Query 024592
Match_columns 265
No_of_seqs 158 out of 553
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 05:51:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024592.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024592hhsearch_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 3.3E-50 7.2E-55 334.8 17.6 240 12-262 13-257 (258)
2 KOG3108 Single-stranded DNA-bi 100.0 3.6E-48 7.8E-53 340.4 20.2 258 2-263 3-265 (265)
3 cd04478 RPA2_DBD_D RPA2_DBD_D: 99.9 3.7E-25 8E-30 167.8 11.6 94 69-162 1-95 (95)
4 cd04483 hOBFC1_like hOBFC1_lik 99.7 7.1E-17 1.5E-21 121.8 10.7 73 71-143 1-91 (92)
5 PF08784 RPA_C: Replication pr 99.7 6.9E-17 1.5E-21 124.2 6.1 58 198-257 44-102 (102)
6 PF10451 Stn1: Telomere regula 99.5 1.7E-12 3.6E-17 115.1 14.9 120 42-164 29-167 (256)
7 PF01336 tRNA_anti-codon: OB-f 99.2 1.5E-10 3.3E-15 82.8 9.5 73 70-144 1-75 (75)
8 cd04492 YhaM_OBF_like YhaM_OBF 98.8 8.5E-08 1.8E-12 69.8 10.1 65 83-150 18-82 (83)
9 PRK13480 3'-5' exoribonuclease 98.6 2.8E-07 6E-12 84.3 10.2 62 82-146 31-92 (314)
10 cd03524 RPA2_OBF_family RPA2_O 98.6 4.2E-07 9.1E-12 63.5 8.4 70 71-142 1-74 (75)
11 cd04485 DnaE_OBF DnaE_OBF: A s 98.5 3.6E-07 7.9E-12 66.0 6.4 72 72-145 2-78 (84)
12 cd04489 ExoVII_LU_OBF ExoVII_L 98.4 4.9E-06 1.1E-10 60.1 10.8 73 70-144 2-77 (78)
13 COG3390 Uncharacterized protei 98.3 3.9E-06 8.5E-11 70.0 9.0 123 42-166 11-151 (196)
14 PRK06461 single-stranded DNA-b 98.3 5.5E-06 1.2E-10 66.3 9.7 84 43-146 4-100 (129)
15 cd04491 SoSSB_OBF SoSSB_OBF: A 98.3 3.6E-06 7.8E-11 61.7 7.6 53 83-140 22-75 (82)
16 cd04482 RPA2_OBF_like RPA2_OBF 98.2 1.4E-05 2.9E-10 60.2 10.0 73 71-146 2-76 (91)
17 cd04487 RecJ_OBF2_like RecJ_OB 98.2 2E-05 4.3E-10 56.8 9.4 72 70-143 1-72 (73)
18 PF13742 tRNA_anti_2: OB-fold 98.1 5.3E-05 1.1E-09 57.8 9.9 75 67-143 21-99 (99)
19 cd04484 polC_OBF polC_OBF: A s 98.0 6.8E-05 1.5E-09 55.2 9.4 72 70-143 2-81 (82)
20 cd04488 RecG_wedge_OBF RecG_we 97.9 8.1E-05 1.7E-09 52.5 8.6 64 72-138 2-69 (75)
21 cd04321 ScAspRS_mt_like_N ScAs 97.7 0.00046 1E-08 51.1 10.0 75 69-144 1-84 (86)
22 COG1107 Archaea-specific RecJ- 97.7 0.00021 4.5E-09 69.2 9.1 77 68-146 214-290 (715)
23 cd04100 Asp_Lys_Asn_RS_N Asp_L 97.7 0.00056 1.2E-08 50.3 9.6 76 69-144 1-83 (85)
24 cd04323 AsnRS_cyto_like_N AsnR 97.6 0.00079 1.7E-08 49.5 10.0 76 69-144 1-82 (84)
25 cd04317 EcAspRS_like_N EcAspRS 97.6 0.00044 9.5E-09 55.5 9.1 78 69-146 16-103 (135)
26 COG4085 Predicted RNA-binding 97.5 0.0007 1.5E-08 57.0 9.1 83 64-146 48-138 (204)
27 cd04320 AspRS_cyto_N AspRS_cyt 97.4 0.0013 2.9E-08 50.1 9.2 79 69-147 1-92 (102)
28 cd04316 ND_PkAspRS_like_N ND_P 97.4 0.0016 3.4E-08 50.3 9.5 80 68-147 13-97 (108)
29 PF13412 HTH_24: Winged helix- 97.4 0.00033 7.1E-09 45.9 4.8 47 199-251 1-47 (48)
30 cd04322 LysRS_N LysRS_N: N-ter 97.4 0.0014 3.1E-08 50.5 9.0 76 69-144 1-80 (108)
31 cd04319 PhAsnRS_like_N PhAsnRS 97.4 0.002 4.3E-08 49.2 9.2 79 69-147 1-83 (103)
32 cd04490 PolII_SU_OBF PolII_SU_ 97.3 0.0028 6.1E-08 46.3 8.9 68 70-140 2-71 (79)
33 cd04318 EcAsnRS_like_N EcAsnRS 97.2 0.0066 1.4E-07 44.2 10.5 74 70-144 2-80 (82)
34 COG1570 XseA Exonuclease VII, 97.2 0.0045 9.7E-08 58.8 11.8 96 67-166 23-121 (440)
35 smart00550 Zalpha Z-DNA-bindin 97.2 0.0016 3.4E-08 46.2 6.5 59 200-262 5-65 (68)
36 PF04076 BOF: Bacterial OB fol 97.2 0.012 2.5E-07 45.3 11.4 83 42-143 21-103 (103)
37 PRK03932 asnC asparaginyl-tRNA 97.1 0.0058 1.2E-07 58.8 11.6 94 42-146 2-99 (450)
38 PRK05673 dnaE DNA polymerase I 97.0 0.0018 3.9E-08 68.6 7.9 77 68-146 978-1059(1135)
39 PRK00286 xseA exodeoxyribonucl 97.0 0.006 1.3E-07 58.4 10.3 112 43-165 5-120 (438)
40 TIGR00237 xseA exodeoxyribonuc 96.9 0.0072 1.6E-07 57.9 10.2 95 67-165 17-114 (432)
41 TIGR00457 asnS asparaginyl-tRN 96.9 0.0088 1.9E-07 57.6 10.7 93 43-145 1-100 (453)
42 PRK07211 replication factor A; 96.9 0.0062 1.4E-07 58.8 9.6 76 68-146 172-261 (485)
43 TIGR00156 conserved hypothetic 96.9 0.039 8.4E-07 43.9 12.4 82 42-142 44-125 (126)
44 PRK07373 DNA polymerase III su 96.8 0.0046 1E-07 59.4 8.3 77 68-146 281-362 (449)
45 PRK10053 hypothetical protein; 96.8 0.055 1.2E-06 43.3 12.8 82 38-142 44-129 (130)
46 PRK07217 replication factor A; 96.6 0.011 2.4E-07 53.8 8.8 73 68-145 83-159 (311)
47 PF04703 FaeA: FaeA-like prote 96.6 0.0024 5.2E-08 44.5 3.1 46 203-253 2-47 (62)
48 PRK07218 replication factor A; 96.6 0.017 3.6E-07 55.1 9.8 72 68-146 173-256 (423)
49 COG0017 AsnS Aspartyl/asparagi 96.5 0.033 7.1E-07 53.1 11.2 89 42-142 3-95 (435)
50 PF01726 LexA_DNA_bind: LexA D 96.5 0.0019 4E-08 45.5 2.2 52 198-252 3-57 (65)
51 PF08220 HTH_DeoR: DeoR-like h 96.5 0.0061 1.3E-07 41.6 4.7 44 203-252 2-45 (57)
52 PF13730 HTH_36: Helix-turn-he 96.5 0.0099 2.1E-07 39.8 5.7 54 198-251 2-55 (55)
53 TIGR00458 aspS_arch aspartyl-t 96.3 0.027 5.9E-07 53.9 9.9 78 68-145 13-95 (428)
54 PRK12445 lysyl-tRNA synthetase 96.3 0.03 6.5E-07 54.7 10.3 77 69-145 67-147 (505)
55 PRK14699 replication factor A; 96.3 0.015 3.2E-07 56.5 7.9 77 68-145 68-157 (484)
56 PF01978 TrmB: Sugar-specific 96.2 0.0062 1.3E-07 42.8 3.8 50 198-253 5-54 (68)
57 TIGR01405 polC_Gram_pos DNA po 96.2 0.025 5.4E-07 60.5 9.8 78 68-145 8-92 (1213)
58 cd04497 hPOT1_OB1_like hPOT1_O 96.2 0.074 1.6E-06 42.8 10.5 69 68-139 15-94 (138)
59 COG3481 Predicted HD-superfami 96.2 0.0038 8.3E-08 56.2 3.1 63 81-146 18-80 (287)
60 PF12802 MarR_2: MarR family; 96.2 0.017 3.7E-07 39.4 5.7 55 198-256 2-57 (62)
61 PRK00448 polC DNA polymerase I 96.2 0.029 6.2E-07 60.9 10.0 79 68-146 237-322 (1437)
62 PRK08402 replication factor A; 96.1 0.031 6.7E-07 52.1 9.0 70 68-139 73-154 (355)
63 PF09339 HTH_IclR: IclR helix- 96.1 0.012 2.6E-07 39.1 4.6 45 204-253 6-50 (52)
64 PRK05159 aspC aspartyl-tRNA sy 96.1 0.039 8.5E-07 52.9 9.8 78 68-145 17-98 (437)
65 KOG3416 Predicted nucleic acid 96.1 0.032 7E-07 44.0 7.4 82 44-139 5-87 (134)
66 PRK14699 replication factor A; 96.1 0.027 6E-07 54.6 8.5 75 69-146 178-265 (484)
67 PRK07211 replication factor A; 96.1 0.034 7.3E-07 53.8 9.0 77 68-146 64-151 (485)
68 TIGR00459 aspS_bact aspartyl-t 96.0 0.041 8.8E-07 54.6 9.5 76 68-144 16-101 (583)
69 PRK00484 lysS lysyl-tRNA synth 96.0 0.045 9.8E-07 53.3 9.6 100 42-144 31-134 (491)
70 PRK05672 dnaE2 error-prone DNA 95.9 0.025 5.4E-07 59.7 8.2 76 69-146 955-1033(1046)
71 PRK06920 dnaE DNA polymerase I 95.9 0.019 4.2E-07 60.7 7.3 75 69-145 945-1024(1107)
72 PRK12366 replication factor A; 95.9 0.031 6.7E-07 56.1 8.3 73 69-146 186-269 (637)
73 PLN02903 aminoacyl-tRNA ligase 95.9 0.056 1.2E-06 54.2 9.9 78 68-145 73-161 (652)
74 COG3111 Periplasmic protein wi 95.8 0.2 4.3E-06 39.5 10.8 81 41-144 43-127 (128)
75 PRK00476 aspS aspartyl-tRNA sy 95.8 0.061 1.3E-06 53.5 10.0 76 68-144 18-103 (588)
76 PRK07374 dnaE DNA polymerase I 95.8 0.03 6.5E-07 59.7 8.1 77 68-146 1001-1082(1170)
77 smart00346 HTH_ICLR helix_turn 95.8 0.033 7E-07 40.9 6.1 55 203-262 7-62 (91)
78 PRK12820 bifunctional aspartyl 95.7 0.06 1.3E-06 54.5 9.6 77 68-144 19-107 (706)
79 smart00420 HTH_DEOR helix_turn 95.7 0.032 6.9E-07 36.3 5.3 45 203-253 2-46 (53)
80 PLN02221 asparaginyl-tRNA synt 95.7 0.13 2.7E-06 51.1 11.3 94 42-144 31-134 (572)
81 TIGR00499 lysS_bact lysyl-tRNA 95.6 0.093 2E-06 51.2 10.3 75 69-143 55-133 (496)
82 PRK06386 replication factor A; 95.6 0.054 1.2E-06 50.5 8.1 70 68-146 118-196 (358)
83 PLN02502 lysyl-tRNA synthetase 95.6 0.099 2.2E-06 51.6 10.4 77 68-144 109-191 (553)
84 PRK15491 replication factor A; 95.6 0.05 1.1E-06 51.2 8.0 75 69-146 178-268 (374)
85 PRK07218 replication factor A; 95.6 0.06 1.3E-06 51.4 8.5 83 43-147 58-152 (423)
86 PF09012 FeoC: FeoC like trans 95.6 0.014 3.1E-07 41.2 3.3 46 204-255 3-48 (69)
87 PRK06826 dnaE DNA polymerase I 95.5 0.046 9.9E-07 58.3 8.3 77 68-146 992-1074(1151)
88 PRK11169 leucine-responsive tr 95.5 0.035 7.6E-07 46.0 5.8 51 197-253 10-62 (164)
89 PLN02603 asparaginyl-tRNA synt 95.5 0.11 2.3E-06 51.5 10.0 96 42-144 88-190 (565)
90 PRK12366 replication factor A; 95.4 0.11 2.4E-06 52.2 10.3 66 68-138 409-485 (637)
91 PF08279 HTH_11: HTH domain; 95.4 0.046 1E-06 36.4 5.3 42 203-249 2-43 (55)
92 smart00347 HTH_MARR helix_turn 95.4 0.046 1E-06 40.3 5.8 62 197-264 6-73 (101)
93 PRK10917 ATP-dependent DNA hel 95.4 0.079 1.7E-06 53.7 9.2 66 68-136 60-129 (681)
94 PLN02850 aspartate-tRNA ligase 95.4 0.13 2.8E-06 50.6 10.2 77 68-144 82-169 (530)
95 PF00392 GntR: Bacterial regul 95.3 0.073 1.6E-06 36.8 6.2 52 202-254 5-57 (64)
96 smart00344 HTH_ASNC helix_turn 95.3 0.039 8.3E-07 42.1 5.3 47 200-252 2-48 (108)
97 cd07377 WHTH_GntR Winged helix 95.3 0.13 2.8E-06 34.9 7.5 39 223-261 27-65 (66)
98 PRK07279 dnaE DNA polymerase I 95.1 0.063 1.4E-06 56.5 7.6 75 69-145 886-966 (1034)
99 PTZ00401 aspartyl-tRNA synthet 95.1 0.17 3.8E-06 49.9 10.3 77 68-144 79-166 (550)
100 COG3355 Predicted transcriptio 95.1 0.06 1.3E-06 42.8 5.7 52 197-253 23-74 (126)
101 cd04479 RPA3 RPA3: A subfamily 95.0 0.7 1.5E-05 35.2 11.4 64 68-146 16-80 (101)
102 PF01022 HTH_5: Bacterial regu 95.0 0.1 2.2E-06 33.8 5.8 46 201-253 2-47 (47)
103 PF13463 HTH_27: Winged helix 95.0 0.056 1.2E-06 37.4 4.8 59 200-263 2-66 (68)
104 COG1571 Predicted DNA-binding 94.9 0.1 2.2E-06 49.5 7.6 75 66-144 265-341 (421)
105 cd04475 RPA1_DBD_B RPA1_DBD_B: 94.8 0.22 4.8E-06 37.5 8.1 64 70-138 2-78 (101)
106 smart00345 HTH_GNTR helix_turn 94.8 0.19 4E-06 33.4 6.8 39 220-258 18-57 (60)
107 COG2176 PolC DNA polymerase II 94.7 0.07 1.5E-06 56.1 6.5 78 68-145 240-324 (1444)
108 PRK15491 replication factor A; 94.7 0.18 4E-06 47.4 8.8 77 68-146 68-158 (374)
109 COG1522 Lrp Transcriptional re 94.7 0.068 1.5E-06 43.2 5.2 49 198-252 5-53 (154)
110 cd04481 RPA1_DBD_B_like RPA1_D 94.7 0.23 5E-06 37.9 7.9 67 72-138 2-82 (106)
111 PRK11179 DNA-binding transcrip 94.6 0.072 1.6E-06 43.5 5.4 50 198-253 6-57 (153)
112 PF08661 Rep_fac-A_3: Replicat 94.6 0.65 1.4E-05 35.7 10.4 70 68-146 19-88 (109)
113 COG1200 RecG RecG-like helicas 94.6 0.24 5.1E-06 49.6 9.6 74 68-144 61-138 (677)
