~q~ki~~~r~~~~ 80 (287)
T COG3481 18 NGKDKLKLTLQDKTGEIEAKLWDALKN---DEEAFKPGMVVHVEGVKEVYRGRKQHKIIRIRLITD 80 (287)
T ss_pred cCChhheeeeccccceecccccccccc---cHhhhCcCceeccccceecccccchheeeecccccc
Confidence 355799999999999999999987653 256799999999999999999999999999999887
No 43
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=97.03 E-value=0.017 Score=42.39 Aligned_cols=74 Identities=18% Similarity=0.154 Sum_probs=54.9
Q ss_pred EEEEEEEEEeeecCCeeEEEEEcCCce--EEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEeeC
Q 023576 73 VTLVGLVYNKEERASDVNFTLDDGTGR--VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVRPV 147 (280)
Q Consensus 73 V~iVG~V~~~~~~~t~~~~~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir~v 147 (280)
|++.|+|.+++......-+.|.|+|+. |.|..-.+.. .......+..|+.|.|.|.+..-. +...|.+..+..+
T Consensus 2 v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~-~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~il 80 (82)
T cd04318 2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELT-NFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEKIEVL 80 (82)
T ss_pred EEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCccc-CHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEEEEEe
Confidence 789999999998777777789999994 9997643321 112346789999999999988753 3466777776654
No 44
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=97.00 E-value=0.0049 Score=59.56 Aligned_cols=94 Identities=21% Similarity=0.251 Sum_probs=73.4
Q ss_pred EeeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC--CeeEEEEEEEee
Q 023576 70 ITNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVRP 146 (280)
Q Consensus 70 i~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir~ 146 (280)
+..|+|.|.|.+.... +..+=|+|-|....|.|.+|...... -...+++|+-|.|.|++..|. |+-||.+..|.|
T Consensus 17 ~~~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~--l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~~i~~ 94 (432)
T TIGR00237 17 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNR--LKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQP 94 (432)
T ss_pred CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhC--CCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEecc
Confidence 5689999999998754 45788899999999999999875421 124579999999999999995 779999999999
Q ss_pred CCCchHHHHHHHHHHHHHHHh
Q 023576 147 VTNFDEVTCHYIECIYFHLQN 167 (280)
Q Consensus 147 v~d~Nei~~H~Le~i~~~l~~ 167 (280)
.- .-++ +--+|-+...|..
T Consensus 95 ~G-~G~l-~~~~~~lk~~L~~ 113 (432)
T TIGR00237 95 AG-EGLL-QLAYEQLKEKLAA 113 (432)
T ss_pred CC-hHHH-HHHHHHHHHHHHH
Confidence 75 4454 4455556666653
No 45
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=96.96 E-value=0.0041 Score=60.25 Aligned_cols=76 Identities=14% Similarity=0.181 Sum_probs=60.4
Q ss_pred eEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 72 NVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 72 ~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
.|+++|.|.+++.. .....++|+|.||.|++.+|.+.-. .....+.++..|-|.|++..-.+..+|.+..|.+
T Consensus 282 ~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~--~~~~~l~~~~~v~v~G~v~~~~~~~~liv~~i~~ 359 (449)
T PRK07373 282 KVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYE--RISELLQVDARLIIWGKVDRRDDQVQLIVEDAEP 359 (449)
T ss_pred EEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeEeec
Confidence 58899999887642 3467789999999999999976421 2235689999999999998755678899999888
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+.+
T Consensus 360 l~~ 362 (449)
T PRK07373 360 IEE 362 (449)
T ss_pred Hhh
Confidence 765
No 46
>PRK07211 replication factor A; Reviewed
Probab=96.94 E-value=0.0058 Score=59.47 Aligned_cols=76 Identities=28% Similarity=0.451 Sum_probs=60.3
Q ss_pred eeEEEEEEEEEeee----------cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEE
Q 023576 71 TNVTLVGLVYNKEE----------RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~----------~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i 139 (280)
..|.|.|+|.++.. ......++|-|.||+|.+.+|.+... ..+.+++|+.|+|. ++++.|++...|
T Consensus 172 ~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad---~~~~le~G~Vv~I~~a~Vre~~g~~EL 248 (485)
T PRK07211 172 SDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRAD---LAEELDAGESVEIVDGYVRERDGSLEL 248 (485)
T ss_pred CceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhh---hhccCCCCCEEEEEeeEEEecCCcEEE
Confidence 45788888876532 11357899999999999999987642 23569999999995 899999999999
Q ss_pred EEE---EEeeCCC
Q 023576 140 VAF---SVRPVTN 149 (280)
Q Consensus 140 ~~~---~ir~v~d 149 (280)
++. .|.++.+
T Consensus 249 sl~~~s~I~~~~d 261 (485)
T PRK07211 249 HVGDRGAVEEVDE 261 (485)
T ss_pred EECCCceEEECCc
Confidence 886 7888766
No 47
>PRK07218 replication factor A; Provisional
Probab=96.77 E-value=0.011 Score=56.91 Aligned_cols=72 Identities=22% Similarity=0.356 Sum_probs=57.9
Q ss_pred eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEEE
Q 023576 71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIVA 141 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~~ 141 (280)
..|.|.|+|.++..+ .......|.|.||+|....|.+. +.+.+|+.|+|.+ .++.|++..+|++
T Consensus 173 ~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~-------~~l~~Gd~v~I~na~v~e~~G~~elnv 245 (423)
T PRK07218 173 RGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPL-------PEIEIGASIRIEDAYVREFRGVPSVNV 245 (423)
T ss_pred CceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEeccc-------ccCCCCCEEEEeeeEEeccCCeEEEEE
Confidence 458888888877431 13556689999999999999863 3589999999998 7788999999999
Q ss_pred E---EEeeCCC
Q 023576 142 F---SVRPVTN 149 (280)
Q Consensus 142 ~---~ir~v~d 149 (280)
. .|.++++
T Consensus 246 ~~~t~I~~~d~ 256 (423)
T PRK07218 246 SEFTTVEALDR 256 (423)
T ss_pred CCceEEEECCC
Confidence 8 7777765
No 48
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=96.73 E-value=0.042 Score=43.50 Aligned_cols=81 Identities=16% Similarity=0.243 Sum_probs=59.2
Q ss_pred eeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEE----EecccccChhhhcc
Q 023576 42 LVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCK----RWASEVFDTREMEA 117 (280)
Q Consensus 42 ~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~----~w~~~~~~~~~~~~ 117 (280)
..-.|+++-+++. ++ ..|.|.|.|+..-... .|..-|+||+|.+- .|.. ..
T Consensus 43 ~~~~TV~~Ak~~~----Dd----------a~V~l~GnIv~qi~~D---~y~FrD~sGeI~VeIdd~~w~g--------~t 97 (128)
T COG3111 43 AKVTTVDQAKTLH----DD----------AWVSLEGNIVRQIGDD---RYVFRDASGEINVDIDDKVWNG--------QT 97 (128)
T ss_pred cceeEHHHhhccc----cC----------CeEEEEeeEEEeeCCc---eEEEEcCCccEEEEecccccCC--------cc
Confidence 3446788877662 22 5788999988866555 56899999987765 4543 35
Q ss_pred CCCCCEEEEEEEEeeeCCeeEEEEEEEeeC
Q 023576 118 IQDGMYVRLIGNLKSFQGKKQIVAFSVRPV 147 (280)
Q Consensus 118 ~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v 147 (280)
+.+.+.|++.|.+-.=-.+..|-+.+|+++
T Consensus 98 v~P~dkV~I~GevDk~~~~~eIdV~~I~k~ 127 (128)
T COG3111 98 VTPKDKVRIQGEVDKDWNSVEIDVKHIEKL 127 (128)
T ss_pred cCcccEEEEEeEEcCCCccceeEhhheEec
Confidence 788899999999987555677777777765
No 49
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=96.62 E-value=0.021 Score=55.51 Aligned_cols=94 Identities=16% Similarity=0.179 Sum_probs=63.9
Q ss_pred eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCC--ceEEEEEecccccC-hhhhccCCC
Q 023576 44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGT--GRVVCKRWASEVFD-TREMEAIQD 120 (280)
Q Consensus 44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgT--G~I~~~~w~~~~~~-~~~~~~~~~ 120 (280)
|.+|+.++.-.... .| ..|+|.|+|.+++.....+-+.|.|+| |.|.|.+-.....+ ......+..
T Consensus 1 ~~~~~~~~~~~~~~--------~g---~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~ 69 (453)
T TIGR00457 1 SAAIKDLLQQVYKF--------VG---DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTT 69 (453)
T ss_pred CccHHHHHhcchhc--------CC---CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCC
Confidence 56788888521111 12 569999999999976666667999999 99999764331111 123457999
Q ss_pred CCEEEEEEEEeee---CCeeEEEEEEEeeCC
Q 023576 121 GMYVRLIGNLKSF---QGKKQIVAFSVRPVT 148 (280)
Q Consensus 121 G~yVrV~G~l~~f---~~~~~i~~~~ir~v~ 148 (280)
|+.|.|.|.+..- .+...|.+..++.+.
T Consensus 70 gs~V~v~G~v~~~~~~~~~~El~~~~i~vl~ 100 (453)
T TIGR00457 70 GSSVSVTGKVVESPGKGQPVELQVKKIEVVG 100 (453)
T ss_pred CcEEEEEEEEEcCCCCCCCEEEEEeEEEEEe
Confidence 9999999998863 234566666665554
No 50
>PF13730 HTH_36: Helix-turn-helix domain
Probab=96.46 E-value=0.01 Score=40.03 Aligned_cols=54 Identities=20% Similarity=0.342 Sum_probs=42.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
+|++....|+-+|..........-.+.+.|++.++++.+.|+.+|.+|.+.|+|
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 467777888888877542222233489999999999999999999999999986
No 51
>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=96.41 E-value=0.0072 Score=41.51 Aligned_cols=46 Identities=35% Similarity=0.537 Sum_probs=40.7
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+..|+++|++. .-+++++|++.|+.++..||.-|..|.++|.|--+
T Consensus 2 ~~~Il~~l~~~------~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEK------GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHc------CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 46799999874 36899999999999999999999999999998654
No 52
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=96.39 E-value=0.002 Score=45.64 Aligned_cols=53 Identities=23% Similarity=0.456 Sum_probs=40.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCcc--CHHHHHHHhCCC-HHHHHHHHHHHHhCCeeee
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGV--HVNELSEQLKIP-QKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv--~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYs 268 (280)
.|++.|++||++|++-- .+.|+ ++.||++.|++. ...|...|..|.+.|+|=.
T Consensus 3 ~LT~rQ~~vL~~I~~~~---~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r 58 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYI---EENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRR 58 (65)
T ss_dssp ---HHHHHHHHHHHHHH---HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEE
T ss_pred CCCHHHHHHHHHHHHHH---HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccC
Confidence 47889999999998731 22344 889999999975 9999999999999999854
No 53
>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=96.39 E-value=0.0088 Score=41.13 Aligned_cols=57 Identities=25% Similarity=0.321 Sum_probs=47.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..+-.||.+|...+ +.++++.+|++.++++...|...|..|...|+|..+-|.+
T Consensus 2 glt~~q~~vL~~l~~~~----~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP----GEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp TSTHHHHHHHHHHHHST----TSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred ccCHHHHHHHHHHHHCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 46778888999998752 3369999999999999999999999999999999887753
No 54
>PRK07217 replication factor A; Reviewed
Probab=96.38 E-value=0.021 Score=52.38 Aligned_cols=74 Identities=18% Similarity=0.280 Sum_probs=56.5
Q ss_pred eeEEEEEEEEEeeecC-CeeEE--EEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE-eeeCCeeEEEEEEEee
Q 023576 71 TNVTLVGLVYNKEERA-SDVNF--TLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL-KSFQGKKQIVAFSVRP 146 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~-t~~~~--~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l-~~f~~~~~i~~~~ir~ 146 (280)
.+|.|.|+|..+-+.. ..+.+ .|.|.||+|....|.+.+ ...+++|+.|++.+-. +.|+|+.+|++.+-..
T Consensus 83 ~~VsV~aKVl~l~e~~~~si~qvGllgDETG~IkfT~W~~s~-----~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~ 157 (311)
T PRK07217 83 QWVDVTAKVVQLWEPSSDSIAQVGLLGDETGTIKFTKWAKSD-----LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTS 157 (311)
T ss_pred CcEEEEEEEEEecCCCCCceEEEEEEEcCCceEEEEEccCCC-----CCcccCCCEEEEEeEEEeeECCEEEEEeCCceE
Confidence 5789999999885422 22222 799999999999998743 4569999999998765 5799999999966444
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
|..
T Consensus 158 I~~ 160 (311)
T PRK07217 158 IEE 160 (311)
T ss_pred EEe
Confidence 443
No 55
>PRK14699 replication factor A; Provisional
Probab=96.36 E-value=0.013 Score=57.27 Aligned_cols=77 Identities=14% Similarity=0.122 Sum_probs=55.0
Q ss_pred eeEEEEEEEEEeee--------cC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576 71 TNVTLVGLVYNKEE--------RA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV 140 (280)
Q Consensus 71 ~~V~iVG~V~~~~~--------~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~ 140 (280)
..|+|.|+|.++.. .. ...++.|.|.||+|.+.+|.+.... -..-.+++||.|+|.|.++...+.+.|+
T Consensus 68 ~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~-~~~g~l~~GDvv~I~~~~r~~~~g~el~ 146 (484)
T PRK14699 68 GPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADL-IKAGKIKAGQTLQISGYAKQGYSGVEVN 146 (484)
T ss_pred ceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccch-hhhcCCCCCCEEEEcceeccCCCCceEE
Confidence 46778888877641 11 3556799999999999999865311 1112599999999999988766667888
Q ss_pred EE---EEeeCC
Q 023576 141 AF---SVRPVT 148 (280)
Q Consensus 141 ~~---~ir~v~ 148 (280)
+. .+++.+
T Consensus 147 ~~~~~~i~~~~ 157 (484)
T PRK14699 147 IGNNGVLTESE 157 (484)
T ss_pred eCCCceeeccC
Confidence 86 455543
No 56
>PRK07211 replication factor A; Reviewed
Probab=96.25 E-value=0.026 Score=55.05 Aligned_cols=77 Identities=19% Similarity=0.287 Sum_probs=58.4
Q ss_pred eeEEEEEEEEEeee------c-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEE
Q 023576 71 TNVTLVGLVYNKEE------R-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i 139 (280)
..|.|.|+|.++.. . ..-..+.|-|.||.|.+.+|.+... .....|++|+.++|.|+++...+...|
T Consensus 64 ~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d~ad--~~~~~Le~GdV~~I~~~~~~~ys~~El 141 (485)
T PRK07211 64 DEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAV--AAEEELEVGQVLRIKGRPKDGYNGLEV 141 (485)
T ss_pred CceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEechHhH--hhhcccCCCCEEEEeceEeccccceEE
Confidence 46778888876532 1 2567889999999999999987542 235679999999999999765555688
Q ss_pred EEEEEeeCCC
Q 023576 140 VAFSVRPVTN 149 (280)
Q Consensus 140 ~~~~ir~v~d 149 (280)
++..+.+..|
T Consensus 142 ~i~~ve~~~d 151 (485)
T PRK07211 142 SVDKVEPDPD 151 (485)
T ss_pred EEeeEEEccc
Confidence 8888777655
No 57
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.24 E-value=0.031 Score=60.30 Aligned_cols=78 Identities=18% Similarity=0.379 Sum_probs=62.5
Q ss_pred eeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe--eeCCeeEEEEEE
Q 023576 71 TNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK--SFQGKKQIVAFS 143 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~--~f~~~~~i~~~~ 143 (280)
..|.|.|.|-.++.+ ..-++|.|.|.|.+|.|+.|.....+.+....+++|++|+|.|.+. .|..+..+.+..
T Consensus 8 ~~~~~~g~i~~~~~~~~~~~~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~~g~~~~d~~~~~~~~~~~~ 87 (1213)
T TIGR01405 8 NRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRDLQMIIKD 87 (1213)
T ss_pred CeEEEEEEEEEEEeEeccCCCEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEEEEEEEEeccCCCCceEEEeee
Confidence 678899999777542 3456899999999999999986654444567899999999999988 567788888888
Q ss_pred EeeCC
Q 023576 144 VRPVT 148 (280)
Q Consensus 144 ir~v~ 148 (280)
|.++.
T Consensus 88 ~~~~~ 92 (1213)
T TIGR01405 88 IEEIP 92 (1213)
T ss_pred eeecC
Confidence 87664
No 58
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.19 E-value=0.0055 Score=42.94 Aligned_cols=46 Identities=20% Similarity=0.379 Sum_probs=39.4
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+++|+++|++. ..+++..|||+.|+++..++|.-|..|..+|.|-.
T Consensus 2 ke~Il~~i~~~-----~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 2 KEKILEYIKEQ-----NGPLKTREIADALGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp HHCHHHHHHHH-----TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred cHHHHHHHHHc-----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 46799999973 34799999999999999999999999999999975
No 59
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=96.17 E-value=0.035 Score=60.78 Aligned_cols=80 Identities=19% Similarity=0.401 Sum_probs=63.2
Q ss_pred eeEEEEEEEEEeeecC-----CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCeeEEEEEE
Q 023576 71 TNVTLVGLVYNKEERA-----SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKKQIVAFS 143 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~-----t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~~i~~~~ 143 (280)
..|.|-|.|-.++.+. .-++|.|.|.|.+|.|+.|.....+.+....++.|++|+|.|++.. |.....+.+..
T Consensus 237 ~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g~~~~d~~~~~~~~~~~~ 316 (1437)
T PRK00448 237 RRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQD 316 (1437)
T ss_pred CeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEEEEEEEEeccCCCCceEEEeee
Confidence 5788999997775432 3568999999999999999865544445678999999999999984 77778888888
Q ss_pred EeeCCCc
Q 023576 144 VRPVTNF 150 (280)
Q Consensus 144 ir~v~d~ 150 (280)
|.++..+
T Consensus 317 ~~~~~~~ 323 (1437)
T PRK00448 317 INEIKHP 323 (1437)
T ss_pred eeecCCc
Confidence 8776543
No 60
>PRK08402 replication factor A; Reviewed
Probab=96.16 E-value=0.027 Score=52.99 Aligned_cols=70 Identities=21% Similarity=0.324 Sum_probs=53.2
Q ss_pred eeEEEEEEEEEeee--------cC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeee-CCeeE
Q 023576 71 TNVTLVGLVYNKEE--------RA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSF-QGKKQ 138 (280)
Q Consensus 71 ~~V~iVG~V~~~~~--------~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f-~~~~~ 138 (280)
..|.++|+|.++.. .+ .-...+|.|.||.|.+.+|.+.... ....+.+|+.|+|. +.++.| +|..+
T Consensus 73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~~--~~~~l~~Gdvi~I~~a~V~e~~~G~~e 150 (355)
T PRK08402 73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAK--YYNKINVGDVIKVIDAQVRESLSGLPE 150 (355)
T ss_pred ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhh--hcccCCCCCEEEEECCEEeecCCCcEE
Confidence 56888999988742 11 1344799999999999999876421 13468999999986 888875 88889
Q ss_pred EEEE
Q 023576 139 IVAF 142 (280)
Q Consensus 139 i~~~ 142 (280)
|++.
T Consensus 151 Lsvg 154 (355)
T PRK08402 151 LHIN 154 (355)
T ss_pred EEEC
Confidence 9884
No 61
>PRK07218 replication factor A; Provisional
Probab=96.16 E-value=0.037 Score=53.23 Aligned_cols=72 Identities=22% Similarity=0.323 Sum_probs=56.7
Q ss_pred eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEE
Q 023576 71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVA 141 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~ 141 (280)
..|.|.|+|.++.++ .......|-|.||+|...+|.+. .+++|+.|+|. +.++.|+++.+|++
T Consensus 69 ~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~--------~l~~Gdvv~I~na~vre~~g~~el~i 140 (423)
T PRK07218 69 KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF--------GLSPGDTVTIGNAGVREWDGRPELNI 140 (423)
T ss_pred ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC--------CCCCCCEEEEeccEeeccCCceEEec
Confidence 567888888877421 24667799999999999999842 29999999999 57889999999986
Q ss_pred ---EEEeeCCCc
Q 023576 142 ---FSVRPVTNF 150 (280)
Q Consensus 142 ---~~ir~v~d~ 150 (280)
..|..+++.
T Consensus 141 g~~t~I~~~de~ 152 (423)
T PRK07218 141 GESTTVSLLDDS 152 (423)
T ss_pred cCcceEEEcCcc
Confidence 456665553
No 62
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=96.11 E-value=0.051 Score=53.53 Aligned_cols=101 Identities=17% Similarity=0.153 Sum_probs=65.8
Q ss_pred eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCC
Q 023576 45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDG 121 (280)
Q Consensus 45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G 121 (280)
.++++|.+....- ....+.-.| ..|+|.|+|.+++......-+.|.|++|.|.|.+-.+...+. .....+..|
T Consensus 44 ~~~~~~~~~~~~~-~~~~~~~~~---~~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~G 119 (505)
T PRK12445 44 HTSDQLHEEFDAK-DNQELESLN---IEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG 119 (505)
T ss_pred cCHHHHHHHhhcc-CcchhhcCC---CEEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCC
Confidence 5578886653211 011111112 249999999999887777777999999999987643321111 123568999
Q ss_pred CEEEEEEEEee-eCCeeEEEEEEEeeCCC
Q 023576 122 MYVRLIGNLKS-FQGKKQIVAFSVRPVTN 149 (280)
Q Consensus 122 ~yVrV~G~l~~-f~~~~~i~~~~ir~v~d 149 (280)
+.|.|.|.+.. -.+...|.+..+..+..
T Consensus 120 d~V~v~G~~~~t~~gelel~~~~~~llsk 148 (505)
T PRK12445 120 DIIGARGTLFKTQTGELSIHCTELRLLTK 148 (505)
T ss_pred CEEEEEEEEEecCCCcEEEEEeEEEEEec
Confidence 99999999864 34667777766655443
No 63
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=96.11 E-value=0.022 Score=60.64 Aligned_cols=76 Identities=20% Similarity=0.307 Sum_probs=59.8
Q ss_pred eEEEEEEEEEeeecCC---eeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCC
Q 023576 72 NVTLVGLVYNKEERAS---DVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVT 148 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t---~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~ 148 (280)
.|+|+|+|..+....| ...++|+|.||.++|.+|.+.-. .....+.++..|.|.|+++.-++..++.+..|.++.
T Consensus 955 ~v~v~g~i~~~~~~~TkkGmaf~~leD~~g~~e~~ifp~~~~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~i~~~~ 1032 (1046)
T PRK05672 955 RVRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWE--RQRREALGARLLLVRGRVQNAEGVRHLVADRLEDLS 1032 (1046)
T ss_pred EEEEEEEEEEEEEecCCCceEEEEEecCCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeeechH
Confidence 4889999988765322 57789999999999999976421 123568999999999999976777899998888775
Q ss_pred C
Q 023576 149 N 149 (280)
Q Consensus 149 d 149 (280)
+
T Consensus 1033 ~ 1033 (1046)
T PRK05672 1033 P 1033 (1046)
T ss_pred H
Confidence 4
No 64
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=96.10 E-value=0.048 Score=52.65 Aligned_cols=79 Identities=18% Similarity=0.182 Sum_probs=58.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEe
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVR 145 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir 145 (280)
..|+|.|+|.+++.....+-+.|.|++|.|.|..-.+...+. .....+..|+.|.|.|.+..-+ +...|.+.++.
T Consensus 13 ~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~i~ 92 (428)
T TIGR00458 13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEKAPGGFEIIPTKIE 92 (428)
T ss_pred CEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCCCCCcEEEEEeEEE
Confidence 458999999999987776777999999999998754321111 1235799999999999998643 45667777666
Q ss_pred eCCC
Q 023576 146 PVTN 149 (280)
Q Consensus 146 ~v~d 149 (280)
.+..
T Consensus 93 vl~~ 96 (428)
T TIGR00458 93 VINE 96 (428)
T ss_pred EEec
Confidence 5543
No 65
>PRK12366 replication factor A; Reviewed
Probab=96.04 E-value=0.023 Score=57.49 Aligned_cols=74 Identities=22% Similarity=0.301 Sum_probs=58.8
Q ss_pred eEEEEEEEEEeeec----------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe-eeCCeeEEE
Q 023576 72 NVTLVGLVYNKEER----------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK-SFQGKKQIV 140 (280)
Q Consensus 72 ~V~iVG~V~~~~~~----------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~-~f~~~~~i~ 140 (280)
.|.|+|.|.++... .....++|.|.||+|.+.+|.+.+. ..+.+|+.|+|.|..+ .|++...|.
T Consensus 186 ~v~v~G~V~~~~~~~~f~rkdg~~~~~r~~~l~D~TG~irvTlW~~~a~-----~~~~~g~vv~i~g~~~~~~~~~~el~ 260 (637)
T PRK12366 186 SATIEGEVTKAYPIKEFTRKDGSEGKLKSFILKDDTGSIRVTLWNDLTD-----IEVNKGDIVRVKGYVKQGYRTGLEIS 260 (637)
T ss_pred eEEEEEEEEEccCcEEEEEcCCCeeEEEEEEEEcCCCcEEEEEEChhhc-----ccCCCCCEEEEEeEEecCcCCceEEE
Confidence 78999999886531 2467899999999999999987642 3589999999999855 477888888
Q ss_pred EEEEeeCCCc
Q 023576 141 AFSVRPVTNF 150 (280)
Q Consensus 141 ~~~ir~v~d~ 150 (280)
+.+...+...
T Consensus 261 ~~~~~~i~~~ 270 (637)
T PRK12366 261 ANNIEILEKL 270 (637)
T ss_pred eCCceeeccc
Confidence 8777766543
No 66
>PRK14699 replication factor A; Provisional
Probab=96.03 E-value=0.03 Score=54.85 Aligned_cols=75 Identities=24% Similarity=0.322 Sum_probs=55.5
Q ss_pred eEEEEEEEEEeee-c------C---CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-Ee--eeCCeeE
Q 023576 72 NVTLVGLVYNKEE-R------A---SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LK--SFQGKKQ 138 (280)
Q Consensus 72 ~V~iVG~V~~~~~-~------~---t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~--~f~~~~~ 138 (280)
.|.|.|+|.++.. + . .-..+.|-|.||+|.+..|.+... ..+.|++|++|+|.+. ++ .|++...
T Consensus 178 ~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~---~~~~l~~Gd~v~I~~a~vr~~~~~~~~e 254 (484)
T PRK14699 178 DLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTD---FLNQIEYGDTVELINAYARENAFTQKVE 254 (484)
T ss_pred ceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECcccc---cccccCCCCEEEEecceEeecccCCceE
Confidence 4888888887643 1 1 244579999999999999987531 2457999999998744 43 5888999
Q ss_pred EEEEEEeeCCC
Q 023576 139 IVAFSVRPVTN 149 (280)
Q Consensus 139 i~~~~ir~v~d 149 (280)
|++.....+..
T Consensus 255 l~~~~~s~i~~ 265 (484)
T PRK14699 255 LQVGNRSIIRK 265 (484)
T ss_pred EEecCceEeec
Confidence 99876665554
No 67
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=96.01 E-value=0.019 Score=61.36 Aligned_cols=76 Identities=12% Similarity=0.102 Sum_probs=60.2
Q ss_pred eEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 72 NVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 72 ~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
.|+++|.|.+++. ......++|+|.||.+++.+|.+.-. .....+.++..|.|.|++..-++..++.+..|.+
T Consensus 945 ~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~~~~~~i~~ 1022 (1107)
T PRK06920 945 VQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPETYI--HFSDKLQEGAIVLVDGTIELRNHKLQWIVNGLYP 1022 (1107)
T ss_pred EEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCcEEEEEeeccc
Confidence 5889999988753 23467789999999999999976421 2235689999999999998767778999988877
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+.+
T Consensus 1023 l~~ 1025 (1107)
T PRK06920 1023 LEE 1025 (1107)
T ss_pred HHH
Confidence 743
No 68
>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=96.00 E-value=0.015 Score=38.92 Aligned_cols=44 Identities=20% Similarity=0.403 Sum_probs=38.1
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.||++|.+. +.++++.+|+++++++...+...|..|.+.|.|..
T Consensus 7 ~iL~~l~~~-----~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAES-----GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCT-----BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 578888774 45789999999999999999999999999999875
No 69
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.99 E-value=0.029 Score=60.37 Aligned_cols=77 Identities=10% Similarity=0.157 Sum_probs=60.9
Q ss_pred eeEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576 71 TNVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR 145 (280)
Q Consensus 71 ~~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir 145 (280)
..|.++|.|.+++. +.....++|+|.||.++|.+|.+.-. .....+.+|..|-|.|++..-.++.+|.+..|.
T Consensus 1001 ~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~~y~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~i~ 1078 (1170)
T PRK07374 1001 AKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYE--RLSDHLMTDTRLLVWAKVDRRDDRVQLIIDDCR 1078 (1170)
T ss_pred CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeee
Confidence 36889999988753 22467789999999999999976421 123568999999999999875577899999998
Q ss_pred eCCC
Q 023576 146 PVTN 149 (280)
Q Consensus 146 ~v~d 149 (280)
++.+
T Consensus 1079 ~l~~ 1082 (1170)
T PRK07374 1079 EIDD 1082 (1170)
T ss_pred cHhh
Confidence 8755
No 70
>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=95.96 E-value=0.0062 Score=43.08 Aligned_cols=52 Identities=23% Similarity=0.388 Sum_probs=44.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
+|++...+|+..|-. ..++++.+|++.++++...|..+|..|.+.|.|...-
T Consensus 5 gLs~~E~~vy~~Ll~------~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 5 GLSENEAKVYLALLK------NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHHHHHHHHHHHHHH------HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CcCHHHHHHHHHHHH------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 456777889888763 2488999999999999999999999999999997753
No 71
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=95.90 E-value=0.063 Score=51.96 Aligned_cols=79 Identities=15% Similarity=0.187 Sum_probs=57.5
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEee
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVRP 146 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir~ 146 (280)
..|+|-|+|.+++.....+-+.|.|++|.|.|.+=.+...+ ......+..|+.|.|.|.+..-+ +...|.+..|..
T Consensus 17 ~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~~~~~~~~el~~~~i~v 96 (437)
T PRK05159 17 EEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPKAPGGVEVIPEEIEV 96 (437)
T ss_pred CEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcCCCCCCCEEEEEeEEEE
Confidence 45889999999988776666799999999999764332111 12346799999999999999754 446677766665
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+..
T Consensus 97 ls~ 99 (437)
T PRK05159 97 LNK 99 (437)
T ss_pred EeC
Confidence 543
No 72
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.81 E-value=0.031 Score=41.43 Aligned_cols=54 Identities=19% Similarity=0.327 Sum_probs=45.0
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
..|+++|... +.++++.+|++.++++...|...|..|.+.|.|...-++..|..
T Consensus 8 ~~Il~~l~~~-----~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l 61 (91)
T smart00346 8 LAVLRALAEE-----PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRL 61 (91)
T ss_pred HHHHHHHHhC-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceee
Confidence 4578888653 24799999999999999999999999999999998655556754
No 73
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.76 E-value=0.04 Score=59.22 Aligned_cols=77 Identities=13% Similarity=0.171 Sum_probs=60.2
Q ss_pred eeEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576 71 TNVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF-QGKKQIVAFSV 144 (280)
Q Consensus 71 ~~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i 144 (280)
..|.++|.|.+++. +.....++|+|.||.+++.+|.+.-. .....+..|..|.|.|++... ++..++.+..|
T Consensus 992 ~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~g~~e~~vfp~~~~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~~~ 1069 (1151)
T PRK06826 992 DKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPKVYE--KYRSLLNEDNIVLIKGRVSLREDEEPKLICEEI 1069 (1151)
T ss_pred cEEEEEEEEEEeEeeccCCCCeEEEEEEEECCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCCceEEEEeee
Confidence 36789999988764 22467789999999999999976421 123568999999999999865 56689999999
Q ss_pred eeCCC
Q 023576 145 RPVTN 149 (280)
Q Consensus 145 r~v~d 149 (280)
.++.+
T Consensus 1070 ~~l~~ 1074 (1151)
T PRK06826 1070 EPLVI 1074 (1151)
T ss_pred ecHhh
Confidence 88764
No 74
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=95.74 E-value=0.11 Score=42.13 Aligned_cols=69 Identities=17% Similarity=0.275 Sum_probs=52.9
Q ss_pred eeEEEEEEEEEeee------cCCeeEEEEEcCCce----EEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEE
Q 023576 71 TNVTLVGLVYNKEE------RASDVNFTLDDGTGR----VVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~------~~t~~~~~LdDgTG~----I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i 139 (280)
..|.|+|+|+++.. +.-.++|+|-|.|.. |.|.+|.+.. +..+.+.+||.|.+.+ +|+.|+++.+.
T Consensus 15 ~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~---~~LP~v~~GDVIll~~~kv~~~~g~~~~ 91 (138)
T cd04497 15 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNE---ESLPIVKVGDIILLRRVKIQSYNGKPQG 91 (138)
T ss_pred CeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCCh---hhCCCCCCCCEEEEEEEEEEEECCceEE
Confidence 56789999988743 234788999998872 9999998864 2356579999999986 56789988766
Q ss_pred EEE
Q 023576 140 VAF 142 (280)
Q Consensus 140 ~~~ 142 (280)
...
T Consensus 92 ~~~ 94 (138)
T cd04497 92 ISN 94 (138)
T ss_pred EEC
Confidence 654
No 75
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=95.73 E-value=0.076 Score=51.00 Aligned_cols=91 Identities=19% Similarity=0.189 Sum_probs=65.5
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-ChhhhccCCCC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DTREMEAIQDG 121 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~G 121 (280)
+.++|++|.+.. + + +.|+|-|+|.+++......-..|-|+||.|.|+.-.+... +......+..+
T Consensus 3 ~~~~i~di~~~~-----~------~---~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~e 68 (435)
T COG0017 3 KRTYIKDIKPHV-----G------G---QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLE 68 (435)
T ss_pred ceeeHHhhhccC-----C------C---cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCc
Confidence 356778876531 1 1 7899999999999888777779999999999998754221 11114578999
Q ss_pred CEEEEEEEEeeeCC---eeEEEEEEEeeC
Q 023576 122 MYVRLIGNLKSFQG---KKQIVAFSVRPV 147 (280)
Q Consensus 122 ~yVrV~G~l~~f~~---~~~i~~~~ir~v 147 (280)
+.|.|.|.|+.-.. .-.|.+.+|..+
T Consensus 69 s~v~V~G~v~~~~~a~~g~El~v~~i~Vl 97 (435)
T COG0017 69 SSVVVTGIVKASPKAPQGFELQVEKIEVL 97 (435)
T ss_pred cEEEEEEEEEcCCCCCCCEEEEEEEEEEe
Confidence 99999999997652 234666555443
No 76
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=95.71 E-value=0.083 Score=51.92 Aligned_cols=101 Identities=18% Similarity=0.162 Sum_probs=66.4
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhccCCC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEAIQD 120 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~~~~ 120 (280)
+..+|++|......-. ..... ..-..|+|.|+|.+++.....+-+.|.|+||.|.|.+-.+...+. .....+..
T Consensus 31 ~~~~~~~~~~~~~~~~-~~~~~---~~~~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~ 106 (491)
T PRK00484 31 RTHTAAELRAKYDDKE-KEELE---ELEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDL 106 (491)
T ss_pred CccCHHHHHHHhcccc-chhhc---ccCcEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCC
Confidence 3467899876543210 00110 001569999999999887766777999999999997643321111 12345999
Q ss_pred CCEEEEEEEEee-eCCeeEEEEEEEeeC
Q 023576 121 GMYVRLIGNLKS-FQGKKQIVAFSVRPV 147 (280)
Q Consensus 121 G~yVrV~G~l~~-f~~~~~i~~~~ir~v 147 (280)
|+.|.|.|.+.. -.+...|.+..++.+
T Consensus 107 g~~v~v~G~v~~t~~ge~el~~~~~~vl 134 (491)
T PRK00484 107 GDIIGVEGTLFKTKTGELSVKATELTLL 134 (491)
T ss_pred CCEEEEEEEEEEcCCCcEEEEEeEEEEE
Confidence 999999999985 346666766666554
No 77
>PRK15491 replication factor A; Provisional
Probab=95.70 E-value=0.069 Score=50.68 Aligned_cols=75 Identities=20% Similarity=0.383 Sum_probs=55.8
Q ss_pred eEEEEEEEEEeee-------c-C--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-Ee--eeCCeeE
Q 023576 72 NVTLVGLVYNKEE-------R-A--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LK--SFQGKKQ 138 (280)
Q Consensus 72 ~V~iVG~V~~~~~-------~-~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~--~f~~~~~ 138 (280)
.|.|.|+|.++.. . . ......|.|.||.|.+.+|.+... ....+++|+.|++... +| .|+++..