114 PRK06386 replication factor A; 94.5 0.23 5E-06 46.4 9.0 65 68-139 13-86 (358)
115 PF02765 POT1: Telomeric singl 94.5 0.51 1.1E-05 38.3 10.0 71 68-141 13-101 (146)
116 PRK08402 replication factor A; 94.4 0.14 3E-06 47.9 7.3 75 85-161 246-352 (355)
117 PF03100 CcmE: CcmE; InterPro 94.4 0.67 1.5E-05 37.0 10.4 65 68-141 51-119 (131)
118 PTZ00385 lysyl-tRNA synthetase 94.4 0.33 7.1E-06 48.8 10.2 77 69-145 109-190 (659)
119 PF01047 MarR: MarR family; I 94.4 0.11 2.4E-06 34.9 5.0 52 200-257 2-54 (59)
120 cd00090 HTH_ARSR Arsenical Res 94.4 0.19 4E-06 34.6 6.3 55 201-262 7-64 (78)
121 PF12840 HTH_20: Helix-turn-he 94.3 0.1 2.2E-06 35.7 4.7 48 200-253 9-56 (61)
122 cd00092 HTH_CRP helix_turn_hel 94.3 0.28 6.1E-06 33.6 7.0 44 219-262 23-66 (67)
123 TIGR00643 recG ATP-dependent D 94.2 0.28 6E-06 49.3 9.5 65 68-136 33-102 (630)
124 PF14947 HTH_45: Winged helix- 94.1 0.1 2.2E-06 37.7 4.6 55 201-263 6-60 (77)
125 PTZ00425 asparagine-tRNA ligas 93.9 0.17 3.6E-06 50.2 7.1 61 68-129 82-146 (586)
126 cd04486 YhcR_OBF_like YhcR_OBF 93.8 0.27 5.9E-06 35.7 6.3 64 72-140 2-70 (78)
127 TIGR00498 lexA SOS regulatory 93.7 0.097 2.1E-06 44.5 4.4 55 198-253 3-58 (199)
128 PRK09834 DNA-binding transcrip 93.7 0.18 3.9E-06 44.9 6.3 54 204-262 14-68 (263)
129 cd04474 RPA1_DBD_A RPA1_DBD_A: 93.6 0.19 4.2E-06 38.3 5.6 62 68-131 10-82 (104)
130 PRK02983 lysS lysyl-tRNA synth 93.6 0.55 1.2E-05 50.1 10.6 73 69-141 653-729 (1094)
131 PRK12423 LexA repressor; Provi 93.5 0.094 2E-06 44.9 4.0 52 199-253 4-58 (202)
132 smart00419 HTH_CRP helix_turn_ 93.4 0.26 5.6E-06 31.3 5.2 41 220-261 7-47 (48)
133 PRK13254 cytochrome c-type bio 93.3 0.98 2.1E-05 37.0 9.5 55 68-128 52-109 (148)
134 PRK10163 DNA-binding transcrip 93.2 0.24 5.2E-06 44.3 6.4 54 204-262 28-82 (271)
135 PRK11512 DNA-binding transcrip 93.2 0.29 6.3E-06 39.3 6.3 53 198-256 37-90 (144)
136 TIGR01884 cas_HTH CRISPR locus 93.1 0.38 8.2E-06 41.1 7.1 63 197-265 139-203 (203)
137 PRK08486 single-stranded DNA-b 92.9 0.74 1.6E-05 39.0 8.4 78 67-146 2-107 (182)
138 PF13404 HTH_AsnC-type: AsnC-t 92.9 0.22 4.7E-06 31.8 4.0 41 200-246 2-42 (42)
139 PF02082 Rrf2: Transcriptional 92.8 0.32 6.9E-06 35.4 5.5 49 202-253 9-57 (83)
140 PHA02701 ORF020 dsRNA-binding 92.8 0.28 6E-06 41.4 5.7 52 201-257 4-55 (183)
141 PF06163 DUF977: Bacterial pro 92.7 0.28 6E-06 38.9 5.2 48 200-253 11-58 (127)
142 PF00325 Crp: Bacterial regula 92.7 0.24 5.2E-06 29.8 3.8 30 222-251 3-32 (32)
143 COG2345 Predicted transcriptio 92.6 0.25 5.5E-06 43.0 5.4 47 201-253 11-57 (218)
144 TIGR02325 C_P_lyase_phnF phosp 92.6 0.38 8.3E-06 41.7 6.7 51 202-253 13-64 (238)
145 TIGR02404 trehalos_R_Bsub treh 92.6 0.38 8.3E-06 41.7 6.6 51 202-253 5-56 (233)
146 PF10007 DUF2250: Uncharacteri 92.5 0.29 6.3E-06 36.8 4.9 52 199-256 5-56 (92)
147 TIGR02431 pcaR_pcaU beta-ketoa 92.4 0.38 8.3E-06 42.3 6.4 51 205-261 13-63 (248)
148 PF01325 Fe_dep_repress: Iron 92.3 0.25 5.3E-06 34.0 4.0 35 219-253 20-54 (60)
149 PTZ00417 lysine-tRNA ligase; P 92.3 0.69 1.5E-05 46.0 8.7 75 69-143 134-215 (585)
150 TIGR02018 his_ut_repres histid 92.3 0.43 9.4E-06 41.4 6.6 51 202-253 6-57 (230)
151 PRK09764 DNA-binding transcrip 92.2 0.46 9.9E-06 41.6 6.7 51 202-253 10-61 (240)
152 PRK05813 single-stranded DNA-b 92.2 1.7 3.7E-05 37.9 10.1 79 67-149 8-105 (219)
153 smart00418 HTH_ARSR helix_turn 92.2 0.48 1E-05 31.5 5.5 44 206-256 2-46 (66)
154 COG1349 GlpR Transcriptional r 92.2 0.21 4.5E-06 44.4 4.5 46 201-252 5-50 (253)
155 PF10771 DUF2582: Protein of u 92.2 0.38 8.3E-06 33.8 4.9 49 203-257 10-59 (65)
156 PRK10434 srlR DNA-bindng trans 92.2 0.22 4.8E-06 44.3 4.7 47 201-253 5-51 (256)
157 COG1190 LysU Lysyl-tRNA synthe 92.2 0.96 2.1E-05 43.8 9.1 76 70-145 64-143 (502)
158 PRK14999 histidine utilization 92.1 0.49 1.1E-05 41.4 6.7 52 201-253 16-68 (241)
159 PRK15090 DNA-binding transcrip 92.0 0.45 9.7E-06 42.1 6.5 52 205-262 18-70 (257)
160 PF03444 HrcA_DNA-bdg: Winged 92.0 0.27 5.9E-06 35.7 4.1 54 199-253 2-55 (78)
161 TIGR03879 near_KaiC_dom probab 92.0 0.17 3.7E-06 36.4 3.0 49 197-251 14-62 (73)
162 TIGR01889 Staph_reg_Sar staphy 91.9 0.61 1.3E-05 35.7 6.3 54 198-253 22-75 (109)
163 PRK10906 DNA-binding transcrip 91.9 0.28 6.1E-06 43.5 5.0 47 201-253 5-51 (252)
164 PRK10079 phosphonate metabolis 91.9 0.5 1.1E-05 41.3 6.6 31 223-253 37-67 (241)
165 COG1414 IclR Transcriptional r 91.8 0.45 9.8E-06 42.0 6.2 54 204-262 7-61 (246)
166 PRK11402 DNA-binding transcrip 91.7 0.58 1.3E-05 40.9 6.7 31 223-253 35-65 (241)
167 COG2188 PhnF Transcriptional r 91.5 0.58 1.2E-05 41.0 6.5 52 201-253 11-63 (236)
168 PRK11569 transcriptional repre 91.4 0.51 1.1E-05 42.3 6.1 52 205-261 32-84 (274)
169 TIGR02337 HpaR homoprotocatech 91.4 0.64 1.4E-05 35.9 6.0 53 198-256 25-78 (118)
170 PRK03573 transcriptional regul 91.3 0.67 1.4E-05 37.1 6.2 55 198-257 28-83 (144)
171 PRK07459 single-stranded DNA-b 91.3 0.82 1.8E-05 36.0 6.5 61 67-129 3-76 (121)
172 PF06969 HemN_C: HemN C-termin 91.1 0.47 1E-05 32.7 4.5 57 202-265 7-64 (66)
173 PRK06751 single-stranded DNA-b 91.1 0.9 1.9E-05 38.2 6.9 61 67-129 2-79 (173)
174 PRK07275 single-stranded DNA-b 91.0 1.4 3.1E-05 36.5 8.0 61 67-129 2-79 (162)
175 TIGR02944 suf_reg_Xantho FeS a 90.9 0.62 1.3E-05 36.8 5.5 47 203-253 11-57 (130)
176 cd07153 Fur_like Ferric uptake 90.8 0.64 1.4E-05 35.7 5.4 47 202-253 2-53 (116)
177 PRK02801 primosomal replicatio 90.7 2.3 5.1E-05 32.3 8.4 33 97-131 50-82 (101)
178 TIGR00738 rrf2_super rrf2 fami 90.7 0.79 1.7E-05 36.0 6.0 46 219-264 23-70 (132)
179 PRK06863 single-stranded DNA-b 90.6 1.9 4.2E-05 36.0 8.4 80 67-148 4-112 (168)
180 PRK03902 manganese transport t 90.6 0.6 1.3E-05 37.5 5.3 59 201-265 8-66 (142)
181 PF10264 Stork_head: Winged he 90.4 1 2.2E-05 32.9 5.7 63 198-262 8-78 (80)
182 PF02295 z-alpha: Adenosine de 90.3 0.53 1.2E-05 33.1 4.2 51 200-254 3-53 (66)
183 PRK13509 transcriptional repre 90.3 0.53 1.1E-05 41.7 5.1 47 201-253 5-51 (251)
184 PRK04424 fatty acid biosynthes 90.3 0.29 6.3E-06 41.4 3.3 45 201-251 7-51 (185)
185 KOG0555 Asparaginyl-tRNA synth 90.2 0.48 1E-05 44.6 4.9 67 66-133 122-189 (545)
186 PF08679 DsrD: Dissimilatory s 90.0 0.93 2E-05 31.8 5.0 49 202-252 2-51 (67)
187 PRK09954 putative kinase; Prov 90.0 0.56 1.2E-05 43.4 5.3 46 200-251 2-47 (362)
188 PRK10411 DNA-binding transcrip 89.9 0.6 1.3E-05 41.2 5.1 45 201-251 4-48 (240)
189 PRK13159 cytochrome c-type bio 89.8 6.7 0.00015 32.3 10.7 84 43-146 37-124 (155)
190 PRK06752 single-stranded DNA-b 89.7 3 6.5E-05 32.2 8.4 77 68-146 3-105 (112)
191 PRK08763 single-stranded DNA-b 89.7 1.8 4E-05 36.0 7.6 61 67-129 5-84 (164)
192 PRK09802 DNA-binding transcrip 89.7 0.55 1.2E-05 42.1 4.8 47 201-253 17-63 (269)
193 COG1725 Predicted transcriptio 89.7 1.4 3.1E-05 35.0 6.6 32 222-253 36-67 (125)
194 COG0735 Fur Fe2+/Zn2+ uptake r 89.6 1.4 3E-05 35.8 6.7 54 199-257 19-78 (145)
195 PRK06293 single-stranded DNA-b 89.6 3 6.5E-05 34.6 8.7 61 68-130 2-76 (161)
196 PF14394 DUF4423: Domain of un 89.5 1.5 3.2E-05 36.7 6.9 56 202-263 25-83 (171)
197 TIGR00122 birA_repr_reg BirA b 89.4 1.8 3.9E-05 30.1 6.3 50 204-261 3-53 (69)
198 PRK11886 bifunctional biotin-- 89.4 1.2 2.5E-05 40.9 6.8 52 203-260 6-58 (319)
199 PHA02943 hypothetical protein; 89.3 1.1 2.4E-05 36.7 5.8 46 201-253 11-56 (165)
200 TIGR00617 rpa1 replication fac 89.3 2.8 6E-05 42.1 9.9 65 69-138 312-389 (608)
201 PF01475 FUR: Ferric uptake re 89.3 0.8 1.7E-05 35.5 4.9 49 200-253 7-60 (120)
202 PRK06958 single-stranded DNA-b 89.1 2.9 6.4E-05 35.4 8.4 61 67-129 4-84 (182)
203 PF14502 HTH_41: Helix-turn-he 88.9 0.84 1.8E-05 30.0 3.9 32 222-253 7-38 (48)
204 TIGR03337 phnR transcriptional 88.7 1.5 3.3E-05 37.7 6.8 51 202-253 6-57 (231)
205 PRK00215 LexA repressor; Valid 88.6 0.66 1.4E-05 39.5 4.3 54 199-253 2-56 (205)
206 PRK09462 fur ferric uptake reg 88.2 1.9 4.1E-05 34.9 6.6 51 199-253 15-70 (148)
207 PF08646 Rep_fac-A_C: Replicat 88.0 1.9 4.1E-05 34.8 6.4 62 85-146 55-139 (146)
208 smart00088 PINT motif in prote 87.9 1 2.2E-05 32.7 4.5 38 220-257 23-61 (88)
209 smart00753 PAM PCI/PINT associ 87.9 1 2.2E-05 32.7 4.5 38 220-257 23-61 (88)
210 PRK09010 single-stranded DNA-b 87.9 2.8 6E-05 35.3 7.5 66 66-133 5-92 (177)
211 PRK10870 transcriptional repre 87.9 2.2 4.8E-05 35.7 7.0 57 197-257 51-108 (176)
212 TIGR00621 ssb single stranded 87.9 2 4.3E-05 35.6 6.6 61 67-129 4-83 (164)
213 PF13601 HTH_34: Winged helix 87.6 0.72 1.6E-05 33.6 3.4 45 203-253 2-46 (80)
214 PRK11050 manganese transport r 87.6 2 4.2E-05 35.1 6.3 44 220-263 50-93 (152)
215 TIGR01610 phage_O_Nterm phage 87.4 2.3 5E-05 31.8 6.2 36 218-253 44-79 (95)
216 TIGR03338 phnR_burk phosphonat 87.3 1.2 2.6E-05 37.8 5.2 36 218-253 31-66 (212)
217 PRK13165 cytochrome c-type bio 87.1 4.6 0.0001 33.4 8.2 55 68-128 58-116 (160)
218 PRK06266 transcription initiat 87.1 1.4 2.9E-05 37.2 5.2 47 201-253 22-68 (178)
219 PF15072 DUF4539: Domain of un 87.0 1.9 4.2E-05 31.9 5.4 49 71-121 6-54 (86)
220 PRK04984 fatty acid metabolism 86.9 2.1 4.5E-05 37.2 6.5 51 202-253 12-63 (239)
221 PRK05733 single-stranded DNA-b 86.9 2.7 5.9E-05 35.2 6.9 62 67-130 5-86 (172)
222 PRK11014 transcriptional repre 86.6 1.2 2.5E-05 35.8 4.4 33 221-253 25-57 (141)
223 PF04182 B-block_TFIIIC: B-blo 86.6 1.8 3.9E-05 31.0 5.0 49 201-253 2-50 (75)
224 PRK14165 winged helix-turn-hel 86.6 1.4 3E-05 38.4 5.1 41 217-257 17-58 (217)
225 PRK10681 DNA-binding transcrip 86.4 1.4 3E-05 39.1 5.2 47 201-253 7-53 (252)
226 PF05158 RNA_pol_Rpc34: RNA po 86.4 0.87 1.9E-05 42.1 4.0 54 197-254 80-133 (327)
227 PRK11639 zinc uptake transcrip 86.3 2.3 4.9E-05 35.4 6.2 57 199-260 24-86 (169)
228 PRK13150 cytochrome c-type bio 86.3 5.5 0.00012 33.0 8.2 65 68-141 58-126 (159)
229 PRK13777 transcriptional regul 86.1 2.4 5.2E-05 36.0 6.3 54 197-256 41-95 (185)
230 TIGR02787 codY_Gpos GTP-sensin 86.1 1.9 4.2E-05 38.0 5.8 45 204-253 186-230 (251)
231 PRK07274 single-stranded DNA-b 85.9 3.4 7.4E-05 32.9 6.7 61 67-129 2-79 (131)
232 PHA03103 double-strand RNA-bin 85.8 2.4 5.1E-05 35.9 6.0 50 202-257 14-63 (183)
233 PRK07217 replication factor A; 85.7 2.2 4.8E-05 39.0 6.2 57 85-145 218-296 (311)
234 PF02002 TFIIE_alpha: TFIIE al 85.7 0.71 1.5E-05 35.1 2.6 45 201-251 13-57 (105)
235 smart00421 HTH_LUXR helix_turn 85.6 3.1 6.6E-05 26.8 5.5 41 199-247 4-44 (58)
236 PF09202 Rio2_N: Rio2, N-termi 85.6 2.3 5E-05 31.2 5.1 65 199-265 4-70 (82)
237 COG1654 BirA Biotin operon rep 85.6 2.5 5.4E-05 30.8 5.3 56 202-261 4-60 (79)
238 PRK08182 single-stranded DNA-b 85.6 3.8 8.2E-05 33.4 7.0 60 68-129 3-86 (148)
239 COG3888 Predicted transcriptio 85.1 1.9 4E-05 38.6 5.2 49 201-253 4-52 (321)
240 PF00436 SSB: Single-strand bi 85.1 1.9 4.1E-05 32.1 4.7 62 67-130 1-81 (104)
241 cd04476 RPA1_DBD_C RPA1_DBD_C: 85.0 3.7 7.9E-05 33.8 6.8 72 85-158 69-164 (166)
242 PRK13732 single-stranded DNA-b 85.0 3.5 7.5E-05 34.7 6.6 61 67-129 6-86 (175)
243 COG0173 AspS Aspartyl-tRNA syn 85.0 2.2 4.7E-05 41.9 6.1 63 68-130 16-79 (585)
244 PF13545 HTH_Crp_2: Crp-like h 84.9 1.7 3.7E-05 30.5 4.1 33 220-252 27-59 (76)
245 PRK07772 single-stranded DNA-b 84.7 3.3 7.1E-05 35.2 6.4 32 96-129 54-85 (186)
246 PRK04172 pheS phenylalanyl-tRN 84.6 1.9 4.2E-05 42.0 5.7 61 198-264 3-65 (489)
247 COG2512 Predicted membrane-ass 84.5 1.8 4E-05 38.6 5.0 50 197-252 191-241 (258)
248 PRK10046 dpiA two-component re 84.1 2.8 6E-05 35.9 5.9 45 204-253 165-209 (225)
249 PF00196 GerE: Bacterial regul 84.0 2.3 4.9E-05 28.5 4.3 42 198-247 3-44 (58)
250 smart00529 HTH_DTXR Helix-turn 83.9 2.1 4.6E-05 31.5 4.5 39 224-263 2-41 (96)
251 PF04545 Sigma70_r4: Sigma-70, 83.9 4.5 9.7E-05 26.1 5.5 41 198-245 4-44 (50)
252 TIGR02010 IscR iron-sulfur clu 83.5 4.6 9.9E-05 32.1 6.5 43 220-262 24-68 (135)
253 PRK07135 dnaE DNA polymerase I 83.2 3.6 7.8E-05 43.5 7.2 58 69-129 899-960 (973)
254 PF08281 Sigma70_r4_2: Sigma-7 83.2 3 6.6E-05 27.3 4.5 40 198-244 10-49 (54)
255 TIGR00373 conserved hypothetic 83.1 2.4 5.3E-05 34.9 4.9 42 204-251 17-58 (158)
256 PF02760 HIN: HIN-200/IF120x d 83.0 6 0.00013 32.7 7.0 43 77-124 123-165 (170)
257 PRK04036 DNA polymerase II sma 83.0 4.5 9.8E-05 39.6 7.5 61 68-128 154-215 (504)
258 PRK11414 colanic acid/biofilm 83.0 3.4 7.4E-05 35.4 6.0 37 217-253 30-66 (221)
259 PF02796 HTH_7: Helix-turn-hel 82.9 2.5 5.3E-05 27.1 3.8 33 203-243 11-43 (45)
260 TIGR02147 Fsuc_second hypothet 82.8 4.4 9.4E-05 36.5 6.7 43 221-263 136-181 (271)
261 cd04496 SSB_OBF SSB_OBF: A sub 82.7 3.6 7.8E-05 30.2 5.3 36 93-130 42-77 (100)
262 PF05331 DUF742: Protein of un 82.6 3.4 7.4E-05 32.3 5.2 49 197-253 39-87 (114)
263 COG4189 Predicted transcriptio 82.4 2.2 4.8E-05 37.5 4.5 47 201-253 23-69 (308)
264 PF07106 TBPIP: Tat binding pr 82.4 2.5 5.4E-05 35.0 4.8 46 203-253 3-50 (169)
265 PTZ00111 DNA replication licen 82.4 3 6.4E-05 43.6 6.1 42 219-260 857-910 (915)
266 PRK10141 DNA-binding transcrip 82.2 3.7 8E-05 32.2 5.4 47 201-253 16-62 (117)
267 PF07381 DUF1495: Winged helix 82.0 5 0.00011 30.0 5.7 61 200-264 8-82 (90)
268 PRK05813 single-stranded DNA-b 81.7 5.7 0.00012 34.6 6.8 81 65-148 107-211 (219)
269 PRK03837 transcriptional regul 81.6 4.9 0.00011 34.7 6.6 35 219-253 34-69 (241)
270 PF01399 PCI: PCI domain; Int 81.6 2.1 4.6E-05 31.6 3.7 39 219-257 58-97 (105)
271 COG1497 Predicted transcriptio 81.6 3.8 8.2E-05 36.2 5.6 59 202-265 11-69 (260)
272 COG2996 Predicted RNA-bindinin 81.5 5.3 0.00011 35.9 6.6 62 198-260 222-284 (287)
273 PRK06642 single-stranded DNA-b 81.5 6.1 0.00013 32.4 6.6 61 67-129 5-86 (152)
274 cd06170 LuxR_C_like C-terminal 81.4 5.2 0.00011 25.8 5.2 40 200-247 2-41 (57)
275 PF08221 HTH_9: RNA polymerase 81.4 3.5 7.6E-05 28.4 4.4 47 201-253 13-59 (62)
276 PF04492 Phage_rep_O: Bacterio 81.2 6.3 0.00014 30.0 6.2 57 197-253 28-86 (100)
277 PRK10421 DNA-binding transcrip 81.1 4 8.6E-05 35.8 5.8 35 219-253 23-58 (253)
278 PRK09990 DNA-binding transcrip 81.0 4.5 9.8E-05 35.3 6.2 37 217-253 26-63 (251)
279 PRK04214 rbn ribonuclease BN/u 80.9 3.3 7.1E-05 39.4 5.6 57 206-264 297-353 (412)
280 PHA00738 putative HTH transcri 80.6 4.7 0.0001 31.1 5.3 48 200-253 11-58 (108)
281 PF13936 HTH_38: Helix-turn-he 80.6 3 6.5E-05 26.6 3.6 38 199-243 5-42 (44)
282 PF09106 SelB-wing_2: Elongati 80.3 2.1 4.4E-05 29.1 2.9 36 218-253 14-52 (59)
283 TIGR02812 fadR_gamma fatty aci 79.9 6 0.00013 34.2 6.5 36 218-253 26-62 (235)
284 PRK10430 DNA-binding transcrip 79.9 5 0.00011 34.6 6.0 54 199-256 159-214 (239)
285 COG1321 TroR Mn-dependent tran 79.8 6 0.00013 32.5 6.1 46 220-265 23-68 (154)
286 COG0587 DnaE DNA polymerase II 79.3 3.6 7.7E-05 44.1 5.6 63 69-133 978-1046(1139)
287 PRK10225 DNA-binding transcrip 79.2 6.3 0.00014 34.6 6.5 37 217-253 28-65 (257)
288 PF08461 HTH_12: Ribonuclease 79.1 3.8 8.2E-05 28.7 4.0 41 205-250 2-47 (66)
289 PF05491 RuvB_C: Holliday junc 79.1 4.2 9.2E-05 29.4 4.3 53 197-252 4-57 (76)
290 PF04255 DUF433: Protein of un 79.1 4.1 8.8E-05 27.4 4.1 32 205-244 23-55 (56)
291 COG1339 Transcriptional regula 79.0 3.6 7.8E-05 35.2 4.5 58 205-263 4-64 (214)
292 PRK11534 DNA-binding transcrip 79.0 5.7 0.00012 34.0 6.0 35 219-253 28-62 (224)
293 PF04967 HTH_10: HTH DNA bindi 78.8 8.1 0.00018 25.9 5.4 45 199-243 1-45 (53)
294 PF12869 tRNA_anti-like: tRNA_ 78.5 6.2 0.00013 31.3 5.7 85 43-131 44-133 (144)
295 PRK09464 pdhR transcriptional 77.8 6.6 0.00014 34.3 6.2 35 219-253 31-66 (254)
296 PRK10857 DNA-binding transcrip 77.6 6.5 0.00014 32.6 5.7 44 219-262 23-68 (164)
297 PF00538 Linker_histone: linke 77.5 6.6 0.00014 28.1 5.1 50 201-253 4-63 (77)
298 PRK15481 transcriptional regul 77.5 6.7 0.00015 37.1 6.6 34 220-253 27-61 (431)
299 PF08280 HTH_Mga: M protein tr 77.4 4.1 9E-05 27.6 3.7 39 203-247 7-45 (59)
300 COG1846 MarR Transcriptional r 77.2 7.3 0.00016 29.2 5.6 52 199-256 20-72 (126)
301 PRK11523 DNA-binding transcrip 76.5 8.9 0.00019 33.6 6.6 37 217-253 27-64 (253)
302 PRK11920 rirA iron-responsive 76.5 6.9 0.00015 32.0 5.5 34 220-253 23-56 (153)
303 PF05584 Sulfolobus_pRN: Sulfo 76.4 9.4 0.0002 27.3 5.4 45 202-253 6-50 (72)
304 COG4190 Predicted transcriptio 75.9 8.1 0.00018 31.0 5.4 50 198-253 61-110 (144)
305 PRK06474 hypothetical protein; 75.1 7.9 0.00017 32.5 5.7 51 200-255 10-61 (178)
306 COG2332 CcmE Cytochrome c-type 74.8 21 0.00046 29.2 7.7 55 68-128 52-110 (153)
307 KOG2411 Aspartyl-tRNA syntheta 74.5 9.5 0.00021 37.2 6.5 63 68-130 48-111 (628)
308 KOG1885 Lysyl-tRNA synthetase 74.4 8.2 0.00018 37.3 6.0 73 69-141 106-184 (560)
309 COG4565 CitB Response regulato 74.0 9.3 0.0002 33.2 5.8 52 197-253 153-205 (224)
310 PLN02853 Probable phenylalanyl 73.6 7.1 0.00015 38.1 5.6 60 201-265 3-64 (492)
311 PRK06341 single-stranded DNA-b 73.6 14 0.0003 30.9 6.6 65 67-133 5-92 (166)
312 TIGR00644 recJ single-stranded 73.6 48 0.001 32.8 11.5 73 54-138 460-534 (539)
313 PTZ00326 phenylalanyl-tRNA syn 73.5 7.1 0.00015 38.1 5.6 61 200-265 5-67 (494)
314 PF13518 HTH_28: Helix-turn-he 73.4 11 0.00024 24.1 4.9 30 221-250 12-41 (52)
315 TIGR01714 phage_rep_org_N phag 73.0 9.2 0.0002 30.1 5.1 41 222-262 52-92 (119)
316 PF13384 HTH_23: Homeodomain-l 72.8 3.5 7.6E-05 26.5 2.4 29 221-249 17-45 (50)
317 COG4901 Ribosomal protein S25 72.8 9.1 0.0002 29.3 4.8 55 202-258 42-96 (107)
318 COG2442 Uncharacterized conser 72.7 7.9 0.00017 28.2 4.4 35 205-247 35-70 (79)
319 PRK15411 rcsA colanic acid cap 72.6 8.2 0.00018 32.9 5.3 42 198-247 137-178 (207)
320 PF04157 EAP30: EAP30/Vps36 fa 72.6 7.5 0.00016 33.7 5.1 50 199-252 172-221 (223)
321 PRK09334 30S ribosomal protein 72.3 6.1 0.00013 29.3 3.7 36 219-254 39-74 (86)
322 PRK11753 DNA-binding transcrip 72.2 8.1 0.00018 32.3 5.1 40 222-262 169-208 (211)
323 PRK15201 fimbriae regulatory p 72.1 11 0.00023 32.1 5.5 82 139-247 93-174 (198)
324 PF09104 BRCA-2_OB3: BRCA2, ol 71.9 21 0.00045 29.0 7.0 73 43-125 3-77 (143)
325 PRK00082 hrcA heat-inducible t 71.8 8.5 0.00018 35.7 5.5 49 199-253 4-59 (339)
326 TIGR02063 RNase_R ribonuclease 71.7 11 0.00024 38.5 6.8 56 201-260 2-61 (709)
327 PF01638 HxlR: HxlR-like helix 71.4 6.5 0.00014 28.9 3.8 54 203-263 7-67 (90)
328 PF05158 RNA_pol_Rpc34: RNA po 71.1 3.4 7.4E-05 38.2 2.7 53 198-253 6-59 (327)
329 KOG0554 Asparaginyl-tRNA synth 71.0 9.9 0.00022 36.0 5.6 70 68-143 21-95 (446)
330 COG4742 Predicted transcriptio 70.7 11 0.00025 33.6 5.8 57 199-263 11-67 (260)
331 smart00526 H15 Domain in histo 70.5 17 0.00037 25.0 5.6 50 201-253 6-63 (66)
332 PF11994 DUF3489: Protein of u 70.4 19 0.00041 25.8 5.8 47 201-253 10-58 (72)
333 PHA02591 hypothetical protein; 70.0 5.1 0.00011 29.1 2.8 26 219-244 57-82 (83)
334 PRK10402 DNA-binding transcrip 69.9 11 0.00023 32.4 5.5 51 201-252 150-200 (226)
335 PF09681 Phage_rep_org_N: N-te 69.6 12 0.00027 29.4 5.2 42 221-262 53-94 (121)
336 TIGR02698 CopY_TcrY copper tra 69.2 15 0.00033 29.1 5.8 57 199-261 2-65 (130)
337 PRK13719 conjugal transfer tra 68.7 13 0.00028 32.4 5.6 43 197-247 142-184 (217)
338 smart00531 TFIIE Transcription 68.7 6.5 0.00014 31.9 3.6 31 221-251 15-45 (147)
339 PRK10840 transcriptional regul 68.6 11 0.00025 31.6 5.3 43 197-247 149-191 (216)
340 TIGR00617 rpa1 replication fac 68.4 13 0.00027 37.5 6.2 61 69-131 192-262 (608)
341 TIGR00721 tfx DNA-binding prot 68.2 13 0.00029 30.0 5.2 39 197-243 5-43 (137)
342 PF09756 DDRGK: DDRGK domain; 68.1 4.7 0.0001 34.3 2.7 50 202-257 100-150 (188)
343 PRK11475 DNA-binding transcrip 68.0 12 0.00026 32.1 5.3 42 198-247 134-175 (207)
344 TIGR00635 ruvB Holliday juncti 67.9 8.6 0.00019 34.4 4.6 53 197-253 234-288 (305)
345 PF08222 HTH_CodY: CodY helix- 67.5 12 0.00027 25.5 4.0 31 223-253 6-36 (61)
346 COG3432 Predicted transcriptio 67.2 6.1 0.00013 29.9 2.8 59 203-265 17-78 (95)
347 PF03965 Penicillinase_R: Peni 67.2 14 0.00031 28.3 5.1 58 199-262 1-65 (115)
348 TIGR03697 NtcA_cyano global ni 67.2 8 0.00017 31.8 4.0 32 222-253 144-175 (193)