T Consensus 178 ~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~---~~~~l~~Gd~V~i~~~~~r~~~~~g~~E 254 (374)
T PRK15491 178 DINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTD---LADKLENGDSVEIINGYARTNNYSQEVE 254 (374)
T ss_pred cEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhc---ccccCCCCCEEEEEeceEEEeccCCCEE
Confidence 4888888877642 1 1 356689999999999999987542 2357999999999663 55 4668888
Q ss_pred EEEE---EEeeCCC
Q 023576 139 IVAF---SVRPVTN 149 (280)
Q Consensus 139 i~~~---~ir~v~d 149 (280)
|++. .|.++++
T Consensus 255 l~~~~~s~I~~~~~ 268 (374)
T PRK15491 255 IQIGNHGSLRKTDR 268 (374)
T ss_pred EEeCCCceEEECCc
Confidence 8874 5777765
No 78
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=95.70 E-value=0.077 Score=53.10 Aligned_cols=75 Identities=20% Similarity=0.225 Sum_probs=56.1
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee----------eCCeeEEEE
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS----------FQGKKQIVA 141 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~----------f~~~~~i~~ 141 (280)
.|+|.|+|.+++....-+-+.|.|+||.|.|..-.+ .........+..|+.|.|.|.+.. -.+...|.+
T Consensus 17 ~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~-~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~~ 95 (583)
T TIGR00459 17 TVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPD-ADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEILA 95 (583)
T ss_pred EEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC-HHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEEE
Confidence 699999999998877767779999999999876333 111123467999999999999974 235567777
Q ss_pred EEEeeC
Q 023576 142 FSVRPV 147 (280)
Q Consensus 142 ~~ir~v 147 (280)
..+..+
T Consensus 96 ~~i~iL 101 (583)
T TIGR00459 96 ESITLL 101 (583)
T ss_pred eEEEEe
Confidence 777654
No 79
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=95.65 E-value=0.16 Score=50.64 Aligned_cols=77 Identities=12% Similarity=0.094 Sum_probs=56.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCCCEEEEEEEEeee--------CCeeEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDGMYVRLIGNLKSF--------QGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G~yVrV~G~l~~f--------~~~~~i 139 (280)
..|+|.|+|.+++.....+-+.|-|++|.|.|.+-.....+. .....+..+++|.|.|.+..- .+...|
T Consensus 79 ~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~V~G~v~~~~~~~~~~~~~~~El 158 (550)
T PTZ00401 79 KTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIEL 158 (550)
T ss_pred CEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEEEEEEEEecCccCCCCCCccEEE
Confidence 359999999999887777777999999999998743321111 123578999999999998862 344567
Q ss_pred EEEEEeeC
Q 023576 140 VAFSVRPV 147 (280)
Q Consensus 140 ~~~~ir~v 147 (280)
.+.+|..+
T Consensus 159 ~v~~i~vl 166 (550)
T PTZ00401 159 KVKKIHTV 166 (550)
T ss_pred EeeEEEEE
Confidence 66666544
No 80
>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=95.60 E-value=0.016 Score=41.25 Aligned_cols=47 Identities=26% Similarity=0.342 Sum_probs=38.4
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
.+|.++|++. .-++.++|+.+|+.+++.|+..|+.|+.-|+|-...+
T Consensus 3 ~~i~~~l~~~------~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRER------GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-------SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 3688888863 3689999999999999999999999999999987543
No 81
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=95.56 E-value=0.12 Score=50.77 Aligned_cols=99 Identities=10% Similarity=0.095 Sum_probs=63.0
Q ss_pred eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh-h-hh-ccCCCC
Q 023576 45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT-R-EM-EAIQDG 121 (280)
Q Consensus 45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~-~-~~-~~~~~G 121 (280)
.+++++......-. .....-.| ..|+|.|+|.+++......-+.|.|+||.|.+.+-.+...+. . .. ..+..|
T Consensus 32 ~~~~~~~~~~~~~~-~~~~~~~~---~~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~g 107 (496)
T TIGR00499 32 HSSQEFQEEYADLS-NEELEDKN---IEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLG 107 (496)
T ss_pred cCHHHHHHHhhccC-ccchhcCC---CEEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCC
Confidence 67888876543210 11111111 248999999999977766777999999999987643321111 1 11 237999
Q ss_pred CEEEEEEEEeeeC-CeeEEEEEEEeeC
Q 023576 122 MYVRLIGNLKSFQ-GKKQIVAFSVRPV 147 (280)
Q Consensus 122 ~yVrV~G~l~~f~-~~~~i~~~~ir~v 147 (280)
+.|.|.|.+..-+ +...|.+.+|..+
T Consensus 108 d~V~v~G~~~~t~~gelel~~~~i~il 134 (496)
T TIGR00499 108 DIIGVTGYPFKTKTGELSVHVTELQIL 134 (496)
T ss_pred CEEEEEEEEEECCCCcEEEEeeEEEEE
Confidence 9999999997543 4466666655443
No 82
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.54 E-value=0.04 Score=36.07 Aligned_cols=46 Identities=35% Similarity=0.502 Sum_probs=39.8
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+..|+++|.+. .++++.+|++.++++...+...|..|...|.|...
T Consensus 2 ~~~il~~l~~~------~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 2 QQQILELLAQQ------GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45688888652 36999999999999999999999999999999863
No 83
>PRK06386 replication factor A; Reviewed
Probab=95.53 E-value=0.065 Score=50.38 Aligned_cols=70 Identities=16% Similarity=0.263 Sum_probs=52.9
Q ss_pred eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE-eeeCCeeEEEE
Q 023576 71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL-KSFQGKKQIVA 141 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l-~~f~~~~~i~~ 141 (280)
..|.|.|+|.++.+. ..-....|.|.||+|....|.+ .+.+|+.|+|.+-. +.|++..+|++
T Consensus 118 ~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~---------~l~eGd~v~i~na~v~e~~G~~el~v 188 (358)
T PRK06386 118 PYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK---------PLEDNRFVRIENARVSQYNGYIEISV 188 (358)
T ss_pred CceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc---------cccCCCEEEEeeeEEEccCCeEEEEe
Confidence 356788888776331 2345789999999999999964 37899999998765 47899999998
Q ss_pred EEEeeCCC
Q 023576 142 FSVRPVTN 149 (280)
Q Consensus 142 ~~ir~v~d 149 (280)
.....|..
T Consensus 189 ~~~t~I~~ 196 (358)
T PRK06386 189 GNKSVIKE 196 (358)
T ss_pred CCeEEEEE
Confidence 66554444
No 84
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=95.53 E-value=0.087 Score=53.83 Aligned_cols=66 Identities=21% Similarity=0.273 Sum_probs=51.4
Q ss_pred eeEEEEEEEEEeeec---CCeeEEEEEcCCceEEEEEec-ccccChhhhccCCCCCEEEEEEEEeeeCCeeEE
Q 023576 71 TNVTLVGLVYNKEER---ASDVNFTLDDGTGRVVCKRWA-SEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~---~t~~~~~LdDgTG~I~~~~w~-~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i 139 (280)
..|+|+|.|.++... ...+.+.+.|+||.|.+++|. +.. .-...|++|+.|.|+|+++.+++++++
T Consensus 60 ~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n~~---~~~~~l~~G~~~~v~Gkv~~~~~~~qm 129 (681)
T PRK10917 60 EKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFNQP---YLKKQLKVGKRVAVYGKVKRGKYGLEM 129 (681)
T ss_pred CEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccCcH---HHHhhCCCCCEEEEEEEEEecCCeEEE
Confidence 468899998876432 357899999999999998773 221 224679999999999999998877665
No 85
>PLN02903 aminoacyl-tRNA ligase
Probab=95.52 E-value=0.11 Score=52.67 Aligned_cols=78 Identities=24% Similarity=0.278 Sum_probs=56.0
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeee----------CCeeEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSF----------QGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i 139 (280)
..|+|.|+|.+++....-+-+.|-|+||.|.|++-.+...+ ......+..++.|.|.|.|+.- .+...|
T Consensus 73 k~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~n~~~~tGeiEl 152 (652)
T PLN02903 73 SRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEV 152 (652)
T ss_pred CEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCcCCCCCCCCEEE
Confidence 36999999999988776667799999999998764332111 1123579999999999999853 144666
Q ss_pred EEEEEeeCC
Q 023576 140 VAFSVRPVT 148 (280)
Q Consensus 140 ~~~~ir~v~ 148 (280)
.+..|..+.
T Consensus 153 ~~~~i~VL~ 161 (652)
T PLN02903 153 VAESVDILN 161 (652)
T ss_pred EEeEEEEEe
Confidence 666665543
No 86
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=95.45 E-value=0.12 Score=51.95 Aligned_cols=77 Identities=17% Similarity=0.250 Sum_probs=55.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee----------CCeeEEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF----------QGKKQIV 140 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i~ 140 (280)
..|+|.|+|.+++.....+-+.|.|+||.|.|.+-. ....-.....+..|+.|.|.|.+..- .+...|.
T Consensus 18 ~~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~-~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~~~~g~~El~ 96 (588)
T PRK00476 18 QTVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDP-DAEAFEVAESLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVL 96 (588)
T ss_pred CEEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeC-CHHHHHHHhCCCCCCEEEEEEEEEecCCcccCccCCCCcEEEE
Confidence 359999999999987777777999999999987632 11111234679999999999999863 2345566
Q ss_pred EEEEeeCC
Q 023576 141 AFSVRPVT 148 (280)
Q Consensus 141 ~~~ir~v~ 148 (280)
+..|+.+.
T Consensus 97 ~~~i~il~ 104 (588)
T PRK00476 97 ASELEVLN 104 (588)
T ss_pred EeEEEEEe
Confidence 66655443
No 87
>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=95.41 E-value=0.045 Score=36.78 Aligned_cols=46 Identities=28% Similarity=0.421 Sum_probs=36.5
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCC-eeee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEG-LIYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG-~IYs 268 (280)
+.+|+.+|.+. ...++.++|++.|+++...|+..|..|.+.| .|.+
T Consensus 2 ~~~il~~L~~~-----~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~ 48 (55)
T PF08279_consen 2 QKQILKLLLES-----KEPITAKELAEELGVSRRTIRRDIKELREWGIPIES 48 (55)
T ss_dssp HHHHHHHHHHT-----TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHHHHc-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEe
Confidence 45788888542 2349999999999999999999999999999 4433
No 88
>PLN02502 lysyl-tRNA synthetase
Probab=95.38 E-value=0.16 Score=50.56 Aligned_cols=77 Identities=16% Similarity=0.191 Sum_probs=55.1
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh----hhh-ccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT----REM-EAIQDGMYVRLIGNLKSF-QGKKQIVAFSV 144 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~----~~~-~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i 144 (280)
..|+|.|+|.+++.....+-+.|.|++|.|.|..-.+...+. ... ..+..|+.|.|.|.+..- .+...|.+..|
T Consensus 109 ~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~~i 188 (553)
T PLN02502 109 VSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPTSF 188 (553)
T ss_pred CEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEeEE
Confidence 359999999999988777778999999999987643321111 112 358999999999988753 35566666655
Q ss_pred eeC
Q 023576 145 RPV 147 (280)
Q Consensus 145 r~v 147 (280)
..+
T Consensus 189 ~vL 191 (553)
T PLN02502 189 EVL 191 (553)
T ss_pred EEE
Confidence 443
No 89
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.35 E-value=0.065 Score=56.88 Aligned_cols=75 Identities=11% Similarity=0.220 Sum_probs=57.5
Q ss_pred EEEEEEEEEee----e--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 73 VTLVGLVYNKE----E--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 73 V~iVG~V~~~~----~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
+.++|+|.++. . ......++|+|.||.|+|.+|.+.-. .....+.++..|.|.|++..-++..++.+..+.+
T Consensus 887 ~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~l~~~~i~~ 964 (1034)
T PRK07279 887 ATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPETYR--QYKDELKEGKFYYLKGKIQERDGRLQMVLQQIQE 964 (1034)
T ss_pred ceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeeEEEEeeeec
Confidence 56667766543 2 23567889999999999999976421 2235689999999999999767788999999988
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+..
T Consensus 965 l~~ 967 (1034)
T PRK07279 965 ASS 967 (1034)
T ss_pred ccc
Confidence 753
No 90
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.32 E-value=0.038 Score=42.44 Aligned_cols=47 Identities=26% Similarity=0.492 Sum_probs=42.5
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
.+++++||..|+.. ..++..+|++.+++++..|+..+..|.+.|.|.
T Consensus 2 d~~D~~il~~L~~~------~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 2 DEIDRKILEELQKD------ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CHHHHHHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45788999999874 268999999999999999999999999999987
No 91
>PRK15491 replication factor A; Provisional
Probab=95.30 E-value=0.11 Score=49.38 Aligned_cols=77 Identities=18% Similarity=0.200 Sum_probs=55.6
Q ss_pred eeEEEEEEEEEeee--------c--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe-eeCCeeEE
Q 023576 71 TNVTLVGLVYNKEE--------R--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK-SFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~--------~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~-~f~~~~~i 139 (280)
..|.|.|+|.++.. . .....+.|-|-||+|.+.+|.+.... .....+++|+.|+|.|..+ .|++ ..|
T Consensus 68 ~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~-~~~~~le~G~v~~I~~~~~~~y~g-~Ei 145 (374)
T PRK15491 68 SNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADL-IKTGDIEVGKSLNISGYAKEGYSG-IEV 145 (374)
T ss_pred CceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhh-hccCCcCCCCEEEEeeeeccCccc-EEE
Confidence 56888888887621 1 23556699999999999999865421 1114589999999999988 4655 688
Q ss_pred EEE---EEeeCCC
Q 023576 140 VAF---SVRPVTN 149 (280)
Q Consensus 140 ~~~---~ir~v~d 149 (280)
++. .|.+.++
T Consensus 146 ~i~~~~~i~~~~~ 158 (374)
T PRK15491 146 NIGRYGGISESDE 158 (374)
T ss_pred EeCCCceeeeccc
Confidence 886 4666654
No 92
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=95.29 E-value=0.12 Score=52.66 Aligned_cols=77 Identities=14% Similarity=0.145 Sum_probs=56.0
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeee----------CCeeE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSF----------QGKKQ 138 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f----------~~~~~ 138 (280)
..|+|.|+|.+++....-+-+.|-|+||.|.|.+-.+...+ ......+..++.|.|.|.++.- .+...
T Consensus 19 ~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~r~~~~~n~~~~tg~iE 98 (706)
T PRK12820 19 REVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETENPHIETGDIE 98 (706)
T ss_pred CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEeccCccccCCCCCCCcEE
Confidence 45999999999988777677799999999998764332111 1124579999999999999872 14456
Q ss_pred EEEEEEeeC
Q 023576 139 IVAFSVRPV 147 (280)
Q Consensus 139 i~~~~ir~v 147 (280)
|.+..+..+
T Consensus 99 l~~~~i~iL 107 (706)
T PRK12820 99 VFVRELSIL 107 (706)
T ss_pred EEeeEEEEE
Confidence 666666554
No 93
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.27 E-value=0.056 Score=40.21 Aligned_cols=53 Identities=25% Similarity=0.401 Sum_probs=46.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
+++..+-.||.+|... .+++..+|++.++++...|..+|..|.+.|.|+.+-|
T Consensus 7 ~l~~~~~~il~~l~~~------~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 7 GLTPTQFLVLRILYEE------GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence 5677888899999863 2689999999999999999999999999999998755
No 94
>PLN02603 asparaginyl-tRNA synthetase
Probab=95.19 E-value=0.16 Score=50.73 Aligned_cols=77 Identities=19% Similarity=0.247 Sum_probs=54.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCc--eEEEEEecccccChhhhc--cCCCCCEEEEEEEEeeeCCe---eEEEEEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTG--RVVCKRWASEVFDTREME--AIQDGMYVRLIGNLKSFQGK---KQIVAFS 143 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~--~~~~G~yVrV~G~l~~f~~~---~~i~~~~ 143 (280)
..|+|.|+|++++......-..|.|+|+ .|.|++=.+ ........ .+..|+.|.|.|.+..-.+. ..|.+.+
T Consensus 108 ~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~-~~~~~~l~~~~l~~gs~V~V~G~v~~~~~~~~~~EL~v~~ 186 (565)
T PLN02603 108 KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPD-AEGYDQVESGLITTGASVLVQGTVVSSQGGKQKVELKVSK 186 (565)
T ss_pred CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECc-HHHHHHHhhcCCCCCCEEEEEEEEEecCCCCccEEEEEeE
Confidence 4699999999999877777779999998 499886322 11111222 38899999999999865432 5666666
Q ss_pred EeeCC
Q 023576 144 VRPVT 148 (280)
Q Consensus 144 ir~v~ 148 (280)
|..+.
T Consensus 187 i~vlg 191 (565)
T PLN02603 187 IVVVG 191 (565)
T ss_pred EEEEE
Confidence 65443
No 95
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=95.09 E-value=0.041 Score=45.95 Aligned_cols=51 Identities=27% Similarity=0.487 Sum_probs=45.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee--eec
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI--YST 269 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I--YsT 269 (280)
.+.++..+||++|+.++ -++..+|++++++++..|+..++.|.++|.| |..
T Consensus 11 ~lD~~D~~IL~~Lq~d~------R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~ 63 (164)
T PRK11169 11 DLDRIDRNILNELQKDG------RISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTA 63 (164)
T ss_pred hHHHHHHHHHHHhccCC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEE
Confidence 46789999999999753 5799999999999999999999999999998 554
No 96
>PRK08402 replication factor A; Reviewed
Probab=95.06 E-value=0.11 Score=49.01 Aligned_cols=75 Identities=21% Similarity=0.210 Sum_probs=54.5
Q ss_pred eeEEEEEcCCceEEEEEecccccC-----h---hhh-----------c-----------cCCCCCEEEEEEEEe--eeCC
Q 023576 88 DVNFTLDDGTGRVVCKRWASEVFD-----T---REM-----------E-----------AIQDGMYVRLIGNLK--SFQG 135 (280)
Q Consensus 88 ~~~~~LdDgTG~I~~~~w~~~~~~-----~---~~~-----------~-----------~~~~G~yVrV~G~l~--~f~~ 135 (280)
.+.+.|+|+||.+.|.+|.+.... . ... + .-..|.+..|+|+++ .|++
T Consensus 246 il~~~l~D~TG~~~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~ 325 (355)
T PRK08402 246 ILDFGLDDGTGYIRVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLG 325 (355)
T ss_pred EEEEEEEcCCCcEEEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCC
Confidence 456789999999999999865421 0 000 0 023488999999998 5777
Q ss_pred eeEEEEEEEeeCCCchHHHHHHHHHHHHH
Q 023576 136 KKQIVAFSVRPVTNFDEVTCHYIECIYFH 164 (280)
Q Consensus 136 ~~~i~~~~ir~v~d~Nei~~H~Le~i~~~ 164 (280)
.. +.+..+.|| |+....-|+++-+...
T Consensus 326 ~~-~~v~~~~~v-d~~~e~~~l~~~i~~~ 352 (355)
T PRK08402 326 LI-LKASSWDEV-DYKREIERVRAELEEL 352 (355)
T ss_pred eE-EEEEEcccC-CHHHHHHHHHHHHHHh
Confidence 65 899999999 5777778888877543
No 97
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=95.06 E-value=0.18 Score=50.79 Aligned_cols=75 Identities=25% Similarity=0.245 Sum_probs=59.9
Q ss_pred eeEEEEEEEEEeeec----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 71 TNVTLVGLVYNKEER----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
..|+++|.|.++... ...+.+++.|+||.|.+++|.-.. .-...+++|.-|.|+|+++.|++.+++.--.+..
T Consensus 61 ~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~---~l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~ 137 (677)
T COG1200 61 EIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPA---YLKKKLKVGERVIVYGKVKRFKGGLQITHPEYIV 137 (677)
T ss_pred ceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccH---HHHhhCCCCCEEEEEEEEeeccCceEEEcceEEe
Confidence 578999999887543 468899999999999999887653 2346799999999999999999888876555554
Q ss_pred CC
Q 023576 147 VT 148 (280)
Q Consensus 147 v~ 148 (280)
..
T Consensus 138 ~~ 139 (677)
T COG1200 138 ND 139 (677)
T ss_pred cC
Confidence 43
No 98
>PLN02850 aspartate-tRNA ligase
Probab=95.05 E-value=0.21 Score=49.55 Aligned_cols=78 Identities=17% Similarity=0.163 Sum_probs=56.5
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-Ch---hhhccCCCCCEEEEEEEEeee-------CCeeEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DT---REMEAIQDGMYVRLIGNLKSF-------QGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~---~~~~~~~~G~yVrV~G~l~~f-------~~~~~i 139 (280)
..|+|.|+|.+++.....+-+.|-|++|.|.|.+-..... .. .....+..|++|.|.|.|+.- .+...|
T Consensus 82 ~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~t~~~El 161 (530)
T PLN02850 82 SEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKGTTQQVEI 161 (530)
T ss_pred CEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEEEEEEEEEccCcCCCCCCccEEE
Confidence 4699999999998877766779999999999987544321 11 124579999999999999842 123566
Q ss_pred EEEEEeeCC
Q 023576 140 VAFSVRPVT 148 (280)
Q Consensus 140 ~~~~ir~v~ 148 (280)
.+.+|..+.
T Consensus 162 ~~~~i~vls 170 (530)
T PLN02850 162 QVRKIYCVS 170 (530)
T ss_pred EEeEEEEEe
Confidence 666666443
No 99
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=95.04 E-value=0.42 Score=39.06 Aligned_cols=71 Identities=18% Similarity=0.267 Sum_probs=54.6
Q ss_pred eeEEEEEEEEEeeec--------CCeeEEEEEcCCc--------eEEEEEecccccChhhhccCCC-CCEEEEE-EEEee
Q 023576 71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTG--------RVVCKRWASEVFDTREMEAIQD-GMYVRLI-GNLKS 132 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG--------~I~~~~w~~~~~~~~~~~~~~~-G~yVrV~-G~l~~ 132 (280)
..|.|+|+|+....- .-.++++|-|.|- .|.|.+|.+.. +..+.+.. ||.|++. =+|+.
T Consensus 13 ~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~---~~LP~v~~~GDii~l~r~kv~~ 89 (146)
T PF02765_consen 13 KFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHK---ESLPNVKSVGDIIRLRRVKVQS 89 (146)
T ss_dssp EEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSH---HHSCTTCSTTHEEEEEEEEEEE
T ss_pred CEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCH---HHCCCCCCCCCEEEEEEEEEEE
Confidence 578899999886432 2367899999883 69999997654 34566776 9999998 78999
Q ss_pred eCCeeEEEEEEE
Q 023576 133 FQGKKQIVAFSV 144 (280)
Q Consensus 133 f~~~~~i~~~~i 144 (280)
|+++.++....-
T Consensus 90 ~~~~~~~~~~~~ 101 (146)
T PF02765_consen 90 YNGKPQGLSNST 101 (146)
T ss_dssp ETTEEEEEEECE
T ss_pred ECCEEEEEecCC
Confidence 999998776543
No 100
>PLN02221 asparaginyl-tRNA synthetase
Probab=94.98 E-value=0.24 Score=49.55 Aligned_cols=95 Identities=20% Similarity=0.177 Sum_probs=62.5
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCC--eeEEEEEcCC--ceEEEEEecccccChhhhccC
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERAS--DVNFTLDDGT--GRVVCKRWASEVFDTREMEAI 118 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t--~~~~~LdDgT--G~I~~~~w~~~~~~~~~~~~~ 118 (280)
..++|+.|+...-.. -...| ..|+|.|||.+++.... .+-+.|.|+| |.|.|++-.+.. .....+
T Consensus 31 ~~~~~~~~~~~~~~~-----~~~~g---~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~---~~~~~L 99 (572)
T PLN02221 31 DRVLIRSILDRPDGG-----AGLAG---QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLY---DLSTLV 99 (572)
T ss_pred CceEHHHHhccccCC-----hhcCC---CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchh---hHHhcC
Confidence 566899998542211 11122 46999999999987763 4556899999 899997632211 111357
Q ss_pred CCCCEEEEEEEEeeeC------CeeEEEEEEEeeCC
Q 023576 119 QDGMYVRLIGNLKSFQ------GKKQIVAFSVRPVT 148 (280)
Q Consensus 119 ~~G~yVrV~G~l~~f~------~~~~i~~~~ir~v~ 148 (280)
..++.|.|.|.|+.-. +...|.+..|..+.
T Consensus 100 ~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~ 135 (572)
T PLN02221 100 ATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVG 135 (572)
T ss_pred CCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEe
Confidence 8999999999998642 23456666554443
No 101
>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=94.94 E-value=0.047 Score=38.12 Aligned_cols=53 Identities=23% Similarity=0.327 Sum_probs=41.3
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
+.-+-.||.+|.. ....++..+|++.++++...+..+|+.|.+.|.|...-|+
T Consensus 2 t~~q~~vL~~l~~-----~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~ 54 (68)
T PF13463_consen 2 TRPQWQVLRALAH-----SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDP 54 (68)
T ss_dssp -HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEES
T ss_pred CHHHHHHHHHHHc-----cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCC
Confidence 3456778999982 2458899999999999999999999999999999877555
No 102
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.94 E-value=0.067 Score=56.64 Aligned_cols=79 Identities=20% Similarity=0.418 Sum_probs=63.2
Q ss_pred EeeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCeeEEEEE
Q 023576 70 ITNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKKQIVAF 142 (280)
Q Consensus 70 i~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~~i~~~ 142 (280)
..+|.|.|.|-.++.. .+-+.|.+-|.|-++.|+.|.....+......++.|+.|+|.|.|.. |....++.+.
T Consensus 239 ~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g~v~~d~f~~~l~m~i~ 318 (1444)
T COG2176 239 ETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVKARGNVQLDTFTRDLTMIIN 318 (1444)
T ss_pred ccceEEEEEEEEEeeeecccCcEEEEEEEecCchheeehhhccccccHHHHhhcccCcEEEEEEEEEecccccceEEEhh
Confidence 3569999999877542 35688999999999999999987766677889999999999999985 4566677766
Q ss_pred EEeeCC
Q 023576 143 SVRPVT 148 (280)
Q Consensus 143 ~ir~v~ 148 (280)
.|.+|.
T Consensus 319 ~I~ei~ 324 (1444)
T COG2176 319 DINEIE 324 (1444)
T ss_pred hhhhhh
Confidence 665554
No 103
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.94 E-value=0.12 Score=49.34 Aligned_cols=75 Identities=13% Similarity=0.153 Sum_probs=58.7
Q ss_pred EEeeEEEEEEEEEe--eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 69 EITNVTLVGLVYNK--EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 69 ~i~~V~iVG~V~~~--~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
+-+...++|+|... .....-+.+.|.|++|.|.|..+............+..||.|.+.|.++... |++.+++.
T Consensus 265 ~~~~~~v~g~v~~~p~~ieGghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G~~~~~~----~n~ek~~v 340 (421)
T COG1571 265 DYSKYRVVGRVEAEPRAIEGGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYGSVKPGT----LNLEKFQV 340 (421)
T ss_pred hccceEEEEEEecccEEeeCCEEEEEecCCCceEEEEEecccccchHHHHhcCCCCEEEEecCccccc----eeEEEEEE
Confidence 34568889988764 3345678899999999999999987665545568899999999999999866 66666555
Q ss_pred C
Q 023576 147 V 147 (280)
Q Consensus 147 v 147 (280)
+
T Consensus 341 ~ 341 (421)
T COG1571 341 L 341 (421)
T ss_pred E
Confidence 4
No 104
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=94.93 E-value=0.052 Score=44.29 Aligned_cols=48 Identities=33% Similarity=0.545 Sum_probs=43.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
.+.++..+||++|+..+ -++..+|++++++++..+..-+..|.++|.|
T Consensus 5 ~lD~~D~~IL~~L~~d~------r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 5 KLDDIDRRILRLLQEDA------RISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred cccHHHHHHHHHHHHhC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 46789999999999863 2899999999999999999999999999977
No 105
>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=94.92 E-value=0.11 Score=34.04 Aligned_cols=46 Identities=26% Similarity=0.411 Sum_probs=39.3
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+.+|+.+|.+ .-.++.+|++.++++.+.|..-|..|.+.|.|.+
T Consensus 2 ~~R~~Il~~L~~-------~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 2 PTRLRILKLLSE-------GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHHTT-------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHh-------CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 456789999876 2479999999999999999999999999999864
No 106
>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=94.92 E-value=0.11 Score=36.13 Aligned_cols=50 Identities=18% Similarity=0.256 Sum_probs=37.2
Q ss_pred hHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 218 DQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
-..|.+.|.... -..++=+ +..+|+++++.+...|++||..|.++|.|+.
T Consensus 6 ~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 6 YDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 345555555532 2334567 8999999999999999999999999999986
No 107
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.91 E-value=0.055 Score=44.64 Aligned_cols=51 Identities=20% Similarity=0.330 Sum_probs=45.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee--eec
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI--YST 269 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I--YsT 269 (280)
.+.++.++||++|+.++ =.+..+|++++++++..|+..++.|.++|.| |..
T Consensus 6 ~lD~~D~~Il~~Lq~d~------R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~ 58 (153)
T PRK11179 6 QIDNLDRGILEALMENA------RTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRV 58 (153)
T ss_pred ccCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEE
Confidence 36789999999999853 4699999999999999999999999999999 554
No 108
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=94.81 E-value=0.44 Score=36.59 Aligned_cols=64 Identities=22% Similarity=0.258 Sum_probs=46.3
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN 149 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d 149 (280)
+.|+|||+|.+.+.. .+++.+.-| .++|++-.+. ....+.||.|+|++.. ...|.+......-+
T Consensus 16 k~V~ivGkV~~~~~~----~~~~~~~Dg~~v~v~l~~~~--------~~~~~~~vEViG~V~~---~~~I~~~~~~~~g~ 80 (101)
T cd04479 16 KTVRIVGKVEKVDGD----SLTLISSDGVNVTVELNRPL--------DLPISGYVEVIGKVSP---DLTIRVLSYIDFGD 80 (101)
T ss_pred CEEEEEEEEEEecCC----eEEEEcCCCCEEEEEeCCCC--------CcccCCEEEEEEEECC---CCeEEEEEEEECCC
Confidence 689999999998654 355655555 7888855432 3577899999999985 46677777666654
No 109
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.68 E-value=0.085 Score=42.21 Aligned_cols=51 Identities=25% Similarity=0.391 Sum_probs=44.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+|+++.-+||..|=+. +.+.++++|++.|+.+.+.|..+|..|.+-|.|+-
T Consensus 24 GLs~~Dv~v~~~LL~~-----~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 24 GLSELDVEVYKALLEE-----NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred CCcHHHHHHHHHHHhh-----cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 7888998988877642 35889999999999999999999999999999874
No 110
>PRK12366 replication factor A; Reviewed
Probab=94.64 E-value=0.12 Score=52.44 Aligned_cols=75 Identities=13% Similarity=0.322 Sum_probs=56.3
Q ss_pred eeEEEEEEEEEeee------c----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-EeeeCCeeEE
Q 023576 71 TNVTLVGLVYNKEE------R----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LKSFQGKKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~------~----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~~f~~~~~i 139 (280)
..|.|.|+|.++.. . .....+.|-|.||+|.+.+|.+... ....|++|+.++|.+. ++.|++...|
T Consensus 74 ~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG~Ir~t~W~~~~~---~~~~le~G~v~~i~~~~v~~~~~~~el 150 (637)
T PRK12366 74 INVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAK---LLKGLKEGDVIKIENARSRKWNNDVEL 150 (637)
T ss_pred cceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCCEEEEEEEchhhh---hhccCCCCCEEEEeccEecccCCceEE
Confidence 45777788766531 1 2357889999999999999987542 2467999999998876 7889999888
Q ss_pred EEE---EEeeCC
Q 023576 140 VAF---SVRPVT 148 (280)
Q Consensus 140 ~~~---~ir~v~ 148 (280)
++. .|.+++
T Consensus 151 ~~~~~t~I~~~~ 162 (637)
T PRK12366 151 NSGSETRIDKLE 162 (637)
T ss_pred EcCCcceEEEcc
Confidence 763 466665
No 111
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=94.59 E-value=0.26 Score=49.96 Aligned_cols=65 Identities=22% Similarity=0.248 Sum_probs=49.1
Q ss_pred eEEEEEEEEEeee----cCCeeEEEEEc-CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576 72 NVTLVGLVYNKEE----RASDVNFTLDD-GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV 140 (280)
Q Consensus 72 ~V~iVG~V~~~~~----~~t~~~~~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~ 140 (280)
.+.++|.|.+... ....+.+.+.| +||.|.+++|... .....+++|+.|.|+|+++.+++++++.
T Consensus 34 ~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~~----~~~~~~~~g~~~~~~Gk~~~~~~~~~~~ 103 (630)
T TIGR00643 34 RATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRA----FLKKKFKVGSKVVVYGKVKSSKFKAYLI 103 (630)
T ss_pred EEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECCH----HHHhhCCCCCEEEEEEEEEeeCCEEEEE
Confidence 5677777765421 12468899999 9999999888521 2346799999999999999998876643
No 112
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=94.47 E-value=0.047 Score=39.78 Aligned_cols=55 Identities=20% Similarity=0.312 Sum_probs=40.7
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
.+-.+||++++ +.+.++.+|+...+++...+.+.|.+|.+.|.| +-++..|+.|+
T Consensus 6 ~Ii~~IL~~l~-------~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI--~~~~~~Y~lTe 60 (77)
T PF14947_consen 6 EIIFDILKILS-------KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI--KKKDGKYRLTE 60 (77)
T ss_dssp HHHHHHHHHH--------TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE--EEETTEEEE-H
T ss_pred HHHHHHHHHHH-------cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe--eCCCCEEEECc
Confidence 35556777765 247889999999999999999999999999999 44788998874
No 113
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=94.45 E-value=0.36 Score=42.37 Aligned_cols=80 Identities=23% Similarity=0.240 Sum_probs=57.2
Q ss_pred EEeeEEEEEEEEEe-----e-ecCCeeEEEEE-----cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---
Q 023576 69 EITNVTLVGLVYNK-----E-ERASDVNFTLD-----DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--- 134 (280)
Q Consensus 69 ~i~~V~iVG~V~~~-----~-~~~t~~~~~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--- 134 (280)
+-+.|.|+|.+.+= + ....+.+|+|. |.|-.|.|..|..-.+ ...+..|+.|.|.|+|++|+
T Consensus 7 ~~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae----~~~l~kG~~v~VeGqlrsy~~~~ 82 (219)
T PRK05813 7 ENNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLA----GMDLKVGTLVIVEGQLRSYNKFI 82 (219)
T ss_pred hcCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhh----hhcccCCCEEEEEEEEEEeccCC
Confidence 45789999999652 1 23456677665 8888999999977542 22399999999999999884
Q ss_pred -Ce----eEEEEEEEeeCCCchH
Q 023576 135 -GK----KQIVAFSVRPVTNFDE 152 (280)
Q Consensus 135 -~~----~~i~~~~ir~v~d~Ne 152 (280)
++ ..|.+..|..+...++
T Consensus 83 ~G~~R~vl~V~a~~i~~l~~~~~ 105 (219)
T PRK05813 83 DGKNRLILTVFARNIEYCDERSD 105 (219)
T ss_pred CCcEEEEEEEEEEEEEEccCCCc
Confidence 33 2356667777777544
No 114
>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=94.29 E-value=0.14 Score=35.63 Aligned_cols=50 Identities=28% Similarity=0.382 Sum_probs=42.9
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
..+..|+.+|... +++..+|++.++++...|..+|+.|.+.|.|...-+.
T Consensus 7 ~~~~~il~~l~~~-------~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 7 PTRLRILRLLLEG-------PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred hHHHHHHHHHHHC-------CcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 4677889888752 2899999999999999999999999999999976544
No 115
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.18 E-value=0.23 Score=33.20 Aligned_cols=34 Identities=26% Similarity=0.489 Sum_probs=31.3
Q ss_pred cc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 236 GV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 236 Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
-+ +..+|++.++++...|+++|..|.++|.|...
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 56 89999999999999999999999999998753
No 116
>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=94.16 E-value=0.31 Score=33.29 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=32.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 238 HVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
++.+|++.++++...|+++|..|.++|.|... ...+|.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~-~~~~~~ 64 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVERR-PGRGTF 64 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec-CCCeEE
Confidence 59999999999999999999999999998764 333443
No 117
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=94.16 E-value=0.47 Score=48.12 Aligned_cols=78 Identities=12% Similarity=0.094 Sum_probs=57.5
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccc-cC-h-hh-hccCCCCCEEEEEEEEeee-CCeeEEEEEEEee
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEV-FD-T-RE-MEAIQDGMYVRLIGNLKSF-QGKKQIVAFSVRP 146 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~-~~-~-~~-~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~ 146 (280)
.|+|-|+|.+++....-.-+.|-|.||.|.|.+-.+.. .+ . .. ...+..|+.|.|.|.+..- .+...|.+..+..
T Consensus 109 ~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~~GeleI~~~~i~l 188 (659)
T PTZ00385 109 TVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASRMLI 188 (659)
T ss_pred EEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecCCceEEEEeeEEEE
Confidence 49999999999877766667899999999998865431 11 1 11 2468999999999988865 4777777777665
Q ss_pred CCC
Q 023576 147 VTN 149 (280)
Q Consensus 147 v~d 149 (280)
+..
T Consensus 189 Lsk 191 (659)
T PTZ00385 189 LSP 191 (659)
T ss_pred ech
Confidence 543
No 118
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=94.06 E-value=0.48 Score=40.41 Aligned_cols=78 Identities=17% Similarity=0.183 Sum_probs=49.5
Q ss_pred EeeEEEEEEEEEe-e-----ecCCeeEEEEE-------------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576 70 ITNVTLVGLVYNK-E-----ERASDVNFTLD-------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL 130 (280)
Q Consensus 70 i~~V~iVG~V~~~-~-----~~~t~~~~~Ld-------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l 130 (280)
++.|.|||.|..- + .....+.|+|- +.|--|.|.+|...++ .....++.|+.|-|.|+|
T Consensus 2 ~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE--~~~~~l~KG~~V~VeGrL 79 (182)
T PRK08486 2 FNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAE--IANQYLSKGSKVLIEGRL 79 (182)
T ss_pred eeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHH--HHHHHcCCCCEEEEEEEE
Confidence 4678888888541 1 12345566661 2345689999976432 234669999999999999
Q ss_pred ee--eCCe-------eEEEEEEEeeCCC
Q 023576 131 KS--FQGK-------KQIVAFSVRPVTN 149 (280)
Q Consensus 131 ~~--f~~~-------~~i~~~~ir~v~d 149 (280)
+. |.++ ..|.+..|..+..