349 PRK11642 exoribonuclease R; Pr 67.2 14 0.00031 38.4 6.4 53 203-260 21-77 (813)
350 PRK13918 CRP/FNR family transc 67.0 7.9 0.00017 32.2 3.9 31 222-252 150-180 (202)
351 PF14493 HTH_40: Helix-turn-he 67.0 9.2 0.0002 28.2 3.8 31 220-250 12-42 (91)
352 PF09105 SelB-wing_1: Elongati 66.7 32 0.00069 22.7 5.7 51 206-261 7-59 (61)
353 PF10557 Cullin_Nedd8: Cullin 66.7 10 0.00022 26.4 3.8 47 201-253 8-62 (68)
354 cd00131 PAX Paired Box domain 66.4 14 0.0003 29.2 5.0 45 201-253 21-65 (128)
355 PF11662 DUF3263: Protein of u 66.0 22 0.00047 25.8 5.4 49 198-249 2-50 (77)
356 PRK05472 redox-sensing transcr 65.8 12 0.00025 32.1 4.8 46 201-250 16-61 (213)
357 TIGR00594 polc DNA-directed DN 65.6 13 0.00027 39.8 5.8 35 68-102 982-1022(1022)
358 PRK10736 hypothetical protein; 65.6 21 0.00046 33.7 6.8 51 204-261 311-361 (374)
359 PRK05638 threonine synthase; V 65.6 13 0.00029 35.6 5.6 59 199-264 369-433 (442)
360 COG1959 Predicted transcriptio 65.1 18 0.0004 29.4 5.6 33 221-253 25-57 (150)
361 COG5071 RPN5 26S proteasome re 65.0 9.9 0.00021 35.0 4.2 53 199-256 332-389 (439)
362 PRK04217 hypothetical protein; 64.8 16 0.00034 28.3 4.9 40 197-243 41-80 (110)
363 COG2197 CitB Response regulato 64.7 14 0.00031 31.6 5.1 42 198-247 148-189 (211)
364 COG1802 GntR Transcriptional r 64.6 6.3 0.00014 34.0 2.9 53 201-253 16-71 (230)
365 PRK15320 transcriptional activ 64.6 16 0.00034 31.7 5.1 43 197-247 163-205 (251)
366 PRK15431 ferrous iron transpor 63.2 14 0.0003 26.9 3.9 45 205-255 6-50 (78)
367 TIGR00331 hrcA heat shock gene 63.1 16 0.00034 33.9 5.4 35 219-253 19-55 (337)
368 smart00351 PAX Paired Box doma 62.9 18 0.0004 28.4 5.0 44 201-252 21-64 (125)
369 PF13567 DUF4131: Domain of un 62.8 40 0.00086 26.5 7.2 60 68-132 76-146 (176)
370 PRK15466 carboxysome structura 62.8 10 0.00023 31.4 3.7 46 203-253 111-156 (166)
371 PF04218 CENP-B_N: CENP-B N-te 62.7 3.4 7.3E-05 27.6 0.7 25 219-243 20-44 (53)
372 COG3398 Uncharacterized protei 62.3 16 0.00036 31.9 4.9 49 199-253 99-147 (240)
373 cd00073 H15 linker histone 1 a 62.3 29 0.00063 25.5 5.7 52 200-254 5-64 (88)
374 PRK10100 DNA-binding transcrip 62.2 18 0.00038 31.2 5.3 43 197-247 154-196 (216)
375 PF13542 HTH_Tnp_ISL3: Helix-t 61.7 22 0.00047 22.9 4.5 37 201-245 15-51 (52)
376 COG0478 RIO-like serine/threon 61.1 27 0.00059 31.8 6.3 66 198-265 10-77 (304)
377 PF07848 PaaX: PaaX-like prote 61.0 8.9 0.00019 27.2 2.6 45 219-263 18-68 (70)
378 TIGR03882 cyclo_dehyd_2 bacter 60.9 14 0.00029 31.5 4.2 33 221-253 42-76 (193)
379 PF09397 Ftsk_gamma: Ftsk gamm 60.5 26 0.00057 24.5 4.9 50 200-255 5-54 (65)
380 PRK09483 response regulator; P 60.5 21 0.00046 29.3 5.4 43 197-247 147-189 (217)
381 cd06171 Sigma70_r4 Sigma70, re 60.5 31 0.00068 21.2 5.1 41 199-246 11-51 (55)
382 PF07638 Sigma70_ECF: ECF sigm 60.2 17 0.00036 30.4 4.7 40 199-245 136-175 (185)
383 TIGR00475 selB selenocysteine- 60.1 24 0.00051 35.3 6.4 51 202-259 476-526 (581)
384 TIGR02937 sigma70-ECF RNA poly 60.0 20 0.00044 27.4 4.9 42 198-246 110-151 (158)
385 PRK09391 fixK transcriptional 59.5 13 0.00028 32.0 4.0 31 222-252 180-210 (230)
386 PF12658 Ten1: Telomere cappin 59.5 86 0.0019 24.7 11.1 78 68-147 26-114 (124)
387 PF07223 DUF1421: Protein of u 59.4 11 0.00025 35.2 3.7 33 218-250 315-350 (358)
388 cd04438 DEP_dishevelled DEP (D 59.4 21 0.00046 26.2 4.5 38 223-260 35-75 (84)
389 PF10668 Phage_terminase: Phag 58.9 17 0.00038 25.0 3.7 35 201-240 7-41 (60)
390 PF03297 Ribosomal_S25: S25 ri 58.3 16 0.00034 28.2 3.8 39 219-257 57-95 (105)
391 PLN02532 asparagine-tRNA synth 58.3 45 0.00097 33.7 7.9 64 79-145 129-199 (633)
392 COG2186 FadR Transcriptional r 57.2 31 0.00068 30.2 6.1 51 202-253 15-66 (241)
393 TIGR02999 Sig-70_X6 RNA polyme 56.8 18 0.00039 29.6 4.3 39 198-243 134-172 (183)
394 PF12324 HTH_15: Helix-turn-he 56.8 29 0.00064 25.1 4.7 43 199-247 22-64 (77)
395 PRK00118 putative DNA-binding 56.8 29 0.00063 26.6 5.0 40 198-244 17-56 (104)
396 TIGR02952 Sig70_famx2 RNA poly 56.6 26 0.00056 28.1 5.1 42 197-245 121-162 (170)
397 PRK03975 tfx putative transcri 56.2 30 0.00065 28.0 5.3 39 197-243 5-43 (141)
398 PRK00135 scpB segregation and 55.6 13 0.00029 31.5 3.3 30 219-248 18-47 (188)
399 PRK09642 RNA polymerase sigma 55.5 19 0.00041 28.8 4.1 39 198-243 106-144 (160)
400 PRK11924 RNA polymerase sigma 55.0 21 0.00046 28.7 4.4 41 197-244 124-164 (179)
401 cd04448 DEP_PIKfyve DEP (Dishe 55.0 27 0.00059 25.3 4.4 37 224-260 35-73 (81)
402 PF10078 DUF2316: Uncharacteri 55.0 13 0.00029 27.7 2.8 25 219-243 21-45 (89)
403 PRK09047 RNA polymerase factor 55.0 21 0.00045 28.4 4.3 40 197-243 105-144 (161)
404 PRK11161 fumarate/nitrate redu 54.5 17 0.00037 31.0 3.9 33 221-253 184-216 (235)
405 COG2390 DeoR Transcriptional r 54.4 25 0.00055 32.4 5.1 41 220-260 25-66 (321)
406 PF06971 Put_DNA-bind_N: Putat 54.0 18 0.0004 23.9 3.0 33 206-242 17-49 (50)
407 COG2771 CsgD DNA-binding HTH d 53.6 48 0.001 21.8 5.4 41 198-246 4-44 (65)
408 PRK12547 RNA polymerase sigma 53.5 26 0.00056 28.3 4.6 41 198-245 112-152 (164)
409 PF04297 UPF0122: Putative hel 53.3 33 0.00072 26.2 4.8 39 199-244 18-56 (101)
410 PRK06759 RNA polymerase factor 53.0 27 0.00058 27.6 4.6 40 198-244 106-145 (154)
411 PRK08898 coproporphyrinogen II 52.8 34 0.00074 32.3 5.9 46 219-265 336-381 (394)
412 TIGR02719 repress_PhaQ poly-be 52.7 25 0.00053 28.4 4.2 60 201-264 24-94 (138)
413 PRK12539 RNA polymerase sigma 52.3 22 0.00048 29.3 4.1 41 197-244 130-170 (184)
414 PRK05660 HemN family oxidoredu 52.2 29 0.00063 32.5 5.3 46 219-265 319-364 (378)
415 PRK15369 two component system 52.0 35 0.00076 27.3 5.3 42 198-247 149-190 (211)
416 PF04539 Sigma70_r3: Sigma-70 51.8 19 0.00041 25.3 3.1 25 222-246 21-45 (78)
417 PRK12529 RNA polymerase sigma 51.8 22 0.00049 29.2 4.1 40 197-243 126-165 (178)
418 TIGR02985 Sig70_bacteroi1 RNA 51.6 33 0.00072 26.9 4.9 41 198-245 113-153 (161)
419 PF04079 DUF387: Putative tran 51.6 16 0.00035 30.2 3.0 28 219-247 11-38 (159)
420 PRK09652 RNA polymerase sigma 51.3 26 0.00057 28.2 4.4 39 198-243 128-166 (182)
421 TIGR03209 P21_Cbot clostridium 51.1 13 0.00029 29.1 2.5 37 197-240 106-142 (142)
422 cd04449 DEP_DEPDC5-like DEP (D 51.0 35 0.00076 24.8 4.5 38 223-260 35-75 (83)
423 PRK13239 alkylmercury lyase; P 50.8 31 0.00067 29.8 4.8 41 200-246 21-61 (206)
424 PRK12523 RNA polymerase sigma 50.8 26 0.00055 28.5 4.2 41 197-244 118-158 (172)
425 PRK12546 RNA polymerase sigma 50.6 26 0.00056 29.3 4.3 41 197-244 112-152 (188)
426 PF03551 PadR: Transcriptional 50.5 8.6 0.00019 27.1 1.1 33 232-264 28-68 (75)
427 PF01853 MOZ_SAS: MOZ/SAS fami 50.5 15 0.00034 31.2 2.8 52 201-258 133-184 (188)
428 PRK10360 DNA-binding transcrip 50.2 40 0.00086 27.1 5.3 42 198-247 137-178 (196)
429 KOG3818 DNA polymerase epsilon 50.2 37 0.00081 32.7 5.5 73 64-146 173-245 (525)
430 PRK00080 ruvB Holliday junctio 49.9 23 0.0005 32.3 4.2 54 197-253 255-309 (328)
431 PRK12520 RNA polymerase sigma 49.8 26 0.00057 29.0 4.2 39 198-243 131-169 (191)
432 KOG3341 RNA polymerase II tran 49.7 34 0.00074 29.8 4.8 51 197-253 172-222 (249)
433 TIGR02716 C20_methyl_CrtF C-20 49.5 35 0.00075 30.7 5.2 55 201-263 10-64 (306)
434 PRK13919 putative RNA polymera 49.4 30 0.00066 28.3 4.5 40 197-243 134-173 (186)
435 PRK09645 RNA polymerase sigma 48.9 28 0.00061 28.2 4.2 39 197-242 117-155 (173)
436 PF12793 SgrR_N: Sugar transpo 48.5 27 0.0006 27.1 3.8 33 219-251 17-49 (115)
437 KOG1498 26S proteasome regulat 48.5 27 0.00059 33.2 4.3 56 199-256 332-389 (439)
438 PRK12516 RNA polymerase sigma 48.3 29 0.00064 28.9 4.3 38 198-242 116-153 (187)
439 TIGR02948 SigW_bacill RNA poly 48.3 30 0.00065 28.3 4.3 41 198-245 136-176 (187)
440 PF11948 DUF3465: Protein of u 48.1 1.4E+02 0.0031 23.9 8.7 63 69-135 38-105 (131)
441 PRK12536 RNA polymerase sigma 48.1 29 0.00062 28.5 4.1 25 220-244 144-168 (181)
442 PRK09637 RNA polymerase sigma 47.5 35 0.00076 28.2 4.6 38 198-242 106-143 (181)
443 TIGR02989 Sig-70_gvs1 RNA poly 47.2 34 0.00074 27.1 4.4 40 198-244 111-150 (159)
444 PRK10188 DNA-binding transcrip 47.2 43 0.00093 29.3 5.3 41 198-246 179-219 (240)
445 PRK09415 RNA polymerase factor 47.2 32 0.00069 28.2 4.3 39 198-243 127-165 (179)
446 PF04057 Rep-A_N: Replication 47.0 1.2E+02 0.0027 22.8 8.7 79 65-144 18-99 (101)
447 COG3398 Uncharacterized protei 47.0 41 0.00089 29.5 4.9 46 201-252 174-219 (240)
448 PRK00117 recX recombination re 47.0 37 0.00079 27.5 4.5 46 199-251 10-58 (157)
449 PRK09647 RNA polymerase sigma 46.8 35 0.00075 28.9 4.5 40 198-244 138-177 (203)
450 PRK09649 RNA polymerase sigma 46.7 34 0.00073 28.3 4.4 39 198-243 130-168 (185)
451 TIGR02392 rpoH_proteo alternat 46.5 45 0.00097 29.6 5.4 44 198-246 218-265 (270)
452 PRK12542 RNA polymerase sigma 46.4 31 0.00067 28.4 4.1 39 198-243 122-160 (185)
453 PRK10651 transcriptional regul 46.3 48 0.001 26.8 5.3 43 198-248 155-197 (216)
454 COG3682 Predicted transcriptio 46.3 43 0.00094 26.5 4.6 56 199-260 4-64 (123)
455 PRK12512 RNA polymerase sigma 46.1 36 0.00077 27.9 4.4 41 197-244 130-170 (184)
456 PRK12524 RNA polymerase sigma 46.0 38 0.00082 28.2 4.6 40 198-244 136-175 (196)
457 PRK07037 extracytoplasmic-func 46.0 35 0.00075 27.3 4.2 39 198-243 109-147 (163)
458 PRK10512 selenocysteinyl-tRNA- 46.0 33 0.00072 34.5 4.9 39 222-260 507-545 (614)
459 TIGR02844 spore_III_D sporulat 45.8 37 0.00081 24.7 3.9 35 202-243 7-41 (80)
460 COG3413 Predicted DNA binding 45.6 51 0.0011 28.2 5.4 51 197-247 154-208 (215)
461 TIGR02983 SigE-fam_strep RNA p 45.6 42 0.00091 26.7 4.7 41 198-245 110-150 (162)
462 PRK12545 RNA polymerase sigma 45.6 34 0.00073 28.8 4.3 39 198-243 139-177 (201)
463 PRK12531 RNA polymerase sigma 45.4 31 0.00068 28.7 4.0 40 198-244 141-180 (194)
464 PF13551 HTH_29: Winged helix- 45.2 33 0.00071 25.4 3.8 30 220-249 10-40 (112)
465 PRK12527 RNA polymerase sigma 45.2 38 0.00082 27.0 4.4 39 198-243 105-143 (159)
466 TIGR02959 SigZ RNA polymerase 45.1 36 0.00078 27.7 4.3 39 197-242 99-137 (170)