T Consensus 80 ~~~~y~dkdG~~r~~~eI~a~~v~~L~~ 107 (182)
T PRK08486 80 TFESWMDQNGQKRSKHTITAESMQMLDS 107 (182)
T ss_pred EeCcEECCCCcEEEEEEEEEeEEEECCC
Confidence 75 5332 3466666666554
No 119
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=93.99 E-value=0.56 Score=36.38 Aligned_cols=69 Identities=22% Similarity=0.247 Sum_probs=41.1
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCC-ceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGT-GRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN 149 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d 149 (280)
..|+|||+|.++..... .++|.-.. +.|.+..-.+. .+..+.||.|+|++..-.+-..|....+.+..+
T Consensus 19 k~VrivGkv~~~~~~g~--~~~l~~~d~~~V~v~l~~~~--------~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~ 88 (109)
T PF08661_consen 19 KTVRIVGKVESVDPDGG--SATLSTSDGGQVTVSLNPPS--------DEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGD 88 (109)
T ss_dssp SEEEEEEEEEEE-TTSS--EEEEE-TTS-EEEEEESS----------SS---SEEEEEEEE-TTS-EEEEEEEE---SSS
T ss_pred CeEEEEEEEeeEcCCCC--EEEEEcCCCCEEEEEeCCCC--------CCCCCCEEEEEEEEcCCCCceEEEEEEeccCCC
Confidence 58999999999875444 44566433 35776654322 345689999999999877666888877777666
No 120
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=93.98 E-value=0.48 Score=36.44 Aligned_cols=68 Identities=19% Similarity=0.287 Sum_probs=42.1
Q ss_pred cCCeeEEEEEcCCc-eEEEEEecccccChhh-h-ccCCCCCEEEE-E-EEEeeeCCeeEE----EEEEEeeCCCchH
Q 023576 85 RASDVNFTLDDGTG-RVVCKRWASEVFDTRE-M-EAIQDGMYVRL-I-GNLKSFQGKKQI----VAFSVRPVTNFDE 152 (280)
Q Consensus 85 ~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~-~-~~~~~G~yVrV-~-G~l~~f~~~~~i----~~~~ir~v~d~Ne 152 (280)
...+..|+|.|.+| .|+|..|-+.+.+-.. . .....+-.|-| . .+++.|++.+.| .+.++..=.|..|
T Consensus 21 ~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v~inp~ipe 97 (106)
T cd04481 21 PSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKVYINPDIPE 97 (106)
T ss_pred cceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEEEECCCcHH
Confidence 34589999999998 6999999765422110 1 12345555555 3 699999986665 3444444333333
No 121
>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=93.97 E-value=0.13 Score=35.46 Aligned_cols=48 Identities=31% Similarity=0.391 Sum_probs=41.0
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++...+||..|.. ..++++.+|++.++++...+..-|..|.+.|.|=.
T Consensus 9 ~p~R~~Il~~L~~------~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 9 DPTRLRILRLLAS------NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp SHHHHHHHHHHHH------CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHhc------CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 4678889999943 35899999999999999999999999999999854
No 122
>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=93.96 E-value=0.31 Score=33.59 Aligned_cols=44 Identities=20% Similarity=0.355 Sum_probs=38.0
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
...++..+|++.++++...|..+|..|.++|.|...- ..+|..+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~-~~~~~l~ 66 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG-RGKYRVN 66 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC-CCeEEeC
Confidence 3568999999999999999999999999999998753 4577654
No 123
>PRK06386 replication factor A; Reviewed
Probab=93.88 E-value=0.46 Score=44.77 Aligned_cols=65 Identities=23% Similarity=0.242 Sum_probs=49.4
Q ss_pred eeEEEEEEEEEeee--------cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-EeeeCCeeEEEE
Q 023576 71 TNVTLVGLVYNKEE--------RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LKSFQGKKQIVA 141 (280)
Q Consensus 71 ~~V~iVG~V~~~~~--------~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~~f~~~~~i~~ 141 (280)
..|.|.++|+++.. ......-.|-|.||.|....|... ..+++|+.|++..- ++.|+++.+|++
T Consensus 13 ~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~~-------~~l~~Gd~v~i~na~v~~~~G~~~Lnv 85 (358)
T PRK06386 13 QNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP-------DAVKSGDVIEIKYCYSKEYNGKIRIYF 85 (358)
T ss_pred CcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCCc-------ccCCCCCEEEEEeEEEeeECCEEEEEE
Confidence 45677777776542 123445589999999999999742 46899999999865 558999999998
Q ss_pred E
Q 023576 142 F 142 (280)
Q Consensus 142 ~ 142 (280)
.
T Consensus 86 ~ 86 (358)
T PRK06386 86 D 86 (358)
T ss_pred c
Confidence 5
No 124
>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=93.84 E-value=0.1 Score=35.44 Aligned_cols=52 Identities=31% Similarity=0.379 Sum_probs=43.4
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
..+-.||.+|.+. .+++..+|++.++++...+...++.|...|.|-...|.+
T Consensus 3 ~~q~~iL~~l~~~------~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 3 PSQFRILRILYEN------GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp HHHHHHHHHHHHH------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHHHHHHHHHc------CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 3456688888764 379999999999999999999999999999998876654
No 125
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=93.60 E-value=0.61 Score=39.05 Aligned_cols=78 Identities=21% Similarity=0.391 Sum_probs=48.5
Q ss_pred EeeEEEEEEEEE-ee-----ecCCeeEEEEE------c-----CCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576 70 ITNVTLVGLVYN-KE-----ERASDVNFTLD------D-----GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 70 i~~V~iVG~V~~-~~-----~~~t~~~~~Ld------D-----gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~ 132 (280)
++.|.|+|.+.. .+ .....+.|+|- + .|--|.|+.|...++ .....++.|+.|-|.|+|+.
T Consensus 2 ~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae--~~~~~l~KG~~V~VeGrl~~ 79 (162)
T PRK07275 2 INNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAE--NLANWAKKGALIGVTGRIQT 79 (162)
T ss_pred eeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence 467888888854 11 12245566662 2 234599999987542 23467899999999999975
Q ss_pred --eCC---e----eEEEEEEEeeCCC
Q 023576 133 --FQG---K----KQIVAFSVRPVTN 149 (280)
Q Consensus 133 --f~~---~----~~i~~~~ir~v~d 149 (280)
|.+ + ..|.+..|..+..
T Consensus 80 r~y~dkdG~k~~~~evva~~i~~l~~ 105 (162)
T PRK07275 80 RNYENQQGQRVYVTEVVADNFQMLES 105 (162)
T ss_pred ceEECCCCCEEEEEEEEEeEEEECCC
Confidence 533 2 2355555555443
No 126
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=93.49 E-value=0.29 Score=35.75 Aligned_cols=64 Identities=20% Similarity=0.200 Sum_probs=41.4
Q ss_pred EEEEEEEeeecCCeeEEEEEcCCce-----EEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEE
Q 023576 75 LVGLVYNKEERASDVNFTLDDGTGR-----VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFS 143 (280)
Q Consensus 75 iVG~V~~~~~~~t~~~~~LdDgTG~-----I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ 143 (280)
+-|+|..+......--|-|.|.++- -++++-... . ...+++|+.|+|.|+++.|++..||....
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~----~-~~~~~~Gd~V~vtG~v~ey~g~tql~~~~ 70 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTG----S-GADVAVGDLVRVTGTVTEYYGLTQLTAVS 70 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecC----C-CCCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence 4577877765433345568886432 122211111 0 35689999999999999999988887644
No 127
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.48 E-value=0.24 Score=40.16 Aligned_cols=55 Identities=11% Similarity=0.100 Sum_probs=47.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..|-.||.+|.. +.|++..+|++.++++...|..+|+.|...|.|+...|.+
T Consensus 37 glt~~q~~vL~~l~~------~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~ 91 (144)
T PRK11512 37 DITAAQFKVLCSIRC------AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPN 91 (144)
T ss_pred CCCHHHHHHHHHHHH------cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcc
Confidence 467778889998864 2489999999999999999999999999999999987753
No 128
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=93.45 E-value=0.23 Score=38.23 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=40.3
Q ss_pred eeEEEEEEEEEeee---------cCCeeEEEEEcC-CceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576 71 TNVTLVGLVYNKEE---------RASDVNFTLDDG-TGRVVCKRWASEVFDTREMEAIQDGMYVRLIG 128 (280)
Q Consensus 71 ~~V~iVG~V~~~~~---------~~t~~~~~LdDg-TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G 128 (280)
..++|+|+|+.+.. ....+.+.|-|. +|.|.|.+|.+..+ .....|++|+.+.+.+
T Consensus 10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~--~f~~~l~eG~vy~i~~ 75 (104)
T cd04474 10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVD--KFYDLLEVGKVYYISK 75 (104)
T ss_pred CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHH--HhhcccccccEEEEec
Confidence 45778888876421 134578999999 88999999986432 2356789998887764
No 129
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=93.43 E-value=0.7 Score=49.79 Aligned_cols=73 Identities=19% Similarity=0.161 Sum_probs=52.8
Q ss_pred eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576 72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDGMYVRLIGNLKSF-QGKKQIVAFSV 144 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i 144 (280)
.|+|.|+|.+++......-+.|.|+||.|.|..=.+...+. .....+..|+.|.|.|.+..- .+...|.+..+
T Consensus 653 ~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~~~~i 729 (1094)
T PRK02983 653 EVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVTSW 729 (1094)
T ss_pred EEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEEEeEE
Confidence 59999999999887776777999999999997643321111 112358899999999998753 35555655554
No 130
>PRK12423 LexA repressor; Provisional
Probab=93.37 E-value=0.1 Score=45.06 Aligned_cols=53 Identities=17% Similarity=0.307 Sum_probs=44.8
Q ss_pred CCchhHHHHHHhcCCCCCCCCCcc--CHHHHHHHhC-CCHHHHHHHHHHHHhCCeeeec
Q 023576 214 LKDCDQMILDYLQQPSSSERERGV--HVNELSEQLK-IPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv--~v~~I~~~l~-~~~~~v~~al~~L~~eG~IYsT 269 (280)
|++-|++||++|++. ..+.|+ ++.||+++|+ .+...|+++|+.|...|+|-.+
T Consensus 4 lt~~q~~il~~l~~~---i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 4 LTPKRAAILAFIRER---IAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence 678899999999874 123455 9999999999 5899999999999999999864
No 131
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=93.33 E-value=0.17 Score=32.49 Aligned_cols=41 Identities=29% Similarity=0.408 Sum_probs=32.6
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.++..+||+.|+.. .-.+..+|++.+++++..|...+..|.
T Consensus 2 D~~D~~Il~~Lq~d------~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 2 DELDRKILRLLQED------GRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp -HHHHHHHHHHHH-------TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHc------CCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 46889999999975 246999999999999999999998873
No 132
>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=93.26 E-value=0.25 Score=36.24 Aligned_cols=48 Identities=29% Similarity=0.403 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
-.+|-+|.... .+.-++.++|+++++.++..+++.+..|...|.|-++
T Consensus 11 l~~l~~la~~~---~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 11 LRILLYLARHP---DGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHCTT---TSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHhCC---CCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 44666666542 2223999999999999999999999999999999765
No 133
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=93.21 E-value=0.65 Score=35.22 Aligned_cols=64 Identities=19% Similarity=0.284 Sum_probs=42.5
Q ss_pred EEEEEEEEEeee-----------cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEE
Q 023576 73 VTLVGLVYNKEE-----------RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQI 139 (280)
Q Consensus 73 V~iVG~V~~~~~-----------~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i 139 (280)
|-|+|.|.++.. ......+.|.|.|+ .|++.+|.+.+.. .....|+.|.+.+ +++.|+ .+.+
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~----~~~~~~~vv~~~~~~i~~~~-~~~l 76 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAEL----FDGSENPVIAIKGVKVSEFN-GKSL 76 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhh----cccCCCCEEEEEeeEEEecC-CeEE
Confidence 567787776531 12578899999999 8999999875421 1112277777765 455677 4566
Q ss_pred EE
Q 023576 140 VA 141 (280)
Q Consensus 140 ~~ 141 (280)
+.
T Consensus 77 ~~ 78 (101)
T cd04475 77 ST 78 (101)
T ss_pred ee
Confidence 55
No 134
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=93.18 E-value=0.2 Score=32.10 Aligned_cols=41 Identities=22% Similarity=0.304 Sum_probs=34.7
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
-.++..+|++.++++...+..+|..|.++|.|... ..+|..
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~--~~~~~i 47 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE--GGRIVI 47 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCEEEE
Confidence 35789999999999999999999999999999753 346643
No 135
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=93.07 E-value=0.22 Score=39.69 Aligned_cols=48 Identities=10% Similarity=0.296 Sum_probs=43.9
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..|+..|++++++.+ =+++.+++..++.+...++..+.+|+..|+||-
T Consensus 11 ~eLk~rIvElVRe~G------RiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 11 EELKARIVELVREHG------RITIKQLVAKTGASRNTVKRYLRELVARGDLYR 58 (127)
T ss_pred HHHHHHHHHHHHHcC------CccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence 468899999999863 469999999999999999999999999999996
No 136
>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=93.02 E-value=0.13 Score=44.13 Aligned_cols=56 Identities=16% Similarity=0.251 Sum_probs=46.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCC-HHHHHHHHHHHHhCCeeeec
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIP-QKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYsT 269 (280)
+|++.|.+||++|++... ......++.+|++.++++ ...|...|..|...|.|-..
T Consensus 3 ~lt~~q~~iL~~l~~~~~-~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 3 PLTARQQEVLDLIRAHIE-STGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred ccCHHHHHHHHHHHHHHH-hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 478899999999985311 123457889999999998 99999999999999999874
No 137
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=93.01 E-value=0.81 Score=38.74 Aligned_cols=62 Identities=19% Similarity=0.354 Sum_probs=40.5
Q ss_pred EeeEEEEEEEEE-ee-----ecCCeeEEEEE------cC-----CceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576 70 ITNVTLVGLVYN-KE-----ERASDVNFTLD------DG-----TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 70 i~~V~iVG~V~~-~~-----~~~t~~~~~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~ 132 (280)
++.|.|+|+|.. .+ .....+.|+|- +. |--|.|+.|...++ .....++.|+.|.|.|+|+.
T Consensus 2 mN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae--~~~~~l~KG~~V~VeGrL~~ 79 (173)
T PRK06751 2 MNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAE--NVANYLKKGSLAGVDGRLQT 79 (173)
T ss_pred ceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHH--HHHHHcCCCCEEEEEEEEEe
Confidence 356777887754 11 12245666662 22 23589999986532 23466899999999999996
Q ss_pred e
Q 023576 133 F 133 (280)
Q Consensus 133 f 133 (280)
-
T Consensus 80 r 80 (173)
T PRK06751 80 R 80 (173)
T ss_pred C
Confidence 3
No 138
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=92.94 E-value=0.31 Score=42.03 Aligned_cols=61 Identities=20% Similarity=0.327 Sum_probs=50.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC-CCccccccC
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI-DEFHYKFAR 279 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi-Dd~hfk~t~ 279 (280)
.++..+..||.+|... .++++.+|++.++++.+.+...|..|.+.|.|...- ....|+.|+
T Consensus 140 ~ls~~~~~IL~~l~~~------g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~ 201 (203)
T TIGR01884 140 GLSREELKVLEVLKAE------GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKGKRYSLTK 201 (203)
T ss_pred CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCccEEEeCC
Confidence 5677888999999763 268999999999999999999999999999999875 334565554
No 139
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=92.93 E-value=0.6 Score=46.82 Aligned_cols=62 Identities=15% Similarity=0.119 Sum_probs=45.0
Q ss_pred eeEEEEEEEEEeeecCC--eeEEEEEcCCc--eEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 71 TNVTLVGLVYNKEERAS--DVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t--~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
..|+|.|||.+++.... .+-..|.|+|| .|.|++- ...........+..|+-|+|.|++..-
T Consensus 82 ~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~-~~~~~~~~l~~l~~gs~v~v~G~v~~~ 147 (586)
T PTZ00425 82 QIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIENYEKLLKCGVGCCFRFTGKLIIS 147 (586)
T ss_pred CEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEEC-CchHHHHHHhcCCCccEEEEEEEEEcC
Confidence 46999999999988653 55668999999 4887652 221111234568899999999999853
No 140
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=92.91 E-value=0.25 Score=44.38 Aligned_cols=55 Identities=18% Similarity=0.360 Sum_probs=46.4
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
-.||++|.+. +.+++..||++.++++.+.+...|..|.++|.|...-|+..|..+
T Consensus 14 l~iL~~l~~~-----~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg 68 (263)
T PRK09834 14 LMVLRALNRL-----DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRLT 68 (263)
T ss_pred HHHHHHHHhc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEEc
Confidence 3478888653 346999999999999999999999999999999987677788754
No 141
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=92.79 E-value=0.51 Score=37.48 Aligned_cols=61 Identities=23% Similarity=0.339 Sum_probs=43.4
Q ss_pred EeeEEEEEEEEEe---e---ecCCeeEEEEE-------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576 70 ITNVTLVGLVYNK---E---ERASDVNFTLD-------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~ 132 (280)
++.|.|+|.+..- . .....+.|+|- +.|--+.|..|...++ .....++.|+.|.|.|+|+.
T Consensus 3 ~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~l~~ 76 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQ--VAADYVKKGSLIGITGSLKF 76 (121)
T ss_pred ccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence 4678888888551 1 22346677765 4566799999976432 23456899999999999995
No 142
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.72 E-value=0.24 Score=43.37 Aligned_cols=47 Identities=30% Similarity=0.461 Sum_probs=41.2
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.-++.||.+|+.. .+++.++|+++|+++...||.-|+.|..+|.|=.
T Consensus 11 ~tr~~il~lL~~~------g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~ 57 (218)
T COG2345 11 STRERILELLKKS------GPVSADELAEELGISPMAVRRHLDDLEAEGLVEV 57 (218)
T ss_pred cHHHHHHHHHhcc------CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceee
Confidence 4677899999874 3889999999999999999999999999997643
No 143
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.71 E-value=0.37 Score=38.96 Aligned_cols=56 Identities=20% Similarity=0.244 Sum_probs=47.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..|-.||..|... +.|++..+|++.++++...|...|+.|...|.|..+-|++
T Consensus 28 glt~~q~~vL~~l~~~-----~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~ 83 (144)
T PRK03573 28 ELTQTHWVTLHNIHQL-----PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCAS 83 (144)
T ss_pred CCCHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCC
Confidence 4566777888888652 2478999999999999999999999999999999998864
No 144
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=92.54 E-value=0.32 Score=43.93 Aligned_cols=54 Identities=19% Similarity=0.354 Sum_probs=45.2
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
-.||++|... +.++++.||++.++++.+.+...|..|.+.|+|+..-+...|..
T Consensus 28 l~IL~~~~~~-----~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~l 81 (271)
T PRK10163 28 IAILQYLEKS-----GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHI 81 (271)
T ss_pred HHHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEe
Confidence 3478888652 35799999999999999999999999999999998655666754
No 145
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=92.54 E-value=0.98 Score=44.11 Aligned_cols=99 Identities=18% Similarity=0.232 Sum_probs=67.3
Q ss_pred eHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC---hhhhccCCCCC
Q 023576 46 TVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD---TREMEAIQDGM 122 (280)
Q Consensus 46 tIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~G~ 122 (280)
++.+|....... ....+ ....+ .|.+.|+|..++......-+.|.|.+|.|.+.+-.+.... ......+..||
T Consensus 41 ~~~~l~~~~~~~-~~~el--~~~~~-~v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGD 116 (502)
T COG1190 41 TSADLREKYADK-TKEEL--EALNI-EVSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGD 116 (502)
T ss_pred cHHHHHHHHhcc-chhhh--hhccc-eeEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCC
Confidence 788888776532 11111 11111 2999999999987776667799999999998877554221 11245678999
Q ss_pred EEEEEEEEeeeC-CeeEEEEEEEeeCC
Q 023576 123 YVRLIGNLKSFQ-GKKQIVAFSVRPVT 148 (280)
Q Consensus 123 yVrV~G~l~~f~-~~~~i~~~~ir~v~ 148 (280)
+|-|.|.+-.-+ |...|.+..++.++
T Consensus 117 iigv~G~~~~T~~GelSv~v~~~~lLs 143 (502)
T COG1190 117 IIGVEGPLFKTKTGELSVSVEELRLLS 143 (502)
T ss_pred EEeeeeeeeecCCCceEEEEEEEeeec
Confidence 999999987665 77777776655443
No 146
>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=92.53 E-value=0.48 Score=36.64 Aligned_cols=58 Identities=22% Similarity=0.345 Sum_probs=47.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
+++..+-.||.+|.-.. ..+.+++..+|+..++++...|..+|+.|...|.|...-|+
T Consensus 22 ~ls~~q~~vL~~l~~~~--~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~ 79 (109)
T TIGR01889 22 NLSLEELLILYYLGKLE--NNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE 79 (109)
T ss_pred CCCHHHHHHHHHHHhhh--ccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc
Confidence 46677778998887210 12458999999999999999999999999999999976665
No 147
>PRK02801 primosomal replication protein N; Provisional
Probab=92.50 E-value=1.1 Score=34.29 Aligned_cols=33 Identities=12% Similarity=0.083 Sum_probs=25.7
Q ss_pred EEEEEecccccChhhhccCCCCCEEEEEEEEeeeC
Q 023576 100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ 134 (280)
Q Consensus 100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~ 134 (280)
|+|+.|-..++ .....+..|+.|.|.|.|+.+.
T Consensus 50 i~~va~G~~Ae--~~~~~l~kGs~v~V~G~L~~~~ 82 (101)
T PRK02801 50 MPVIVSGNQFQ--AITQSITVGSKITVQGFISCHQ 82 (101)
T ss_pred EEEEEEcHHHH--HHHhhcCCCCEEEEEEEEEEeE
Confidence 89999986542 2234699999999999999853
No 148
>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=92.49 E-value=0.21 Score=34.65 Aligned_cols=35 Identities=17% Similarity=0.382 Sum_probs=31.3
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
...+...+||+.|+++...|.++|..|.++|.|--
T Consensus 20 ~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEe
Confidence 45899999999999999999999999999999854
No 149
>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=92.46 E-value=0.28 Score=29.63 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=26.0
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
++.+||++.++.+.+.|-.+|..|..+|.|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 578999999999999999999999999987
No 150
>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=92.42 E-value=0.32 Score=43.13 Aligned_cols=51 Identities=10% Similarity=0.189 Sum_probs=43.2
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
.||++|... ..++++.||++.++++.+.+...|..|.+.|.+.. |+..|..
T Consensus 13 ~IL~~l~~~-----~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~--~~~~Y~l 63 (248)
T TIGR02431 13 AVIEAFGAE-----RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS--DGRLFWL 63 (248)
T ss_pred HHHHHHhcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--CCCEEEe
Confidence 477777652 45899999999999999999999999999999987 5567764
No 151
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=92.35 E-value=0.32 Score=32.67 Aligned_cols=44 Identities=30% Similarity=0.414 Sum_probs=36.8
Q ss_pred HHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576 221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 221 Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
|+++|. . ..++..+|++.++++...+..+|+.|.+.|.|...-+
T Consensus 2 il~~l~-~------~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 2 ILKLLA-E------GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred HHHHhh-c------CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 566665 2 3579999999999999999999999999999986543
No 152
>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=92.32 E-value=0.42 Score=37.28 Aligned_cols=55 Identities=24% Similarity=0.317 Sum_probs=47.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..|-.||.+|... .++++.+|++.++++...|...|+.|...|.|-..-|..
T Consensus 25 ~lt~~q~~iL~~l~~~------~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~ 79 (118)
T TIGR02337 25 GLTEQQWRILRILAEQ------GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN 79 (118)
T ss_pred CCCHHHHHHHHHHHHc------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC
Confidence 4566777899998753 378999999999999999999999999999999987653
No 153
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=92.30 E-value=0.32 Score=36.80 Aligned_cols=49 Identities=27% Similarity=0.474 Sum_probs=41.2
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++++...||..|.... .+ +..-|+++++++.++|+.+|+.|.+.|.|=.
T Consensus 5 ~~~l~~~IL~hl~~~~---~D---y~k~ia~~l~~~~~~v~~~l~~Le~~GLler 53 (92)
T PF10007_consen 5 LDPLDLKILQHLKKAG---PD---YAKSIARRLKIPLEEVREALEKLEEMGLLER 53 (92)
T ss_pred cChhHHHHHHHHHHHC---CC---cHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 3567888999998752 33 6678999999999999999999999999855
No 154
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=92.30 E-value=0.24 Score=44.39 Aligned_cols=48 Identities=27% Similarity=0.430 Sum_probs=41.5
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+=+++|+++|++.+ -+++.|+++.|+.++..||.-|.+|.++|.|..+
T Consensus 5 eR~~~Il~~L~~~~------~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 5 QRQAAILEYLQKQG------KTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHHcC------CEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 35678999999742 4899999999999999999999999999987553
No 155
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=92.02 E-value=0.28 Score=43.92 Aligned_cols=48 Identities=19% Similarity=0.321 Sum_probs=42.5
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+-+++|+++|++. .-+++.+|+++|++++..||.-|.+|.++|.|..+
T Consensus 5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 5 QRHDAIIELVKQQ------GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHHc------CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4567899999874 25899999999999999999999999999999775
No 156
>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=92.02 E-value=0.49 Score=41.41 Aligned_cols=32 Identities=22% Similarity=0.397 Sum_probs=30.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 238 HVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+..+++++++.+...||+||+.|.+||.|+.-
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~ 65 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAE 65 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 78999999999999999999999999999873
No 157
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=92.01 E-value=0.17 Score=36.58 Aligned_cols=49 Identities=12% Similarity=0.220 Sum_probs=41.7
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
..+.+..++++.+.+. .+|+++.||++.+++++..|+..+..+.++|.+
T Consensus 14 ~~l~~~~r~af~L~R~------~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 14 TWVDSLAEAAAALARE------EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred hcCCHHHHHHHHHHHH------HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 3567788888888754 259999999999999999999999999888865
No 158
>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=91.99 E-value=0.48 Score=41.48 Aligned_cols=51 Identities=14% Similarity=0.151 Sum_probs=37.5
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+.|.+-|.+..- ....=+ +-.+++++++.+...||+||+.|.+||.|+.
T Consensus 5 i~~~l~~~I~~g~~-~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 56 (233)
T TIGR02404 5 IYQDLEQKITHGQY-KEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQK 56 (233)
T ss_pred HHHHHHHHHHhCCC-CCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44556666654211 111123 7899999999999999999999999999986
No 159
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=91.88 E-value=1 Score=45.27 Aligned_cols=101 Identities=14% Similarity=0.102 Sum_probs=63.0
Q ss_pred eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCC-eeEEEEEcCCceEEEEEecccc---cCh-hh-hc
Q 023576 43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERAS-DVNFTLDDGTGRVVCKRWASEV---FDT-RE-ME 116 (280)
Q Consensus 43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t-~~~~~LdDgTG~I~~~~w~~~~---~~~-~~-~~ 116 (280)
+..+|+++.+....-..+ .. ..+ ..|+|-|+|.+++.... -.-+.|.|.+|.|.|..-.+.. .+. .. ..
T Consensus 110 ~~~~~~~~~~~~~~~~~~-~~-~~~---~~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~ 184 (585)
T PTZ00417 110 RTITVPEFVEKYQDLASG-EH-LED---TILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYD 184 (585)
T ss_pred CCcCHHHHHHHhhccCcc-cc-ccC---CeEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHh
Confidence 346788887654321001 11 111 23899999999988764 4455777888899988754321 111 11 24
Q ss_pred cCCCCCEEEEEEEEeee-CCeeEEEEEEEeeCC
Q 023576 117 AIQDGMYVRLIGNLKSF-QGKKQIVAFSVRPVT 148 (280)
Q Consensus 117 ~~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~v~ 148 (280)
.+..|+.|.|.|.+..- .+...|.+..|..+.
T Consensus 185 ~l~~Gd~V~V~G~~~~t~~gel~i~~~~i~lls 217 (585)
T PTZ00417 185 KIRRGDIVGIVGFPGKSKKGELSIFPKETIILS 217 (585)
T ss_pred cCCCCCEEEEEeEEcCCCCceEEEEEEEEEEEe
Confidence 68999999999997654 466777776655443
No 160
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=91.86 E-value=0.52 Score=41.58 Aligned_cols=51 Identities=8% Similarity=0.173 Sum_probs=37.5
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+.|.+-|.+..- ....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus 10 i~~~L~~~I~~g~~-~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r 61 (240)
T PRK09764 10 IADRIREQIARGEL-KPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILES 61 (240)
T ss_pred HHHHHHHHHHcCCC-CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44555555544211 112234 6799999999999999999999999999985
No 161
>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=91.78 E-value=0.52 Score=41.22 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=37.6
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+.|.+-|....- ....=+ +..+++++++.+...||+||+.|.+||.||.
T Consensus 6 i~~~l~~~I~~g~~-~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 57 (230)
T TIGR02018 6 IKQDILERIRSGEW-PPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLER 57 (230)
T ss_pred HHHHHHHHHHhCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44555555544211 112224 7899999999999999999999999999986
No 162
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=91.72 E-value=1.8 Score=33.72 Aligned_cols=77 Identities=16% Similarity=0.309 Sum_probs=47.1
Q ss_pred eeEEEEEEEEEe---e---ecCCeeEEEEE------cC-----CceEEEEEecccccChhhhccCCCCCEEEEEEEEee-
Q 023576 71 TNVTLVGLVYNK---E---ERASDVNFTLD------DG-----TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS- 132 (280)
Q Consensus 71 ~~V~iVG~V~~~---~---~~~t~~~~~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~- 132 (280)
+.|.|+|.+..- . ....++.|+|- |. |--+.|..|...++ .....+..|+.|.|.|+|+.
T Consensus 3 N~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~l~~~ 80 (112)
T PRK06752 3 NRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAE--NVTEYCTKGSLVGITGRIHTR 80 (112)
T ss_pred eEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHH--HHHHhcCCCCEEEEEEEEEeC
Confidence 566777776441 1 12234555554 21 33588999976432 23456899999999999986
Q ss_pred -eCC---e----eEEEEEEEeeCCC
Q 023576 133 -FQG---K----KQIVAFSVRPVTN 149 (280)
Q Consensus 133 -f~~---~----~~i~~~~ir~v~d 149 (280)
|.+ + ..|.+..|..++.
T Consensus 81 ~~~~~~G~~~~~~ei~a~~i~~l~~ 105 (112)
T PRK06752 81 NYEDDQGKRIYITEVVIESITFLER 105 (112)
T ss_pred ccCCCCCcEEEEEEEEEEEEEECCC
Confidence 432 2 2366777776654
No 163
>PRK14999 histidine utilization repressor; Provisional
Probab=91.70 E-value=0.56 Score=41.38 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=38.2
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+...|.+-|.+.. -....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus 17 i~~~i~~~I~~g~-~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 68 (241)
T PRK14999 17 VKQDICKKIAGGV-WQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVR 68 (241)
T ss_pred HHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4455555555421 1122234 7899999999999999999999999999985
No 164
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=91.67 E-value=0.51 Score=33.29 Aligned_cols=48 Identities=17% Similarity=0.372 Sum_probs=35.9
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 266 (280)
+++.|+++|+.... .-.=.=+.|+++.+ ...+.+|++++..|++||.+
T Consensus 2 ~K~~Ile~L~~k~~--~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l 50 (67)
T PF08679_consen 2 AKQKILEFLEAKKK--KKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL 50 (67)
T ss_dssp HHHHHHHHHSSCCC--HSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHhccC--CCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence 67889999985421 22345678999977 69999999999999999976
No 165
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=91.64 E-value=1.7 Score=36.29 Aligned_cols=61 Identities=20% Similarity=0.229 Sum_probs=41.1
Q ss_pred eeEEEEEEEEE-ee-----ecCCeeEEEEE--------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 71 TNVTLVGLVYN-KE-----ERASDVNFTLD--------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 71 ~~V~iVG~V~~-~~-----~~~t~~~~~Ld--------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
+.|.|+|.+.. .+ ....++.|+|- +.|--|.|..|...++ .....++.|+.|-|.|+|+.-
T Consensus 2 N~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae--~v~~yL~KG~~V~VeGrL~~~ 76 (161)
T PRK06293 2 MFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYD--KMLPYLKKGSGVIVAGEMSPE 76 (161)
T ss_pred eEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHH--HHHHhCCCCCEEEEEEEEEeC
Confidence 46778888754 11 12346666665 2455699999976431 224569999999999999964
No 166
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=91.63 E-value=1.5 Score=35.20 Aligned_cols=54 Identities=24% Similarity=0.311 Sum_probs=39.5
Q ss_pred eeEEEEEEEE--Eeee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576 71 TNVTLVGLVY--NKEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL 130 (280)
Q Consensus 71 ~~V~iVG~V~--~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l 130 (280)
..|+|-|.|. ++.. ....++|.|.|+...|.|.+--. .++.|++|.-|-|.|++
T Consensus 51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~------~Pd~F~eg~~VVv~G~~ 108 (131)
T PF03100_consen 51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGP------LPDLFREGQGVVVEGRL 108 (131)
T ss_dssp SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--------CTT--TTSEEEEEEEE
T ss_pred ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCC------CCccccCCCeEEEEEEE
Confidence 5788899998 4555 46899999999988898886543 24679999999999998
No 167
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=91.60 E-value=1.6 Score=36.70 Aligned_cols=81 Identities=20% Similarity=0.197 Sum_probs=50.1
Q ss_pred EeeEEEEEEEEEe---e---ecCCeeEEEEE------c-C-------CceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576 70 ITNVTLVGLVYNK---E---ERASDVNFTLD------D-G-------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129 (280)
Q Consensus 70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-g-------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~ 129 (280)
+++|.|+|.+..- + .....+.|+|- | . |--+.|..|....+ .....++.|+.|.|.|+
T Consensus 4 ~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE--~v~~~LkKGs~V~VeGr 81 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAE--VAGEYLRKGSQVYVEGR 81 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHH--HHHHHCCCCCEEEEEEE
Confidence 6788888888652 1 12234555543 1 1 22477888875431 23466999999999999
Q ss_pred Eeee--CC---e----eEEEEEEEeeCCCchH
Q 023576 130 LKSF--QG---K----KQIVAFSVRPVTNFDE 152 (280)
Q Consensus 130 l~~f--~~---~----~~i~~~~ir~v~d~Ne 152 (280)
|+.- .+ + ..|.+..|..+...++
T Consensus 82 L~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~~ 113 (168)
T PRK06863 82 LKTRKWQDQNGQDRYTTEIQGDVLQMLGGRNQ 113 (168)
T ss_pred EEeCCccCCCCCEEEEEEEEEeEEEECCCCCc
Confidence 9974 32 2 3466666766665443
No 168
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=91.44 E-value=0.58 Score=41.26 Aligned_cols=31 Identities=13% Similarity=0.313 Sum_probs=29.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 238 HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-.+++++++.+...||+||+.|.+||.||.
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 67 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQR 67 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7799999999999999999999999999986
No 169
>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=91.38 E-value=0.39 Score=33.97 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=40.1
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
-.|+++|.+. ..+++.+|.+..+++..++.-||-.|..|+.|+---.+
T Consensus 11 G~Vw~~L~~~------~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~ 58 (65)
T PF10771_consen 11 GKVWQLLNEN------GEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN 58 (65)
T ss_dssp HHHHHHHCCS------SSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred HHHHHHHhhC------CCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence 3689999873 36899999999999999999999999999999865433
No 170
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=91.34 E-value=1.8 Score=36.93 Aligned_cols=62 Identities=19% Similarity=0.176 Sum_probs=40.9
Q ss_pred EeeEEEEEEEEEe-e-----ecCCeeEEEEE--------------cCCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576 70 ITNVTLVGLVYNK-E-----ERASDVNFTLD--------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129 (280)
Q Consensus 70 i~~V~iVG~V~~~-~-----~~~t~~~~~Ld--------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~ 129 (280)
++.|.|+|.|..- + .....+.|+|- +.|--+.|.+|...++ .....++.|+.|.|.|+
T Consensus 4 ~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE--~v~~~LkKGs~V~VeGr 81 (182)
T PRK06958 4 VNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAE--IVGEYLKKGSSVYIEGR 81 (182)
T ss_pred ccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHH--HHHHHhCCCCEEEEEEE
Confidence 5788888888552 1 12245566662 1244577888865431 23457899999999999
Q ss_pred Eeee
Q 023576 130 LKSF 133 (280)
Q Consensus 130 l~~f 133 (280)
|+..
T Consensus 82 L~~~ 85 (182)
T PRK06958 82 IRTR 85 (182)
T ss_pred EEeC
Confidence 9964
No 171
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=91.34 E-value=0.31 Score=43.70 Aligned_cols=46 Identities=30% Similarity=0.481 Sum_probs=40.9
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
=+++|+++|++. .=++++++++.|+.++..||.-|.+|.++|.+=.
T Consensus 6 R~~~Il~~l~~~------g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R 51 (253)
T COG1349 6 RHQKILELLKEK------GKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR 51 (253)
T ss_pred HHHHHHHHHHHc------CcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence 567899999974 2579999999999999999999999999998754
No 172
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=91.29 E-value=1.2 Score=33.56 Aligned_cols=62 Identities=21% Similarity=0.269 Sum_probs=35.7
Q ss_pred EeeEEEEEEEEE---eee---cCCeeEEEEE--c-----------CCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576 70 ITNVTLVGLVYN---KEE---RASDVNFTLD--D-----------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL 130 (280)
Q Consensus 70 i~~V~iVG~V~~---~~~---~~t~~~~~Ld--D-----------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l 130 (280)
++.|.|+|.|.. +.. ...++.|.|. + .|--+.|..|.+.++ .....++.|+.|.|.|++
T Consensus 1 mN~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l 78 (104)
T PF00436_consen 1 MNKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAE--NVAEYLKKGDRVYVEGRL 78 (104)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHH--HHHHH--TT-EEEEEEEE
T ss_pred CcEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeeccc--ccceEEcCCCEEEEEEEE
Confidence 467888888844 211 1234444432 2 122488888866431 224569999999999999
Q ss_pred eee
Q 023576 131 KSF 133 (280)
Q Consensus 131 ~~f 133 (280)
+..