467 cd04480 RPA1_DBD_A_like RPA1_D 45.0 82 0.0018 22.6 5.7 41 83-125 18-59 (86)
468 PRK09392 ftrB transcriptional 45.0 34 0.00074 29.2 4.3 31 222-252 174-204 (236)
469 PRK12528 RNA polymerase sigma 44.6 37 0.00081 27.1 4.2 40 198-244 113-152 (161)
470 COG2524 Predicted transcriptio 44.5 26 0.00055 31.5 3.4 64 198-262 3-68 (294)
471 cd05694 S1_Rrp5_repeat_hs2_sc2 44.5 71 0.0015 22.5 5.2 48 71-125 7-54 (74)
472 PRK12543 RNA polymerase sigma 44.4 40 0.00086 27.6 4.4 39 197-242 116-154 (179)
473 TIGR03020 EpsA transcriptional 44.2 54 0.0012 29.0 5.5 43 197-247 189-231 (247)
474 PRK09958 DNA-binding transcrip 44.1 54 0.0012 26.5 5.2 42 198-247 143-184 (204)
475 PRK09651 RNA polymerase sigma 44.1 38 0.00083 27.5 4.3 40 198-244 119-158 (172)
476 PF04433 SWIRM: SWIRM domain; 44.1 39 0.00085 24.4 3.9 47 201-251 37-84 (86)
477 PRK11923 algU RNA polymerase s 43.9 41 0.00089 27.7 4.5 24 220-243 153-176 (193)
478 smart00843 Ftsk_gamma This dom 43.9 62 0.0013 22.5 4.6 47 201-253 5-51 (63)
479 PRK06811 RNA polymerase factor 43.7 39 0.00085 28.0 4.3 40 197-243 130-169 (189)
480 PRK12522 RNA polymerase sigma 43.7 36 0.00078 27.6 4.0 24 220-243 134-157 (173)
481 PRK12511 RNA polymerase sigma 43.6 37 0.0008 28.1 4.2 39 198-243 111-149 (182)
482 PRK12530 RNA polymerase sigma 43.6 36 0.00079 28.2 4.1 24 220-243 149-172 (189)
483 PRK05853 hypothetical protein; 43.6 15 0.00032 30.5 1.7 35 93-129 41-75 (161)
484 PF00888 Cullin: Cullin family 43.5 17 0.00037 35.7 2.4 48 199-252 518-565 (588)
485 PF12651 RHH_3: Ribbon-helix-h 43.1 40 0.00086 21.5 3.3 23 225-247 18-41 (44)
486 PRK12533 RNA polymerase sigma 43.1 35 0.00076 29.3 4.0 40 198-244 134-173 (216)
487 PRK12514 RNA polymerase sigma 43.1 35 0.00077 27.8 3.9 25 220-244 144-168 (179)
488 PF04282 DUF438: Family of unk 43.0 49 0.0011 23.6 4.0 31 220-250 11-46 (71)
489 PRK09639 RNA polymerase sigma 43.0 51 0.0011 26.3 4.8 39 198-244 112-150 (166)
490 PRK12541 RNA polymerase sigma 42.8 38 0.00083 27.0 4.0 40 198-244 112-151 (161)
491 PRK12525 RNA polymerase sigma 42.8 38 0.00083 27.4 4.1 39 198-243 118-156 (168)
492 PRK09643 RNA polymerase sigma 42.8 41 0.0009 28.0 4.4 39 198-243 134-172 (192)
493 PRK12540 RNA polymerase sigma 42.8 39 0.00084 28.0 4.2 39 198-243 111-149 (182)
494 PLN03239 histone acetyltransfe 42.7 43 0.00092 31.3 4.6 43 202-246 267-309 (351)
495 COG3065 Slp Starvation-inducib 42.6 1E+02 0.0022 26.2 6.4 61 67-133 53-127 (191)
496 PF14338 Mrr_N: Mrr N-terminal 42.4 75 0.0016 23.2 5.2 30 236-265 55-84 (92)
497 PRK09646 RNA polymerase sigma 42.4 39 0.00085 28.1 4.1 40 197-243 141-180 (194)
498 PRK12526 RNA polymerase sigma 42.4 51 0.0011 27.8 4.9 40 198-244 153-192 (206)
499 PRK14136 recX recombination re 42.3 30 0.00066 31.7 3.6 47 198-251 160-209 (309)
500 PRK12534 RNA polymerase sigma 42.3 38 0.00083 27.8 4.0 40 198-244 137-176 (187)
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=3.3e-50 Score=334.77 Aligned_cols=240 Identities=26% Similarity=0.407 Sum_probs=188.0
Q ss_pred cCCcccCCCCCCCCCCCCCCcCcCCcccceeeeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEE
Q 024592 12 FAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLI 90 (265)
Q Consensus 12 ~~gGGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~L 90 (265)
..+|||.+++++++ ...........+|||||||||+++ +.+.++.|.+++.++.+|++||+||+++.+.++.+|+|
T Consensus 13 it~g~~~~~~s~p~---~drseg~~~vntLrpvTIKQIl~~~qd~~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~i 89 (258)
T COG5235 13 ITRGQIFGTGSPPP---MDRSEGGYIVNTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVI 89 (258)
T ss_pred eeccceecCCCCCC---CCccccCceeeeeeeeEHHHhhcccccccCCceeecceEEeeEEEEEEEEeeeecccceEEEE
Confidence 45789986555422 112223456899999999999999 77788999999999999999999999999999999999
Q ss_pred EcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhccCCCC
Q 024592 91 DDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGG 170 (265)
Q Consensus 91 dDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~~~~~~ 170 (265)
+||||.|+|++|...+.+.+.....+++.||||+|.||.|+||++|.+.+|++|+|+||+++|+||||+.||.+++....
T Consensus 90 EDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~~I~d~NeV~~HfLe~I~~Hl~~t~~~~~ 169 (258)
T COG5235 90 EDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQR 169 (258)
T ss_pred ecCCceEEEEecCCCchHHHhccccccccEEEEecceeeeCCeeEEehhheeeccccchhHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999987766666677889999999999999999999999999999999999999999999999999876432
Q ss_pred C--CCCCCCCCCCCccccccccCCCCCCCCCChhHHHHHHHhcCcC-CCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 171 S--SNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPE-FLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 171 ~--~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~~~~~Vl~~i~~~~-~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
. .+.+..+.+. ...+ .|-. +.+.++||+.++.+.|.+. ......+|++..|++.++.++ .+..++.|.+
T Consensus 170 ple~~~~n~GqSl-f~k~----dNdt-Ssgss~lq~~~~~c~~~~~~~~~~~~~V~I~~lsqs~~~de--t~v~~d~L~~ 241 (258)
T COG5235 170 PLEEEVKNDGQSL-FAKL----DNDT-SSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQSYSEDE--TRVNIDVLLR 241 (258)
T ss_pred hhhhhcCCCccce-eeec----cCcc-ccccccccHHHHHHHHHhcCCCCcccceeehHhhhhcCccc--eeeeeeeehh
Confidence 1 1111111110 0011 1111 1345689999999998763 112346777777777777554 4444999999
Q ss_pred CCeEEe-ecCCceeec
Q 024592 248 NSLVYS-IDEFHYKSA 262 (265)
Q Consensus 248 eG~IYs-iDd~hyk~t 262 (265)
+|+||. +|++|||++
T Consensus 242 ~g~iYpTvD~n~fkt~ 257 (258)
T COG5235 242 DGHIYPTVDGNEFKTT 257 (258)
T ss_pred CceEEeeecCcceeec
Confidence 999999 999999987
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=3.6e-48 Score=340.38 Aligned_cols=258 Identities=34% Similarity=0.514 Sum_probs=203.2
Q ss_pred CCCCCCCCCccCCcccCCCCCCCCCCCCCCcCcCCcccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeee
Q 024592 2 YSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQD 81 (265)
Q Consensus 2 ~~~~~~~~~~~~gGGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~ 81 (265)
++..|.+..++.+||+++++.+....++......+..+.++|+||+||+++....+..|++++.++.+|++||+|+++++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~v~~~ti~qi~s~~~~~~~~~~i~~~~v~~v~~VGivr~~e~ 82 (265)
T KOG3108|consen 3 SSYTFEDYNGQSSGGQGPGQFTTSRPPSSQSITNRRVQGVVPLTIKQILSSTQDDDSVFKIGGVEVSAVSIVGIVRNIEK 82 (265)
T ss_pred ccccceecccccccccCCCcccccCCccccccccceeccccccceeeeccccccccccEEEccEEEEEEEEEEEEEecee
Confidence 34466677777888888766532111111222357889999999999999944333399999999999999999999999
Q ss_pred CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHH
Q 024592 82 KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQ 161 (265)
Q Consensus 82 ~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~ 161 (265)
.+++++|+|+|+||.|+|++|..+..+..+.+.+++|.||||+|.||.|+|+++|.+++|+||+|+||+++|+|||+++|
T Consensus 83 ~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~pv~D~Nevt~h~LE~i~~h 162 (265)
T KOG3108|consen 83 SATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRPVEDFNEVTTHFLEVINAH 162 (265)
T ss_pred cCcceEEEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecccCCCCceeEEEEeeeeeecCCceeEEeehhhHHH
Confidence 99999999999999999999998776666778999999999999999999999999999999999999999999999999
Q ss_pred HHhccCCCCCCCCCCCCCCCCcccccc--ccCCCCC-CCCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHH
Q 024592 162 LYNTRLRGGSSNQPQMTNSNHLKEYNA--ISSNHYS-FDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDK 237 (265)
Q Consensus 162 l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~n~~~-~~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~ 237 (265)
|.+++......+.... .+.+.+.... ..++... ...|..+++.|++.++++.+ .+|+|+.+|+++|+ .....
T Consensus 163 l~~s~~~~~~sa~~~~-~~~~~~s~~~~~~~~~~s~~~~~l~~i~~~v~~~~~~~~h---~eGv~~~~i~~~l~~~~~~~ 238 (265)
T KOG3108|consen 163 LSLSKSPSQSSAGNDP-VGFPGMSEAADSGYSQESGQSSQLERIQQRVLQAIESGLH---IEGVHIKEIAAQLREPSVSE 238 (265)
T ss_pred HHhhhcccccccccCC-CCCcccccccccccCcccccchhhhHHHHHHHHhhhcCcc---cccccHHHHHHHhcccchhh
Confidence 9999876543222111 1111110000 0011110 12367899999999998753 48999999999997 56678
Q ss_pred HHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592 238 LMEALESLNENSLVYS-IDEFHYKSAV 263 (265)
Q Consensus 238 v~~al~~L~~eG~IYs-iDd~hyk~t~ 263 (265)
+++++++|.+|||||+ +||+|||+|+
T Consensus 239 ~~~~~~~l~~eG~iy~TvD~~hFks~~ 265 (265)
T KOG3108|consen 239 LREAVDFLLNEGHIYSTVDEEHFKSTN 265 (265)
T ss_pred HHHHHHHHhcCCeEEEeechhheeecC
Confidence 9999999999999999 9999999984
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=3.7e-25 Score=167.80 Aligned_cols=94 Identities=46% Similarity=0.893 Sum_probs=86.2
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCCh
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDF 147 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~ 147 (265)
+|++||+|++++..++++.|+|+|+||+|+|++|.+++.+ ....+.+++|+||+|.|+++.|+++++|.++.++|++|+
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 4899999999999999999999999999999999876421 124677999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHH
Q 024592 148 NEITSHFVECIYVQL 162 (265)
Q Consensus 148 Nei~~H~Levi~~~l 162 (265)
||+++|+|||+++||
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=99.71 E-value=7.1e-17 Score=121.85 Aligned_cols=73 Identities=25% Similarity=0.545 Sum_probs=64.3
Q ss_pred EEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc------------------ccccccCCCCEEEEEEEeeeeCC
Q 024592 71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF------------------NEVNQISKGMYVRVYGHLKAFQD 132 (265)
Q Consensus 71 ~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~------------------~~~~~~~~g~yVrV~G~i~~f~~ 132 (265)
.|||+|+++++.++++.|+|+|+||+|+|++|.+...+. +..+.+++|+||||.|+|+.|++
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 ccEEEEEEeee
Q 024592 133 KRSLNAYSLRP 143 (265)
Q Consensus 133 ~~~i~~~~i~~ 143 (265)
+++|++..+..