T Consensus 79 ~~~ 81 (104)
T PF00436_consen 79 RTR 81 (104)
T ss_dssp EEE
T ss_pred Eee
Confidence 975
No 173
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=91.24 E-value=0.54 Score=41.92 Aligned_cols=54 Identities=24% Similarity=0.451 Sum_probs=46.1
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
-+||++|.+. +.++++.+|+++++++.+.+...|..|.+.|.+...-++.+|..
T Consensus 7 l~iL~~l~~~-----~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~L 60 (246)
T COG1414 7 LAILDLLAEG-----PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRL 60 (246)
T ss_pred HHHHHHHHhC-----CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEee
Confidence 3588888862 35789999999999999999999999999999999755557764
No 174
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.24 E-value=2 Score=35.96 Aligned_cols=36 Identities=14% Similarity=0.057 Sum_probs=27.3
Q ss_pred CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 96 GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 96 gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
.|--|.|+.|...+. .....++.|+.|.|.|+|+.-
T Consensus 49 ~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L~~~ 84 (164)
T TIGR00621 49 ETEWHDIVIFGRLAE--VAAQYLKKGSLVYVEGRLRTR 84 (164)
T ss_pred cceEEEEEEehHHHH--HHHHhCCCCCEEEEEEEEEec
Confidence 355799999976432 234579999999999999963
No 175
>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=91.02 E-value=0.25 Score=34.42 Aligned_cols=55 Identities=18% Similarity=0.379 Sum_probs=39.8
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHH-HHHHHHHHHhCCeeeecCCCccccccC
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKK-IMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~-v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
+.+.|+.-|+- ..|++++++.++++.+..+ +.+.|+.|.++|.| ++|+++++.|.
T Consensus 7 ~~e~i~~~LR~------~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll--~~~~~~l~lT~ 62 (66)
T PF06969_consen 7 LREYIMLGLRC------NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL--EIDGGRLRLTE 62 (66)
T ss_dssp HHHHHHHHHHH------HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE--EE-SSEEEE-T
T ss_pred HHHHHHHHHHh------HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE--EEeCCEEEECc
Confidence 44556666664 2599999999999977555 58889999999999 56788998875
No 176
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=90.90 E-value=0.74 Score=40.53 Aligned_cols=31 Identities=26% Similarity=0.431 Sum_probs=29.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 238 HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-.+++++++.+...||+||+.|.+||.|+.
T Consensus 35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r 65 (241)
T PRK11402 35 TENELCTQYNVSRITIRKAISDLVADGVLIR 65 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7799999999999999999999999999986
No 177
>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=90.89 E-value=0.62 Score=37.07 Aligned_cols=48 Identities=19% Similarity=0.274 Sum_probs=39.8
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
-.+|..|... .+..+++++|+++++++..-+++.|..|...|.|.+.-
T Consensus 12 l~~l~~la~~----~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 12 TLVLTTLAQN----DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred HHHHHHHHhC----CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence 3466666542 34579999999999999999999999999999998753
No 178
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=90.88 E-value=0.65 Score=41.45 Aligned_cols=52 Identities=17% Similarity=0.340 Sum_probs=43.5
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
.||++|.+. .++++.||+++++++.+.+...|..|.+.|.|+..-++..|..
T Consensus 18 ~IL~~l~~~------~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~l 69 (257)
T PRK15090 18 GILQALGEE------REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSL 69 (257)
T ss_pred HHHHHhhcC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEe
Confidence 477777541 3689999999999999999999999999999998655667764
No 179
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=90.81 E-value=0.75 Score=37.44 Aligned_cols=65 Identities=17% Similarity=0.341 Sum_probs=37.0
Q ss_pred eeEEEEEcCCceEEEEEecccccC----------------hhh----hcc-CCCCCEEEEEEEEeeeCCe--eEEEEEEE
Q 023576 88 DVNFTLDDGTGRVVCKRWASEVFD----------------TRE----MEA-IQDGMYVRLIGNLKSFQGK--KQIVAFSV 144 (280)
Q Consensus 88 ~~~~~LdDgTG~I~~~~w~~~~~~----------------~~~----~~~-~~~G~yVrV~G~l~~f~~~--~~i~~~~i 144 (280)
.+.+.|.|+||.+.+..|.+.... ... ... +-..-.++|.++...|+++ ..+++.+|
T Consensus 55 ~l~~~i~D~tg~~~~~~F~~~a~~l~G~~a~el~~~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~i 134 (146)
T PF08646_consen 55 RLSLKISDGTGSIWVTLFDEEAEQLLGMSADELKELKEEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVRI 134 (146)
T ss_dssp EEEEEEEETTEEEEEEEEHHHHHHHHCCHHCCCHHHCCC-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEEE
T ss_pred EEEEEEEeCCCeEEEEEEhHHHHHHhCCCHHHHHHHHhhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEEe
Confidence 466789999999999999864320 000 111 1222457899999999865 56888999
Q ss_pred eeCCCchH
Q 023576 145 RPVTNFDE 152 (280)
Q Consensus 145 r~v~d~Ne 152 (280)
.||+-..|
T Consensus 135 ~~vd~~~e 142 (146)
T PF08646_consen 135 EPVDYAEE 142 (146)
T ss_dssp EE--HHHH
T ss_pred EeCCHHHH
Confidence 99854333
No 180
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=90.78 E-value=0.73 Score=40.72 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=37.2
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
|...|.+-|.+-.- ....-+ +-.+++++++.+...||+||+.|.++|.|+.
T Consensus 12 I~~~i~~~I~~G~~-~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r 63 (236)
T COG2188 12 IAEDIRQRIESGEL-PPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVR 63 (236)
T ss_pred HHHHHHHHHHhCCC-CCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEE
Confidence 45555555554211 111123 6799999999999999999999999999985
No 181
>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=90.52 E-value=1.1 Score=31.40 Aligned_cols=50 Identities=20% Similarity=0.258 Sum_probs=40.3
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
.+|++++++. -++..+|+++++++...|+..+..|.++|...... ...|.
T Consensus 3 ~~il~~L~~~-------~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~-~~g~~ 52 (69)
T TIGR00122 3 LRLLALLADN-------PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV-GKGYR 52 (69)
T ss_pred HHHHHHHHcC-------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec-CCceE
Confidence 4678887742 36799999999999999999999999999976554 44554
No 182
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=90.50 E-value=0.68 Score=39.35 Aligned_cols=51 Identities=18% Similarity=0.344 Sum_probs=44.8
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
+..+.||.+|+.. +.+++.-+|+++|+++-.+|+..|-.|..+|.||.+ |+
T Consensus 4 ~~~~~i~~~l~~~-----~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~-~~ 54 (183)
T PHA02701 4 DCASLILTLLSSS-----GDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCE-DG 54 (183)
T ss_pred hHHHHHHHHHHhc-----CCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC-CC
Confidence 4678899999974 335999999999999999999999999999999987 44
No 183
>PRK09954 putative kinase; Provisional
Probab=90.41 E-value=0.5 Score=44.22 Aligned_cols=46 Identities=24% Similarity=0.427 Sum_probs=40.7
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
++...+||++|++++ =++..+|+++|+++...|+..|..|.++|.|
T Consensus 2 ~~~~~~il~~l~~~~------~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 2 NNREKEILAILRRNP------LIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred ChHHHHHHHHHHHCC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 456778999999752 4799999999999999999999999999876
No 184
>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=90.37 E-value=0.75 Score=35.61 Aligned_cols=49 Identities=22% Similarity=0.343 Sum_probs=41.0
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecC
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
.+..||++|.+. +.-++.++|.+++ +++...|-.+|+.|.+.|.|=...
T Consensus 2 qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 2 QRLAILEVLLES-----DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHHHHHhC-----CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 356799999863 3578999999998 489999999999999999987643
No 185
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=90.35 E-value=3.3 Score=36.42 Aligned_cols=81 Identities=14% Similarity=0.203 Sum_probs=56.3
Q ss_pred EEEeeEEEEEEEEEe---e---ecCCeeEEEEEc-----CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee--C
Q 023576 68 LEITNVTLVGLVYNK---E---ERASDVNFTLDD-----GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--Q 134 (280)
Q Consensus 68 ~~i~~V~iVG~V~~~---~---~~~t~~~~~LdD-----gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~ 134 (280)
..++.|.|+|.+..- . .....+.|+|-= .|--|.|..|...+. .+..++.|+.|.|.|+|+.. .
T Consensus 107 ~~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae---~~~~l~KG~~V~V~GrL~sr~y~ 183 (219)
T PRK05813 107 KNPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNAR---FCKTLEVGDNIRVWGRVQSREYQ 183 (219)
T ss_pred CCccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhH---HHhhCCCCCEEEEEEEEEecceE
Confidence 457899999999652 1 123466666652 255799999987542 24469999999999999974 3
Q ss_pred C--------e---eEEEEEEEeeCCCch
Q 023576 135 G--------K---KQIVAFSVRPVTNFD 151 (280)
Q Consensus 135 ~--------~---~~i~~~~ir~v~d~N 151 (280)
+ + -.|.+.+|..+...+
T Consensus 184 ~k~g~~~g~kr~~~eV~v~~i~~l~~~~ 211 (219)
T PRK05813 184 KKLSEGEVVTKVAYEVSISKMEKVEKEE 211 (219)
T ss_pred cCCCCccceEEEEEEEEEEEEEEcCChh
Confidence 2 2 247778887776644
No 186
>PRK11569 transcriptional repressor IclR; Provisional
Probab=90.34 E-value=0.69 Score=41.76 Aligned_cols=53 Identities=15% Similarity=0.396 Sum_probs=44.2
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
.||++|.+. +.++++.||++.++++.+.+...|..|.++|.+...-+...|..
T Consensus 32 ~IL~~l~~~-----~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~l 84 (274)
T PRK11569 32 KLLEWIAES-----NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAI 84 (274)
T ss_pred HHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEec
Confidence 478887652 45799999999999999999999999999999987555566753
No 187
>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=90.22 E-value=1.2 Score=35.30 Aligned_cols=45 Identities=27% Similarity=0.355 Sum_probs=38.0
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC-CCcccccc
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI-DEFHYKFA 278 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi-Dd~hfk~t 278 (280)
+..++.++|++.++++...|++.|+.|...|.|-++- .+..|+.+
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~ 68 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLA 68 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCC
Confidence 3489999999999999999999999999999998753 33467654
No 188
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=90.20 E-value=0.84 Score=38.50 Aligned_cols=56 Identities=25% Similarity=0.240 Sum_probs=43.5
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHh--CCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQL--KIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
....|++++.-.+ |. ...+|+++| +++.++|+++|++|..-|.|=-.-| ..|+.|+
T Consensus 25 ~~~~ir~l~~l~~------~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~-g~y~~t~ 83 (171)
T PF14394_consen 25 YHPAIRELLPLMP------FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD-GKYVQTD 83 (171)
T ss_pred HHHHHHHHhhcCC------CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC-CcEEEec
Confidence 3445666665432 33 899999999 7999999999999999999987544 4777665
No 189
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=90.08 E-value=3.1 Score=34.85 Aligned_cols=61 Identities=21% Similarity=0.164 Sum_probs=41.1
Q ss_pred EeeEEEEEEEEE---ee---ecCCeeEEEEE------cC-------CceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576 70 ITNVTLVGLVYN---KE---ERASDVNFTLD------DG-------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL 130 (280)
Q Consensus 70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld------Dg-------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l 130 (280)
++.|.|+|.|.+ +. .....+.|+|- |. |--+.|.+|...++ .....++.|+.|.|.|+|
T Consensus 5 ~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae--~v~~~L~KGs~V~VeGrL 82 (164)
T PRK08763 5 INKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGE--IAGEYLRKGSQCYIEGSI 82 (164)
T ss_pred ceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHH--HHHHhcCCCCEEEEEEEE
Confidence 788899998866 21 12345666664 22 22388889965321 234568999999999999
Q ss_pred ee
Q 023576 131 KS 132 (280)
Q Consensus 131 ~~ 132 (280)
+.
T Consensus 83 ~~ 84 (164)
T PRK08763 83 RY 84 (164)
T ss_pred Ee
Confidence 86
No 190
>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=90.07 E-value=0.49 Score=34.62 Aligned_cols=54 Identities=28% Similarity=0.318 Sum_probs=41.9
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
|++-|++||..|=+.= ....+-|.=.+|++.++.++..||..+..|.+.|+|.+
T Consensus 2 Lt~rq~~IL~alV~~Y-~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 2 LTERQREILKALVELY-IETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred CCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 5667777777553321 12345677799999999999999999999999999985
No 191
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=89.76 E-value=0.37 Score=41.09 Aligned_cols=47 Identities=13% Similarity=0.113 Sum_probs=41.2
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
-++.|+++|++.+ =+++.++++.|+.++..||.-|.+|..+|++=.|
T Consensus 8 R~~~Il~~l~~~~------~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENP------FITDEELAEKFGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCC------CEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence 5677999998742 4799999999999999999999999999988655
No 192
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=89.69 E-value=1.8 Score=35.92 Aligned_cols=72 Identities=14% Similarity=0.230 Sum_probs=45.5
Q ss_pred eeEEEEEcCCceEEEEEecccccC-----h--------h-------hhccCCCCC--EEEEEEEEeeeCC--eeEEEEEE
Q 023576 88 DVNFTLDDGTGRVVCKRWASEVFD-----T--------R-------EMEAIQDGM--YVRLIGNLKSFQG--KKQIVAFS 143 (280)
Q Consensus 88 ~~~~~LdDgTG~I~~~~w~~~~~~-----~--------~-------~~~~~~~G~--yVrV~G~l~~f~~--~~~i~~~~ 143 (280)
.+.+.|.|+||.+.+..|.+.... . . ....+ .|. .++|..+...|++ +...++.+
T Consensus 69 ~l~~~i~D~Tg~~~~~~F~~~ae~l~G~sa~el~~~~~~~~~~~~~~i~~~-~gk~~~f~v~~~~~~y~~e~~~~~~v~~ 147 (166)
T cd04476 69 ILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDL-VGKTFLFRVSVKEETYNDEGRIRYTVVK 147 (166)
T ss_pred EEEEEEEeCCCCEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHHh-hCceEEEEEEEEehhcCCcceEEEEEEE
Confidence 467899999999999999754320 0 0 01111 233 4566666778887 66677777
Q ss_pred EeeCCCchHHHHHHHHHH
Q 023576 144 VRPVTNFDEVTCHYIECI 161 (280)
Q Consensus 144 ir~v~d~Nei~~H~Le~i 161 (280)
|.|+.- .+...++|+-+
T Consensus 148 i~~~~~-~~~~~~l~~~i 164 (166)
T cd04476 148 VAPVDY-KKESKRLIQSI 164 (166)
T ss_pred cccCCH-HHHHHHHHHHh
Confidence 777743 45566666654
No 193
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=89.66 E-value=2.7 Score=31.23 Aligned_cols=36 Identities=14% Similarity=0.152 Sum_probs=27.5
Q ss_pred CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 96 GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 96 gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
.+--+.|..|.+.+. .....++.|+.|.|.|+++..
T Consensus 42 ~~~~~~v~~~g~~a~--~~~~~~~kG~~V~v~G~l~~~ 77 (100)
T cd04496 42 ETDWIRVVAFGKLAE--NAAKYLKKGDLVYVEGRLRTR 77 (100)
T ss_pred ccEEEEEEEEhHHHH--HHHHHhCCCCEEEEEEEEEec
Confidence 445699999987432 234569999999999999975
No 194
>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=89.42 E-value=0.64 Score=32.89 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=38.6
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+++++||++|++.+ ......-+++..|+.+..+|+..|-.|..+|.|+.
T Consensus 4 ~~ee~Il~~L~~~g----~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k 52 (66)
T PF02295_consen 4 DLEEKILDFLKELG----GSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCK 52 (66)
T ss_dssp HHHHHHHHHHHHHT----SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hHHHHHHHHHHhcC----CccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEee
Confidence 57889999999852 33555555666677889999999999999999985
No 195
>PHA02943 hypothetical protein; Provisional
Probab=89.28 E-value=1.1 Score=36.96 Aligned_cols=46 Identities=13% Similarity=0.225 Sum_probs=38.6
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-..+||++|+. -..+..+||+.++++-.+++-+|--|..||.|-+
T Consensus 11 ~R~~eILE~Lk~-------G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr 56 (165)
T PHA02943 11 TRMIKTLRLLAD-------GCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK 56 (165)
T ss_pred HHHHHHHHHHhc-------CCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE
Confidence 345678888832 1467999999999999999999999999999865
No 196
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=89.12 E-value=0.73 Score=41.66 Aligned_cols=47 Identities=28% Similarity=0.429 Sum_probs=41.1
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-+.+|+++|++.+ -+++.+|++.|+.++..||.-|.+|.++|.+..
T Consensus 17 eR~~~Il~~L~~~~------~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r 63 (269)
T PRK09802 17 ERREQIIQRLRQQG------SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVR 63 (269)
T ss_pred HHHHHHHHHHHHcC------CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEE
Confidence 45677999998742 399999999999999999999999999999865
No 197
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=89.08 E-value=0.66 Score=34.06 Aligned_cols=39 Identities=15% Similarity=0.334 Sum_probs=36.2
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
.=+++++|++.++++.++++..|-.|+.+|.|.-.||..
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00088 23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 468999999999999999999999999999999999863
No 198
>smart00753 PAM PCI/PINT associated module.
Probab=89.08 E-value=0.66 Score=34.06 Aligned_cols=39 Identities=15% Similarity=0.334 Sum_probs=36.2
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
.=+++++|++.++++.++++..|-.|+.+|.|.-.||..
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00753 23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 468999999999999999999999999999999999863
No 199
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=88.98 E-value=1.7 Score=34.86 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=31.8
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
-|+.++|..+++++..|..|..+|..+|.||+--
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~r 69 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELEREGIVETKR 69 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4999999999999999999999999999999853
No 200
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=88.75 E-value=3.1 Score=34.27 Aligned_cols=55 Identities=24% Similarity=0.257 Sum_probs=42.8
Q ss_pred eeEEEEEEEEE--eee-cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576 71 TNVTLVGLVYN--KEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK 131 (280)
Q Consensus 71 ~~V~iVG~V~~--~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~ 131 (280)
..|++-|.|.. +.. ....++|.|.|+...|.|.+--. .++.|++|.-|-|.|++.
T Consensus 52 ~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~------lPd~F~eg~~VVv~G~~~ 109 (148)
T PRK13254 52 RRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGI------LPDLFREGQGVVAEGRLQ 109 (148)
T ss_pred CeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCC------CCccccCCCEEEEEEEEC
Confidence 56788888864 444 56789999999987888776432 256799999999999985
No 201
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=88.74 E-value=4.3 Score=34.75 Aligned_cols=35 Identities=26% Similarity=0.383 Sum_probs=26.5
Q ss_pred CceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 97 TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 97 TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
|--|+|..|...++ .....|+.|+.|.|.|+|+.-
T Consensus 52 t~fi~V~~Wg~~Ae--~va~~L~KGd~V~V~GrL~~r 86 (186)
T PRK07772 52 ALFLRCSIWRQAAE--NVAESLTKGMRVIVTGRLKQR 86 (186)
T ss_pred ceEEEEEEecHHHH--HHHHhcCCCCEEEEEEEEEcC
Confidence 33589999976432 234569999999999999963
No 202
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=88.48 E-value=1.4 Score=36.05 Aligned_cols=55 Identities=24% Similarity=0.268 Sum_probs=46.5
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++.+..||++|.+.. + .++.++|.+.+ +++...|-.+|+.|.+.|.|...-.++
T Consensus 19 ~T~qR~~vl~~L~~~~----~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 19 LTPQRLAVLELLLEAD----G-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred cCHHHHHHHHHHHhcC----C-CCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 5778899999999752 3 49999999988 399999999999999999998766544
No 203
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=88.47 E-value=1.3 Score=32.57 Aligned_cols=54 Identities=17% Similarity=0.216 Sum_probs=42.8
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----C---CCHHHHHHHHHHHHhCCeeeec
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----K---IPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~---~~~~~v~~al~~L~~eG~IYsT 269 (280)
+.+|-+.|..+|.+.. ..+..++.+.|.+.| + =+.+-|+.+|..|+.|+.||-|
T Consensus 9 fiPL~EvlC~~I~dln--~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~t 70 (80)
T PF10264_consen 9 FIPLPEVLCWVISDLN--AAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHT 70 (80)
T ss_pred ceeHHHHHHHHHHHHh--ccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeC
Confidence 4667888888887753 346678999999888 2 2455599999999999999998
No 204
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=88.45 E-value=0.98 Score=40.35 Aligned_cols=48 Identities=25% Similarity=0.327 Sum_probs=41.9
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+-+++|+++|++. .-+++.+|++.|+.++..||.-|..|.++|.|-.+
T Consensus 5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 5 QRHQILLELLAQL------GFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 3567899999874 36899999999999999999999999999998653
No 205
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=88.33 E-value=0.9 Score=40.37 Aligned_cols=46 Identities=26% Similarity=0.433 Sum_probs=40.2
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
+-+++|+++|++. ..+++++|++.|++++..||.-|.+|.++|.|-
T Consensus 4 ~R~~~Il~~l~~~------~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNH------TSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3567899999863 378999999999999999999999999998773
No 206
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=88.25 E-value=2.2 Score=36.27 Aligned_cols=63 Identities=24% Similarity=0.243 Sum_probs=40.5
Q ss_pred EEeeEEEEEEEEEe---e---ecCCeeEEEEE------c-CCc-------eEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576 69 EITNVTLVGLVYNK---E---ERASDVNFTLD------D-GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIG 128 (280)
Q Consensus 69 ~i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G 128 (280)
-++.|.|||.|..- + .....+.|+|- | .+| -+.|.+|...++ .....|+.|+.|.|.|
T Consensus 5 ~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae--~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAE--VAGEYLRKGSQVYIEG 82 (177)
T ss_pred CceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHH--HHHHhcCCCCEEEEEE
Confidence 36788888888552 1 12244555553 2 123 378888875431 2346799999999999
Q ss_pred EEeee
Q 023576 129 NLKSF 133 (280)
Q Consensus 129 ~l~~f 133 (280)
+|+.-
T Consensus 83 rL~~~ 87 (177)
T PRK09010 83 QLRTR 87 (177)
T ss_pred EEEec
Confidence 99863
No 207
>PRK10870 transcriptional repressor MprA; Provisional
Probab=88.07 E-value=2.2 Score=36.00 Aligned_cols=57 Identities=21% Similarity=0.225 Sum_probs=48.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..|-.||..|... .+.+++..+|++.++++...|...|+.|...|.|...-|.+
T Consensus 52 gLt~~q~~iL~~L~~~----~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~ 108 (176)
T PRK10870 52 GINETLFMALITLESQ----ENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN 108 (176)
T ss_pred CCCHHHHHHHHHHhcC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 4666777899988753 24578999999999999999999999999999999877654
No 208
>PRK09462 fur ferric uptake regulator; Provisional
Probab=88.03 E-value=1.4 Score=35.94 Aligned_cols=51 Identities=20% Similarity=0.367 Sum_probs=42.9
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs 268 (280)
++..+..||++|.+. .+.-++.++|.++| +++...|-.+|+.|.+.|.|-.
T Consensus 15 ~T~qR~~Il~~l~~~----~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 15 VTLPRLKILEVLQEP----DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 577888999999863 23478999999988 2789999999999999999954
No 209
>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]
Probab=87.94 E-value=1.1 Score=42.41 Aligned_cols=87 Identities=15% Similarity=0.155 Sum_probs=62.3
Q ss_pred eeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCc--eEEEEEecccccChhhhccCC
Q 023576 42 LVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQ 119 (280)
Q Consensus 42 ~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~ 119 (280)
+.+|.++.+...... -..+.|-|+|++++......-+.|+|||- .+.|+.=. .....+.
T Consensus 5 ~~~v~~~~~~~~~~~-------------g~~~~i~GWvKsvr~~~~~~Fl~i~DGs~~~~lQvVv~~------~~~q~la 65 (446)
T KOG0554|consen 5 SLSVLSGRILGHPRA-------------GDTISIGGWVKSVRKLKKVTFLDINDGSCPSPLQVVVDS------EQSQLLA 65 (446)
T ss_pred eeeeeccccccCCCC-------------CCceeecchhhhcccccceEEEEecCCCCCcceEEEech------HHhhhcc
Confidence 456666666554433 25678889999999888888889999996 47777544 2356789
Q ss_pred CCCEEEEEEEEeeeCCe---eEEEEEEEeeC
Q 023576 120 DGMYVRLIGNLKSFQGK---KQIVAFSVRPV 147 (280)
Q Consensus 120 ~G~yVrV~G~l~~f~~~---~~i~~~~ir~v 147 (280)
.|+-|.|.|.++.-++- ..+++.+|..|
T Consensus 66 ~Gt~i~~~g~l~~~~~~~q~iel~~eki~~v 96 (446)
T KOG0554|consen 66 TGTCISAEGVLKVSKGAKQQIELNAEKIKVV 96 (446)
T ss_pred ccceEEEEeeEEeccchheeeeeeeeEEEEE
Confidence 99999999999987632 33555555443
No 210
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=87.83 E-value=0.46 Score=37.22 Aligned_cols=51 Identities=22% Similarity=0.356 Sum_probs=41.2
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecC
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
+..+..||++|.+. +.-++.++|.+.+ +++...|-.+|+.|.+.|.|-...
T Consensus 7 T~~R~~Il~~l~~~-----~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~ 62 (120)
T PF01475_consen 7 TPQRLAILELLKES-----PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIE 62 (120)
T ss_dssp HHHHHHHHHHHHHH-----SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHcC-----CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEE
Confidence 55778899999985 2379999999988 388899999999999999986643
No 211
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=87.81 E-value=5.2 Score=32.90 Aligned_cols=61 Identities=15% Similarity=0.156 Sum_probs=39.2
Q ss_pred eeEEEEEEEEEe---e--ecCC-----eeEEEEE------cCCc--------eEEEEEecccccChhhhccCCCCCEEEE
Q 023576 71 TNVTLVGLVYNK---E--ERAS-----DVNFTLD------DGTG--------RVVCKRWASEVFDTREMEAIQDGMYVRL 126 (280)
Q Consensus 71 ~~V~iVG~V~~~---~--~~~t-----~~~~~Ld------DgTG--------~I~~~~w~~~~~~~~~~~~~~~G~yVrV 126 (280)
+.|.|+|.+..- . .... .+.|+|- +.+| -+.|..|...++ .....++.|+.|-|
T Consensus 3 N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae--~v~~~l~KG~~V~V 80 (148)
T PRK08182 3 THFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAE--HWARLYQKGMRVLV 80 (148)
T ss_pred cEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHH--HHHHhcCCCCEEEE
Confidence 567788877541 1 1122 5677772 2222 488999975432 23456899999999
Q ss_pred EEEEeee
Q 023576 127 IGNLKSF 133 (280)
Q Consensus 127 ~G~l~~f 133 (280)
.|+|+.-
T Consensus 81 ~GrL~~~ 87 (148)
T PRK08182 81 EGRMERD 87 (148)
T ss_pred EEEEEec
Confidence 9999753
No 212
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=87.79 E-value=2.7 Score=33.78 Aligned_cols=62 Identities=18% Similarity=0.233 Sum_probs=39.4
Q ss_pred EeeEEEEEEEEEe---e---ecCCeeEEEEE------cCCc-----eEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576 70 ITNVTLVGLVYNK---E---ERASDVNFTLD------DGTG-----RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~ 132 (280)
++.|.|+|.+..- . ....++.|+|- |..| -+.|..|...++ .-...++.|+.|.|.|+|+.
T Consensus 2 mN~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae--~v~~~l~KG~~V~V~Grl~~ 79 (131)
T PRK07274 2 YNKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAE--TLASYASKGSLISIDGELRT 79 (131)
T ss_pred eeEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence 3567777777542 1 12245566654 3223 488888965321 23456999999999999986
Q ss_pred e
Q 023576 133 F 133 (280)
Q Consensus 133 f 133 (280)
-
T Consensus 80 ~ 80 (131)
T PRK07274 80 R 80 (131)
T ss_pred c
Confidence 3
No 213
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=87.79 E-value=1.8 Score=37.56 Aligned_cols=52 Identities=19% Similarity=0.308 Sum_probs=38.7
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+.+.+.+.|++..-. ...=+ +..+++++|+.+.-.|++||..|.++|.||..
T Consensus 6 i~~~l~~~I~~g~~~-~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~ 58 (231)
T TIGR03337 6 IKDHLSYQIRAGALL-PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRE 58 (231)
T ss_pred HHHHHHHHHHcCCCC-CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEe
Confidence 455666666553211 11123 67999999999999999999999999999974
No 214
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=87.78 E-value=2.3 Score=36.00 Aligned_cols=62 Identities=21% Similarity=0.220 Sum_probs=41.8
Q ss_pred EeeEEEEEEEEEe---e---ecCCeeEEEEEc-------CCc-------eEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576 70 ITNVTLVGLVYNK---E---ERASDVNFTLDD-------GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129 (280)
Q Consensus 70 i~~V~iVG~V~~~---~---~~~t~~~~~LdD-------gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~ 129 (280)
++.|.|+|.|..- . .....+.|+|-- .+| -+.|..|...++ .....++.|+.|.|.|+
T Consensus 6 mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae--~v~~~L~KG~~V~VeGr 83 (175)
T PRK13732 6 INKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAE--VAGEYLRKGAQVYIEGQ 83 (175)
T ss_pred ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHH--HHHHhcCCCCEEEEEEE
Confidence 6889999998652 1 223466666642 233 468888875431 23456899999999999
Q ss_pred Eeee
Q 023576 130 LKSF 133 (280)
Q Consensus 130 l~~f 133 (280)
|+.-
T Consensus 84 L~~r 87 (175)
T PRK13732 84 LRTR 87 (175)
T ss_pred EEee
Confidence 9864
No 215
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=87.71 E-value=0.73 Score=33.80 Aligned_cols=45 Identities=22% Similarity=0.333 Sum_probs=36.9
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-.|+.+|... ..+++.+|.+.++++...+...|..|.++|.|=.
T Consensus 2 Rl~Il~~L~~~------~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~ 46 (80)
T PF13601_consen 2 RLAILALLYAN------EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEV 46 (80)
T ss_dssp HHHHHHHHHHH------SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhhc------CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE
Confidence 45678888752 4799999999999999999999999999999854
No 216
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=87.55 E-value=2.7 Score=35.57 Aligned_cols=62 Identities=21% Similarity=0.247 Sum_probs=40.6
Q ss_pred EeeEEEEEEEEEe---e---ecCCeeEEEEE------c-CCc-------eEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576 70 ITNVTLVGLVYNK---E---ERASDVNFTLD------D-GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129 (280)
Q Consensus 70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~ 129 (280)
++.|.|+|.|..- . .....+.|+|- | .+| -+.|.+|...++ .....++.|+.|.|.|+
T Consensus 5 mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae--~v~~~l~KGs~V~VeGr 82 (172)
T PRK05733 5 VNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAE--IAGEYLRKGSQVYIEGK 82 (172)
T ss_pred ceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHH--HHHHHhCCCCEEEEEEE
Confidence 6788888888552 1 12234555543 1 133 388889975432 23467899999999999
Q ss_pred Eeee
Q 023576 130 LKSF 133 (280)
Q Consensus 130 l~~f 133 (280)
|+.-
T Consensus 83 Lr~~ 86 (172)
T PRK05733 83 LQTR 86 (172)
T ss_pred EEeC
Confidence 9974
No 217
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=87.45 E-value=0.99 Score=36.56 Aligned_cols=34 Identities=15% Similarity=0.342 Sum_probs=32.1
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
=++.++|+++++++..-|++++..|..+|.|.++
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 4799999999999999999999999999999875
No 218
>PRK00215 LexA repressor; Validated
Probab=87.37 E-value=0.77 Score=39.48 Aligned_cols=56 Identities=21% Similarity=0.360 Sum_probs=45.0
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCC-CHHHHHHHHHHHHhCCeeeecC
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKI-PQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~-~~~~v~~al~~L~~eG~IYsTi 270 (280)
+++.|.+||++|++.- .......++.+|++.+++ +...+...|..|.+.|.|-...
T Consensus 2 lt~~q~~il~~i~~~~-~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHI-EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence 4678899999997521 012356799999999999 9999999999999999996543
No 219
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=87.32 E-value=1.3 Score=40.90 Aligned_cols=45 Identities=31% Similarity=0.369 Sum_probs=39.3
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCe-eee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL-IYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~-IYs 268 (280)
..+||++|++ +..++.++|+++|+++...|..+|..|.++|. |++
T Consensus 6 ~~~il~~L~~------~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 6 MLQLLSLLAD------GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred HHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence 4578888875 24789999999999999999999999999999 766
No 220
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=86.93 E-value=2.1 Score=36.65 Aligned_cols=55 Identities=16% Similarity=0.148 Sum_probs=47.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
+++..|-.||.+|... .|++..+|++.+.++...|...|+.|...|.|.-..|.+
T Consensus 42 gLt~~q~~iL~~L~~~------~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~ 96 (185)
T PRK13777 42 DLNINEHHILWIAYHL------KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKED 96 (185)
T ss_pred CCCHHHHHHHHHHHhC------CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence 5677788899998763 389999999999999999999999999999999876653
No 221
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=86.86 E-value=1.7 Score=38.01 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=31.6
Q ss_pred CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~ 63 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTI 63 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3456 6889999999999999999999999999985
No 222
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=86.78 E-value=1.5 Score=37.97 Aligned_cols=36 Identities=14% Similarity=0.183 Sum_probs=32.5
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=++..+|+++|+++..-||+||..|..+|.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~ 66 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVREALLRLVSVNALSV 66 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe
Confidence 445678899999999999999999999999999975
No 223
>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=86.77 E-value=1.7 Score=31.28 Aligned_cols=49 Identities=29% Similarity=0.483 Sum_probs=43.8
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+++-.||+.|... .+.|+...++.+.++++...+--.+..|.+.|.|.-
T Consensus 2 ~~~~~~Le~I~rs----R~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k 50 (75)
T PF04182_consen 2 DIQYCLLERIARS----RYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVK 50 (75)
T ss_pred chHHHHHHHHHhc----CCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEE
Confidence 5678899999874 578999999999999999999999999999999864
No 224
>PF14502 HTH_41: Helix-turn-helix domain
Probab=86.75 E-value=1.4 Score=29.21 Aligned_cols=32 Identities=25% Similarity=0.399 Sum_probs=29.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
-+++|.+++|+.+.-.|..||.+|.++|-|..
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~L 38 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKL 38 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEe
Confidence 47899999999999999999999999998864
No 225
>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=86.65 E-value=1 Score=42.83 Aligned_cols=65 Identities=20% Similarity=0.221 Sum_probs=48.2
Q ss_pred EEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 68 LEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 68 ~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
..=++|++-|||-+.+.+.+-+-..|-||||.+.|++-..-.. +.+.-.+..-.-|.|+|.|+..
T Consensus 121 ~r~qrVkv~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~-~yd~~~Ls~essv~vYG~i~~~ 185 (545)
T KOG0555|consen 121 NRGQRVKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQ-SYDALTLSTESSVTVYGTIKKL 185 (545)
T ss_pred ccCceEEeehhhHhhhhcCceEEEEEecCCceEEEEEcchhhh-hhccccccccceEEEEEEEecC
Confidence 3346899999998888777777779999999999997654321 1122345566789999999876
No 226
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=86.46 E-value=1.6 Score=37.66 Aligned_cols=47 Identities=13% Similarity=0.218 Sum_probs=40.6
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
++|+.++.+. ..|.+.++|+++|++++..|+.-+.+|...|.+=..+
T Consensus 165 r~Vl~~~~~g-----~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 165 NAVRKLFKEP-----GVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred HHHHHHHHcC-----CCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence 4789888752 3489999999999999999999999999999987654
No 227
>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=86.41 E-value=1.6 Score=37.41 Aligned_cols=36 Identities=14% Similarity=0.380 Sum_probs=31.8
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=++..+++++|+++..-||+||..|..+|.|-.
T Consensus 31 pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 345668899999999999999999999999999853
No 228
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=86.09 E-value=1.7 Score=34.17 Aligned_cols=49 Identities=22% Similarity=0.396 Sum_probs=43.8
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..+..-++.|+++.+. -.|+.||+..++++..-++--+..|.+.|+|-.
T Consensus 39 ~~l~pE~~~Il~lC~~--------~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 39 AGLGPEHRAILELCRR--------PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred CCCCHHHHHHHHHHCC--------CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 4678889999998764 569999999999999999999999999999864
No 229
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=85.88 E-value=2.9 Score=27.18 Aligned_cols=41 Identities=22% Similarity=0.435 Sum_probs=32.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
+++.+..|+.++. .|.+..+|++.++++...|+..+..+..
T Consensus 4 l~~~e~~i~~~~~--------~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 4 LTPREREVLRLLA--------EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5566667776653 3789999999999999999998887643
No 230
>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=85.87 E-value=3 Score=31.46 Aligned_cols=35 Identities=20% Similarity=0.380 Sum_probs=32.9
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
...++..+|++.++++...|..+|..|...|.|..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 46899999999999999999999999999999985
No 231
>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=85.69 E-value=2.1 Score=38.09 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=39.1
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+.||+.|+.. +.-++..+|+++++++..-|++|+..|...|.|.+-
T Consensus 186 ~~IL~~L~~~-----egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 186 EHIFEELDGN-----EGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHHHhccc-----cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4577777652 345789999999999999999999999999999874
No 232
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=85.67 E-value=2.3 Score=34.30 Aligned_cols=57 Identities=11% Similarity=0.178 Sum_probs=42.8
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
+.-+.|+.++... ..+++.+|++.++++...|..+|..|...|.|... ....|..|+
T Consensus 8 dyL~~I~~l~~~~------~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~-~~~~i~LT~ 64 (142)
T PRK03902 8 DYIEQIYLLIEEK------GYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE-KYRGLVLTP 64 (142)
T ss_pred HHHHHHHHHHhcC------CCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe-cCceEEECH
Confidence 3445566666542 36799999999999999999999999999999643 234555553
No 233
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.66 E-value=1.8 Score=36.74 Aligned_cols=46 Identities=20% Similarity=0.162 Sum_probs=39.5
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
.....||.+|...+ -++.++|+..|+++..+||+.|..|.++|.|-
T Consensus 22 ~~~~~Vl~~L~~~g------~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 22 EEGFEVLKALIKKG------EVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred ccHhHHHHHHHHcC------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 34567888887632 37999999999999999999999999999987
No 234
>PRK03837 transcriptional regulator NanR; Provisional
Probab=85.52 E-value=2.3 Score=37.14 Aligned_cols=35 Identities=14% Similarity=0.289 Sum_probs=31.8
Q ss_pred CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 3456 7899999999999999999999999999976
No 235
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=85.51 E-value=1.9 Score=37.40 Aligned_cols=36 Identities=11% Similarity=0.239 Sum_probs=31.7
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=++..+++++|+++..-||+||..|..+|.|-.
T Consensus 27 pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~ 62 (224)
T PRK11534 27 PDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTV 62 (224)
T ss_pred CCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEE
Confidence 344678899999999999999999999999999853
No 236
>PRK07217 replication factor A; Reviewed
Probab=85.35 E-value=2.8 Score=38.68 Aligned_cols=58 Identities=24% Similarity=0.254 Sum_probs=41.6
Q ss_pred CeeEEEEEcCCceEEEEEecccccC--------h--------------hhhccCCCCCEEEEEEEEeeeCCeeEEEEEEE
Q 023576 87 SDVNFTLDDGTGRVVCKRWASEVFD--------T--------------REMEAIQDGMYVRLIGNLKSFQGKKQIVAFSV 144 (280)
Q Consensus 87 t~~~~~LdDgTG~I~~~~w~~~~~~--------~--------------~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~i 144 (280)
-++.+.||||||.++|++..+.-.. . ......-.|.|++|+|.+ | -++|.+..+
T Consensus 217 Lrik~vlDDGt~~~~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~--~--g~~l~~~~~ 292 (311)
T PRK07217 217 LRIKGVLDDGEEVQEVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT--L--GRYLLADSV 292 (311)
T ss_pred eEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc--C--CcEEEeeEe
Confidence 3889999999999999998653210 0 011224689999999976 3 368888888
Q ss_pred eeCC
Q 023576 145 RPVT 148 (280)
Q Consensus 145 r~v~ 148 (280)
.+.+
T Consensus 293 ~~~~ 296 (311)
T PRK07217 293 EPLT 296 (311)
T ss_pred eccc
Confidence 7774
No 237
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=85.27 E-value=4 Score=33.70 Aligned_cols=62 Identities=21% Similarity=0.208 Sum_probs=42.5
Q ss_pred EeeEEEEEEEEE---ee---ecCCeeEEEEE------c---C-----CceEEEEEecc-cccChhhhccCCCCCEEEEEE
Q 023576 70 ITNVTLVGLVYN---KE---ERASDVNFTLD------D---G-----TGRVVCKRWAS-EVFDTREMEAIQDGMYVRLIG 128 (280)
Q Consensus 70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld------D---g-----TG~I~~~~w~~-~~~~~~~~~~~~~G~yVrV~G 128 (280)
++.|.|+|.+.. +. .....+.|+|- | + |--+.|..|.. .+. .....++.|+.|.|.|
T Consensus 5 ~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae--~~~~~l~KG~~V~V~G 82 (152)
T PRK06642 5 LNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVS--VVERYVTKGSKLYIEG 82 (152)
T ss_pred ceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHH--HHHHhCCCCCEEEEEE
Confidence 688999999965 22 22357777776 2 1 33488888874 221 2345689999999999
Q ss_pred EEeee
Q 023576 129 NLKSF 133 (280)
Q Consensus 129 ~l~~f 133 (280)
+|+..
T Consensus 83 rL~~~ 87 (152)
T PRK06642 83 SLQTR 87 (152)
T ss_pred EEEeC
Confidence 99864
No 238
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=85.24 E-value=2.2 Score=37.72 Aligned_cols=37 Identities=16% Similarity=0.357 Sum_probs=32.4
Q ss_pred CCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 232 ERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 232 ~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+..-+ +..+|+++|+++..-||+||..|..+|.|-.
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~ 63 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIET 63 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 344567 6899999999999999999999999999854
No 239
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=85.08 E-value=3.6 Score=26.79 Aligned_cols=41 Identities=15% Similarity=0.277 Sum_probs=31.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++-++.|+...-. +|.+..+|++.++++...|+.....-
T Consensus 4 ~L~~~er~vi~~~y~-------~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-------EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHT-------ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-------CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 477888888886542 48899999999999999988776543
No 240
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=85.05 E-value=2.6 Score=31.49 Aligned_cols=65 Identities=15% Similarity=0.150 Sum_probs=44.7
Q ss_pred EEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---CeeEEEE
Q 023576 74 TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---GKKQIVA 141 (280)
Q Consensus 74 ~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~ 141 (280)
++++.|+++.........+|.|.||+|.|.+-.+--. +....+..|..+-+. .+..|. .+.+|++
T Consensus 6 ~l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~v~~--~y~~~l~~GavLlLk-~V~Vf~ps~~~~yLnI 73 (86)
T PF15072_consen 6 CLVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRKVLE--EYGDELSPGAVLLLK-DVTVFSPSPRSHYLNI 73 (86)
T ss_pred EEEEEEEEeeccCCCeEEEEECCCCcEEEEEeHHHHh--hcCCccccCEEEEEe-eeeEEecCCCccEEEE
Confidence 5788999998777788999999999999998754321 134567888755544 444443 3344544
No 241
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=85.01 E-value=2.3 Score=28.14 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=28.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+..- .|.+..+|++.++++++.|+..+..
T Consensus 10 ~L~~~~r~i~~l~~~-------~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-------QGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp CS-HHHHHHHHHHHT-------S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-------HCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 467788888887654 4999999999999999999887653
No 242
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=84.79 E-value=1.8 Score=38.65 Aligned_cols=46 Identities=11% Similarity=0.214 Sum_probs=39.3
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
+-+.+|+++|++. .-+++.++++.|+.++..||.-|.+|...+.+|
T Consensus 7 eR~~~I~~~l~~~------~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~ 52 (252)
T PRK10681 7 ERIGQLLQALKRS------DKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLL 52 (252)
T ss_pred HHHHHHHHHHHHc------CCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEE
Confidence 3567899999874 358999999999999999999999999877643
No 243
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=84.56 E-value=7.4 Score=32.49 Aligned_cols=55 Identities=22% Similarity=0.274 Sum_probs=42.2
Q ss_pred eeEEEEEEEE--EeeecC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576 71 TNVTLVGLVY--NKEERA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK 131 (280)
Q Consensus 71 ~~V~iVG~V~--~~~~~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~ 131 (280)
..+++=|.|. ++.... ..+.|+|-|+...|.+.+=-. -++.|++|.=|-|.|++.
T Consensus 58 ~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~ 116 (160)
T PRK13165 58 QRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGI------LPDLFREGQGIVAQGVLE 116 (160)
T ss_pred CEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEccc------CCccccCCCeEEEEEEEC
Confidence 5677778887 455433 378999999999988875432 246799999999999986
No 244
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=84.40 E-value=2.3 Score=28.70 Aligned_cols=41 Identities=24% Similarity=0.397 Sum_probs=33.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.|++.+.+|+.++.. |.+..+|++.+++++..|+.-+..+.
T Consensus 3 ~LT~~E~~vl~~l~~--------G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--------GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp SS-HHHHHHHHHHHT--------TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--------cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 367888899999864 89999999999999999988877664
No 245
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=84.12 E-value=3.7 Score=43.71 Aligned_cols=59 Identities=12% Similarity=0.028 Sum_probs=44.0
Q ss_pred eEEEEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 72 NVTLVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 72 ~V~iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
.|+++|.|.+++. +.+...++|+|.||.|+|.+|.+.- .....+.+++++.|.|+...-
T Consensus 899 ~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~~~---~~~~~l~~~~~~~~~~~~~~~ 961 (973)
T PRK07135 899 EYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDNDY---LLFETLKKGDIYEFLISKSKN 961 (973)
T ss_pred eEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHHHH---HHHHHhhcCCEEEEEEEEcCC
Confidence 4677888876532 3467778999999999999997642 123358889999999887763
No 246
>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=84.09 E-value=2 Score=30.40 Aligned_cols=34 Identities=18% Similarity=0.374 Sum_probs=31.0
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..++.++|+..++.+...|...|..|.++|.|=.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4578999999999999999999999999998853
No 247
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=84.07 E-value=2.1 Score=37.55 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=36.3
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
...+++..+|++.++++...+...|..|.++|.|.-..|.
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~ 57 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVP 57 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcC
Confidence 3458999999999999999999999999999999987764
No 248
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=84.01 E-value=5.9 Score=32.99 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=26.0
Q ss_pred eeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE
Q 023576 82 KEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI 127 (280)
Q Consensus 82 ~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~ 127 (280)
......++.|.|.|.||.++|...-.-. .-..++||-+|++
T Consensus 125 K~v~~~~~~YeI~DnTG~MeVvv~G~~~-----ni~CEeGDKLrL~ 165 (170)
T PF02760_consen 125 KTVNKKNTIYEIQDNTGKMEVVVYGKWH-----NIKCEEGDKLRLF 165 (170)
T ss_dssp EEEESSEEEEEEEETTEEEEEEEEGGGC-----GCC--TT-EEEEE
T ss_pred EEEcCCeEEEEEecCCCcEEEEEeccCc-----ccccCCCCeEEEE
Confidence 3445678999999999999999754321 2346777755543
No 249
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=83.80 E-value=2.3 Score=38.32 Aligned_cols=46 Identities=15% Similarity=0.463 Sum_probs=42.0
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
++++|+..|+.. .+.|+..-||-+..+++.+.+-+||..|.++|.|
T Consensus 5 ~reklir~Lk~a----~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv 50 (321)
T COG3888 5 LREKLIRELKRA----GPEGIDQTEIEELMGLSKSTVSEALSELEKQGIV 50 (321)
T ss_pred HHHHHHHHHHhc----CCCCccHHHHHHHhCcchhHHHHHHHHHHhcCee
Confidence 678899999985 4679999999999999999999999999999987
No 250
>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=83.78 E-value=0.94 Score=34.72 Aligned_cols=44 Identities=23% Similarity=0.336 Sum_probs=33.5
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
-.-.|+++|-.. ..++-++|++.++++..+||.+|..|.++|.|
T Consensus 14 ~~~~Il~~L~~~------~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv 57 (105)
T PF02002_consen 14 EAVRILDALLRK------GELTDEDLAKKLGLKPKEVRKILYKLYEDGLV 57 (105)
T ss_dssp TTHHHHHHHHHH--------B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-
T ss_pred hHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence 445788888753 25788999999999999999999999999998
No 251
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=83.67 E-value=2.2 Score=27.44 Aligned_cols=33 Identities=12% Similarity=0.340 Sum_probs=23.9
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.+.|++++++ |+++.+||+.++++...|...|.
T Consensus 11 ~~~i~~l~~~--------G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYAE--------GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHHT--------T--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHC--------CCCHHHHHHHHCcCHHHHHHHHh
Confidence 4567777653 89999999999999999887663
No 252
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=83.55 E-value=8.6 Score=32.06 Aligned_cols=55 Identities=24% Similarity=0.325 Sum_probs=42.5
Q ss_pred eeEEEEEEEE--Eeeec--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576 71 TNVTLVGLVY--NKEER--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK 131 (280)
Q Consensus 71 ~~V~iVG~V~--~~~~~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~ 131 (280)
..+++=|.|. ++... ...+.|.|.|+...|.+.+=-. -++.|++|.=|-|.|++.
T Consensus 58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~ 116 (159)
T PRK13150 58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI------LPDLFREGQGVVVQGTLE 116 (159)
T ss_pred CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc------CCccccCCCeEEEEEEEC
Confidence 5677888887 45543 3579999999999998875432 246799999999999985
No 253
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=83.54 E-value=2.9 Score=37.02 Aligned_cols=35 Identities=23% Similarity=0.452 Sum_probs=31.1
Q ss_pred CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+=+ +..+|+++|+++..-||+||..|..+|.|-.
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~ 66 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLR 66 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 3455 6899999999999999999999999999864
No 254
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=83.54 E-value=3.1 Score=36.92 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=31.8
Q ss_pred CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+=+ +..+++++|+++..-||+||..|..+|.|..
T Consensus 29 pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~ 65 (257)
T PRK10225 29 PGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEV 65 (257)
T ss_pred CCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 44567 5889999999999999999999999999964
No 255
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.47 E-value=4.6 Score=40.90 Aligned_cols=73 Identities=18% Similarity=0.285 Sum_probs=49.9
Q ss_pred eEEEEEcCCceEEEEEecccccC----------------hhhh-ccCC----CCCEEEEEEEEeeeCCee--EEEEEEEe
Q 023576 89 VNFTLDDGTGRVVCKRWASEVFD----------------TREM-EAIQ----DGMYVRLIGNLKSFQGKK--QIVAFSVR 145 (280)
Q Consensus 89 ~~~~LdDgTG~I~~~~w~~~~~~----------------~~~~-~~~~----~G~yVrV~G~l~~f~~~~--~i~~~~ir 145 (280)
+.+.|.|.||.+.+..|.+.... .... ..|. .--.+||.-+...|+++. ..++.++.
T Consensus 512 l~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~~v~~~~ 591 (608)
T TIGR00617 512 LQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVD 591 (608)
T ss_pred EEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHHhcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEEEEEEee
Confidence 56789999999999999864320 0000 1111 223567777788898774 46777888
Q ss_pred eCCCchHHHHHHHHHHH
Q 023576 146 PVTNFDEVTCHYIECIY 162 (280)
Q Consensus 146 ~v~d~Nei~~H~Le~i~ 162 (280)
|| |+.+...++|+.|.
T Consensus 592 ~v-d~~~e~~~L~~~i~ 607 (608)
T TIGR00617 592 PV-NYRAEAKYLLQEIE 607 (608)
T ss_pred eC-CHHHHHHHHHHHhc
Confidence 88 57888999998763
No 256
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=83.42 E-value=2.4 Score=35.61 Aligned_cols=51 Identities=12% Similarity=0.208 Sum_probs=43.1
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.+..+..||++|.+. +.-++.++|.++| +++...|-..|+.|.+.|.|-.-
T Consensus 24 ~T~qR~~IL~~l~~~-----~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 24 LTPQRLEVLRLMSLQ-----PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred CCHHHHHHHHHHHhc-----CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 466788899999873 3578999999988 37899999999999999998653
No 257
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.33 E-value=6.5 Score=39.84 Aligned_cols=65 Identities=20% Similarity=0.360 Sum_probs=45.6
Q ss_pred eEEEEEEEEEeee------c-----CCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeE
Q 023576 72 NVTLVGLVYNKEE------R-----ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQ 138 (280)
Q Consensus 72 ~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~ 138 (280)
.|.|+|+|.++.. + .....++|.|.|| .|++.+|.+.+.. . ....+..|.+. .+++.|++ +.
T Consensus 312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~---~-~~~~~~Vva~kg~~V~~f~g-~s 386 (608)
T TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK---F-DVSVQPVIAIKGVRVSDFGG-KS 386 (608)
T ss_pred CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh---c-CCCCCCEEEEEeEEEEecCC-ce
Confidence 5778888877632 1 1357899999999 5999999876421 1 25677888777 56778865 46
Q ss_pred EEE
Q 023576 139 IVA 141 (280)
Q Consensus 139 i~~ 141 (280)
|..
T Consensus 387 Ls~ 389 (608)
T TIGR00617 387 LST 389 (608)
T ss_pred Eec
Confidence 653
No 258
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=83.17 E-value=4 Score=26.55 Aligned_cols=40 Identities=18% Similarity=0.334 Sum_probs=31.3
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
++.+..|+.++. .|++..+|++.++++...|+..+..+..
T Consensus 2 ~~~e~~i~~~~~--------~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 2 TPREREVLRLLA--------EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 345666776653 3789999999999999999998887643
No 259
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=83.14 E-value=2.2 Score=27.43 Aligned_cols=38 Identities=13% Similarity=0.331 Sum_probs=20.3
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
|+.-++..+..+.+ .|.++.+||+.|+.+.+.|...|.
T Consensus 5 Lt~~eR~~I~~l~~-------~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 5 LTPEERNQIEALLE-------QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp -------HHHHHHC-------S---HHHHHHHTT--HHHHHHHHH
T ss_pred hhhhHHHHHHHHHH-------cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 45555555555543 499999999999999999988764
No 260
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=83.03 E-value=2.7 Score=44.21 Aligned_cols=42 Identities=17% Similarity=0.188 Sum_probs=35.9
Q ss_pred CCccCHHHHHHHh------------CCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 234 ERGVHVNELSEQL------------KIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 234 e~Gv~v~~I~~~l------------~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
..++++++|.+.+ ++++++++++|+.|..+|.||.+-+. +||
T Consensus 857 ~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i~~~~~g-~y~ 910 (915)
T PTZ00111 857 NKSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTAVRENNS-YYL 910 (915)
T ss_pred CCceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeEeeeCCC-chh
Confidence 3589999998664 59999999999999999999998555 776
No 261
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=82.79 E-value=2.3 Score=38.37 Aligned_cols=49 Identities=27% Similarity=0.477 Sum_probs=44.1
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCc-cCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERG-VHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~G-v~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
..|++-.+.|+++|++.+ | +...||.+.+++|...|-.+|..|...|.|
T Consensus 191 ~~L~~~e~~il~~i~~~G------Gri~Q~eL~r~lglsktTvsR~L~~LEk~GlI 240 (258)
T COG2512 191 YDLNEDEKEILDLIRERG------GRITQAELRRALGLSKTTVSRILRRLEKRGLI 240 (258)
T ss_pred CCCCHHHHHHHHHHHHhC------CEEeHHHHHHhhCCChHHHHHHHHHHHhCCce
Confidence 367888899999999853 5 789999999999999999999999999987
No 262
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=82.75 E-value=2.8 Score=37.73 Aligned_cols=57 Identities=19% Similarity=0.385 Sum_probs=50.2
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
+++.++.||-+|++. -.+++||...++.+...|.-.|..|.+.|.|-.. ++.|+.|+
T Consensus 11 ~SekRk~lLllL~eg-------Pkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~--~~~Y~LS~ 67 (260)
T COG4742 11 LSEKRKDLLLLLKEG-------PKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE--GDRYSLSS 67 (260)
T ss_pred ccHHHHHHHHHHHhC-------CCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEec--CCEEEecc
Confidence 467888999999873 3589999999999999999999999999999995 77998875
No 263
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=82.29 E-value=2 Score=29.39 Aligned_cols=37 Identities=24% Similarity=0.365 Sum_probs=31.8
Q ss_pred CCCccCHHHHHHHh---CCCHHHHHHHHHHHHhCCeeeec
Q 023576 233 RERGVHVNELSEQL---KIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~IYsT 269 (280)
...|++.+++.+++ +++...+...|+.|+.+|.|-.+
T Consensus 14 lr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 14 LRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVE 53 (59)
T ss_dssp TSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEE
T ss_pred CccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeE
Confidence 56799999999998 68999999999999999999875
No 264
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=82.18 E-value=2.6 Score=35.18 Aligned_cols=45 Identities=22% Similarity=0.493 Sum_probs=39.1
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhC--CCHHHHHHHHHHHHhCCeee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLK--IPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~--~~~~~v~~al~~L~~eG~IY 267 (280)
...|+++|+.. ..-.++.+|...|+ ++-..|.++|+.|..+|.|-
T Consensus 3 e~~Il~y~~~q-----NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~ 49 (169)
T PF07106_consen 3 EDAILEYMKEQ-----NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIV 49 (169)
T ss_pred HHHHHHHHHHc-----CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCee
Confidence 45799999974 35789999999994 99999999999999999863
No 265
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=82.10 E-value=5.6 Score=31.88 Aligned_cols=87 Identities=13% Similarity=0.204 Sum_probs=42.2
Q ss_pred eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecC-CeeEEEEEcCCc--eEEEEEecccccChhhhccCCC
Q 023576 44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERA-SDVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQD 120 (280)
Q Consensus 44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~-t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~ 120 (280)
.++..+|.+.....+....=.+.| ..|.|-|.|.++.... .+......+..+ .|.|.+-.+.. .......++.
T Consensus 44 ~~sa~~L~~~y~~N~~~A~~kY~g---K~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~-~~~~~~~l~~ 119 (144)
T PF12869_consen 44 SVSAEELYKDYKDNEVAADKKYKG---KIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQE-KRASVAKLKK 119 (144)
T ss_dssp EEEHHHHHHHHHH-HHHHHHHHTT----EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGG-GHHHHHH--T
T ss_pred eecHHHHHHHHHhCHHHHHhhcCC---CEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchh-hhhhHhcCCC
Confidence 899999988764431111122344 4567789999987633 333223333233 35544433331 1112345999
Q ss_pred CCEEEEEEEEeeeC
Q 023576 121 GMYVRLIGNLKSFQ 134 (280)
Q Consensus 121 G~yVrV~G~l~~f~ 134 (280)
|+.|.|.|++..|.
T Consensus 120 G~~Vti~G~~~g~~ 133 (144)
T PF12869_consen 120 GQKVTIKGICTGYS 133 (144)
T ss_dssp TSEEEEEEE-----
T ss_pred CCEEEEEEEEEeee
Confidence 99999999999985
No 266
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=82.09 E-value=4 Score=36.13 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=31.4
Q ss_pred CCCccC-HHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGVH-VNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv~-v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=++ ..+|+++|+++..-||+||..|..+|.|-.
T Consensus 28 pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~ 64 (253)
T PRK11523 28 VGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEV 64 (253)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 445664 789999999999999999999999999964
No 267
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=82.07 E-value=3.7 Score=32.47 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=41.8
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.+...+||.+|... ..+++.+|++.++++.+.|..-|..|.+-|.|-..
T Consensus 15 dptRl~IL~~L~~~------~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 15 DETRLGIVLLLRES------GELCVCDLCTALDQSQPKISRHLALLRESGLLLDR 63 (117)
T ss_pred CHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 45777899998742 25899999999999999999999999999999544
No 268
>PRK04036 DNA polymerase II small subunit; Validated
Probab=81.91 E-value=5.4 Score=39.42 Aligned_cols=61 Identities=16% Similarity=0.218 Sum_probs=42.8
Q ss_pred eeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccCh-hhhccCCCCCEEEEEEEEee
Q 023576 71 TNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDT-REMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~-~~~~~~~~G~yVrV~G~l~~ 132 (280)
..|.|||.|.++... .....+.|+|.||+|.+..-.+.. +- .....+..|..|-|.|++..
T Consensus 154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~-~~~~~~~~lvtg~vv~v~G~~~~ 216 (504)
T PRK04036 154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDRE-DLAELADELLLDEVIGVEGTLSG 216 (504)
T ss_pred ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchh-hhhhhhhcccCceEEEEEEEEcC
Confidence 458999999887543 334578999999999987632210 11 11346889999999998753
No 269
>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=81.90 E-value=1.8 Score=40.40 Aligned_cols=53 Identities=21% Similarity=0.496 Sum_probs=44.5
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+|++-++.||.+|++. ...||-..+|.++.+++...|.++|..|.+.++|=+
T Consensus 80 ~~l~~~e~lvy~~I~~a----g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~ 132 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEA----GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS 132 (327)
T ss_dssp -SSSCCHHHHHHHHHHH----TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred cCCCHHHHHHHHHHHHh----CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence 46788889999999985 467999999999999999999999999999998865
No 270
>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=81.88 E-value=4.1 Score=32.69 Aligned_cols=47 Identities=21% Similarity=0.231 Sum_probs=37.4
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.++-+|.... .+.-++.++|++++++|..-+++.|..|...|.|-++
T Consensus 12 ~~l~~La~~~---~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 12 TAMLDLALNA---ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred HHHHHHHhCC---CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 3455554321 2346899999999999999999999999999999774
No 271
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=81.83 E-value=3.2 Score=30.24 Aligned_cols=55 Identities=27% Similarity=0.289 Sum_probs=43.1
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH-HHHhCCeeeec
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA-SLENEGLIYST 269 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~-~L~~eG~IYsT 269 (280)
.+|..+++++|++|.+.- ...-|.++-||..++.+.+.|++.++ +|+..|.|--|
T Consensus 4 ~GLd~~D~~yL~~l~~~f---~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT 59 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENF---KGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRT 59 (76)
T ss_dssp TS-BHHHHHHHHHHHHCS---TTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEE
T ss_pred ccCCHHHHHHHHHHHHHc---CCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhC
Confidence 468899999999998752 23457899999999999999998887 89999998766
No 272
>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=81.82 E-value=3 Score=34.64 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
-.|++.|-.. .-++.++||..|+++..+||.+|..|.+.|.|
T Consensus 17 v~Vl~aL~~~------~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv 58 (158)
T TIGR00373 17 GLVLFSLGIK------GEFTDEEISLELGIKLNEVRKALYALYDAGLA 58 (158)
T ss_pred HHHHHHHhcc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4577765432 24899999999999999999999999999998
No 273
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=81.80 E-value=7.3 Score=28.57 Aligned_cols=57 Identities=25% Similarity=0.289 Sum_probs=43.4
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
....++.++... ...-+|=++|++.|+++...|.+.++.|-++|.=-.+.-..-|+.
T Consensus 4 ~~~~~~~ll~~~----~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L 60 (79)
T COG1654 4 TSQMLLLLLLLL----TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYLL 60 (79)
T ss_pred hHHHHHHHHHHc----CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCceec
Confidence 445566666553 345789999999999999999999999999998666555545553
No 274
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=81.76 E-value=4.4 Score=36.81 Aligned_cols=43 Identities=26% Similarity=0.284 Sum_probs=36.0
Q ss_pred cc-CHHHHHHHhC--CCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 236 GV-HVNELSEQLK--IPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 236 Gv-~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
|- ...+|+++|+ ++.++|+++|++|..-|.|=-.- +-.|+.|+
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~-~g~y~~t~ 181 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE-DGFYKQTD 181 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC-CCcEEeec
Confidence 44 7889999996 99999999999999999998753 33677765
No 275
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=81.53 E-value=3 Score=28.27 Aligned_cols=33 Identities=27% Similarity=0.393 Sum_probs=23.7
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhC-CCHHHHHHHHHH
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIAS 259 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~-~~~~~v~~al~~ 259 (280)
..|++.++ .|.+.++|++.+. ++.++|+.||.+
T Consensus 22 ~~i~~~~~--------~G~s~eeI~~~yp~Lt~~~i~aAl~y 55 (56)
T PF04255_consen 22 RDILDLLA--------AGESPEEIAEDYPSLTLEDIRAALAY 55 (56)
T ss_dssp HHHHHHHH--------TT--HHHHHHHSTT--HHHHHHHHHH
T ss_pred HHHHHHHH--------cCCCHHHHHHHCCCCCHHHHHHHHHh
Confidence 34667663 3899999999996 999999999986
No 276
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=81.27 E-value=3.7 Score=36.35 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=31.6
Q ss_pred CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 22 pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~ 58 (253)
T PRK10421 22 AGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLS 58 (253)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 34456 5889999999999999999999999999964
No 277
>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=81.20 E-value=4.2 Score=35.49 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=32.1
Q ss_pred CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~ 62 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI 62 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34457 6899999999999999999999999999975
No 278
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=81.08 E-value=4.6 Score=36.52 Aligned_cols=61 Identities=21% Similarity=0.264 Sum_probs=48.6
Q ss_pred CCchhHHHHHHhcCCCCC-CCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 214 LKDCDQMILDYLQQPSSS-ERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~-~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
+.+.-+.||.+|++.... .-..=-+-++|-+.|+++-.+.+.||-.|.-.|.||. |-+.|+
T Consensus 223 l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q--~g~~t~ 284 (287)
T COG2996 223 LDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ--DGDGTE 284 (287)
T ss_pred hhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE--cCceEE
Confidence 566778999999886422 1123347899999999999999999999999999999 555554
No 279
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=81.07 E-value=3.8 Score=36.43 Aligned_cols=57 Identities=23% Similarity=0.318 Sum_probs=44.2
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
..-+||..|... ..-++..||++.++++...|-+-+.+|++||+|=+ ----||+.|.
T Consensus 11 t~fqIL~ei~~~-----qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~-~gR~~Y~iTk 67 (260)
T COG1497 11 TRFQILSEIAVR-----QPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK-EGRGEYEITK 67 (260)
T ss_pred hHHHHHHHHHHh-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee-cCCeeEEEeh
Confidence 345677766542 12578999999999999999999999999999987 3334777764
No 280
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=80.86 E-value=4.9 Score=30.46 Aligned_cols=55 Identities=27% Similarity=0.366 Sum_probs=45.5
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFH 274 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~h 274 (280)
++..+-.||.+|...+ +++..+|++.++++...|...|+.|...|+|....|.+-
T Consensus 20 lt~~q~~~L~~l~~~~------~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~D 74 (126)
T COG1846 20 LTPPQYQVLLALYEAG------GITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPED 74 (126)
T ss_pred CCHHHHHHHHHHHHhC------CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccc
Confidence 6677888888887642 322299999999999999999999999999999888643
No 281
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=80.73 E-value=3.9 Score=39.10 Aligned_cols=34 Identities=24% Similarity=0.368 Sum_probs=31.0
Q ss_pred Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.=+ ++.+++++|+.+...|++|++.|..||.|+.
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~ 61 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQS 61 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 345 6899999999999999999999999999985
No 282
>PHA00738 putative HTH transcription regulator
Probab=80.67 E-value=4.5 Score=31.47 Aligned_cols=49 Identities=16% Similarity=0.217 Sum_probs=42.9
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.+.+++||++|... ..+.+.+|+..++++-+.|-.-|.-|.+-|.|-+.
T Consensus 11 dptRr~IL~lL~~~------e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr 59 (108)
T PHA00738 11 KILRRKILELIAEN------YILSASLISHTLLLSYTTVLRHLKILNEQGYIELY 59 (108)
T ss_pred CHHHHHHHHHHHHc------CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE
Confidence 56889999999762 25899999999999999999999999999988554
No 283
>PRK11050 manganese transport regulator MntR; Provisional
Probab=80.52 E-value=4.2 Score=33.40 Aligned_cols=35 Identities=14% Similarity=0.306 Sum_probs=32.6
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.+++..+|++.++++...|..+|..|...|.|...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 47899999999999999999999999999999864
No 284
>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=80.07 E-value=5.6 Score=30.50 Aligned_cols=56 Identities=13% Similarity=0.243 Sum_probs=42.7
Q ss_pred CCCchhHHHHH-HhcCC-CCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 213 GLKDCDQMILD-YLQQP-SSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 213 ~l~~~~~~Vl~-~i~~~-~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+++.-+-+|+. ++|.. +......-|+..+|+...+++.+.|.+++.+|++.|.|..
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 45666655544 45543 2334556899999999999999999999999999999954
No 285
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=79.91 E-value=11 Score=31.24 Aligned_cols=64 Identities=22% Similarity=0.233 Sum_probs=44.6
Q ss_pred eeEEEEEEEE--Eeeec--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEE
Q 023576 71 TNVTLVGLVY--NKEER--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSV 144 (280)
Q Consensus 71 ~~V~iVG~V~--~~~~~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~i 144 (280)
..+++=|.|. ++... ...+.|+|-|+...|.|.+=-- -++.|++|.=|-+.|++. ++ .+.+..|
T Consensus 52 ~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEGqgVVaeG~~~--~g--~F~A~~v 119 (155)
T PRK13159 52 QQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGI------LPDLFRDNQSVIANGRMQ--GG--RFVANEV 119 (155)
T ss_pred CeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccC------CCccccCCCeEEEEEEEc--CC--EEEEeEE
Confidence 4555556665 44443 3479999999999998775422 246799999999999997 33 4555544
No 286
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=79.86 E-value=3 Score=37.02 Aligned_cols=48 Identities=33% Similarity=0.520 Sum_probs=41.6
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+..+-+||++|+.. .++++.|||+.++++-+.+..-+.-|..-|.|-+
T Consensus 22 S~vRv~Il~lL~~k------~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 22 SKVRVAILQLLHRK------GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHHh------CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence 34677899999874 3689999999999999999999999999998754
No 287
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=79.73 E-value=2.4 Score=45.73 Aligned_cols=63 Identities=22% Similarity=0.259 Sum_probs=45.9
Q ss_pred eEEEEEEEEEeeec------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe
Q 023576 72 NVTLVGLVYNKEER------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK 136 (280)
Q Consensus 72 ~V~iVG~V~~~~~~------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~ 136 (280)
.+.++|.|+.++.. .....++|+|.||.++|..|...-. .....+.++..+.|.|+++.-+..
T Consensus 978 ~~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~~g~~e~v~f~~~~~--~~~~~l~~~~~~~v~g~v~~~~~~ 1046 (1139)
T COG0587 978 RVVLAGGIVAVRQRPTKAKGNKMAFLTLEDETGILEVVVFPSEYE--RYRRLLLEGRLLIVKGKVQRREDG 1046 (1139)
T ss_pred eeEEEEEEEEEEEeeccCCCCEEEEEEEecCCCcEEEEEcHHHHH--HHHHHhccCcEEEEEEEEEecccc
Confidence 46777777776432 2367789999999999999965431 234567788999999999984433
No 288
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=79.51 E-value=3.8 Score=40.26 Aligned_cols=51 Identities=25% Similarity=0.464 Sum_probs=45.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+++..+..||..|... .+++..+|++.++++.+.|..+++.|...|.|-.+
T Consensus 3 ~Lt~~e~~vL~~L~~~------~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~ 53 (489)
T PRK04172 3 ELHPNEKKVLKALKEL------KEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVE 53 (489)
T ss_pred CCCHHHHHHHHHHHhC------CCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEE
Confidence 4678899999999642 37899999999999999999999999999999876
No 289
>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=79.37 E-value=2.9 Score=37.86 Aligned_cols=54 Identities=24% Similarity=0.286 Sum_probs=42.3
Q ss_pred CCCchhHHHHH-HhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH-HHHhCCeeeecC
Q 023576 213 GLKDCDQMILD-YLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA-SLENEGLIYSTI 270 (280)
Q Consensus 213 ~l~~~~~~Vl~-~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~-~L~~eG~IYsTi 270 (280)
++...++..|. +++... ....++++|++.++.+...++..++ .|++.|.||.|-
T Consensus 235 ~l~~~~~~~L~al~~~~~----~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~ 290 (305)
T TIGR00635 235 GLDEIDRKLLSVLIEQFQ----GGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTP 290 (305)
T ss_pred CCCHHHHHHHHHHHHHhC----CCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCC
Confidence 45666677777 445431 2247899999999999999999999 799999999763
No 290
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=79.03 E-value=5.8 Score=39.40 Aligned_cols=63 Identities=16% Similarity=0.209 Sum_probs=48.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-ChhhhccCCCCCEEEEEEEEeee
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
..|+|.|||-.++....-+-..|-|.+|.+.+..=.+... .-.....++.-..|+|.|.++.-
T Consensus 16 ~~V~L~GWV~r~Rd~GgliFiDLRDr~GivQvv~~~~~~~~~~~~a~~lr~E~vi~V~G~V~~R 79 (585)
T COG0173 16 QTVTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEFVIQVTGTVRAR 79 (585)
T ss_pred CEEEEEeeeeeccccCCeEEEEcccCCCeEEEEECCccCHHHHHHHHhcCceEEEEEEEEEEec
Confidence 5799999998888877777779999999888776543221 11345678888999999998875
No 291
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=78.87 E-value=2.5 Score=31.48 Aligned_cols=39 Identities=21% Similarity=0.473 Sum_probs=35.9
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
..-+++++|++.+++++++++..|..|+.+|.|=-.||.
T Consensus 58 y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~ 96 (105)
T PF01399_consen 58 YSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQ 96 (105)
T ss_dssp -SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEET
T ss_pred hcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEEC
Confidence 457999999999999999999999999999999988886
No 292
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=78.74 E-value=4.6 Score=35.18 Aligned_cols=52 Identities=19% Similarity=0.349 Sum_probs=39.4
Q ss_pred hhHHHHHHhcCC---CCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQP---SSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~---~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+...|++.|++. +.-.+.+=++..+|+++|+.+..=||+||..|..||.|-.
T Consensus 17 ~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~ 71 (230)
T COG1802 17 LADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEI 71 (230)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEe
Confidence 445555555441 1223456789999999999999999999999999999864
No 293
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=78.59 E-value=8.3 Score=26.02 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=31.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
|++-|+++|..--+.+-=.....++.++|++.|+++...+.+-|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHH
Confidence 456777777755444332345799999999999988877655443
No 294
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=78.53 E-value=5.5 Score=32.81 Aligned_cols=35 Identities=11% Similarity=0.269 Sum_probs=32.6
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.-++.++|++++++|..-+++++..|...|.|-++
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 35899999999999999999999999999999875
No 295
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=78.39 E-value=7.6 Score=27.98 Aligned_cols=46 Identities=24% Similarity=0.346 Sum_probs=39.8
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+.+.||.++... .++.+++.+..+++.+++--.|..|..+|.|+..