T Consensus 81 ~~ql~i~~~~~ 91 (92)
T cd04483 81 EREINASVVYK 91 (92)
T ss_pred eeEEEEEEEEe
Confidence 99999998764
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=99.67 E-value=6.9e-17 Score=124.16 Aligned_cols=58 Identities=29% Similarity=0.510 Sum_probs=49.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
++++++++||++||+. ..+++|||+++|+++|++++++||++|++|++||+||+ |||+
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 6889999999999993 26789999999999999999999999999999999999 9996
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=99.46 E-value=1.7e-12 Score=115.08 Aligned_cols=120 Identities=21% Similarity=0.369 Sum_probs=92.6
Q ss_pred eeeeHHHHhcC--CC----------CCCCCeEECCeEEeEEEEEEEEEEeeeC----CCeEEEEEEcCCC--eEEEEEec
Q 024592 42 LPMTVKQLSEL--SS----------NDESSASIDGADVNTITVVGIVCDMQDK----EPQFIFLIDDGTG--RIECSRWA 103 (265)
Q Consensus 42 ~PvtIkqi~~a--~~----------~~~~~f~i~g~~v~~V~iVG~V~~v~~~----~t~~~y~LdDgTG--~I~~~~w~ 103 (265)
.||.|++|+.. .+ ...+.|.+.++||..|+|||.|+.+... ..++.|+|||+|| .|.|+.|.
T Consensus 29 ~PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~ 108 (256)
T PF10451_consen 29 VPLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSK 108 (256)
T ss_dssp -E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEH
T ss_pred CcEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEc
Confidence 39999999993 11 2245788999999999999999999865 7899999999999 89999997
Q ss_pred cccccc-ccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHh
Q 024592 104 HEQMEF-NEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYN 164 (265)
Q Consensus 104 ~~~~~~-~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~ 164 (265)
+..... .....+ .|..|+|.|.++ ++.++|.+..|..+.|+++...||.+++..+-.+
T Consensus 109 ~~~~~~~l~~~~~-~G~~V~VkG~vs--r~~~ql~ve~i~~~~~l~~Ei~fW~~~~~~R~~L 167 (256)
T PF10451_consen 109 SSYLSMGLPINDL-IGKVVEVKGTVS--RNERQLDVERIELVRDLNAEIEFWKERMRFRKEL 167 (256)
T ss_dssp HHHHCCCHHCTT--TT-EEEEEEEEE--SSSEEEEEEEEEEETSCCHHHHHHHHHHHHHHHC
T ss_pred ccccccCCCccCC-CCcEEEEEEEEc--cCcEEEEEEEEEccCChHHHHHHHHHHHHHHHHc
Confidence 632211 123344 999999999999 8899999999999999999999999999986544
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=99.20 E-value=1.5e-10 Score=82.83 Aligned_cols=73 Identities=25% Similarity=0.367 Sum_probs=63.2
Q ss_pred EEEEEEEEEe-eeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc-cEEEEEEeeeC
Q 024592 70 ITVVGIVCDM-QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK-RSLNAYSLRPI 144 (265)
Q Consensus 70 V~iVG~V~~v-~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~-~~i~~~~i~~v 144 (265)
|+|.|+|.++ ......+.|+|+|+||.|+|+.|.+.. ......+++|+.|+|.|+++.+++. .+|.+..+++|
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 777899999999999999999998322 1346789999999999999999987 99999998764
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=98.78 E-value=8.5e-08 Score=69.77 Aligned_cols=65 Identities=20% Similarity=0.464 Sum_probs=56.7
Q ss_pred CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHH
Q 024592 83 EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEI 150 (265)
Q Consensus 83 ~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei 150 (265)
..++.++|+|+||.|+|++|.+.. .....+++|.+|.|.|+++.+++..++.+..+.+++|.|+.
T Consensus 18 ~~~~~~~l~D~tg~i~~~~f~~~~---~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~l~~~~~~ 82 (83)
T cd04492 18 KPYLALTLQDKTGEIEAKLWDASE---EDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTEEDGV 82 (83)
T ss_pred CcEEEEEEEcCCCeEEEEEcCCCh---hhHhhCCCCCEEEEEEEEEEeCCceeEEEEEEEECCcccCC
Confidence 368999999999999999997543 12467899999999999999999899999999999998864
No 9
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=98.60 E-value=2.8e-07 Score=84.28 Aligned_cols=62 Identities=18% Similarity=0.397 Sum_probs=54.9
Q ss_pred CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 82 KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 82 ~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
...|+.++|.|.||+|+|++|...+. ....+++|++|+|.|++..|+++.|+.+..+++++.
T Consensus 31 G~~yl~l~l~D~tG~I~ak~W~~~~~---~~~~~~~g~vv~v~G~v~~y~g~~Ql~i~~i~~~~~ 92 (314)
T PRK13480 31 GKPFLTLILQDKSGDIEAKLWDVSPE---DEATYVPETIVHVKGDIINYRGRKQLKVNQIRLATE 92 (314)
T ss_pred CCeEEEEEEEcCCcEEEEEeCCCChh---hHhhcCCCCEEEEEEEEEEECCcceEEEEEeEECCC
Confidence 34699999999999999999986542 357799999999999999999999999999998754
No 10
>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=98.57 E-value=4.2e-07 Score=63.51 Aligned_cols=70 Identities=29% Similarity=0.465 Sum_probs=57.7
Q ss_pred EEEEEEEEeeeCC---CeEEEEEEcCC-CeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 71 TVVGIVCDMQDKE---PQFIFLIDDGT-GRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 71 ~iVG~V~~v~~~~---t~~~y~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
+++|.|.+++... .+..++|+|+| |.|+|..|.+... .....++.|..|.|.|+++.++++.++.+..++
T Consensus 1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~--~~~~~~~~g~~v~v~g~v~~~~~~~~l~~~~~~ 74 (75)
T cd03524 1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAE--ELENLLKEGQVVYIKGKVKKFRGRLQLIVESIE 74 (75)
T ss_pred CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHH--HHHhhccCCCEEEEEEEEEecCCeEEEEeeeec
Confidence 4789999997665 68999999999 9999999976432 123568999999999999999988888887654
No 11
>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=98.49 E-value=3.6e-07 Score=66.02 Aligned_cols=72 Identities=17% Similarity=0.215 Sum_probs=56.6
Q ss_pred EEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCC
Q 024592 72 VVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPII 145 (265)
Q Consensus 72 iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~ 145 (265)
++|.|.++... ..++.++|+|+||.++|++|.+.-. .....+++|.+|.|.|+++.|++..++.+..+.++.
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 67788775421 2369999999999999999964311 124568999999999999999988999998887765
No 12
>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=98.42 E-value=4.9e-06 Score=60.05 Aligned_cols=73 Identities=19% Similarity=0.368 Sum_probs=59.1
Q ss_pred EEEEEEEEEeee-CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeeeC
Q 024592 70 ITVVGIVCDMQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRPI 144 (265)
Q Consensus 70 V~iVG~V~~v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~v 144 (265)
+.+.|.|.+++. ......++|+|.||.|+|..|.+... .....+++|+.|.|.|++..+. +..++.+..+.|.
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 578899988875 33478999999999999999986432 2346789999999999999874 7789999888764
No 13
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.31 E-value=3.9e-06 Score=70.05 Aligned_cols=123 Identities=19% Similarity=0.255 Sum_probs=91.0
Q ss_pred eeeeHHHHhcCC---CC-C---CCCeE--ECCeEEeEEEEEEEEEEeee---CCCeEEEEEEcCCCeEEEE--Eeccccc
Q 024592 42 LPMTVKQLSELS---SN-D---ESSAS--IDGADVNTITVVGIVCDMQD---KEPQFIFLIDDGTGRIECS--RWAHEQM 107 (265)
Q Consensus 42 ~PvtIkqi~~a~---~~-~---~~~f~--i~g~~v~~V~iVG~V~~v~~---~~t~~~y~LdDgTG~I~~~--~w~~~~~ 107 (265)
+-|.++.|.++. .. + .-+|. --|..+++|-|||.|.+... ..+...+.+.|+||.+-|- ++..++
T Consensus 11 ~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~Vyag~yqPEa- 89 (196)
T COG3390 11 YRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYVYAGQYQPEA- 89 (196)
T ss_pred HHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEEEcCCCChHH-
Confidence 347788888881 11 1 12344 36899999999999999764 3568999999999998871 122221
Q ss_pred ccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee----CCChhHHHHHHHHHHHHHHHhcc
Q 024592 108 EFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP----IIDFNEITSHFVECIYVQLYNTR 166 (265)
Q Consensus 108 ~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~----v~d~Nei~~H~Levi~~~l~~~~ 166 (265)
..-.+.++.+++|-|+|+++.|++.--...++||| ..|++-..+|-+++.+..|..-+
T Consensus 90 -~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siRpE~vs~vde~~r~~Wv~eta~~tl~Ri~ 151 (196)
T COG3390 90 -KAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKVDEEARDLWVLETAEQTLERIK 151 (196)
T ss_pred -HHHHHhccCCceEEEecccceeecCCCceEEEechhhhhhcCHHHHHHHHHHHHHHHHHHHH
Confidence 12356789999999999999999887777777877 44678888999999988775543
No 14
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.31 E-value=5.5e-06 Score=66.28 Aligned_cols=84 Identities=19% Similarity=0.273 Sum_probs=65.7
Q ss_pred eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeee-------C--CCeEEEEEEcCCCeEEEEEeccccccccccc
Q 024592 43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQD-------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVN 113 (265)
Q Consensus 43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~-------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~ 113 (265)
++.|++|.... ..|.++++|.++.. . ..+..++|.|.||+|.++.|.+. ..
T Consensus 4 ~~kI~dL~~g~--------------~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~------a~ 63 (129)
T PRK06461 4 ITKIKDLKPGM--------------ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQ------AG 63 (129)
T ss_pred ceEHHHcCCCC--------------CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCc------cc
Confidence 56788875321 35777788876532 1 23778899999999999999863 34
Q ss_pred ccCCCCEEEEE-EEeeeeCCccEEEEE---EeeeCCC
Q 024592 114 QISKGMYVRVY-GHLKAFQDKRSLNAY---SLRPIID 146 (265)
Q Consensus 114 ~~~~g~yVrV~-G~i~~f~~~~~i~~~---~i~~v~d 146 (265)
.+++|+.|+|. |.++.|+++.+|++. .|+++.+
T Consensus 64 ~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 64 SLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred cCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 68999999999 889999999999998 5888875
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=98.29 E-value=3.6e-06 Score=61.73 Aligned_cols=53 Identities=21% Similarity=0.345 Sum_probs=46.8
Q ss_pred CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEEEEE
Q 024592 83 EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLNAYS 140 (265)
Q Consensus 83 ~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~~~~ 140 (265)
..+..++|.|.||+|.+++|.+.+ ...+++|+.|++. |.++.|++..+|.+..
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 368899999999999999998653 4678999999999 9999999999998754
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=1.4e-05 Score=60.16 Aligned_cols=73 Identities=30% Similarity=0.415 Sum_probs=59.6
Q ss_pred EEEEEEEEeee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 71 TVVGIVCDMQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 71 ~iVG~V~~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
.|.|.|.++.. .+..+-|+|.|.++.|.|.+|............+++|+-|.|.|+++.|. +|.+..++++--
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 57899998865 46789999999999999999976521112356789999999999999997 899999988654
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=98.19 E-value=2e-05 Score=56.84 Aligned_cols=72 Identities=19% Similarity=0.327 Sum_probs=59.4
Q ss_pred EEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592 70 ITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 70 V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~ 143 (265)
|.+-|.|.+....+..+-|+|.|.++.|.|.+|..... .....+++|+-|.|.|++...+|+-++.+..|+.
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 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGV--RAYPEVEVGDIVRVTGEVEPRDGQLQIEVESLEV 72 (73)
T ss_pred CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhcc--CCcCCCCCCCEEEEEEEEecCCeEEEEEEeeEEE
Confidence 46788898876555679999999999999999976542 1346789999999999999888888999888764
No 18
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=98.05 E-value=5.3e-05 Score=57.81 Aligned_cols=75 Identities=17% Similarity=0.294 Sum_probs=63.8
Q ss_pred EeEEEEEEEEEEeee-CCCeEEEEEEcCCCeEEEEEecccccccccc-cccCCCCEEEEEEEeeeeC--CccEEEEEEee
Q 024592 67 VNTITVVGIVCDMQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEV-NQISKGMYVRVYGHLKAFQ--DKRSLNAYSLR 142 (265)
Q Consensus 67 v~~V~iVG~V~~v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~-~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~ 142 (265)
+..|.|.|.|.+++. .+..+-|+|-|+...|.|.+|..... .-. ..+++|+-|.|.|++..|. |+-++.+..|+
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 478999999999988 67889999999999999999986542 112 5789999999999999985 67889999888
Q ss_pred e
Q 024592 143 P 143 (265)
Q Consensus 143 ~ 143 (265)
|
T Consensus 99 P 99 (99)
T PF13742_consen 99 P 99 (99)
T ss_pred C
Confidence 7
No 19
>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=98.01 E-value=6.8e-05 Score=55.22 Aligned_cols=72 Identities=24% Similarity=0.407 Sum_probs=55.1
Q ss_pred EEEEEEEEEeeeCC-----CeEEEEEEcCCCeEEEEEecccccccccccccC-CCCEEEEEEEee--eeCCccEEEEEEe
Q 024592 70 ITVVGIVCDMQDKE-----PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQIS-KGMYVRVYGHLK--AFQDKRSLNAYSL 141 (265)
Q Consensus 70 V~iVG~V~~v~~~~-----t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~g~yVrV~G~i~--~f~~~~~i~~~~i 141 (265)
|.|-|.|-.++.+. .-++|.|.|.|.+|.|+.|.. .+......++ +|++|+|.|++. .|.....+.+..|
T Consensus 2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~--~~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~~i~~i 79 (82)
T cd04484 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLR--KDEKDKEELKSKGDWVRVRGKVQYDTFSKELVLMINDI 79 (82)
T ss_pred EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEecc--CChhHHhhcccCCCEEEEEEEEEEccCCCceEEEeeeE
Confidence 77899998876422 356899999999999999985 1123346789 999999999987 4667777777666
Q ss_pred ee
Q 024592 142 RP 143 (265)
Q Consensus 142 ~~ 143 (265)
.+
T Consensus 80 ~~ 81 (82)
T cd04484 80 EE 81 (82)
T ss_pred EE
Confidence 54
No 20
>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=97.94 E-value=8.1e-05 Score=52.46 Aligned_cols=64 Identities=23% Similarity=0.348 Sum_probs=48.7
Q ss_pred EEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEE
Q 024592 72 VVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNA 138 (265)
Q Consensus 72 iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~ 138 (265)
+.|.|.++.. ....+.+.|.|+||.|+|+.|.... .....++.|+.+.|+|+++.|++..++.-
T Consensus 2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~---~~~~~~~~G~~~~v~Gkv~~~~~~~qi~~ 69 (75)
T cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQP---YLKKQLPPGTRVRVSGKVKRFRGGLQIVH 69 (75)
T ss_pred EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCH---HHHhcCCCCCEEEEEEEEeecCCeeEEeC
Confidence 5666666532 2357999999999999999996322 12457899999999999999988766653
No 21
>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=97.74 E-value=0.00046 Score=51.08 Aligned_cols=75 Identities=17% Similarity=0.203 Sum_probs=54.4
Q ss_pred EEEEEEEEEEeee-CCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeC-------CccEEEEE
Q 024592 69 TITVVGIVCDMQD-KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ-------DKRSLNAY 139 (265)
Q Consensus 69 ~V~iVG~V~~v~~-~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~-------~~~~i~~~ 139 (265)
.|++.|||.+++. ......+.|.|+|| .|.|.. ............+..|+-|.|.|.+..=. +...|.+.
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 3789999999998 56777889999999 588753 32211112235689999999999998743 45677777
Q ss_pred EeeeC
Q 024592 140 SLRPI 144 (265)
Q Consensus 140 ~i~~v 144 (265)
.+..+
T Consensus 80 ~i~il 84 (86)
T cd04321 80 DIQTL 84 (86)
T ss_pred EEEEe
Confidence 77655
No 22
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.67 E-value=0.00021 Score=69.23 Aligned_cols=77 Identities=17% Similarity=0.307 Sum_probs=68.4
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
.+|+|.|.|+.++..+.-..|+|.|+||.|.|--|....- ..-+.++.|++|+|.|.++.-.|+.||-+..+..++-
T Consensus 214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv--RAyP~IevGdiV~ViG~V~~r~g~lQiE~~~me~L~G 290 (715)
T COG1107 214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV--RAYPEIEVGDIVEVIGEVTRRDGRLQIEIEAMEKLTG 290 (715)
T ss_pred ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc--ccCCCCCCCceEEEEEEEeecCCcEEEeehhhHHhhC
Confidence 6899999999999999999999999999999888875432 3357899999999999999999999999999888874
No 23
>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=97.67 E-value=0.00056 Score=50.31 Aligned_cols=76 Identities=22% Similarity=0.282 Sum_probs=56.1
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeee------CCccEEEEEEe
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAF------QDKRSLNAYSL 141 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f------~~~~~i~~~~i 141 (265)
.|+|.|+|.+++.......+.|.|+||.+.|..-.+...+ ......+..|++|.|.|.+..- .+...|.+..+
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 3889999999998888788899999999998764332211 1234578999999999998863 34456666666
Q ss_pred eeC
Q 024592 142 RPI 144 (265)
Q Consensus 142 ~~v 144 (265)
+.+
T Consensus 81 ~il 83 (85)
T cd04100 81 EVL 83 (85)
T ss_pred EEE
Confidence 544
No 24
>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=97.64 E-value=0.00079 Score=49.49 Aligned_cols=76 Identities=22% Similarity=0.353 Sum_probs=54.7
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc------cEEEEEEee
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK------RSLNAYSLR 142 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~------~~i~~~~i~ 142 (265)
.|+|.|+|.+++.......+.|.|++|.|.|..-.+...+......+..|+.|.|.|.+..-... ..|.+..++
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 37899999999988888888999999999986533221111234568899999999999874332 456665554
Q ss_pred eC
Q 024592 143 PI 144 (265)
Q Consensus 143 ~v 144 (265)
.+
T Consensus 81 vl 82 (84)
T cd04323 81 II 82 (84)
T ss_pred EE
Confidence 43
No 25
>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=97.62 E-value=0.00044 Score=55.48 Aligned_cols=78 Identities=18% Similarity=0.213 Sum_probs=57.3
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee----------CCccEEEE
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF----------QDKRSLNA 138 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i~~ 138 (265)
.|+|.|||.+++.....+.+.|.|++|.+.|..-.+...+......+..|++|.|.|.+..- .+...|.+
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 49999999999988877888999999999987643322111234568999999999998852 23356777
Q ss_pred EEeeeCCC
Q 024592 139 YSLRPIID 146 (265)
Q Consensus 139 ~~i~~v~d 146 (265)
..++.+..
T Consensus 96 ~~i~vl~~ 103 (135)
T cd04317 96 SELEVLNK 103 (135)
T ss_pred eEEEEEEC
Confidence 66665553
No 26
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=97.52 E-value=0.0007 Score=57.02 Aligned_cols=83 Identities=20% Similarity=0.268 Sum_probs=62.6
Q ss_pred CeEEeEEEEEEEEEEeee--CCCeEEEEEEcCCCeEEEEEecccccc---cccccccCCCCEEEEEEEeeeeCCccEEEE
Q 024592 64 GADVNTITVVGIVCDMQD--KEPQFIFLIDDGTGRIECSRWAHEQME---FNEVNQISKGMYVRVYGHLKAFQDKRSLNA 138 (265)
Q Consensus 64 g~~v~~V~iVG~V~~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~ 138 (265)
|.-+.-|.+=|.|.+.+. ........|+|+||.|++..+...+.. ..-.+-+.+|++|.|.|++..|+|+..|.+
T Consensus 48 G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~yrG~~eVkv 127 (204)
T COG4085 48 GRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEYRGSSEVKV 127 (204)
T ss_pred ceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccCcEEEEEEEEEEeCCCceeec
Confidence 444566778888888763 457788899999999999999765432 122456789999999999999999988877
Q ss_pred EE---eeeCCC
Q 024592 139 YS---LRPIID 146 (265)
Q Consensus 139 ~~---i~~v~d 146 (265)
.. ++|+.-
T Consensus 128 nq~~d~~~l~k 138 (204)
T COG4085 128 NQPNDSRPLPK 138 (204)
T ss_pred cCccccccccc
Confidence 43 444443
No 27
>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=97.44 E-value=0.0013 Score=50.07 Aligned_cols=79 Identities=13% Similarity=0.083 Sum_probs=58.7
Q ss_pred EEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc--cc--cccccccCCCCEEEEEEEeeee-C-------CccE
Q 024592 69 TITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ--ME--FNEVNQISKGMYVRVYGHLKAF-Q-------DKRS 135 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~--~~--~~~~~~~~~g~yVrV~G~i~~f-~-------~~~~ 135 (265)
.|+|.|||.+++... ..+.+.|.|+||.|.|..-.+.. .+ ......+..|+.|.|.|.++.- . +...
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 378999999999887 77888999999999998864421 11 1123568999999999998863 1 3467
Q ss_pred EEEEEeeeCCCh
Q 024592 136 LNAYSLRPIIDF 147 (265)
Q Consensus 136 i~~~~i~~v~d~ 147 (265)
|.+..++.+...
T Consensus 81 l~~~~i~il~~~ 92 (102)
T cd04320 81 LHIEKIYVVSEA 92 (102)
T ss_pred EEEEEEEEEecC
Confidence 777777766543
No 28
>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=97.43 E-value=0.0016 Score=50.26 Aligned_cols=80 Identities=19% Similarity=0.266 Sum_probs=58.7
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-c-cccccccCCCCEEEEEEEeeeeCC---ccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-E-FNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~ 142 (265)
..|+|.|||.+++.......+.|.|+||.|.|..-..... + ......+..++.|.|.|.+..-.. ...|.+..++
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 3599999999999888888889999999999865432111 0 123356899999999999886432 3567777777
Q ss_pred eCCCh
Q 024592 143 PIIDF 147 (265)
Q Consensus 143 ~v~d~ 147 (265)
.+...
T Consensus 93 il~~~ 97 (108)
T cd04316 93 VLSEA 97 (108)
T ss_pred EEeCC
Confidence 66543
No 29
>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=97.42 E-value=0.00033 Score=45.89 Aligned_cols=47 Identities=17% Similarity=0.385 Sum_probs=39.4
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
|+..+.+||++|.+. .+++..+|++.++++...|...|..|.++|.|
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 356788999999874 47999999999999999999999999999987
No 30
>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=97.40 E-value=0.0014 Score=50.46 Aligned_cols=76 Identities=14% Similarity=0.187 Sum_probs=53.6
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccc-cCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQ-ISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI 144 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~-~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v 144 (265)
.|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+ ...... +..|+.|.|.|.+..- .+...|.+..+.-+
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 3789999999999888888899999999998764332111 112223 8999999999998753 34455555444443
No 31
>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=97.35 E-value=0.002 Score=49.24 Aligned_cols=79 Identities=19% Similarity=0.228 Sum_probs=56.8
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeCC---ccEEEEEEeeeC
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLRPI 144 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~~v 144 (265)
.|+|.|||.+++.....+.+.|.|+||.+.|..-.+...+ ......+..|+.|.|.|.++.-.. ...|.+..+..+
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 3889999999998888888899999999998664321111 122356889999999999886322 245666666666
Q ss_pred CCh
Q 024592 145 IDF 147 (265)
Q Consensus 145 ~d~ 147 (265)
...
T Consensus 81 ~~a 83 (103)
T cd04319 81 QNV 83 (103)
T ss_pred ecC
Confidence 543
No 32
>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=97.28 E-value=0.0028 Score=46.25 Aligned_cols=68 Identities=22% Similarity=0.340 Sum_probs=48.3
Q ss_pred EEEEEEEEEee--eCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEE
Q 024592 70 ITVVGIVCDMQ--DKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYS 140 (265)
Q Consensus 70 V~iVG~V~~v~--~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~ 140 (265)
|.++|.|.+++ ..... .++|+|.||+++|..|.+.-.--.....++++..|-|.|++.. ++. .+.+..
T Consensus 2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~-~~~-~l~~~~ 71 (79)
T cd04490 2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSK-DGG-LIFADE 71 (79)
T ss_pred EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEec-CCC-EEEEEE
Confidence 67889998875 22234 9999999999999999754210012457899999999999966 444 444443
No 33
>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=97.23 E-value=0.0066 Score=44.22 Aligned_cols=74 Identities=23% Similarity=0.289 Sum_probs=54.9
Q ss_pred EEEEEEEEEeeeCCCeEEEEEEcCCCe--EEEEEecccccccccccccCCCCEEEEEEEeeeeC---CccEEEEEEeeeC
Q 024592 70 ITVVGIVCDMQDKEPQFIFLIDDGTGR--IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLRPI 144 (265)
Q Consensus 70 V~iVG~V~~v~~~~t~~~y~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~~v 144 (265)
|++.|||.+++.......+.|.|+||. |.|..-.+.. .......+..|+.|.|.|.+..-. +...|.+..+..+
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 789999999998888888899999994 9987543321 112345789999999999988743 3456666666544
No 34
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=97.22 E-value=0.0045 Score=58.80 Aligned_cols=96 Identities=17% Similarity=0.218 Sum_probs=77.7
Q ss_pred EeEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeee
Q 024592 67 VNTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRP 143 (265)
Q Consensus 67 v~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~ 143 (265)
+.+|.|-|.|.+++... ...-|+|-|....|.|.+|..... .-...+++|+.|-|.|+|..|. |.-+|.+..++|
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 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNR--RLKFRPEEGMQVLVRGKISLYEPRGDYQIVAESMEP 100 (440)
T ss_pred CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCccc--ccCCCccCCCEEEEEEEEEEEcCCCceEEEEecCCc
Confidence 68999999999998544 478999999999999999986543 2234579999999999999995 678999999998
Q ss_pred CCChhHHHHHHHHHHHHHHHhcc
Q 024592 144 IIDFNEITSHFVECIYVQLYNTR 166 (265)
Q Consensus 144 v~d~Nei~~H~Levi~~~l~~~~ 166 (265)
.-. --.+--+|.++..|..+.
T Consensus 101 ~G~--G~L~~~~E~lK~kL~aEG 121 (440)
T COG1570 101 AGL--GALYLAFEQLKAKLAAEG 121 (440)
T ss_pred CCh--hHHHHHHHHHHHHHHhCC
Confidence 754 234667788888886653
No 35
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.19 E-value=0.0016 Score=46.16 Aligned_cols=59 Identities=20% Similarity=0.312 Sum_probs=49.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC-Cceeec
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE-FHYKSA 262 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd-~hyk~t 262 (265)
...+++||.+|++.+ +.|++..+|++.|+++...|+..|..|.++|.|.. -+. ..|..+
T Consensus 5 ~~~~~~IL~~L~~~g----~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~ 65 (68)
T smart00550 5 DSLEEKILEFLENSG----DETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLT 65 (68)
T ss_pred hHHHHHHHHHHHHCC----CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEee
Confidence 467889999999742 34799999999999999999999999999999988 544 455543
No 36
>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=97.15 E-value=0.012 Score=45.30 Aligned_cols=83 Identities=18% Similarity=0.229 Sum_probs=54.9
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV 121 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV 121 (265)
...|++|++++.. + ..|.|-|.|++....+ .|...|+||+|.+..=.+.- ....+.+++.|
T Consensus 21 ~~~TV~~a~~~~D--d----------~~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~w----~g~~vt~~~~V 81 (103)
T PF04076_consen 21 TVTTVAQAKNAKD--D----------TPVTLEGNIVKQLGDD---KYLFRDATGEIEVEIDDDVW----RGQTVTPDDKV 81 (103)
T ss_dssp ----HHHHTTS-S--S----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEE--GGGS----TT----TTSEE
T ss_pred CeEeHHHHhhCcC--C----------CeEEEEEEEEEEecCC---EEEEECCCCcEEEEEChhhc----CCcccCCCCEE
Confidence 4478999987632 3 7899999988866544 56899999999887532210 12456788999
Q ss_pred EEEEEeeeeCCccEEEEEEeee
Q 024592 122 RVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 122 rV~G~i~~f~~~~~i~~~~i~~ 143 (265)
+|+|.|..--.+..|-+.+|++
T Consensus 82 ri~GeVDk~~~~~~IdV~~I~K 103 (103)
T PF04076_consen 82 RISGEVDKDWNKTEIDVDRIEK 103 (103)
T ss_dssp EEEEEEEEETTEEEEEEEEEEE
T ss_pred EEEEEEeCCCCceEEEEEEEEC
Confidence 9999999655678888887764
No 37
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=97.10 E-value=0.0058 Score=58.84 Aligned_cols=94 Identities=19% Similarity=0.222 Sum_probs=67.9
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCE
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMY 120 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~y 120 (265)
.+++|++|+..... + ..|+|.|+|.+++.....+.+.|.|+||.|.+..-.+...+ ......+..|+.
T Consensus 2 ~~~~~~~~~~~~~~-~----------~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~ 70 (450)
T PRK03932 2 MRVSIKDILKGKYV-G----------QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSS 70 (450)
T ss_pred CcEEHHHhcccccC-C----------CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcE
Confidence 46789998732111 1 67999999999998887788899999999877765433111 123456899999
Q ss_pred EEEEEEeeeeC---CccEEEEEEeeeCCC
Q 024592 121 VRVYGHLKAFQ---DKRSLNAYSLRPIID 146 (265)
Q Consensus 121 VrV~G~i~~f~---~~~~i~~~~i~~v~d 146 (265)
|.|.|.+..-. +...|.+..++.+..
T Consensus 71 v~v~G~v~~~~~~~~~~el~~~~i~vl~~ 99 (450)
T PRK03932 71 VIVTGTVVESPRAGQGYELQATKIEVIGE 99 (450)
T ss_pred EEEEEEEEcCCCCCCCEEEEEEEEEEccC
Confidence 99999998643 346777777766653
No 38
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=97.02 E-value=0.0018 Score=68.65 Aligned_cols=77 Identities=19% Similarity=0.270 Sum_probs=61.8
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
..|.++|.|.+++.. .....++|+|.||.|+++.|.+.-. .....+.+|..|.|.|++..++++.++.+..+.