T Consensus 6 ~~~~IL~~ls~~-------c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQKILIILSKR-------CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHHHhc-------cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 456688887652 6799999999999999999999999999999863
No 296
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=78.35 E-value=6.2 Score=31.85 Aligned_cols=51 Identities=24% Similarity=0.366 Sum_probs=44.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
-|++-..++|+.|++. .-.|+.|+|+..+...++|-..|..|.+-|.|+--
T Consensus 61 vLsp~nleLl~~Ia~~------~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 61 VLSPRNLELLELIAQE------EPASINELAELVGRDVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HhChhHHHHHHHHHhc------CcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEe
Confidence 4677778888888874 35699999999999999999999999999999864
No 297
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=78.34 E-value=7.6 Score=27.96 Aligned_cols=51 Identities=12% Similarity=0.301 Sum_probs=40.8
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHh--C----CCH----HHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQL--K----IPQ----KKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l--~----~~~----~~v~~al~~L~~eG~IYsT 269 (280)
+..++|++.|+... +..|.+...|.+-+ + .+. ..++.+|..|+++|.+-.+
T Consensus 4 ~y~~mI~eAI~~l~---er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~ 64 (77)
T PF00538_consen 4 PYSDMILEAIKALK---ERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQV 64 (77)
T ss_dssp CHHHHHHHHHHHCC---SSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEEC
T ss_pred CHHHHHHHHHHHcC---CCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEee
Confidence 46788999998863 45799999999877 2 333 4599999999999999775
No 298
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=78.22 E-value=5 Score=27.86 Aligned_cols=47 Identities=11% Similarity=0.178 Sum_probs=36.6
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++-.+|.++|-.. ...++.+|.+..+++.++|+++|--|+.-+.++-
T Consensus 13 ~~~~~V~~~Ll~~------G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 13 EIVAKVGEVLLSR------GRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHHHHHHC-------SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred hHHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeee
Confidence 4556788877653 2558999999999999999999999999988764
No 299
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=78.01 E-value=3.6 Score=35.45 Aligned_cols=50 Identities=26% Similarity=0.358 Sum_probs=40.3
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 270 (280)
.+|.-|...+.... .+++..+++++++.+....-..|.+|.++|+|+-|+
T Consensus 4 ~~lk~l~~~~a~~~-~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~ 53 (214)
T COG1339 4 RLLKKLALRGAVRG-VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTI 53 (214)
T ss_pred HHHHHHHHhhhhcC-ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEe
Confidence 45555555432222 579999999999999999999999999999999887
No 300
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=77.99 E-value=3.4 Score=35.04 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=35.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
++..+||+.++++...|..+|..|.++|.|- ++..+++.+|
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~--~~~~~i~i~~ 209 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLIS--AHGKTIVVYG 209 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE--ecCCEEEEec
Confidence 5679999999999999999999999999884 5667777654
No 301
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=77.87 E-value=5.7 Score=34.50 Aligned_cols=54 Identities=13% Similarity=0.278 Sum_probs=42.8
Q ss_pred CCchh-HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576 214 LKDCD-QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 214 l~~~~-~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
+++.. +.++.++.++ ...|.+.++|+++|++++..|+.-+.+|.+-|.+..-++
T Consensus 159 Lt~re~~~l~~~i~~~----~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~ 213 (239)
T PRK10430 159 LTPQTLRTLCQWIDAH----QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIH 213 (239)
T ss_pred CCHHHHHHHHHHHHhC----CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEee
Confidence 55544 3456777653 246999999999999999999999999999999966443
No 302
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.55 E-value=6.6 Score=32.84 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=33.6
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+.-++.++|++++++|..-+++.|..|...|.|-++
T Consensus 23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 23 AGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 347999999999999999999999999999999986
No 303
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=76.93 E-value=5.3 Score=29.32 Aligned_cols=35 Identities=17% Similarity=0.299 Sum_probs=29.2
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhC-CCHHHHHHHHHHHHh
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIASLEN 262 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~-~~~~~v~~al~~L~~ 262 (280)
.|++.++ .|.+.+||+.-+. ++.++|++||.+=..
T Consensus 35 ~Il~~l~--------~G~s~eeil~dyp~Lt~~dI~aal~ya~~ 70 (79)
T COG2442 35 DILEMLA--------AGESIEEILADYPDLTLEDIRAALRYAAD 70 (79)
T ss_pred HHHHHHH--------CCCCHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 4666665 3899999999996 999999999997554
No 304
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=76.78 E-value=6.9 Score=33.40 Aligned_cols=38 Identities=26% Similarity=0.572 Sum_probs=35.0
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
.++++..+|+++|+++-.+|+..|-.|..+|.||.+ |+
T Consensus 25 ~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~-~~ 62 (183)
T PHA03103 25 GEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMS-DS 62 (183)
T ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecC-CC
Confidence 359999999999999999999999999999999986 44
No 305
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=76.71 E-value=7 Score=33.33 Aligned_cols=42 Identities=14% Similarity=0.277 Sum_probs=35.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||.++.+ |.+..+||+.|++++..|+.-+..+..
T Consensus 133 ~LSpRErEVLrLLAq--------GkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 133 HFSVTERHLLKLIAS--------GYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCCHHHHHHHHHHHC--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 478889999999864 999999999999999999887766543
No 306
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=76.61 E-value=4.4 Score=27.65 Aligned_cols=39 Identities=23% Similarity=0.468 Sum_probs=31.7
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
+-+++++|-.. .-+++++|++.++.++..|+..|++|.+
T Consensus 7 q~~Ll~~L~~~------~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLKN------KWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHH------TSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHcC------CCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34578877642 4789999999999999999999999985
No 307
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=76.53 E-value=13 Score=31.32 Aligned_cols=62 Identities=15% Similarity=0.175 Sum_probs=39.2
Q ss_pred EeeEEEEEEEEE---eee---cCCeeEEEEEc--------------CCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576 70 ITNVTLVGLVYN---KEE---RASDVNFTLDD--------------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129 (280)
Q Consensus 70 i~~V~iVG~V~~---~~~---~~t~~~~~LdD--------------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~ 129 (280)
++.|.|+|.|.. ++. ...++.|+|-= .|--+.|..|.+... ......++.|+.|.|.|+
T Consensus 5 mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~A-e~~~~~LkKG~~V~VeGr 83 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLC-KVAEQYLKKGAKVYIEGQ 83 (166)
T ss_pred ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHH-HHHHHhcCCCCEEEEEEE
Confidence 678888888865 221 22355555532 122478888974211 122357899999999999
Q ss_pred Eee
Q 023576 130 LKS 132 (280)
Q Consensus 130 l~~ 132 (280)
|+.
T Consensus 84 L~~ 86 (166)
T PRK06341 84 LQT 86 (166)
T ss_pred EEe
Confidence 975
No 308
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=76.42 E-value=5.2 Score=35.02 Aligned_cols=50 Identities=28% Similarity=0.492 Sum_probs=41.0
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
++..+..|++++... ...+++..++++.++.+..-.+++|+.|+.+|.+.
T Consensus 172 ~~~~~~~il~~~~~~----~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 172 LSKDQSRILELAEEE----NGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp H-HHHHHHHHHH--T----TTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred hhHHHHHHHHHHHhh----cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 457889999999321 23599999999999999999999999999999986
No 309
>smart00526 H15 Domain in histone families 1 and 5.
Probab=75.99 E-value=11 Score=26.14 Aligned_cols=51 Identities=10% Similarity=0.214 Sum_probs=39.4
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHh--CCC--H----HHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQL--KIP--Q----KKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l--~~~--~----~~v~~al~~L~~eG~IYsT 269 (280)
....+|++.|.... +..|.++..|.+-+ ++. . .-++.+|..+++.|.+..+
T Consensus 6 ~~~~mI~eAI~~l~---er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 6 PYSEMITEAISALK---ERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred CHHHHHHHHHHHcC---CCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 46778999998863 46799999999877 232 2 3388999999999998754
No 310
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=75.94 E-value=5.2 Score=29.58 Aligned_cols=39 Identities=18% Similarity=0.354 Sum_probs=32.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 239 VNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 239 v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
+.+|++.++++...|..+|..|...|.|...-+. -|..|
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~~-~~~lT 40 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPYR-GITLT 40 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCCC-ceEec
Confidence 4689999999999999999999999999997653 34443
No 311
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=75.87 E-value=5.8 Score=34.16 Aligned_cols=42 Identities=17% Similarity=0.303 Sum_probs=36.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||.++.+ |.+..+||++|++++..|+.-+..+..
T Consensus 137 ~LT~RE~eVL~lla~--------G~snkeIA~~L~iS~~TVk~h~~~I~~ 178 (207)
T PRK15411 137 SLSRTESSMLRMWMA--------GQGTIQISDQMNIKAKTVSSHKGNIKR 178 (207)
T ss_pred cCCHHHHHHHHHHHc--------CCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 388899999999864 999999999999999999888766543
No 312
>PF13518 HTH_28: Helix-turn-helix domain
Probab=75.15 E-value=9.6 Score=24.56 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=27.4
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCe
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGL 265 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~ 265 (280)
|.++.+|++.++++...|..-+.....+|.
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 569999999999999999999999988884
No 313
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=74.76 E-value=21 Score=29.43 Aligned_cols=56 Identities=23% Similarity=0.275 Sum_probs=44.1
Q ss_pred eeEEEEEEEEE--eee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576 71 TNVTLVGLVYN--KEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132 (280)
Q Consensus 71 ~~V~iVG~V~~--~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~ 132 (280)
.++++.|.|.. +.. ....+.|++.|+-..|++.+=-.- ++-|++|+=|-+.|.+..
T Consensus 52 ~rlR~GGlV~~GSv~R~~~~~~v~F~vtD~~~~v~V~Y~GiL------PDLFREGQgVVa~G~~~~ 111 (153)
T COG2332 52 QRLRLGGLVEAGSVQRDPGSLKVSFVVTDGNKSVTVSYEGIL------PDLFREGQGVVAEGQLQG 111 (153)
T ss_pred cEEEEeeeEeeceEEecCCCcEEEEEEecCCceEEEEEeccC------chhhhcCCeEEEEEEecC
Confidence 67888899865 333 568999999999999998865332 467999999999999843
No 314
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=74.27 E-value=5.3 Score=29.83 Aligned_cols=34 Identities=21% Similarity=0.255 Sum_probs=31.5
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
..=|+...|+++|++..+--+.+|.+|.++|.|=
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik 72 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLV 72 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEE
Confidence 4578999999999999999999999999999983
No 315
>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=74.21 E-value=6.6 Score=27.62 Aligned_cols=40 Identities=20% Similarity=0.488 Sum_probs=33.6
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHh---C--CCHHHHHHHHHHHHhCC
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQL---K--IPQKKIMDSIASLENEG 264 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l---~--~~~~~v~~al~~L~~eG 264 (280)
.||++|++. +.-+...+|++.| + +++..|+--|..|..+|
T Consensus 2 ~IL~~L~~~-----~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~G 46 (66)
T PF08461_consen 2 FILRILAES-----DKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDG 46 (66)
T ss_pred HHHHHHHHc-----CCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCC
Confidence 589999874 3468899999988 3 66789999999999999
No 316
>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=73.92 E-value=2.7 Score=39.19 Aligned_cols=51 Identities=16% Similarity=0.408 Sum_probs=39.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 266 (280)
.+.++.++||+++++. ....|++.++|.+.+ +.+..++..+|..|+++|.|
T Consensus 6 ~~~~~~~~l~~~~~~~---~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~ 57 (327)
T PF05158_consen 6 KLSELEKKLLELCREN---PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLL 57 (327)
T ss_dssp -HHHHHHHHHHHHHH------SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSE
T ss_pred hHHHHHHHHHHHHHHh---cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCE
Confidence 4567999999999885 246799999999996 69999999999999998875
No 317
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=73.84 E-value=7.2 Score=30.95 Aligned_cols=42 Identities=17% Similarity=0.138 Sum_probs=35.3
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
-...+.||..++.+.+.|+-||..|..-|.|.-+ ||..|+.+
T Consensus 51 py~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~-d~g~i~i~ 92 (119)
T TIGR01714 51 PYNAEMLATMFNRNVGDIRITLQTLESLGLIEKK-NNGDIFLE 92 (119)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCcEEeh
Confidence 3467888999999999999999999999999997 55566543
No 318
>PHA02591 hypothetical protein; Provisional
Probab=73.34 E-value=2.8 Score=30.58 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=22.8
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
+.|.++++||+.|+++.+.|++.|+
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4699999999999999999999875
No 319
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=73.10 E-value=12 Score=36.43 Aligned_cols=75 Identities=15% Similarity=0.160 Sum_probs=50.9
Q ss_pred eEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccccC----hhhhccCCCCCEEEEEEEEeee-CCeeEEEEEEEe
Q 023576 72 NVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEVFD----TREMEAIQDGMYVRLIGNLKSF-QGKKQIVAFSVR 145 (280)
Q Consensus 72 ~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~~~----~~~~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~ir 145 (280)
.|.|.|+|.+++... ..+-|.|-++-..|.+..-...-.+ ......++.||+|.|.|....- .+..+|-+..+.
T Consensus 106 ~~svaGRI~s~R~sGsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~pgrt~~gELSi~~~~~~ 185 (560)
T KOG1885|consen 106 IVSVAGRIHSKRESGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGYPGRTKSGELSIIPNEII 185 (560)
T ss_pred eeeeeeeEeeeeccCCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecCCCcCCCceEEEeecchh
Confidence 389999999998766 4556688887667877765433111 1224678999999999988654 355555555543
Q ss_pred e
Q 023576 146 P 146 (280)
Q Consensus 146 ~ 146 (280)
.
T Consensus 186 l 186 (560)
T KOG1885|consen 186 L 186 (560)
T ss_pred e
Confidence 3
No 320
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=72.72 E-value=9.3 Score=33.52 Aligned_cols=43 Identities=9% Similarity=0.148 Sum_probs=36.4
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
..|++-+.+||.+|.+ |.+..+||++|++++..|+.-+..+..
T Consensus 142 ~~LS~RE~eVL~Lia~--------G~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 142 NKVTKYQNDVFILYSF--------GFSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred CCCCHHHHHHHHHHHC--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3578889999999864 999999999999999999887766543
No 321
>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=72.59 E-value=4.3 Score=30.13 Aligned_cols=49 Identities=27% Similarity=0.337 Sum_probs=38.4
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEF 273 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd~ 273 (280)
.-.||..|.. .-..+.+|.+++ +++...+.+.|.+|.+.|.|-.+....
T Consensus 7 ~~~IL~~l~~-------g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~ 56 (90)
T PF01638_consen 7 TLLILRALFQ-------GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPE 56 (90)
T ss_dssp HHHHHHHHTT-------SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHHHHHHHh-------CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccC
Confidence 3456666654 246899999999 799999999999999999998876543
No 322
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=72.41 E-value=3.9 Score=26.46 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=19.5
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEG 264 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 264 (280)
|.+..+|++.|+++...|..-+....++|
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 89999999999999999999998887777
No 323
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=72.28 E-value=8.3 Score=32.76 Aligned_cols=42 Identities=21% Similarity=0.252 Sum_probs=36.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||.++.+ |.+..+|+++|++++..|+.-+..+..
T Consensus 150 ~Lt~rE~evl~~~~~--------G~s~~eIA~~l~iS~~TV~~h~~~i~~ 191 (216)
T PRK10840 150 RLSPKESEVLRLFAE--------GFLVTEIAKKLNRSIKTISSQKKSAMM 191 (216)
T ss_pred cCCHHHHHHHHHHHC--------CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 588899999999863 999999999999999999887776643
No 324
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=72.20 E-value=14 Score=26.55 Aligned_cols=47 Identities=17% Similarity=0.378 Sum_probs=39.7
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH--HhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL--ENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L--~~eG~IYs 268 (280)
..|..|+.+|+.+ +|.++++|++.++-....||-+|.-| -.-|+-.+
T Consensus 10 tKqa~li~mL~rp------~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~ 58 (72)
T PF11994_consen 10 TKQAQLIAMLRRP------EGATIAEICEATGWQPHTVRGALSGLLKKKLGLTIT 58 (72)
T ss_pred cHHHHHHHHHcCC------CCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEE
Confidence 4788999999874 59999999999999999999999999 55566544
No 325
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=72.12 E-value=8.6 Score=31.83 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=30.9
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.-+...+|++.|+++++.|.+.+..|.+.|.|=-
T Consensus 23 ~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~ 56 (154)
T COG1321 23 GFARTKDIAERLKVSPPSVTEMLKRLERLGLVEY 56 (154)
T ss_pred CcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEE
Confidence 3578999999999999999999999999999844
No 326
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=71.63 E-value=8 Score=29.72 Aligned_cols=50 Identities=26% Similarity=0.308 Sum_probs=38.3
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+++++-++.+- ..+.=|+.-.|++++++..+--+.+|..|.++|.|-.
T Consensus 42 vdee~~~ki~KEV--~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~l 91 (107)
T COG4901 42 VDEELLDKIRKEV--PRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQL 91 (107)
T ss_pred ccHHHHHHHHHhc--ccceeecHHHHHHHhccchHHHHHHHHHHHhCCceee
Confidence 4445555443321 2456899999999999999999999999999998754
No 327
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=71.55 E-value=9 Score=33.13 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=36.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||++|.+ |.+..+|+++|++++..|+.-+..+..
T Consensus 134 ~LT~RE~eVL~ll~~--------G~snkeIA~~L~iS~~TV~~h~~~I~~ 175 (207)
T PRK11475 134 MLSPTEREILRFMSR--------GYSMPQIAEQLERNIKTIRAHKFNVMS 175 (207)
T ss_pred CCCHHHHHHHHHHHC--------CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 488899999999974 999999999999999999887776643
No 328
>PRK06474 hypothetical protein; Provisional
Probab=71.34 E-value=11 Score=31.94 Aligned_cols=50 Identities=18% Similarity=0.335 Sum_probs=43.0
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeec
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsT 269 (280)
++.+.+||++|... ...+++.+|++.+ +++...|-..|..|.+.|.|-..
T Consensus 10 ~p~R~~Il~~L~~~-----~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 10 HPVRMKICQVLMRN-----KEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred CHHHHHHHHHHHhC-----CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 46788899999864 2249999999999 69999999999999999999864
No 329
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=71.21 E-value=10 Score=30.81 Aligned_cols=37 Identities=16% Similarity=0.293 Sum_probs=30.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
-|++.+++|+.+.. .|++.++|++.|+.+...|+..+
T Consensus 6 ~Lte~qr~VL~Lr~--------~GlTq~EIAe~LgiS~stV~~~e 42 (137)
T TIGR00721 6 FLTERQIKVLELRE--------KGLSQKEIAKELKTTRANVSAIE 42 (137)
T ss_pred CCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHH
Confidence 47889999999852 48999999999999999887433
No 330
>PRK04217 hypothetical protein; Provisional
Probab=71.14 E-value=9.9 Score=29.71 Aligned_cols=40 Identities=8% Similarity=0.131 Sum_probs=30.8
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
..|+.-+++|+.++.. +|+++++||+.++++...|...|.
T Consensus 41 ~~Lt~eereai~l~~~-------eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 41 IFMTYEEFEALRLVDY-------EGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3467777777776643 489999999999999988776654
No 331
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=70.78 E-value=14 Score=25.99 Aligned_cols=48 Identities=15% Similarity=0.297 Sum_probs=38.0
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.++-.++.+++.+. .-+|+..|.++|++.-..-...++.|..+|.|=.
T Consensus 5 D~ly~~a~~~V~~~------~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 5 DPLYEEAVEFVIEE------GKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp STTHHHHHHHHHHC------TCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred cHHHHHHHHHHHHc------CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 45677788888763 3689999999999999999999999999998844
No 332
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=70.44 E-value=9.1 Score=33.12 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=35.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||.+|.+ |.+..+||.+|++++..|+.-+..+..
T Consensus 148 ~LT~RE~eVL~lla~--------G~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAE--------GLSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHC--------CCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 578888999999864 999999999999999999887766543
No 333
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=70.20 E-value=8 Score=37.11 Aligned_cols=55 Identities=16% Similarity=0.295 Sum_probs=42.0
Q ss_pred HHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 221 Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
|+..+.+.- ..+++++.++|+++++.+++.+++.++.|.+.|.|-.+ +++.|-.+
T Consensus 297 iL~~l~~~~--~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~-~~g~~~l~ 351 (412)
T PRK04214 297 LLGRLDQAR--KHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRG-ERGQWVLA 351 (412)
T ss_pred HHHHHHHHH--hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEec-CCCceEec
Confidence 555553211 13469999999999999999999999999999999875 44466543
No 334
>PRK15320 transcriptional activator SprB; Provisional
Probab=70.15 E-value=11 Score=32.86 Aligned_cols=43 Identities=16% Similarity=0.188 Sum_probs=37.7
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
..+++-...||++|.+ |.+-++|+++|+++.+.|..-+..|.+
T Consensus 163 ~~LSdREIEVL~LLAk--------G~SNKEIAekL~LS~KTVSTYKnRLLe 205 (251)
T PRK15320 163 PGVTQAKYALLILLSS--------GHPAIELAKKFGLGTKTVSIYRKKVMY 205 (251)
T ss_pred CCCCHHHHHHHHHHHc--------CCCHHHHHHHhccchhhHHHHHHHHHH
Confidence 4688899999999864 999999999999999999988887765
No 335
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=69.76 E-value=6.4 Score=32.88 Aligned_cols=46 Identities=17% Similarity=0.336 Sum_probs=39.0
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+.+|..|.+. ..|++..+++.+|+.+.++-|.+|+.|.++|.+--
T Consensus 111 ~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (166)
T PRK15466 111 ADELLALLTSV-----RQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRK 156 (166)
T ss_pred HHHHHHHHHHH-----HccccHHHHHHHhCCcHHHHHHHHHHHHhccchhh
Confidence 34677777664 36999999999999999999999999999998754
No 336
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=69.36 E-value=9.8 Score=35.63 Aligned_cols=50 Identities=28% Similarity=0.437 Sum_probs=41.9
Q ss_pred CCchhHHHHH-----HhcCCCCCCCCCccCHHHHHHH--hCCCHHHHHHHHHHHHhCCeeeec
Q 023576 214 LKDCDQMILD-----YLQQPSSSERERGVHVNELSEQ--LKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 214 l~~~~~~Vl~-----~i~~~~~~~~e~Gv~v~~I~~~--l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+++-+++||+ +++. ..-|+..+|++. +++++..||..+..|.++|.|..+
T Consensus 4 l~~R~~~Il~~IV~~yi~~------~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 4 LDERQREILRAIVEDYIAT------GEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred cCHHHHHHHHHHHHHHHhc------CCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCC
Confidence 5667888887 6664 346899999977 899999999999999999998764
No 337
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=69.12 E-value=10 Score=26.08 Aligned_cols=31 Identities=23% Similarity=0.480 Sum_probs=25.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 238 HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.-..||.+++++.+-|-.||..|.+-|.|-+
T Consensus 6 vas~iAd~~GiTRSvIVNALRKleSaGvIes 36 (61)
T PF08222_consen 6 VASKIADRVGITRSVIVNALRKLESAGVIES 36 (61)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred hHHHHHHHhCccHHHHHHHHHHHHhcCceee
Confidence 4578999999999999999999999999865
No 338
>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=69.01 E-value=9.2 Score=28.80 Aligned_cols=48 Identities=17% Similarity=0.287 Sum_probs=40.8
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH----------HHHhCCee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA----------SLENEGLI 266 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~----------~L~~eG~I 266 (280)
+.+.++||.+|.+. -.+.....+|++..+.+.++|.-||. -|+.-|.+
T Consensus 8 S~~R~~vl~~L~~~----yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV 65 (90)
T PF07381_consen 8 SKVRKKVLEYLCSI----YPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLV 65 (90)
T ss_pred HHHHHHHHHHHHHc----CCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCe
Confidence 45889999999885 24588999999999999999999995 47777777
No 339
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=68.25 E-value=4.1 Score=30.97 Aligned_cols=56 Identities=20% Similarity=0.321 Sum_probs=42.8
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc---cccccC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF---HYKFAR 279 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~---hfk~t~ 279 (280)
+.|+++|+.. .+.|+.+..|+-.++++-.-.++.++.|++.| +..+-|+. .|..|+
T Consensus 18 eIi~dIL~~~----~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~G-li~~~~~~~~~~y~lT~ 76 (95)
T COG3432 18 EIIFDILKAI----SEGGIGITRIIYGANLNYKRAQKYIEMLVEKG-LIIKQDNGRRKVYELTE 76 (95)
T ss_pred HHHHHHHHHh----cCCCCCceeeeeecCcCHHHHHHHHHHHHhCC-CEEeccCCccceEEECh
Confidence 4567777742 34588888999999999999999999999999 44444554 577775
No 340
>PRK05638 threonine synthase; Validated
Probab=68.08 E-value=10 Score=36.63 Aligned_cols=48 Identities=23% Similarity=0.270 Sum_probs=41.9
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC--CCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLK--IPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYs 268 (280)
+.+.+..||.+|+.. -++..+|++.|+ ++...|...|..|.++|.|-+
T Consensus 369 ~~~~r~~IL~~L~~~-------~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~ 418 (442)
T PRK05638 369 IGGTKLEILKILSER-------EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEE 418 (442)
T ss_pred ccchHHHHHHHHhhC-------CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEE
Confidence 567889999999852 378999999997 889999999999999999955
No 341
>cd00131 PAX Paired Box domain
Probab=67.45 E-value=13 Score=29.68 Aligned_cols=44 Identities=20% Similarity=0.323 Sum_probs=38.0
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
++...|+.+++ +|++..+|+++|+++...|...+....+.|.+-
T Consensus 21 d~R~rIv~~~~--------~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~ 64 (128)
T cd00131 21 SIRQRIVELAQ--------SGIRPCDISRQLRVSHGCVSKILNRYYETGSIR 64 (128)
T ss_pred HHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 47778887764 389999999999999999999999999999653
No 342
>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=67.35 E-value=18 Score=26.71 Aligned_cols=54 Identities=11% Similarity=0.120 Sum_probs=41.1
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+++.+=.||..|...- ..-+=|+.+.|.+..++++.++...|..|...+.|..+
T Consensus 4 L~~~d~rvL~aiE~gm--k~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~ 57 (82)
T PF09202_consen 4 LSKEDFRVLRAIEMGM--KNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRR 57 (82)
T ss_dssp --HHHHHHHHHHHTTT--TT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHHcc--cCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCcccc
Confidence 4555667888887642 23468999999999999999999999999999999874
No 343
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=67.15 E-value=14 Score=31.61 Aligned_cols=33 Identities=18% Similarity=0.465 Sum_probs=29.8
Q ss_pred ccCHHHHHHHh--CCCHHHHHHHHHHHHhCCeeee
Q 023576 236 GVHVNELSEQL--KIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 236 Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYs 268 (280)
.-++++|++.+ .++.++|.++|+.|.+.|+|-.
T Consensus 42 ~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~ 76 (193)
T TIGR03882 42 RRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVE 76 (193)
T ss_pred CCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEec
Confidence 56999999999 3899999999999999999865
No 344
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=67.00 E-value=12 Score=32.45 Aligned_cols=42 Identities=24% Similarity=0.316 Sum_probs=36.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||.++.+ |.+..+|++.|++++..|+.-+..+..
T Consensus 155 ~Lt~rE~~Vl~l~~~--------G~s~~eIA~~L~iS~~TVk~~~~~i~~ 196 (216)
T PRK10100 155 LLTHREKEILNKLRI--------GASNNEIARSLFISENTVKTHLYNLFK 196 (216)
T ss_pred CCCHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 488889999999863 899999999999999999998877654
No 345
>PF14493 HTH_40: Helix-turn-helix domain
Probab=66.99 E-value=9.2 Score=28.40 Aligned_cols=31 Identities=19% Similarity=0.408 Sum_probs=29.3
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCe
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGL 265 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~ 265 (280)
.|.++++||+.-++.++.|..-|..+...|.
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 3999999999999999999999999999997
No 346
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=66.50 E-value=15 Score=31.79 Aligned_cols=52 Identities=8% Similarity=0.169 Sum_probs=39.1
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++..+|..+|...... .....+.++||+.++.+...|..+|..|.++|.|-.
T Consensus 150 ~~~~Rla~~L~~~~~~-~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 150 PLENRLAAFILLTQEG-DLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK 201 (226)
T ss_pred hHHHHHHHHHHhcccC-CcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence 4667777776543211 122357899999999999999999999999998854
No 347
>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=66.35 E-value=8.7 Score=31.89 Aligned_cols=32 Identities=16% Similarity=0.230 Sum_probs=30.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++.++||+.++.+...|..+|..|.++|.|-.
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 68899999999999999999999999999965
No 348
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.17 E-value=8.5 Score=32.30 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=33.1
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
-++.++||..++.+.+.|..+|..|.++|.|- ....|...
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~--~~~~~i~I 188 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIR--SGYGKIQL 188 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE--cCCCEEEE
Confidence 35789999999999999999999999999996 23334443
No 349
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=65.68 E-value=12 Score=26.33 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=34.0
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHh--------CCCHHHHHHHHHHHHhCCeeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQL--------KIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~IYs 268 (280)
.++..|..+|+.. .=++.++|...+ ..+..+|+++|+.|++.++|=-
T Consensus 8 ~I~AaIVrimK~~------k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~R 62 (68)
T PF10557_consen 8 QIDAAIVRIMKQE------KKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIER 62 (68)
T ss_dssp HHHHHHHHHHHHS------SEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEE
T ss_pred hhhhheehhhhhc------CceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhc
Confidence 3677888888874 246777776543 3777889999999999998855
No 350
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=65.50 E-value=12 Score=27.35 Aligned_cols=44 Identities=23% Similarity=0.299 Sum_probs=36.4
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
+|=++|+..+ =++..+|+.+|+.|++-|+.-|+.|+.-|.|-.-
T Consensus 6 qlRd~l~~~g------r~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 6 QVRDLLALRG------RMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHHcC------cccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 3555666532 3589999999999999999999999999999764
No 351
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=65.48 E-value=8.8 Score=35.42 Aligned_cols=55 Identities=24% Similarity=0.257 Sum_probs=44.4
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH-HHHhCCeeeec
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA-SLENEGLIYST 269 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~-~L~~eG~IYsT 269 (280)
.++...+...|..+...- ...-+.++.|+..++.+.+.+.+.++ +|++.|.|..|
T Consensus 255 ~~l~~~~~~~l~~~~~~~---~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~ 310 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKF---GGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRT 310 (328)
T ss_pred CCCCHHHHHHHHHHHHHc---CCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccC
Confidence 467788888887444321 12358999999999999999999999 99999999766
No 352
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.08 E-value=8.8 Score=31.34 Aligned_cols=31 Identities=35% Similarity=0.387 Sum_probs=28.8
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
-++-++|+..++++..+||++|..|-+++++
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcc
Confidence 4789999999999999999999999998775
No 353
>KOG2411 consensus Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]
Probab=64.99 E-value=19 Score=35.50 Aligned_cols=63 Identities=17% Similarity=0.046 Sum_probs=47.2
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh-hhhccCCCCCEEEEEEEEeee
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT-REMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~-~~~~~~~~G~yVrV~G~l~~f 133 (280)
..|.|+||+.....+....-|.|-|.+|.|.+..-.+.-... .....+..-+.|+|.|++..-
T Consensus 48 ~kv~l~GWl~~~~~~k~~~F~~LRD~~G~vq~lls~~s~~l~~~~~~~v~~e~vv~v~gtvv~R 111 (628)
T KOG2411|consen 48 KKVVLCGWLELHRVHKMLTFFNLRDAYGIVQQLLSPDSFPLAQKLENDVPLEDVVQVEGTVVSR 111 (628)
T ss_pred CEEEEeeeeeeeeccccceEEEeeccCcceEEEecchhhhHHhcccCCCChhheEeeeeeEecc
Confidence 578999999988777777788999999999998765432110 112346677999999999875
No 354
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=64.86 E-value=23 Score=22.06 Aligned_cols=41 Identities=15% Similarity=0.235 Sum_probs=31.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
+++.++.++..+-. .|.+..+|++.++++...|...+....
T Consensus 11 l~~~~~~~~~~~~~-------~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRFG-------EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHHh-------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55666777765532 478999999999999999988877643
No 355
>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=64.74 E-value=10 Score=29.39 Aligned_cols=52 Identities=19% Similarity=0.260 Sum_probs=40.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCC
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
|++...+||++|=+. + .+++.+|.+.|. .....|...|..|..-|.|-..-+
T Consensus 1 Ls~~E~~IM~~lW~~-----~-~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 1 LSDLELEIMEILWES-----G-EATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp --HHHHHHHHHHHHH-----S-SEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCHHHHHHHHHHHhC-----C-CCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec
Confidence 356788999999874 2 389999999994 668899999999999999876533
No 356
>smart00351 PAX Paired Box domain.
Probab=64.70 E-value=16 Score=28.91 Aligned_cols=44 Identities=23% Similarity=0.296 Sum_probs=37.0
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
++..+|+.+++ +|.+..+|+++|+++...|...+....+.|.+-
T Consensus 21 ~~R~riv~~~~--------~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 21 EERQRIVELAQ--------NGVRPCDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred HHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 47777887764 378999999999999999999999998888643
No 357
>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=64.56 E-value=24 Score=25.15 Aligned_cols=39 Identities=15% Similarity=0.192 Sum_probs=30.1
Q ss_pred CCccCHHHHHHHh---CCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 234 ERGVHVNELSEQL---KIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 234 e~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
..-+++..+++-+ ++++..+|.||..|..+|.|=++-+.
T Consensus 18 g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~G 59 (70)
T PF07848_consen 18 GGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERRG 59 (70)
T ss_dssp TS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECCC
T ss_pred CCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeecC
Confidence 3467888888776 69999999999999999999876544
No 358
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=64.52 E-value=29 Score=25.67 Aligned_cols=53 Identities=9% Similarity=0.185 Sum_probs=41.6
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh--CCC------HHHHHHHHHHHHhCCeeeecC
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL--KIP------QKKIMDSIASLENEGLIYSTI 270 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l--~~~------~~~v~~al~~L~~eG~IYsTi 270 (280)
.....+|++.|.... ...|.|...|.+-+ ++. ..-++.+|..|++.|.|-.+-
T Consensus 5 P~y~~MI~eAI~~l~---er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~k 65 (88)
T cd00073 5 PPYSEMVTEAIKALK---ERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVK 65 (88)
T ss_pred CCHHHHHHHHHHHcC---CCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeec
Confidence 357789999998863 56899999999877 333 233888999999999998764
No 359
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=64.45 E-value=19 Score=26.32 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=31.2
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
..|.+-+|..|.. ..-|++.+++..++.+.++|+.+|..+-+
T Consensus 23 ~~L~r~LLr~LA~------G~PVt~~~LA~a~g~~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 23 AWLLRPLLRLLAK------GQPVTVEQLAAALGWPVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHHHHHHHTT------TS-B-HHHHHHHHT--HHHHHHHHHH-TT
T ss_pred HHHHHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHhCCC
Confidence 4577888888875 35799999999999999999999998753
No 360
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=64.42 E-value=33 Score=28.08 Aligned_cols=58 Identities=16% Similarity=0.146 Sum_probs=31.3
Q ss_pred EEeeEEEEEEEEEeeecCCeeE-EEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEE
Q 023576 69 EITNVTLVGLVYNKEERASDVN-FTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLI 127 (280)
Q Consensus 69 ~i~~V~iVG~V~~~~~~~t~~~-~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~ 127 (280)
+...|.+||.|+++.....+.. .-|.|..- .+-+++|.+-.. -.-.+-+++|.+|-+.
T Consensus 17 p~~EvD~VG~VvsV~~~~~f~~~vYLsD~~~Nll~Ikfw~~l~~-~~~eDilk~~~liA~S 76 (143)
T PF09104_consen 17 PYGEVDTVGFVVSVSKKQGFQPLVYLSDECHNLLAIKFWTGLNQ-YGYEDILKPGSLIAAS 76 (143)
T ss_dssp CCCEEEEEEEEEEEE--TTS--EEEEE-TTS-EEEEEESS--------SS---TT-EEEEE
T ss_pred CccccceEEEEEEEEecCCCceeEEeecCCccEEEEEeccCccc-cchhhhcCcceEEEEe
Confidence 4688999999999976554433 45677665 688888876431 0112456888888775
No 361
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=64.33 E-value=19 Score=29.55 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=36.1
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.+|-+|.... .+.-+++++|+++.++++.-+++.+..|...|.|-+
T Consensus 12 ~~L~~LA~~~---~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S 57 (150)
T COG1959 12 RALLYLALLP---GGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKS 57 (150)
T ss_pred HHHHHHHhCC---CCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEe
Confidence 3455555431 222478999999999999999999999999999876
No 362
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair.
Probab=64.05 E-value=66 Score=32.02 Aligned_cols=70 Identities=14% Similarity=0.338 Sum_probs=47.6
Q ss_pred CCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCee
Q 023576 60 KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKK 137 (280)
Q Consensus 60 ~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~ 137 (280)
...|.+.+..+..++.+| ...+.+.+.++-..++|+.|.... ....+..+.+|.|.+++.. |+++.
T Consensus 463 ~P~F~~~~~~i~~~~~~g--------~~h~kl~~~~~~~~~~ai~F~~~~----~~~~~~~~~~~~ii~~l~~n~~~g~~ 530 (539)
T TIGR00644 463 EPLFLLKNLRVEDIKLLG--------ENHLKLSLKSGGKNIEAIAFNAGD----LELELNLGRPLDVAGKLSINEWRGRE 530 (539)
T ss_pred CCEEEecCeEEEEEEEcC--------CCEEEEEEecCCEEEEEEEEcCcc----ccccccCCCEEEEEEEEEEEeeCCcc
Confidence 345666777777777665 346788887752259999996542 1234556789999999884 98876
Q ss_pred EEEE
Q 023576 138 QIVA 141 (280)
Q Consensus 138 ~i~~ 141 (280)
.+.+
T Consensus 531 ~~ql 534 (539)
T TIGR00644 531 TPQL 534 (539)
T ss_pred eEEE
Confidence 5544
No 363
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=63.92 E-value=16 Score=29.60 Aligned_cols=41 Identities=10% Similarity=0.002 Sum_probs=32.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++.++.|+.+.-- +|.+..+|++.|++++..|+..+...
T Consensus 122 ~L~~~~r~vl~l~~~-------~g~s~~eIA~~l~is~~tv~~~l~ra 162 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-------QNLPIAEVARILGKTEGAVKILQFRA 162 (170)
T ss_pred hCCHHHHHHHHHHHh-------cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 567777777776432 48999999999999999999887654
No 364
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=63.83 E-value=18 Score=37.34 Aligned_cols=54 Identities=20% Similarity=0.501 Sum_probs=42.8
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCC----HHHHHHHHHHHHhCCeeeecCCCccc
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIP----QKKIMDSIASLENEGLIYSTIDEFHY 275 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~----~~~v~~al~~L~~eG~IYsTiDd~hf 275 (280)
.+.+||++|++. ...++++.+|++.|+++ ..+++.+|+.|..+|.|-.+ ....|
T Consensus 3 ~~~~il~~l~~~----~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~-~~~~~ 60 (709)
T TIGR02063 3 LRELILEFLKSK----KGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKN-RRGLY 60 (709)
T ss_pred cHHHHHHHHHhC----CCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc-CCceE
Confidence 466799999864 35799999999999865 34599999999999999754 43444
No 365
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=63.78 E-value=15 Score=29.13 Aligned_cols=41 Identities=15% Similarity=0.146 Sum_probs=34.9
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF 277 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~ 277 (280)
-.+.++||..++.+.+.|+.||..|..-|.|.-+ ||.-|..
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~-ed~~i~i 93 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQKLGLIEID-EDGVIYI 93 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCeEEe
Confidence 4578999999999999999999999999999885 4555544
No 366
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=63.75 E-value=15 Score=32.24 Aligned_cols=51 Identities=20% Similarity=0.268 Sum_probs=43.2
Q ss_pred CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..|+.-|..||++.... .-+++..|...|+-......++|++|+.||+.+.
T Consensus 172 ~ELn~Dht~ILela~~~------gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~Wi 222 (249)
T KOG3341|consen 172 TELNMDHTVILELAEIL------GYVTISLLKANLGWERSRAIQALEHLVKEGLAWI 222 (249)
T ss_pred chhcccHHHHHHHHHhc------CceeHHHHHHhccchHHHHHHHHHHHHhccceee
Confidence 34666788899987653 2489999999999999999999999999999974
No 367
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=63.32 E-value=19 Score=23.30 Aligned_cols=38 Identities=16% Similarity=0.289 Sum_probs=31.1
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
..++..|++.+++ ..++.+|++.++++.+.|+..++..
T Consensus 14 ~~~~~~i~~~~~~--------~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 14 KRLEQYILKLLRE--------SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHHHhh--------cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3477788888764 2699999999999999999988753
No 368
>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=63.07 E-value=12 Score=33.99 Aligned_cols=53 Identities=6% Similarity=0.102 Sum_probs=43.7
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t 278 (280)
++-.|++.|.+ ...+.++|+++++.++.-++.-|+.|+.-|.+=. +++.|+.|
T Consensus 11 ~~Lglfd~L~~-------gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~--~~~~y~~t 63 (306)
T TIGR02716 11 IELDLFSHMAE-------GPKDLATLAADTGSVPPRLEMLLETLRQMRVINL--EDGKWSLT 63 (306)
T ss_pred HHcCcHHHHhc-------CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEe--cCCcEecc
Confidence 45567888854 2569999999999999999999999999999954 56788866
No 369
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=63.05 E-value=14 Score=31.12 Aligned_cols=40 Identities=18% Similarity=0.347 Sum_probs=31.5
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
+.+-+.+|+++..- .|++++||++.+++++..|+..+...
T Consensus 136 l~~~~~~~v~l~~~-------~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-------EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred cCHHHHHHHHHHHH-------CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45555666666543 49999999999999999999888765
No 370
>PRK00118 putative DNA-binding protein; Validated
Probab=62.99 E-value=18 Score=28.01 Aligned_cols=40 Identities=13% Similarity=0.298 Sum_probs=31.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+..... .|.++.+|++.+++++..|...+..
T Consensus 17 ~L~ekqRevl~L~y~-------eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 17 LLTEKQRNYMELYYL-------DDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467788888866543 4899999999999999988777653
No 371
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=62.71 E-value=13 Score=30.00 Aligned_cols=39 Identities=8% Similarity=0.026 Sum_probs=30.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+..- +|++.++||+.|++++..|+..+.
T Consensus 106 ~Lp~~~r~v~~l~~~-------~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYW-------EDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHH-------hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 566777777765432 499999999999999999886553
No 372
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=62.71 E-value=14 Score=25.59 Aligned_cols=35 Identities=9% Similarity=0.301 Sum_probs=28.0
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHH
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMD 255 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~ 255 (280)
+-.+.-++++.+. ...+...+||.+|++++.+|+.
T Consensus 7 p~rdkA~e~y~~~-----~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 7 PNRDKAFEIYKES-----NGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred cCHHHHHHHHHHh-----CCCccHHHHHHHHCCCHHHHHH
Confidence 3556677777763 3479999999999999999984
No 373
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=62.65 E-value=12 Score=30.25 Aligned_cols=39 Identities=15% Similarity=0.009 Sum_probs=29.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.. -+|++.++|++.+++++..|+..|.
T Consensus 106 ~Lp~~~r~v~~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 106 ELPENYRDVVLAHY-------LEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred hCCHHHHHHHHHHH-------HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666666533 2599999999999999999976653
No 374
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=62.51 E-value=16 Score=34.21 Aligned_cols=46 Identities=28% Similarity=0.457 Sum_probs=38.2
Q ss_pred hHHHHH-----HhcCCCCCCCCCccCHHHHHHH--hCCCHHHHHHHHHHHHhCCeeeec
Q 023576 218 DQMILD-----YLQQPSSSERERGVHVNELSEQ--LKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 218 ~~~Vl~-----~i~~~~~~~~e~Gv~v~~I~~~--l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
++.||. +++. ..-|+..+|++. +++++..||..+..|.++|.|..+
T Consensus 4 ~~~il~aIV~~~l~~------~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 4 QRKILKAIVEEYIKT------GQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred HHHHHHHHHHHHHhc------CCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCC
Confidence 455664 5554 347899999999 899999999999999999999765
No 375
>PRK09483 response regulator; Provisional
Probab=62.42 E-value=18 Score=30.13 Aligned_cols=41 Identities=27% Similarity=0.373 Sum_probs=34.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.|++-..+||.++. .|.+..+|+++|++++..|+.-+..+.
T Consensus 148 ~Lt~rE~~vl~~~~--------~G~~~~~Ia~~l~is~~TV~~~~~~i~ 188 (217)
T PRK09483 148 SLSERELQIMLMIT--------KGQKVNEISEQLNLSPKTVNSYRYRMF 188 (217)
T ss_pred ccCHHHHHHHHHHH--------CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 57888899999874 388999999999999999887776554
No 376
>PRK11642 exoribonuclease R; Provisional
Probab=62.06 E-value=20 Score=37.74 Aligned_cols=53 Identities=23% Similarity=0.376 Sum_probs=42.2
Q ss_pred hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCH----HHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQ----KKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~----~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
++.||++|++. +.++++.+|++.|+++. ..++.+|+.|..+|.|..+ ....|.
T Consensus 21 ~~~Il~~l~~~-----~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~-~~~~~~ 77 (813)
T PRK11642 21 REFILEHLTKR-----EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT-RRQCYA 77 (813)
T ss_pred HHHHHHHHHhc-----CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc-CCceEe
Confidence 56799999763 36899999999998753 3499999999999999865 334564
No 377
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.02 E-value=16 Score=39.37 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=27.4
Q ss_pred eeEEEEEEEEEeeec------CCeeEEEEEcCCceEEEEEe
Q 023576 71 TNVTLVGLVYNKEER------ASDVNFTLDDGTGRVVCKRW 105 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~------~t~~~~~LdDgTG~I~~~~w 105 (280)
..|+++|.|.+++.. .....++|+|.||.|+|.+|
T Consensus 982 ~~v~v~G~i~~~~~~~~tkkG~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594 982 SQVRTLGGLNSVKKKITTKNGKPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred CEEEEEEEEEEEEEecccCCCCEEEEEEEEECCCcEEEEeC
Confidence 357899999765542 23577799999999999987
No 378
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=62.01 E-value=13 Score=30.75 Aligned_cols=40 Identities=13% Similarity=0.189 Sum_probs=31.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+..- +|++.+||++.|++++..|+..|..
T Consensus 134 ~Lp~~~r~v~~l~~~-------~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 134 QVDPRQAEVVELRFF-------AGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred cCCHHHHHHHHHHHH-------cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 367777777766442 5999999999999999998876643
No 379
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=61.84 E-value=18 Score=28.04 Aligned_cols=42 Identities=17% Similarity=0.229 Sum_probs=32.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.|++.++.|+...-- .|.+..+|++.++++++.|+..+....
T Consensus 110 ~L~~~~~~ii~~~~~-------~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPEREREVLVLRYL-------EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHHHHhhHHh-------cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 466777777654321 388999999999999999998887653
No 380
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=61.79 E-value=15 Score=29.95 Aligned_cols=41 Identities=7% Similarity=0.027 Sum_probs=31.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++.++.|+.+..- +|.+.+||++.+++++..|+..|...
T Consensus 112 ~L~~~~r~v~~l~~~-------~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 112 LLSADQREAIILIGA-------SGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 466677777766432 49999999999999999998877653
No 381
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=61.73 E-value=15 Score=31.66 Aligned_cols=46 Identities=20% Similarity=0.187 Sum_probs=38.8
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCe
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL 265 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~ 265 (280)
+.+..||+.|++. ...=++.+++++.++.++..||.-|.+|...|.
T Consensus 16 ~~~~~il~~l~~~----~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 16 PLYYRYLKELKEE----GVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHHHHHHHHc----CCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 4677899999874 234689999999999999999999999988774
No 382
>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=61.66 E-value=7.9 Score=33.22 Aligned_cols=50 Identities=22% Similarity=0.498 Sum_probs=39.0
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 272 (280)
+-...+++|+.. .=|++++|+..|++...++.+.|..|..+|.|---+||
T Consensus 100 lL~~Fi~yIK~~------Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd 149 (188)
T PF09756_consen 100 LLQEFINYIKEH------KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD 149 (188)
T ss_dssp HHHHHHHHHHH-------SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T
T ss_pred HHHHHHHHHHHc------ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC
Confidence 666677999874 36799999999999999999999999999998887777
No 383
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=61.65 E-value=12 Score=28.73 Aligned_cols=52 Identities=27% Similarity=0.442 Sum_probs=40.1
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH-------------hCCeeeecCC
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE-------------NEGLIYSTID 271 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~-------------~eG~IYsTiD 271 (280)
..-.-.|+.+|=+. ..|+-+.+|+..|++++..++.++--|. =-|+||+|.-
T Consensus 20 k~~eI~IY~lLve~-----~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGYiya~~~ 84 (113)
T COG5625 20 KKNEIRIYSLLVEK-----GRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGYIYATTP 84 (113)
T ss_pred CcchhhhhhHHHHh-----cCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceeeEecCCC
Confidence 33344688877663 3599999999999999999999987766 3578888853
No 384
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=61.39 E-value=9.5 Score=29.56 Aligned_cols=35 Identities=31% Similarity=0.373 Sum_probs=31.7
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
..=|+...|+++|++..+--+.+|.+|.+.|.|=.
T Consensus 57 ~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~ 91 (105)
T PF03297_consen 57 MKLITPSVLSERLKINGSLARKALRELESKGLIKP 91 (105)
T ss_dssp SSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEE
T ss_pred CcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEE
Confidence 35789999999999999999999999999998854
No 385
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=61.36 E-value=16 Score=34.03 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=38.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
+|++-+||+++|+++...|...|++..++|.|=-+|+.....
T Consensus 25 ~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~ 66 (321)
T COG2390 25 EGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEG 66 (321)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcc
Confidence 599999999999999999999999999999999999864443
No 386
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=61.26 E-value=22 Score=31.20 Aligned_cols=53 Identities=19% Similarity=0.352 Sum_probs=43.8
Q ss_pred CCCCchh-HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 212 DGLKDCD-QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 212 ~~l~~~~-~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
.+++.+. +.|.+.|+. .+.+.+.+++++.++++.-.+|.-|++|++.|.|..-
T Consensus 153 kGi~~~Tl~~i~~~~~~-----~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 153 KGLDELTLQKVREALKE-----PDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred CCcCHHHHHHHHHHHhC-----cCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence 4555544 568888884 3568999999999999999999999999999988653
No 387
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=60.43 E-value=18 Score=28.87 Aligned_cols=40 Identities=10% Similarity=0.018 Sum_probs=31.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.-- +|.+..||++.+++++..|+..+..
T Consensus 106 ~L~~~~r~ii~l~~~-------~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFF-------VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHh-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466777777654332 4899999999999999999887754
No 388
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=60.38 E-value=23 Score=28.94 Aligned_cols=37 Identities=16% Similarity=0.230 Sum_probs=29.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
-|++-+++||.+. . .|.+.++|++.|+++...|....
T Consensus 6 ~Lt~rqreVL~lr-~-------~GlTq~EIAe~LGiS~~tVs~ie 42 (141)
T PRK03975 6 FLTERQIEVLRLR-E-------RGLTQQEIADILGTSRANVSSIE 42 (141)
T ss_pred CCCHHHHHHHHHH-H-------cCCCHHHHHHHHCCCHHHHHHHH
Confidence 4788999999884 2 48999999999999887655444
No 389
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=60.31 E-value=13 Score=30.83 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=30.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+..- +|.+.+||++.|++++..|+..|.
T Consensus 127 ~Lp~~~R~v~~L~~~-------~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 127 TLRPRVKQAFLMATL-------DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567777777776432 499999999999999998877554
No 390
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=59.65 E-value=14 Score=30.76 Aligned_cols=40 Identities=13% Similarity=0.225 Sum_probs=31.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.-- +|++.++|++.|++|...|+..|..
T Consensus 131 ~L~~~~r~v~~l~~~-------~g~s~~eIA~~lgis~~tV~~~l~r 170 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-------EGLSVAEAATRSGMSESAVKVSVHR 170 (184)
T ss_pred hCCHHHHHHHHHHHH-------cCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 567777777765432 4999999999999999999887653
No 391
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=59.34 E-value=43 Score=26.56 Aligned_cols=60 Identities=28% Similarity=0.318 Sum_probs=34.8
Q ss_pred eeEEEEEEEEEeeec-CCeeEEEEE----cCCc---eEEEEE---ecccccChhhhccCCCCCEEEEEEEEeeeCC
Q 023576 71 TNVTLVGLVYNKEER-ASDVNFTLD----DGTG---RVVCKR---WASEVFDTREMEAIQDGMYVRLIGNLKSFQG 135 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~-~t~~~~~Ld----DgTG---~I~~~~---w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~ 135 (280)
..+.+.|+|.+.... +....|++. ...+ ....+. |..+. ...++.|+.+++.|+++...+
T Consensus 76 ~~~~v~g~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~-----~~~l~~Gd~i~~~g~l~~~~~ 146 (176)
T PF13567_consen 76 KEVTVQGTVESVPQIDGRGQRFTLRVERVLAGGNWIPVSGKILLYLPKDS-----QPRLQPGDRIRVRGKLKPPSG 146 (176)
T ss_pred ceEEEEEEEcccccccCceEEEEEEEEEeeccccccccceeeEEEecccc-----ccccCCCCEEEEEEEEecCCC
Confidence 456688888776443 334456664 1111 222222 22221 126899999999999988654
No 392
>PRK10736 hypothetical protein; Provisional
Probab=59.16 E-value=28 Score=33.09 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=36.3
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
..+|+++|+.+++++..++..+|-+|.-.|.|...-+. .|+
T Consensus 320 ~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~g~-~~~ 360 (374)
T PRK10736 320 EVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGG-YVR 360 (374)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcCCc-EEE
Confidence 36899999999999999999999999999999987654 554
No 393
>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=59.08 E-value=30 Score=27.60 Aligned_cols=49 Identities=10% Similarity=0.190 Sum_probs=40.2
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh----CCCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL----KIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l----~~~~~~v~~al~~L~~eG~IYs 268 (280)
|++.+..||++|=.. ..+++.+|+..| +.....|...|..|..-|.|-.
T Consensus 2 Lt~~E~~VM~vlW~~------~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~ 54 (130)
T TIGR02698 2 ISDAEWEVMRVVWTL------GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTT 54 (130)
T ss_pred CCHHHHHHHHHHHcC------CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceee
Confidence 567788899999653 257999998887 4788899999999999998854
No 394
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=59.04 E-value=33 Score=25.08 Aligned_cols=49 Identities=22% Similarity=0.419 Sum_probs=41.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEG 264 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 264 (280)
+|++.+.+||+|=+.-- .-.|..-+.|...|+++.-..-+.|..|++.-
T Consensus 2 ~Ls~~d~~iL~fE~~ww---~~~GaKe~aIre~fGls~~rYyq~Ln~LiD~p 50 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWW---RHGGAKEEAIREEFGLSPTRYYQRLNALIDDP 50 (77)
T ss_pred CCCHHHHHHHHHHHHhC---cCCCCcHHHHHHHHCCCHHHHHHHHHHHhCCh
Confidence 47889999999987752 34577888999999999999999999999854
No 395
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=58.74 E-value=22 Score=27.31 Aligned_cols=40 Identities=25% Similarity=0.429 Sum_probs=28.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
-|++-|++++++.-. +..|+.+||..++++...|.+.+..
T Consensus 17 LLT~kQ~~~l~lyy~-------eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYE-------EDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCT-------S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHc-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 378899999998754 4789999999999998877766654
No 396
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=58.72 E-value=17 Score=29.59 Aligned_cols=40 Identities=15% Similarity=0.222 Sum_probs=31.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+....- .|++..+|++.+++++..|+..+..
T Consensus 125 ~L~~~~r~i~~l~~~-------~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 125 ALPVKQREVFLLRYV-------EGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred hCCHHHHHHhhHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 567777777766542 4899999999999999998887654
No 397
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.69 E-value=14 Score=32.09 Aligned_cols=32 Identities=16% Similarity=0.380 Sum_probs=29.6
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
-++.++||+.++++...|..+|..|.++|.|-
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 36789999999999999999999999999994
No 398
>KOG3818 consensus DNA polymerase epsilon, subunit B [Replication, recombination and repair]
Probab=57.93 E-value=34 Score=33.26 Aligned_cols=78 Identities=23% Similarity=0.329 Sum_probs=57.4
Q ss_pred CEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576 67 GLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP 146 (280)
Q Consensus 67 g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~ 146 (280)
++.+..+.++|.+....++ .|-|+|-||+++.-+-. .. ....-+.+|.+|-|.|.... +...++...+-|
T Consensus 173 t~~~~~~lvLGlLTq~k~G----~~~lEDpsgsVqlDlsq-a~---fh~glf~egC~VL~EG~f~~--~vf~V~~lg~PP 242 (525)
T KOG3818|consen 173 TRALQSFLVLGLLTQLKEG----KFHLEDPSGSVQLDLSQ-AK---FHHGLFCEGCFVLVEGTFES--GVFHVNELGFPP 242 (525)
T ss_pred cccccceeeeehhhhccCC----cEEEeCCCCcEEEeecc-cc---cccceeccceEEEEeeeeec--ceEEEeeccCCC
Confidence 4567788899998876554 57899999987754332 11 23456899999999999776 888888888888
Q ss_pred CCCchHHHH
Q 023576 147 VTNFDEVTC 155 (280)
Q Consensus 147 v~d~Nei~~ 155 (280)
++. .|++.
T Consensus 243 ~E~-~~~tr 250 (525)
T KOG3818|consen 243 VER-REVTR 250 (525)
T ss_pred CCc-chhHH
Confidence 764 55554
No 399
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=57.73 E-value=17 Score=29.89 Aligned_cols=40 Identities=18% Similarity=0.280 Sum_probs=31.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+..- +|.+..||++.|++++..|+..|..
T Consensus 119 ~Lp~~~r~v~~L~~~-------~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 119 KLSSKARAAFLYNRL-------DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466677777776432 4899999999999999998876543
No 400
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=57.70 E-value=16 Score=33.96 Aligned_cols=54 Identities=19% Similarity=0.334 Sum_probs=40.7
Q ss_pred CCCchhHHHHH----HhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576 213 GLKDCDQMILD----YLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271 (280)
Q Consensus 213 ~l~~~~~~Vl~----~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 271 (280)
.++++++.|.+ +|.+- -.-+|+.+|-.-+.++++++.+-+.+|++.|++|.-|.
T Consensus 331 ~w~DL~krviEHN~RvI~~y-----YSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiN 388 (439)
T COG5071 331 RWSDLRKRVIEHNIRVIANY-----YSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKIN 388 (439)
T ss_pred hHHHHHHHHHHhhHhHHHHH-----hhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEec
Confidence 35667766644 34331 12567888888888999999999999999999998764
No 401
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=57.60 E-value=4.1 Score=27.31 Aligned_cols=24 Identities=4% Similarity=0.288 Sum_probs=17.9
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|.++.+|++.|+++.++|...+.
T Consensus 21 ~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 21 EGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp CTT-HHHHHHHHT--CCHHHHHHH
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 477999999999999988887764
No 402
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=57.37 E-value=9.3 Score=30.31 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=27.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMD 255 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~ 255 (280)
.|++-++.|+.+-.- +|.+.+|||+.|++++..|++
T Consensus 107 ~Lp~~~r~v~~l~~~-------~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-------EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHhhcC
Confidence 466677777766332 589999999999999988863
No 403
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=57.12 E-value=13 Score=31.77 Aligned_cols=30 Identities=20% Similarity=0.487 Sum_probs=27.0
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhC
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENE 263 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 263 (280)
+.|+++.+|++.++.+..+|+++|+.|..+
T Consensus 18 ~pgls~~~La~~l~~~~~~v~~~l~~L~~~ 47 (188)
T PRK00135 18 EEGLSLEQLAEILELEPTEVQQLLEELQEK 47 (188)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 448999999999999999999999999764
No 404
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=57.00 E-value=17 Score=30.41 Aligned_cols=39 Identities=10% Similarity=0.071 Sum_probs=29.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+.. -+|.+.+||++.+++|+..|+..|.
T Consensus 131 ~Lp~~~r~v~~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~ 169 (191)
T PRK12520 131 RLPPRTGRVFMMRE-------WLELETEEICQELQITATNAWVLLY 169 (191)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666665433 2489999999999999999887754
No 405
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=56.91 E-value=13 Score=28.00 Aligned_cols=24 Identities=8% Similarity=0.345 Sum_probs=22.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++|++.|++++.+|.++|+
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 599999999999999999999875
No 406
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=56.81 E-value=27 Score=25.82 Aligned_cols=39 Identities=18% Similarity=0.268 Sum_probs=33.4
Q ss_pred CHHHHHHHhC--CCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 238 HVNELSEQLK--IPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 238 ~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
-|+.+++.+. -+.++-...-..|++.|.|+-..|+.+|+
T Consensus 35 lVdWL~~~~~~~~~R~eAv~~g~~Ll~~G~i~HV~~~h~F~ 75 (84)
T cd04438 35 LVDWLLSHVEGLTDRREARKYASSLLKLGYIRHTVNKITFS 75 (84)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHHHHHCCcEEecCCCcccc
Confidence 5678888774 57778888889999999999999999997
No 407
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=56.44 E-value=18 Score=29.64 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=29.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
.|++-++.|+.+..- +|.+..||++.|++++..|+..+
T Consensus 118 ~L~~~~r~vl~L~~~-------~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-------RGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHH
Confidence 466777777776432 48999999999999999885543
No 408
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=56.41 E-value=24 Score=27.95 Aligned_cols=41 Identities=22% Similarity=0.213 Sum_probs=30.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++-++.|+.+.- -+|.++.+|++.+++++..|+..+...
T Consensus 113 ~L~~~~r~il~l~~-------~~~~~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 113 KLPEQCRKIFILSR-------FEGKSYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred HCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45666666666522 148999999999999999998877654
No 409
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.41 E-value=23 Score=31.16 Aligned_cols=49 Identities=24% Similarity=0.359 Sum_probs=42.7
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
++..++.|+++|+.+ .|.+..|+.+.+.++.+..|=-|..|..++.|=+
T Consensus 99 ~ns~R~~Iy~~i~~n------PG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a 147 (240)
T COG3398 99 LNSKRDGIYNYIKPN------PGFSLSELRANLYINRSTLRYHLRILESNPLIEA 147 (240)
T ss_pred hhhhHHHHHHHhccC------CCccHHHHHHhcCCChHHHHHHHHHHHhCcchhh
Confidence 355788999999975 3999999999999999999999999999887743
No 410
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=56.38 E-value=19 Score=30.32 Aligned_cols=40 Identities=15% Similarity=0.133 Sum_probs=31.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+..- +|.+.++|++.|++++..|+..|..
T Consensus 113 ~Lp~~~r~v~~L~~~-------~g~s~~EIA~~LgiS~~tVk~~l~R 152 (188)
T PRK12546 113 QLPDEQREALILVGA-------SGFSYEEAAEMCGVAVGTVKSRANR 152 (188)
T ss_pred hCCHHHhHHhhhHHh-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 567777777766432 4899999999999999988776643
No 411
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=56.38 E-value=25 Score=28.52 Aligned_cols=42 Identities=21% Similarity=0.306 Sum_probs=34.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.+++.+.+||.++.+ |.+..+|++.+++++..|+..+..|..
T Consensus 149 ~lt~~e~~vl~l~~~--------g~~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 149 LLTPRERQILKLITE--------GYTNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred CCCHHHHHHHHHHHC--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 477888999998753 678999999999999988887776654
No 412
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=55.99 E-value=21 Score=30.01 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=29.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
.|++-++.|+.+.. -+|++..||++.|++++..|+.-|
T Consensus 116 ~Lp~~~r~i~~L~~-------~~g~s~~EIA~~Lgis~~tVk~~l 153 (187)
T PRK12516 116 QLPDDQREAIILVG-------ASGFAYEEAAEICGCAVGTIKSRV 153 (187)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 46666777776543 259999999999999999887654
No 413
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=55.98 E-value=41 Score=22.33 Aligned_cols=41 Identities=20% Similarity=0.325 Sum_probs=33.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.+++-+.+|+..+.+ |.+..+|+..+++++..|+.-+..+.
T Consensus 4 ~Lt~rE~~v~~l~~~--------G~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQ--------GKSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHC--------CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356677788888764 78999999999999999887776553
No 414
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=55.64 E-value=21 Score=29.61 Aligned_cols=39 Identities=15% Similarity=0.255 Sum_probs=29.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.. -+|.+.++|++.+++++..|+..+.
T Consensus 135 ~L~~~~r~vl~l~~-------~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 135 ALSPEERRVIEVLY-------YQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 56677777776533 2489999999999999999986554
No 415
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.62 E-value=22 Score=28.98 Aligned_cols=40 Identities=15% Similarity=0.219 Sum_probs=30.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+..- .|.+.++|++.|++++..|+..+..
T Consensus 128 ~L~~~~r~vl~l~~~-------~~~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 128 SLPEELRTAITLREI-------EGLSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 567777777765432 4899999999999999998766543
No 416
>PLN02532 asparagine-tRNA synthetase
Probab=55.53 E-value=52 Score=33.57 Aligned_cols=64 Identities=11% Similarity=0.004 Sum_probs=43.2
Q ss_pred eeecCCeeEEEEEcCCce--EEEEEecccccChhhhccCCCCCEEEEEEEEeeeC-----CeeEEEEEEEeeCC
Q 023576 82 KEERASDVNFTLDDGTGR--VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ-----GKKQIVAFSVRPVT 148 (280)
Q Consensus 82 ~~~~~t~~~~~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~-----~~~~i~~~~ir~v~ 148 (280)
++......-+.|.|+||. |.|++-.... .....+..+..|.|.|.|+.-+ +...|.+..|..+.
T Consensus 129 ~r~~g~i~FI~LrDGSg~~~lQvVv~~~~~---~~~~~L~~Es~V~V~G~V~~~~~~~~~g~iEl~v~~i~VLg 199 (633)
T PLN02532 129 APPPPSVAYLLISDGSCVASLQVVVDSALA---PLTQLMATGTCILAEGVLKLPLPAQGKHVIELEVEKILHIG 199 (633)
T ss_pred cccCCCcEEEEEECCCCccceEEEEeCCcc---cHhhcCCCceEEEEEEEEEecCCCCCCCcEEEEeeEEEEEe
Confidence 334445556699999998 9997743322 1125789999999999999752 23456666665554
No 417
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=55.40 E-value=90 Score=23.71 Aligned_cols=79 Identities=19% Similarity=0.218 Sum_probs=47.1
Q ss_pred EEEeeEEEEEEEEEe-eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE-eeeC-CeeEEEEEEE
Q 023576 68 LEITNVTLVGLVYNK-EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL-KSFQ-GKKQIVAFSV 144 (280)
Q Consensus 68 ~~i~~V~iVG~V~~~-~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l-~~f~-~~~~i~~~~i 144 (280)
.||-+|.=+-.+... .....+..+.|.||.=.+.|.+-..-+ +.-....++.|.+||+.=-. +..+ +++-|.+..+
T Consensus 18 ~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLatqln-~lv~~g~l~~~siirl~~y~~n~v~~~k~iiiil~l 96 (101)
T PF04057_consen 18 NPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLATQLN-HLVESGELQKGSIIRLKQYTCNTVKNGKKIIIILDL 96 (101)
T ss_dssp -TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESGGGH-HHHHTTSSSTT-EEEEEEEEEEESTTSSEEEEEEEE
T ss_pred CcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHHHhH-HHHhcCCcccCCEEEEeEEEEeeccCCCEEEEEEee
Confidence 455555555554442 234578899999999998885433221 11223579999999998543 3456 7888888777
Q ss_pred eeC
Q 023576 145 RPV 147 (280)
Q Consensus 145 r~v 147 (280)
..|
T Consensus 97 eVv 99 (101)
T PF04057_consen 97 EVV 99 (101)
T ss_dssp EEE
T ss_pred EEE
Confidence 655
No 418
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=55.17 E-value=29 Score=28.24 Aligned_cols=42 Identities=24% Similarity=0.362 Sum_probs=35.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++...+|+.+|.+ |++.++|++++++++..|+..+..|..
T Consensus 137 ~Lt~~E~~il~~l~~--------g~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 137 PLTKRERQVAEKLAQ--------GMAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred CCCHHHHHHHHHHHC--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 467788889998863 789999999999999999988877754
No 419
>PRK14136 recX recombination regulator RecX; Provisional
Probab=55.12 E-value=26 Score=32.42 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=41.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh---CCCHHHHHHHHHHHHhCCeeeecCCCccc
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQL---KIPQKKIMDSIASLENEGLIYSTIDEFHY 275 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~IYsTiDd~hf 275 (280)
....+....|.+|..- --+..||.++| +++++.|..+|++|.++|+| ||.-|
T Consensus 160 ~~~~lk~kAL~lLSrR-------eRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYL----DDeRF 214 (309)
T PRK14136 160 PARSLKGRALGYLSRR-------EYSRAELARKLAPYADESDSVEPLLDALEREGWL----SDARF 214 (309)
T ss_pred cHHHHHHHHHHHhhcc-------cccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCc----CHHHH
Confidence 3456778888888652 35889999999 49999999999999999985 55444
No 420
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=54.68 E-value=20 Score=29.55 Aligned_cols=41 Identities=20% Similarity=0.230 Sum_probs=30.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++-++.|+.+.- -+|.+.++|++.+++++..|+..+...
T Consensus 136 ~L~~~~r~v~~l~~-------~~g~s~~eIA~~lgis~~~v~~~l~Ra 176 (187)
T TIGR02948 136 ALPPKYRMVIVLKY-------MEDLSLKEISEILDLPVGTVKTRIHRG 176 (187)
T ss_pred hCCHHHhHHhhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45556666665422 248999999999999999999887653
No 421
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=54.45 E-value=20 Score=29.80 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=29.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.. -+|++.+||++.|++++..|+..|..
T Consensus 129 ~L~~~~r~v~~l~~-------~~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 129 QLPDRQRLPIVHVK-------LEGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred HCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35555555554432 25999999999999999999887654
No 422
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=54.41 E-value=16 Score=34.50 Aligned_cols=33 Identities=6% Similarity=0.235 Sum_probs=29.3
Q ss_pred CCCccCHHHHHHHh---CCCHHHHHHHHHHHHhCCe
Q 023576 233 RERGVHVNELSEQL---KIPQKKIMDSIASLENEGL 265 (280)
Q Consensus 233 ~e~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~ 265 (280)
....+.++|+++++ ||..|.||..+..|++.|.
T Consensus 315 ~~~~~p~ddvidKv~~MGf~rDqV~a~v~rl~E~GQ 350 (358)
T PF07223_consen 315 SGNRHPYDDVIDKVASMGFRRDQVRATVRRLTENGQ 350 (358)
T ss_pred ccccCcHHHHHHHHHHcCCcHHHHHHHHHHHHhcCC
Confidence 34677899999988 8999999999999999994
No 423
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=54.37 E-value=23 Score=29.55 Aligned_cols=39 Identities=15% Similarity=0.210 Sum_probs=29.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.- -.|++.++||+.+++++..|+..+.
T Consensus 106 ~L~~~~r~i~~l~~-------~~g~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTE-------LEGLSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHH-------hcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 46666777776543 2499999999999999988866543
No 424
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=54.33 E-value=22 Score=29.77 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+-.- +|++.+||++.+++++..|+..|.
T Consensus 130 ~Lp~~~r~v~~L~~~-------~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 130 DLTTDQREALLLTQL-------LGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred hCCHHHhHHhhhHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 466667777665432 489999999999999999887654
No 425
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=54.24 E-value=21 Score=29.59 Aligned_cols=40 Identities=8% Similarity=0.141 Sum_probs=29.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.-- +|.+.++|++.+++++..|+..+..
T Consensus 127 ~L~~~~r~v~~l~~~-------~g~s~~EIA~~l~is~~tv~~~l~R 166 (179)
T PRK09415 127 SLPIKYREVIYLFYY-------EELSIKEIAEVTGVNENTVKTRLKK 166 (179)
T ss_pred hCCHHHhhHhHhHHh-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466666666654322 4999999999999999998876643
No 426
>PRK13239 alkylmercury lyase; Provisional
Probab=54.24 E-value=24 Score=30.75 Aligned_cols=41 Identities=20% Similarity=0.260 Sum_probs=34.5
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
..+..-||..|.. ..-+++.+|++.++.++++|+++|+.|-
T Consensus 21 ~~~~~~llr~la~------G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 21 ATLLVPLLRLLAK------GRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred hHHHHHHHHHHHc------CCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 4577778887763 3478999999999999999999999986
No 427
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=54.10 E-value=8.1 Score=25.70 Aligned_cols=38 Identities=32% Similarity=0.484 Sum_probs=24.1
Q ss_pred ccCHHHHHHHhCCCHHHHHHHH-HHHHhC-CeeeecCCCc
Q 023576 236 GVHVNELSEQLKIPQKKIMDSI-ASLENE-GLIYSTIDEF 273 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al-~~L~~e-G~IYsTiDd~ 273 (280)
.+.|.++|+.++++..+|-+.| .++--. -..=+++|++
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e 42 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEE 42 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETT
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHH
Confidence 6789999999999999887777 435333 3333445544
No 428
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=54.06 E-value=20 Score=29.87 Aligned_cols=39 Identities=13% Similarity=0.287 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+-- -+|.+.++|++.+++++..|+..+.
T Consensus 122 ~L~~~~r~i~~l~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 122 ELNESNRQVFKYKV-------FYNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46667777766532 2489999999999999999887654
No 429
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=53.70 E-value=21 Score=30.34 Aligned_cols=39 Identities=5% Similarity=0.049 Sum_probs=29.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.. -+|.+.++|+..+++++..|+..|.
T Consensus 139 ~Lp~~~r~v~~L~~-------~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 139 HLPEQIGRVFMMRE-------FLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45666666666543 2599999999999999999885543
No 430
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=53.50 E-value=38 Score=29.89 Aligned_cols=51 Identities=16% Similarity=0.252 Sum_probs=36.3
Q ss_pred hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
+-.+|.+.|.+..-. ...=+ +..+++++|+.+..-||+||..|...|.|-.
T Consensus 15 v~~~i~~~I~~g~~~-~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~ 66 (241)
T COG2186 15 VAEQIGALIVSGELP-PGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI 66 (241)
T ss_pred HHHHHHHHHHcCCCC-CCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee
Confidence 334455555543211 12223 5799999999999999999999999999864
No 431
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=53.49 E-value=23 Score=30.28 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=29.7
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.. -+|.+.++|++.|++++..|+..|..
T Consensus 138 ~L~~~~r~v~~L~~-------~~g~s~~EIA~~Lgis~~tV~~~l~R 177 (203)
T PRK09647 138 SLPPEFRAAVVLCD-------IEGLSYEEIAATLGVKLGTVRSRIHR 177 (203)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45666666655432 25999999999999999998877653
No 432
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=53.33 E-value=29 Score=27.79 Aligned_cols=41 Identities=27% Similarity=0.404 Sum_probs=31.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++.++.|+.+.-- +|.+..+|++.+++++..|+..+...
T Consensus 111 ~L~~~~r~v~~l~~~-------~g~~~~eIA~~l~is~~tv~~~l~Ra 151 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-------RGVSLTALAEQLGRTVNAVYKALSRL 151 (159)
T ss_pred HCCHHHHHHHHHHHh-------cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 466677777766322 49999999999999999998876543
No 433
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=53.03 E-value=20 Score=30.15 Aligned_cols=40 Identities=13% Similarity=0.226 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+..- +|.+.++|++.|++++..|+..|..
T Consensus 141 ~Lp~~~r~v~~l~~~-------eg~s~~EIA~~lgis~~tVk~rl~r 180 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-------EELPHQQVAEMFDIPLGTVKSRLRL 180 (194)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 455666666665322 4899999999999999998877653
No 434
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=52.84 E-value=34 Score=24.46 Aligned_cols=57 Identities=28% Similarity=0.256 Sum_probs=35.5
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhC-CCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~-~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
.+..||..|.+.- +...-.+-.||=+.|+ + -++.-..-.+|++.|.+--|-|...|.
T Consensus 12 ~r~~iL~~l~~~f--~~g~~y~E~EVN~~L~~~-~~D~a~LRR~LVd~g~L~R~~dg~~Yw 69 (71)
T PF09860_consen 12 KRLVILEYLASRF--EPGREYSEKEVNEILKRF-FDDYATLRRYLVDYGLLERTRDGSRYW 69 (71)
T ss_pred HHHHHHHHHHHhC--CCCCccCHHHHHHHHHHH-cccHHHHHHHHHHcCCeeecCCCCeee
Confidence 5666888776642 2233444455544442 2 224444557899999999998887774
No 435
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.84 E-value=24 Score=29.23 Aligned_cols=40 Identities=10% Similarity=0.239 Sum_probs=31.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.-- +|.+.++|++.|+++...|+..+..
T Consensus 131 ~L~~~~r~v~~l~~~-------~g~s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 131 TLPPRQRDVVQSISV-------EGASIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 566677777776432 4899999999999999998887654
No 436
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=52.72 E-value=19 Score=30.98 Aligned_cols=34 Identities=9% Similarity=0.261 Sum_probs=31.1
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
-++.++||+.+|++...|..+|..|..+|.|-..
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 3688999999999999999999999999999754
No 437
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=52.70 E-value=22 Score=27.88 Aligned_cols=34 Identities=24% Similarity=0.339 Sum_probs=31.3
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
+.-+++++|+..|.-++..++..|..|.++|-|-
T Consensus 17 ~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 17 PVEVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred CcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 4578999999999999999999999999999873
No 438
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=52.67 E-value=38 Score=23.74 Aligned_cols=48 Identities=17% Similarity=0.277 Sum_probs=38.2
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS 268 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 268 (280)
.++-.++.+++.+. .-.|+..|.++|++.-..-...++.|.++|.|=.
T Consensus 4 D~ly~~a~~~V~~~------~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 4 DELYDEAVELVIET------QKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred cHHHHHHHHHHHHh------CCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 34667788888763 3569999999998777788899999999998743
No 439
>PF13551 HTH_29: Winged helix-turn helix
Probab=52.50 E-value=31 Score=25.77 Aligned_cols=30 Identities=20% Similarity=0.474 Sum_probs=27.6
Q ss_pred CccC-HHHHHHHhCCCHHHHHHHHHHHHhCC
Q 023576 235 RGVH-VNELSEQLKIPQKKIMDSIASLENEG 264 (280)
Q Consensus 235 ~Gv~-v~~I~~~l~~~~~~v~~al~~L~~eG 264 (280)
+|.+ +.+|++.++++...|...+....++|
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 4775 99999999999999999999999888
No 440
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=52.46 E-value=26 Score=29.51 Aligned_cols=40 Identities=15% Similarity=0.193 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+..- +|.+.++|++.|++++..|+..|..
T Consensus 136 ~L~~~~r~i~~L~~~-------~g~s~~eIA~~lgis~~tV~~~l~R 175 (196)
T PRK12524 136 ALPERQRQAVVLRHI-------EGLSNPEIAEVMEIGVEAVESLTAR 175 (196)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 466666666665432 4899999999999999988776643
No 441
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=52.41 E-value=24 Score=28.50 Aligned_cols=39 Identities=10% Similarity=0.178 Sum_probs=30.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.-- +|.+.+||++.+++++..|+..+.
T Consensus 109 ~L~~~~r~v~~l~~~-------~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 109 ELPARTRYAFEMYRL-------HGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567777777765432 489999999999999998877644
No 442
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=52.40 E-value=25 Score=29.09 Aligned_cols=39 Identities=15% Similarity=0.135 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+..- +|.+.++|++.+++|+..|+..+.
T Consensus 117 ~Lp~~~r~i~~l~~~-------e~~s~~EIA~~lgis~~tV~~~l~ 155 (179)
T PRK12543 117 KLPYKLRQVIILRYL-------HDYSQEEIAQLLQIPIGTVKSRIH 155 (179)
T ss_pred hCCHHHHHHHHHHHH-------ccCCHHHHHHHHCCCHHHHHHHHH
Confidence 577777777776332 489999999999999998766543
No 443
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=52.23 E-value=1.2e+02 Score=24.13 Aligned_cols=78 Identities=15% Similarity=0.233 Sum_probs=45.7
Q ss_pred eeEEEEEEEEEeeecCCeeEEEEEcC--C---c-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCC-----eeEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTLDDG--T---G-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQG-----KKQI 139 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~LdDg--T---G-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~-----~~~i 139 (280)
.+|+++|.|.+...... .++|... . . .-.+..+.+.--.+-....++.|..|-|+|-++.-.. ...+
T Consensus 26 ~KVRfLgcV~~Y~~~~~--~L~l~h~~p~~~~~~~~~v~VdI~~vL~tv~~~~~rvG~WvNV~Gy~~~~~~~~~~~~v~V 103 (124)
T PF12658_consen 26 DKVRFLGCVSSYDTSTG--TLTLEHNYPRENDSQPSSVSVDINLVLETVSSEELRVGEWVNVVGYIRGEKPSQTQSPVYV 103 (124)
T ss_dssp EEEEEEEEEEEEECCCT--EEEEEETCCC---S----EEEE-TTTTTTS-GGGGSTT-EEEEEEEEECTT--------EE
T ss_pred CEEEEEEEEeEEecCcc--EEEEeecCCCCcCCCCceEEEEHHHHhhhcCccceecceEEEEEEEecccccccccccceE
Confidence 68999999988765433 5566662 1 1 1234444443222233568999999999999998662 2456
Q ss_pred EEEEEeeCCCc
Q 023576 140 VAFSVRPVTNF 150 (280)
Q Consensus 140 ~~~~ir~v~d~ 150 (280)
.|-.|.++...
T Consensus 104 qai~i~~ag~~ 114 (124)
T PF12658_consen 104 QAIMIWSAGPI 114 (124)
T ss_dssp EEEEEEE-TCG
T ss_pred EEEEEEecCch
Confidence 77777766543
No 444
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=52.01 E-value=28 Score=28.00 Aligned_cols=41 Identities=10% Similarity=0.126 Sum_probs=30.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++-++.|+.+.-- .|++.++|++.+++++..|+..+...
T Consensus 110 ~L~~~~r~i~~l~~~-------~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 110 RLPARQRAVVVLRYY-------EDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred hCCHHHHHHhhhHHH-------hcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 456666666654322 49999999999999999998877654
No 445
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=51.82 E-value=27 Score=28.10 Aligned_cols=39 Identities=15% Similarity=0.187 Sum_probs=30.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-+++|+.+..- +|++.++|++.+++++..|+..|.
T Consensus 105 ~L~~~~r~v~~l~~~-------~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 105 ELPPACRDSFLLRKL-------EGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 467777777776432 489999999999999998776543
No 446
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=51.76 E-value=25 Score=28.43 Aligned_cols=40 Identities=18% Similarity=0.206 Sum_probs=30.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.-- +|.+.++|++.++++...|+.-|..
T Consensus 113 ~L~~~~r~v~~L~~~-------~g~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 113 GLPPLVKRAFLLAQV-------DGLGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred HCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466677777765332 4899999999999999998876654
No 447
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=51.72 E-value=23 Score=29.66 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=29.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
.|++-++.|+.+..- +|++.++|++.|++++..|+..+
T Consensus 111 ~Lp~~~R~v~~L~~~-------eg~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 111 DLPEEQRAALHLVAI-------EGLSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHhCcCHHHHHHHH
Confidence 466666666665332 49999999999999999888765
No 448
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=51.51 E-value=33 Score=30.32 Aligned_cols=41 Identities=15% Similarity=0.260 Sum_probs=35.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
.|++-+.+||..+. +|.+-.||++.|++++..|+..+..+.
T Consensus 179 ~LT~rE~evl~~~a--------~G~t~~eIa~~l~is~~TV~~h~~~~~ 219 (240)
T PRK10188 179 NFSKREKEILKWTA--------EGKTSAEIAMILSISENTVNFHQKNMQ 219 (240)
T ss_pred CCCHHHHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47888999999985 389999999999999999988877654
No 449
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=51.41 E-value=21 Score=25.24 Aligned_cols=25 Identities=16% Similarity=0.280 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576 237 VHVNELSEQLKIPQKKIMDSIASLE 261 (280)
Q Consensus 237 v~v~~I~~~l~~~~~~v~~al~~L~ 261 (280)
-+.++||+.|+++.++|++++....
T Consensus 21 Pt~eEiA~~lgis~~~v~~~l~~~~ 45 (78)
T PF04539_consen 21 PTDEEIAEELGISVEEVRELLQASR 45 (78)
T ss_dssp -BHHHHHHHHTS-HHHHHHHHHHHS
T ss_pred CCHHHHHHHHcccHHHHHHHHHhCC
Confidence 4899999999999999999998654
No 450
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=51.30 E-value=25 Score=28.90 Aligned_cols=40 Identities=18% Similarity=0.262 Sum_probs=29.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.. -+|.+.+||++.+++++..|+..+..
T Consensus 119 ~L~~~~r~i~~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~R 158 (172)
T PRK09651 119 GLNGKTREAFLLSQ-------LDGLTYSEIAHKLGVSVSSVKKYVAK 158 (172)
T ss_pred hCCHHHhHHhhhhh-------ccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45666666655432 25899999999999999998876543
No 451
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=50.95 E-value=22 Score=30.83 Aligned_cols=40 Identities=15% Similarity=0.186 Sum_probs=29.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+..- +|++.+||++.|++++..|+..|..
T Consensus 134 ~Lp~~~R~v~~L~y~-------eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 134 KLPVEYREVLVLREL-------EDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred cCCHHHHhHhhhHHh-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455566666655332 4999999999999999998877653
No 452
>PRK05660 HemN family oxidoreductase; Provisional
Probab=50.92 E-value=24 Score=33.37 Aligned_cols=43 Identities=9% Similarity=0.193 Sum_probs=37.6
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
.|+++..+.++++.+..++...|+.|.++|.+. .|+++++.|+
T Consensus 320 ~G~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~--~~~~~~~lt~ 362 (378)
T PRK05660 320 EAAPRADFEAYTGLPESVIRPQLDEALAQGYLT--ETADHWQITE 362 (378)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EeCCEEEECc
Confidence 599999999999987777889999999999876 5778898875
No 453
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=50.89 E-value=15 Score=28.40 Aligned_cols=33 Identities=27% Similarity=0.367 Sum_probs=29.8
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIY 267 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 267 (280)
.=|+..-|..+|++.-+--+.||.+|.++|.|=
T Consensus 59 k~it~svl~dRlkIngsLAr~alr~L~~kG~Ik 91 (110)
T KOG1767|consen 59 KLITPSVLSDRLKINGSLARAALRELSNKGVIK 91 (110)
T ss_pred eeecHHHhhhhhhhchHHHHHHHHHHHhcchHH
Confidence 468999999999999999999999999999873
No 454
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=50.89 E-value=27 Score=29.10 Aligned_cols=40 Identities=13% Similarity=0.186 Sum_probs=28.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.. -+|.++++|++.+++++..|+..+..
T Consensus 138 ~L~~~~r~v~~l~~-------~~g~s~~eIA~~lgis~~tv~~~l~R 177 (193)
T PRK11923 138 QLPEDLRTALTLRE-------FDGLSYEDIASVMQCPVGTVRSRIFR 177 (193)
T ss_pred hCCHHHhHHHhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34555555554422 25999999999999999988876543
No 455
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=50.85 E-value=29 Score=25.49 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=27.9
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
=+.+|+++|++ + =+++.+|++.++++...|..+|.
T Consensus 7 R~~~I~e~l~~-~------~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-T------KATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-C------CCCHHHHHHHhCCCHHHHHHHhc
Confidence 35678888886 3 35899999999999999988763
No 456
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=50.83 E-value=18 Score=30.07 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=22.3
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
+.+++++|++.++ ++.+|+++|++|..
T Consensus 12 ~pvs~~~La~~l~-~~~~v~~~l~~L~~ 38 (159)
T PF04079_consen 12 EPVSIEELAEILG-SEDEVEEALEELQE 38 (159)
T ss_dssp S-B-HHHHHHHCT--HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhC-CHHHHHHHHHHHHH
Confidence 4699999999999 99999999999975
No 457
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=50.73 E-value=24 Score=29.62 Aligned_cols=39 Identities=5% Similarity=0.044 Sum_probs=27.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+-. -+|.++++||+.|++++..|+..|.
T Consensus 134 ~Lp~~~R~v~~L~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 134 HLPAQQARVFMMRE-------YLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred hCCHHHHHHHhHHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34555555555432 2499999999999999999876543
No 458
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=50.55 E-value=26 Score=29.28 Aligned_cols=40 Identities=18% Similarity=0.288 Sum_probs=30.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.-- +|.+.+||++.++++...|+..+..
T Consensus 131 ~L~~~~r~i~~l~~~-------~g~s~~EIAe~lgis~~~V~~~l~R 170 (189)
T PRK06811 131 DLEKLDREIFIRRYL-------LGEKIEEIAKKLGLTRSAIDNRLSR 170 (189)
T ss_pred hCCHHHHHHHHHHHH-------ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 567777777764321 3899999999999999998877653
No 459
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=50.51 E-value=28 Score=29.10 Aligned_cols=39 Identities=10% Similarity=0.064 Sum_probs=29.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+.. -+|.+..+|++.|++++..|+..|.
T Consensus 111 ~Lp~~~R~v~~L~~-------~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 111 KLPQDQREALILVG-------ASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred hCCHHHHHHhhHHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666665533 2599999999999999998877654
No 460
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=50.06 E-value=30 Score=28.37 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=29.5
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
.|++.++.|+.+..- .|.+.++|++.|++++..|+..|
T Consensus 100 ~L~~~~r~v~~l~~~-------~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-------EGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHH
Confidence 567777777776432 48999999999999999887654
No 461
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=50.05 E-value=1.3e+02 Score=23.82 Aligned_cols=78 Identities=19% Similarity=0.158 Sum_probs=53.4
Q ss_pred eeEEEEEEEEEeeecCCeeEEEE--EcCCce--EEEEEecccccChhhhccCCCCCEEEEEEEEeee--CCeeEEEEEEE
Q 023576 71 TNVTLVGLVYNKEERASDVNFTL--DDGTGR--VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--QGKKQIVAFSV 144 (280)
Q Consensus 71 ~~V~iVG~V~~~~~~~t~~~~~L--dDgTG~--I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~~~~~i~~~~i 144 (280)
..|++.|++.+.+......+.+= .|+--. |+..+ .. ...++.|.++.+.|-+... .+...|.|--+
T Consensus 22 ~svR~~GrL~~yD~~~~~a~l~~~~~~~~~~l~V~t~~-l~-------~~~~~~gslyq~iGEl~~~~~~~~~~L~ARV~ 93 (118)
T PF15490_consen 22 KSVRTFGRLQSYDVATSRATLTAQHESDQHSLKVDTKL-LE-------PFQARVGSLYQFIGELEHQPQDGGIVLKARVL 93 (118)
T ss_pred CeEEEEEEEEEEeccCCEEEEEeeccCCCcEEEEEeeE-cc-------ccccCCCCEEEEEEEEEEEcCCCcEEEEEEEE
Confidence 57899999999876665543311 333222 33222 21 2345899999999999998 45678888889
Q ss_pred eeCCCchHHHHH
Q 023576 145 RPVTNFDEVTCH 156 (280)
Q Consensus 145 r~v~d~Nei~~H 156 (280)
|.|+..|--.|+
T Consensus 94 r~VdG~Dl~Ly~ 105 (118)
T PF15490_consen 94 RCVDGMDLNLYE 105 (118)
T ss_pred EecCCcCHHHHH
Confidence 999888865544
No 462
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=50.03 E-value=37 Score=24.83 Aligned_cols=38 Identities=24% Similarity=0.189 Sum_probs=29.8
Q ss_pred HHHHHHHhC-CCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 239 VNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 239 v~~I~~~l~-~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
|+.+++... .+..+-....+.|++.|.|.-..|+.+|+
T Consensus 35 VdWL~~~~~~~~R~eAv~~gq~Ll~~g~i~hV~~~~~F~ 73 (81)
T cd04448 35 VNWLIRQGKAATRVQAIAIGQALLDAGWIECVSDDDLFR 73 (81)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHCCCEEecCCCCccc
Confidence 445554432 66778888889999999999999998887
No 463
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=49.91 E-value=27 Score=28.77 Aligned_cols=40 Identities=15% Similarity=0.201 Sum_probs=29.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.- -+|.+.++|++.|++++..|+..|..
T Consensus 129 ~L~~~~r~i~~l~~-------~~g~s~~eIA~~lgis~~tV~~~l~R 168 (179)
T PRK12514 129 ELEKDRAAAVRRAY-------LEGLSYKELAERHDVPLNTMRTWLRR 168 (179)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCChHHHHHHHHH
Confidence 45555555555432 24899999999999999999887654
No 464
>PRK10651 transcriptional regulator NarL; Provisional
Probab=49.77 E-value=38 Score=27.76 Aligned_cols=42 Identities=17% Similarity=0.298 Sum_probs=35.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+||+++.+ |.+.++|++.+++++..|+..+..|..
T Consensus 155 ~Lt~rE~~vl~~l~~--------g~~~~~ia~~l~is~~tV~~~~~~l~~ 196 (216)
T PRK10651 155 QLTPRERDILKLIAQ--------GLPNKMIARRLDITESTVKVHVKHMLK 196 (216)
T ss_pred cCCHHHHHHHHHHHc--------CCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 478888899998753 789999999999999999988887765
No 465
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=49.77 E-value=29 Score=29.14 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=30.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+..- +|.+.++|++.++++...|+..|.
T Consensus 134 ~Lp~~~r~i~~l~~~-------~g~s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 134 RLPVEQRAALVAVDM-------QGYSVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 467777777754322 489999999999999998887763
No 466
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=49.71 E-value=26 Score=29.33 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=28.1
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+.. -+|++.++|++.|++++..|+..+.
T Consensus 136 ~L~~~~r~i~~L~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 136 NLPENTARVFTLKE-------ILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred hCCHHHHHHhhhHH-------HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34555555554322 2599999999999999999887664
No 467
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=49.65 E-value=29 Score=28.47 Aligned_cols=38 Identities=21% Similarity=0.224 Sum_probs=27.4
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
|++-++.|+.+.. -+|.+.++||+.+++++..|+..|.
T Consensus 120 L~~~~r~i~~l~~-------~~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 120 LNEKYKTVLVLYY-------YEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred CCHHHHHHHHHHH-------HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4444555554332 2589999999999999999887765
No 468
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=49.60 E-value=86 Score=25.99 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=26.9
Q ss_pred CceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576 97 TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133 (280)
Q Consensus 97 TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f 133 (280)
|--|.|..|...++ .....++.|+.|-|.|+|+..
T Consensus 50 t~~~~vv~wgk~Ae--~~~~yl~KG~~V~VeG~l~~~ 84 (167)
T COG0629 50 TDWIRVVIWGKLAE--NAAEYLKKGSLVYVEGRLQTR 84 (167)
T ss_pred cceEEEEEehHHHH--HHHHHhcCCCEEEEEEEEEee
Confidence 44599999977432 224568899999999999975
No 469
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=49.45 E-value=26 Score=29.47 Aligned_cols=40 Identities=18% Similarity=0.311 Sum_probs=30.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.||.+-. -+|.+.+||++.|++++..|+..+..
T Consensus 142 ~L~~~~r~vl~l~~-------~~~~s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 142 ALTDTQRESVTLAY-------YGGLTYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCChHhHHHHHHH
Confidence 46677777776432 14899999999999999998876643
No 470
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=49.34 E-value=29 Score=29.52 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=29.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+.- -+|.+.++||..+++++..|+..+..
T Consensus 153 ~L~~~~r~vl~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~R 192 (206)
T PRK12526 153 KLPEAQQTVVKGVY-------FQELSQEQLAQQLNVPLGTVKSRLRL 192 (206)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46666666665432 24899999999999999998877543
No 471
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=49.33 E-value=26 Score=28.65 Aligned_cols=39 Identities=21% Similarity=0.288 Sum_probs=30.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+.-- +|.+.+||++.|++++..|+.-|.
T Consensus 118 ~L~~~~r~v~~L~~~-------eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 118 GLSGKARAAFLMSQL-------EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 467777777766432 489999999999999998876654
No 472
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.22 E-value=27 Score=28.22 Aligned_cols=40 Identities=15% Similarity=0.096 Sum_probs=30.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++.++.|+.+-. -+|.+.++|+..+++++..|+..+..
T Consensus 112 ~L~~~~r~v~~l~~-------~~~~s~~eIA~~lgis~~tv~~~l~R 151 (161)
T PRK12541 112 SLPLERRNVLLLRD-------YYGFSYKEIAEMTGLSLAKVKIELHR 151 (161)
T ss_pred HCCHHHHHHhhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46666666666532 24899999999999999999887654
No 473
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=49.16 E-value=21 Score=33.06 Aligned_cols=41 Identities=20% Similarity=0.307 Sum_probs=38.0
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccc
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHY 275 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hf 275 (280)
+|++.+||+++|+++...|...|.+-.++|.|=-+|++...
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~ 68 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFE 68 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCc
Confidence 59999999999999999999999999999999999987543
No 474
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=49.02 E-value=25 Score=29.13 Aligned_cols=41 Identities=15% Similarity=0.124 Sum_probs=30.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++.++.|+...- -+|.+.++|+..|++++..|+..|...
T Consensus 137 ~L~~~~r~i~~l~~-------~~g~s~~eIA~~lgis~~~v~~~l~Ra 177 (187)
T PRK12534 137 ELEPPRSELIRTAF-------FEGITYEELAARTDTPIGTVKSWIRRG 177 (187)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCChhHHHHHHHHH
Confidence 45556666655432 259999999999999999998877543
No 475
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=48.95 E-value=32 Score=32.75 Aligned_cols=53 Identities=23% Similarity=0.345 Sum_probs=41.8
Q ss_pred HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR 279 (280)
Q Consensus 219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~ 279 (280)
+.++.-|+. ..|+....+.++++.+.+++...|+.|.+.|.|. .|+++++.|+
T Consensus 327 ~~~~l~LR~------~~Gld~~~f~~~~g~~~~~~~~~l~~l~~~gll~--~~~~~~~LT~ 379 (394)
T PRK08898 327 EFMLNALRL------TDGVPAHLFQERTGLPLAAIEPQLAAAEQRGLLE--RDHTRIRPTP 379 (394)
T ss_pred HHHHHHHHH------hCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EECCEEEECh
Confidence 445554553 2599999999999988888889999999999987 4677888875
No 476
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.75 E-value=28 Score=28.99 Aligned_cols=39 Identities=15% Similarity=0.086 Sum_probs=30.2
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.+++|+.+.-- +|.+.+||++.+++++..|+..+.
T Consensus 139 ~L~~~~r~i~~l~~~-------~g~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 139 TLPEKQREILILRVV-------VGLSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567777777775432 489999999999999998877654
No 477
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=48.46 E-value=19 Score=30.89 Aligned_cols=41 Identities=20% Similarity=0.484 Sum_probs=31.8
Q ss_pred hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
....|+++|.+.. .+..+++++|.+..++..++|-.+|+.|
T Consensus 134 W~~~i~~~L~~~~---~~~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 134 WRRVILEYLLEFK---GKKSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp HHHHHHHHHHHTS---SE--EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcC---CCCeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 6788999998752 2337999999999999999998888776
No 478
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=48.26 E-value=27 Score=30.63 Aligned_cols=39 Identities=8% Similarity=0.120 Sum_probs=28.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++.++.|+.+.. -+|++.+||++.|++++..|+..|.
T Consensus 171 ~Lp~~~R~v~~L~~-------~eg~s~~EIA~~Lgis~~tVk~~l~ 209 (233)
T PRK12538 171 RLPEQQRIAVILSY-------HENMSNGEIAEVMDTTVAAVESLLK 209 (233)
T ss_pred hCCHHHHHHhhhHH-------hcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45566666655432 2599999999999999998876543
No 479
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=48.24 E-value=40 Score=30.17 Aligned_cols=44 Identities=14% Similarity=0.289 Sum_probs=33.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHH----HHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIM----DSIASLE 261 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~----~al~~L~ 261 (280)
.|++-++.|+.+.-- .++|++..+|++.|+++...|+ .||..|-
T Consensus 218 ~L~~rer~vl~l~y~-----~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 218 SLDARSRRIIEARWL-----DDDKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred cCCHHHHHHHHHHhc-----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566677777776432 1358999999999999999999 6666664
No 480
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=48.22 E-value=44 Score=24.45 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=30.9
Q ss_pred CHHHHHHHhC--CCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576 238 HVNELSEQLK--IPQKKIMDSIASLENEGLIYSTIDEFHYK 276 (280)
Q Consensus 238 ~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYsTiDd~hfk 276 (280)
-|+.+.+.+. -+..+--...+.|.++|.|.-..++.+|+
T Consensus 35 ~VdWL~~~~~~~~~r~eAv~lgq~Ll~~g~I~hv~~~~~F~ 75 (83)
T cd04449 35 AVSWLINNFEDVDTREEAVELGQELMNEGLIEHVSGRHPFL 75 (83)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHHHHHCCCEEecCCCCCcc
Confidence 3556666654 56677888889999999999999988886
No 481
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=47.89 E-value=33 Score=28.88 Aligned_cols=40 Identities=20% Similarity=0.318 Sum_probs=30.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL 260 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L 260 (280)
.|++.++.|+.. -- +|.+.++|++.+++++..|+..+...
T Consensus 155 ~L~~~~r~vl~l-~~-------e~~s~~EIA~~lgis~~tV~~~l~ra 194 (208)
T PRK08295 155 LLSELEKEVLEL-YL-------DGKSYQEIAEELNRHVKSIDNALQRV 194 (208)
T ss_pred hCCHHHHHHHHH-HH-------ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456666666654 21 48999999999999999998887654
No 482
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=47.77 E-value=42 Score=29.96 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=35.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|++-+.+|+..+. +|.+..+|++.|++++..|+.-+..+..
T Consensus 190 ~LT~RE~evl~l~a--------~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 190 LITAREAEILAWVR--------DGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred CCCHHHHHHHHHHH--------CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57888899999864 3899999999999999999988876643
No 483
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=47.39 E-value=44 Score=27.37 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=35.3
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
.|+....+||.+|.+ |.+.++|++.+++++..|+.-+..|..
T Consensus 143 ~lt~~E~~vl~~l~~--------g~~~~~I~~~l~~s~~tv~~~~~~l~~ 184 (204)
T PRK09958 143 SLSKQEISVMRYILD--------GKDNNDIAEKMFISNKTVSTYKSRLME 184 (204)
T ss_pred cCCHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 477778889999874 678999999999999999988877754
No 484
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=46.97 E-value=20 Score=30.06 Aligned_cols=24 Identities=13% Similarity=0.404 Sum_probs=21.0
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
+|.+.++|++.++++...|+..+.
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ 177 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLR 177 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 599999999999999999986543
No 485
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=46.79 E-value=30 Score=28.99 Aligned_cols=40 Identities=13% Similarity=0.164 Sum_probs=28.8
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.- -+|.++++|++.+++++..|+..|..
T Consensus 131 ~L~~~~r~v~~l~~-------~~g~s~~EIA~~lgis~~tvk~rl~R 170 (188)
T TIGR02943 131 HLPEQTARVFMMRE-------VLGFESDEICQELEISTSNCHVLLYR 170 (188)
T ss_pred hCCHHHHHHHHHHH-------HhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35555566655432 24899999999999999988876543
No 486
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=46.66 E-value=84 Score=22.26 Aligned_cols=48 Identities=17% Similarity=0.180 Sum_probs=32.4
Q ss_pred EEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576 74 TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG 128 (280)
Q Consensus 74 ~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G 128 (280)
.+-|.|++++...-++.|.+++=+|-|....-.. ...+++|+-|.+.=
T Consensus 7 ~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~-------~~~~~~Gq~v~~~V 54 (74)
T cd05694 7 VLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN-------FSKLKVGQLLLCVV 54 (74)
T ss_pred EEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc-------ccccCCCCEEEEEE
Confidence 3789999999888777776655566555321111 15689999887764
No 487
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=46.15 E-value=29 Score=28.65 Aligned_cols=25 Identities=12% Similarity=0.321 Sum_probs=21.9
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
+|.+.++|++.|++++..|+..+..
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~r 177 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFR 177 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999999999999998887654
No 488
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=45.98 E-value=43 Score=27.00 Aligned_cols=39 Identities=21% Similarity=0.311 Sum_probs=29.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+.- .|.+..+|++.+++++..|+..+..
T Consensus 112 ~L~~~~r~il~l~~--------~g~s~~eIA~~lgis~~tV~~~i~r 150 (166)
T PRK09639 112 KMTERDRTVLLLRF--------SGYSYKEIAEALGIKESSVGTTLAR 150 (166)
T ss_pred cCCHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45666666666532 4899999999999999988877653
No 489
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=45.97 E-value=35 Score=27.73 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=30.0
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-+++|+.+.- -+|.+..+|++.|++++..|+..+..
T Consensus 119 ~L~~~~r~i~~l~~-------~~g~s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 119 TLNDKYQTAIILRY-------YHDLTIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred hCCHHHhHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45666666665432 24899999999999999998877654
No 490
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=45.75 E-value=37 Score=21.75 Aligned_cols=23 Identities=30% Similarity=0.525 Sum_probs=15.6
Q ss_pred HHHHHHhCCCHHH-HHHHHHHHHh
Q 023576 240 NELSEQLKIPQKK-IMDSIASLEN 262 (280)
Q Consensus 240 ~~I~~~l~~~~~~-v~~al~~L~~ 262 (280)
+++++..+++.++ |++||+.|..
T Consensus 18 ~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 18 KELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4455555666666 7888888765
No 491
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.61 E-value=35 Score=28.39 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=29.6
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.||.+-.- .|.+.++|+..|++++..|+..|.
T Consensus 131 ~L~~~~r~vl~l~~~-------~~~s~~eIA~~lgis~~tV~~~l~ 169 (189)
T PRK12515 131 KLSPAHREIIDLVYY-------HEKSVEEVGEIVGIPESTVKTRMF 169 (189)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 466677777765332 489999999999999999877653
No 492
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=45.41 E-value=32 Score=28.53 Aligned_cols=39 Identities=13% Similarity=0.133 Sum_probs=28.4
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
.|++-++.|+.+.- -+|.+.++|++.++++...|+..+.
T Consensus 128 ~L~~~~r~i~~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 128 ALPERQREAIVLQY-------YQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred hCCHHHHHHhhHHH-------hcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 35555666655432 2499999999999999999877654
No 493
>PHA03068 DNA-binding phosphoprotein; Provisional
Probab=45.27 E-value=56 Score=29.32 Aligned_cols=49 Identities=22% Similarity=0.499 Sum_probs=36.7
Q ss_pred CCEEEEEEEEeeeCCeeE------EEEEEEeeCCCchHHHHHHHHHHHHHHHhcCC
Q 023576 121 GMYVRLIGNLKSFQGKKQ------IVAFSVRPVTNFDEVTCHYIECIYFHLQNSKS 170 (280)
Q Consensus 121 G~yVrV~G~l~~f~~~~~------i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~~ 170 (280)
-.|+-|.|-.+.|++|+. -=-.+|||+. .+-+.|.+|||||..++--+.
T Consensus 73 Sp~I~veGE~KIyknKk~~~~~~d~YFlkIkpt~-aSPmLYQllE~IY~nI~~~~r 127 (270)
T PHA03068 73 STYIMVEGEAKIYKNKKKDFRREDGYFLKIKPTA-ASPMLYQLLECIYGNIKDGKR 127 (270)
T ss_pred cceEEEeeeeEEEecccccccccCcceEEEeecc-cCHHHHHHHHHHHhhhccCCc
Confidence 368889999999987652 1224577764 588999999999999876553
No 494
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=45.24 E-value=34 Score=22.75 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=24.3
Q ss_pred HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHH
Q 023576 220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSI 257 (280)
Q Consensus 220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al 257 (280)
.+|+-|++. ..+-|+=.+|++.+++++.+||+-|
T Consensus 16 r~L~~l~~~----G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 16 RYLEQLKEE----GVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHT----T-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHc----CCeeECHHHHHHHHCCCHHHhcccC
Confidence 455555553 3468899999999999999999865
No 495
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=45.14 E-value=1.6e+02 Score=23.70 Aligned_cols=62 Identities=16% Similarity=0.183 Sum_probs=37.6
Q ss_pred EEEEEEEEEeee----cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeE
Q 023576 73 VTLVGLVYNKEE----RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQ 138 (280)
Q Consensus 73 V~iVG~V~~~~~----~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~ 138 (280)
|.-.|.|+.+-. .+.--.|.|.=.+| +|.+..-.+-. ...+.+++||.|.+.|.. .|+.+..
T Consensus 39 v~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla---prip~l~~GD~V~f~GeY-e~n~kgg 105 (131)
T PF11948_consen 39 VSGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA---PRIPWLQKGDQVEFYGEY-EWNPKGG 105 (131)
T ss_pred EeccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc---ccCcCcCCCCEEEEEEEE-EECCCCC
Confidence 344888888743 22233344444556 46666444432 346779999999999998 4454443
No 496
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.01 E-value=47 Score=29.31 Aligned_cols=48 Identities=15% Similarity=0.200 Sum_probs=41.1
Q ss_pred chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576 216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST 269 (280)
Q Consensus 216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 269 (280)
..++.|+..|+++ .+.+.-.|++.++++...|.=.+..|.+-|.|=++
T Consensus 174 ~~~k~I~~eiq~~------~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~ 221 (240)
T COG3398 174 ETSKAIIYEIQEN------KCNTNLLIAYELNLSVATVAYHLKKLEELGIIPED 221 (240)
T ss_pred hhHHHHHHHHhcC------CcchHHHHHHHcCccHHHHHHHHHHHHHcCCCccc
Confidence 4667788888864 37899999999999999999999999999987654
No 497
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=44.81 E-value=41 Score=26.89 Aligned_cols=44 Identities=20% Similarity=0.388 Sum_probs=33.4
Q ss_pred CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576 215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266 (280)
Q Consensus 215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 266 (280)
..++.+|+++.+ +|+..-+|+++|..+..-|.+.|...-+-|.|
T Consensus 20 ~~~R~rIvela~--------~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi 63 (125)
T PF00292_consen 20 NELRQRIVELAK--------EGVRPCDISRQLRVSHGCVSKILSRYRETGSI 63 (125)
T ss_dssp HHHHHHHHHHHH--------TT--HHHHHHHHT--HHHHHHHHHHHHHHS-S
T ss_pred HHHHHHHHHHhh--------hcCCHHHHHHHHccchhHHHHHHHHHHHhccc
Confidence 458889999875 39999999999999999999999988776654
No 498
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=44.76 E-value=31 Score=28.56 Aligned_cols=40 Identities=15% Similarity=0.142 Sum_probs=28.9
Q ss_pred CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576 213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS 259 (280)
Q Consensus 213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~ 259 (280)
.|++-++.|+.+-. -+|.+.++|++.+++++..|+..+..
T Consensus 133 ~L~~~~r~i~~l~~-------~~~~s~~eIA~~lgis~~tV~~~l~r 172 (182)
T PRK12537 133 QLEPARRNCILHAY-------VDGCSHAEIAQRLGAPLGTVKAWIKR 172 (182)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCChhhHHHHHHH
Confidence 45555555555432 25899999999999999998876654
No 499
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=44.69 E-value=24 Score=23.52 Aligned_cols=42 Identities=24% Similarity=0.356 Sum_probs=27.8
Q ss_pred CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576 214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN 262 (280)
Q Consensus 214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 262 (280)
|++-.+.-++++.+ .|++..+|+++++-+..-|+..|..-++
T Consensus 5 Lt~~Eqaqid~m~q-------lG~s~~~isr~i~RSr~~Ir~yl~dP~~ 46 (50)
T PF11427_consen 5 LTDAEQAQIDVMHQ-------LGMSLREISRRIGRSRTCIRRYLKDPVN 46 (50)
T ss_dssp --HHHHHHHHHHHH-------TT--HHHHHHHHT--HHHHHHHHHSCCC
T ss_pred CCHHHHHHHHHHHH-------hchhHHHHHHHhCccHHHHHHHhcChhh
Confidence 56666667777765 4999999999999999889888765444
No 500
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=44.32 E-value=33 Score=31.29 Aligned_cols=24 Identities=17% Similarity=0.212 Sum_probs=21.2
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 023576 235 RGVHVNELSEQLKIPQKKIMDSIA 258 (280)
Q Consensus 235 ~Gv~v~~I~~~l~~~~~~v~~al~ 258 (280)
+|++.+||++.|++++..|+..|.
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~ 180 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQ 180 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 599999999999999999887654
Done!