T Consensus 978 ~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye--~~~~~L~~g~iV~V~GkVe~~~~~~qlii~~I~ 1055 (1135)
T PRK05673 978 SVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALE--KYRDLLEEDRIVVVKGQVSFDDGGLRLTAREVM 1055 (1135)
T ss_pred ceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeecc
Confidence 368899999887643 3478899999999999999975411 234568999999999999988888899998888
Q ss_pred eCCC
Q 024592 143 PIID 146 (265)
Q Consensus 143 ~v~d 146 (265)
++.+
T Consensus 1056 ~L~~ 1059 (1135)
T PRK05673 1056 DLEE 1059 (1135)
T ss_pred cHHH
Confidence 7754
No 39
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=96.96 E-value=0.006 Score=58.40 Aligned_cols=112 Identities=16% Similarity=0.253 Sum_probs=83.0
Q ss_pred eeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeC-CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCE
Q 024592 43 PMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDK-EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY 120 (265)
Q Consensus 43 PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~-~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~y 120 (265)
|+|+++|... .. .++.. +..|.|.|.|.+++.. +..+=|+|-|.+..|.|.+|..... .-...+++|+-
T Consensus 5 ~~svsel~~~ik~------~le~~-~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~--~~~~~~~~G~~ 75 (438)
T PRK00286 5 ILSVSELNRYVKS------LLERD-LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR--RLKFKPEEGMK 75 (438)
T ss_pred cCcHHHHHHHHHH------HHHhh-CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh--cCCCCCCCCCE
Confidence 5788888775 11 11111 5789999999999865 5678899999999999999986442 12356899999
Q ss_pred EEEEEEeeeeC--CccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhc
Q 024592 121 VRVYGHLKAFQ--DKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNT 165 (265)
Q Consensus 121 VrV~G~i~~f~--~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~ 165 (265)
|.|.|+|..|. |.-+|.+..|.|.-- -++ +--+|-+...|..+
T Consensus 76 v~v~g~~~~y~~~g~~ql~v~~i~~~g~-G~l-~~~~~~lk~~L~~e 120 (438)
T PRK00286 76 VLVRGKVSLYEPRGDYQLIVEEIEPAGI-GAL-AAAFEQLKEKLAAE 120 (438)
T ss_pred EEEEEEEEEECCCCCEEEEEEEeeeCCc-cHH-HHHHHHHHHHHHHC
Confidence 99999999885 668999999998654 343 55556666666544
No 40
>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=96.90 E-value=0.0072 Score=57.89 Aligned_cols=95 Identities=12% Similarity=0.201 Sum_probs=74.6
Q ss_pred EeEEEEEEEEEEeeeC-CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeee
Q 024592 67 VNTITVVGIVCDMQDK-EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRP 143 (265)
Q Consensus 67 v~~V~iVG~V~~v~~~-~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~ 143 (265)
+..|.|.|-|.+++.. +..+=|+|-|....|.|.+|..... .-...+++|+-|.|.|+|..|. |+-+|.+..|.|
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 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNN--RLKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQP 94 (432)
T ss_pred CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhh--CCCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEecc
Confidence 4689999999999764 4578899999999999999987542 1235679999999999999985 668999999998
Q ss_pred CCChhHHHHHHHHHHHHHHHhc
Q 024592 144 IIDFNEITSHFVECIYVQLYNT 165 (265)
Q Consensus 144 v~d~Nei~~H~Levi~~~l~~~ 165 (265)
.- .-+ .+--+|-+...|..+
T Consensus 95 ~G-~G~-l~~~~~~lk~~L~~e 114 (432)
T TIGR00237 95 AG-EGL-LQLAYEQLKEKLAAE 114 (432)
T ss_pred CC-hHH-HHHHHHHHHHHHHHC
Confidence 74 334 355566666666554
No 41
>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=96.89 E-value=0.0088 Score=57.63 Aligned_cols=93 Identities=18% Similarity=0.280 Sum_probs=63.8
Q ss_pred eeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCC--CeEEEEEecccccc-cccccccCCC
Q 024592 43 PMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGT--GRIECSRWAHEQME-FNEVNQISKG 118 (265)
Q Consensus 43 PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgT--G~I~~~~w~~~~~~-~~~~~~~~~g 118 (265)
|.+|+.++.. ... + | ..|+|.|||.+++.....+.+.|.|+| |.|.|..-.....+ ......+..|
T Consensus 1 ~~~~~~~~~~~~~~------~-g---~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~g 70 (453)
T TIGR00457 1 SAAIKDLLQQVYKF------V-G---DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTG 70 (453)
T ss_pred CccHHHHHhcchhc------C-C---CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCC
Confidence 5678888752 111 1 2 569999999999977777888999999 99999764331111 1234568999
Q ss_pred CEEEEEEEeeee---CCccEEEEEEeeeCC
Q 024592 119 MYVRVYGHLKAF---QDKRSLNAYSLRPII 145 (265)
Q Consensus 119 ~yVrV~G~i~~f---~~~~~i~~~~i~~v~ 145 (265)
+.|.|.|.+..- .+...|.+..++.+.
T Consensus 71 s~V~v~G~v~~~~~~~~~~El~~~~i~vl~ 100 (453)
T TIGR00457 71 SSVSVTGKVVESPGKGQPVELQVKKIEVVG 100 (453)
T ss_pred cEEEEEEEEEcCCCCCCCEEEEEeEEEEEe
Confidence 999999998752 233556666555544
No 42
>PRK07211 replication factor A; Reviewed
Probab=96.89 E-value=0.0062 Score=58.79 Aligned_cols=76 Identities=18% Similarity=0.349 Sum_probs=60.7
Q ss_pred eEEEEEEEEEEeee----------CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEE
Q 024592 68 NTITVVGIVCDMQD----------KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~----------~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i 136 (265)
..|.|.|+|.++.. ......+.|-|.||+|.+..|.+.+. ..+.+++|+.|+|. ++++.|++...|
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 56889999987642 11347899999999999999987543 34568999999996 889999999999
Q ss_pred EEE---EeeeCCC
Q 024592 137 NAY---SLRPIID 146 (265)
Q Consensus 137 ~~~---~i~~v~d 146 (265)
++. .|.++.+
T Consensus 249 sl~~~s~I~~~~d 261 (485)
T PRK07211 249 HVGDRGAVEEVDE 261 (485)
T ss_pred EECCCceEEECCc
Confidence 885 6777765
No 43
>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=96.87 E-value=0.039 Score=43.87 Aligned_cols=82 Identities=15% Similarity=0.159 Sum_probs=57.1
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV 121 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV 121 (265)
...|++|++++.. + ..|.|-|.|+..-.. =.|...|+||+|.+..=.+.- .-..+.+++-|
T Consensus 44 ~~~tV~~a~~~~D--d----------t~V~L~G~Iv~~l~~---d~Y~F~D~TG~I~VeId~~~w----~G~~v~p~d~V 104 (126)
T TIGR00156 44 KKMTVDFAKSMHD--G----------ASVTLRGNIISHIGD---DRYVFRDKSGEINVVIPAAVW----NGREVQPKDMV 104 (126)
T ss_pred ceEeHHHHhhCCC--C----------CEEEEEEEEEEEeCC---ceEEEECCCCCEEEEECHHHc----CCCcCCCCCEE
Confidence 3689999988632 3 678888888776543 457999999998887511100 12357789999
Q ss_pred EEEEEeeeeCCccEEEEEEee
Q 024592 122 RVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 122 rV~G~i~~f~~~~~i~~~~i~ 142 (265)
+|.|.|..--....|-+.+|+
T Consensus 105 ~I~GeVDk~~~~~~IdV~~I~ 125 (126)
T TIGR00156 105 NISGSLDKKSAPAEVDVTHIQ 125 (126)
T ss_pred EEEEEECCCCCCeEEEEEEEE
Confidence 999999853334566666664
No 44
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=96.83 E-value=0.0046 Score=59.40 Aligned_cols=77 Identities=13% Similarity=0.255 Sum_probs=60.0
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
..|+++|+|.+++.. .....++|+|.||.++|..|.+.-. .....++++..|.|.|++..-.+..++.+..|.
T Consensus 281 ~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~--~~~~~l~~~~~v~v~G~v~~~~~~~~liv~~i~ 358 (449)
T PRK07373 281 TKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYE--RISELLQVDARLIIWGKVDRRDDQVQLIVEDAE 358 (449)
T ss_pred CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeEee
Confidence 368899999998643 2467889999999999999976321 224568999999999999864466788888888
Q ss_pred eCCC
Q 024592 143 PIID 146 (265)
Q Consensus 143 ~v~d 146 (265)
++.+
T Consensus 359 ~l~~ 362 (449)
T PRK07373 359 PIEE 362 (449)
T ss_pred cHhh
Confidence 7755
No 45
>PRK10053 hypothetical protein; Provisional
Probab=96.79 E-value=0.055 Score=43.28 Aligned_cols=82 Identities=16% Similarity=0.253 Sum_probs=56.8
Q ss_pred ccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEE----eccccccccccc
Q 024592 38 VRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSR----WAHEQMEFNEVN 113 (265)
Q Consensus 38 ~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~----w~~~~~~~~~~~ 113 (265)
+......|++|.+++.. + ..|.|-|.|+.--.. =.|...|+||+|.+.. |.. .
T Consensus 44 p~~~~~~tV~~a~~~~D--d----------~~V~L~G~Iv~~lg~---d~Y~F~D~tG~I~VeID~~~w~G--------~ 100 (130)
T PRK10053 44 TDDARKMTVEQAKTMHD--G----------ATVSLRGNLIDHKGD---DRYVFRDKSGEINVIIPAAVFDG--------R 100 (130)
T ss_pred CcccceEEHHHhhcCcC--C----------CeEEEEEEEEEEeCC---ceEEEECCCCcEEEEeCHHHcCC--------C
Confidence 33334679999887632 3 567788887765443 3578999999988875 532 3
Q ss_pred ccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 114 QISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 114 ~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
.+.+.+.||++|.+..-.....|-+.+|+
T Consensus 101 ~v~p~~kV~I~GevDk~~~~~~IdV~~i~ 129 (130)
T PRK10053 101 EVQPDQMININGSLDKKSAPPVVRVTHLQ 129 (130)
T ss_pred cCCCCCEEEEEEEECCCCCCeEEEEEEEe
Confidence 57889999999999753334566666554
No 46
>PRK07217 replication factor A; Reviewed
Probab=96.64 E-value=0.011 Score=53.76 Aligned_cols=73 Identities=18% Similarity=0.304 Sum_probs=57.1
Q ss_pred eEEEEEEEEEEeeeCC-CeEEE--EEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEEEEeee
Q 024592 68 NTITVVGIVCDMQDKE-PQFIF--LIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~-t~~~y--~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~~~i~~ 143 (265)
..|+|.|+|..+-+.. ..+.+ .|.|.||+|....|.+++ .+.+++|+.|++.+- ++.|+|+.+|++..-..
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 5799999999985432 33333 699999999999998743 467999999999887 66899999999855444
Q ss_pred CC
Q 024592 144 II 145 (265)
Q Consensus 144 v~ 145 (265)
|+
T Consensus 158 I~ 159 (311)
T PRK07217 158 IE 159 (311)
T ss_pred EE
Confidence 43
No 47
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.56 E-value=0.0024 Score=44.48 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=39.5
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+++|+++|++. ..+++..||++.|+++..++|.-|+.|..+|.|-.
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 56799999873 35799999999999999999999999999999864
No 48
>PRK07218 replication factor A; Provisional
Probab=96.55 E-value=0.017 Score=55.10 Aligned_cols=72 Identities=19% Similarity=0.346 Sum_probs=57.4
Q ss_pred eEEEEEEEEEEeee-------CC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccEEEE
Q 024592 68 NTITVVGIVCDMQD-------KE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRSLNA 138 (265)
Q Consensus 68 ~~V~iVG~V~~v~~-------~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~i~~ 138 (265)
..|.|.|+|.++.. .. ......|.|.||+|.+..|.+. +.+.+|+.|+|.+ .++.|+|..+|++
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 45888999988743 11 2455689999999999999852 3589999999998 5889999999999
Q ss_pred E---EeeeCCC
Q 024592 139 Y---SLRPIID 146 (265)
Q Consensus 139 ~---~i~~v~d 146 (265)
. .|.++++
T Consensus 246 ~~~t~I~~~d~ 256 (423)
T PRK07218 246 SEFTTVEALDR 256 (423)
T ss_pred CCceEEEECCC
Confidence 7 6777654
No 49
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=96.49 E-value=0.033 Score=53.06 Aligned_cols=89 Identities=20% Similarity=0.245 Sum_probs=64.6
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-ccccccccCCCCE
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-EFNEVNQISKGMY 120 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~g~y 120 (265)
+.++|++|.+... + ..|+|-|||.+++.........|.|+||.|.|..-.+... +..+...+..++.
T Consensus 3 ~~~~i~di~~~~~---------~---~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~ 70 (435)
T COG0017 3 KRTYIKDIKPHVG---------G---QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESS 70 (435)
T ss_pred ceeeHHhhhccCC---------C---cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccE
Confidence 3567778765321 1 7899999999999988888889999999999998754221 1111457899999
Q ss_pred EEEEEEeeeeCC---ccEEEEEEee
Q 024592 121 VRVYGHLKAFQD---KRSLNAYSLR 142 (265)
Q Consensus 121 VrV~G~i~~f~~---~~~i~~~~i~ 142 (265)
|.|.|.|+.-.. .-.|.+..|.
T Consensus 71 v~V~G~v~~~~~a~~g~El~v~~i~ 95 (435)
T COG0017 71 VVVTGIVKASPKAPQGFELQVEKIE 95 (435)
T ss_pred EEEEEEEEcCCCCCCCEEEEEEEEE
Confidence 999999997542 2345554443
No 50
>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=96.48 E-value=0.0019 Score=45.47 Aligned_cols=52 Identities=23% Similarity=0.352 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCc--CHHHHHHhcCCC-HHHHHHHHHHHhhCCeEE
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGV--HRNVISQQLNLP-MDKLMEALESLNENSLVY 252 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv--~~~~I~~~l~~~-~~~v~~al~~L~~eG~IY 252 (265)
.|++.|.+||++|++- ..+.|+ ++.||++.|++. ...|...|+-|.+.|+|=
T Consensus 3 ~LT~rQ~~vL~~I~~~---~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 3 ELTERQKEVLEFIREY---IEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp ---HHHHHHHHHHHHH---HHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 5788999999999863 223454 789999999975 999999999999999984
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=96.47 E-value=0.0061 Score=41.57 Aligned_cols=44 Identities=16% Similarity=0.348 Sum_probs=39.3
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
+..|+++|++. .-+++.++++.|+.++..||.-|..|.++|.|-
T Consensus 2 ~~~Il~~l~~~------~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 2 QQQILELLKEK------GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHHHHc------CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 46799999874 368999999999999999999999999999874
No 52
>PF13730 HTH_36: Helix-turn-helix domain
Probab=96.46 E-value=0.0099 Score=39.78 Aligned_cols=54 Identities=13% Similarity=0.183 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
+|++....||-+|....+.....-.+.+.|++.++++...|+++|.+|++.|.|
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 466778888888776542222233489999999999999999999999999986
No 53
>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=96.33 E-value=0.027 Score=53.90 Aligned_cols=78 Identities=19% Similarity=0.226 Sum_probs=57.7
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeeeC---CccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~ 142 (265)
..|+|.|+|.+++.....+...|.|++|.|.|..-.+...+ -+....+..|+.|.|.|.+..-+ +...|.+..+.
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 45999999999998888888899999999999775432111 11235689999999999998643 44666666665
Q ss_pred eCC
Q 024592 143 PII 145 (265)
Q Consensus 143 ~v~ 145 (265)
.+.
T Consensus 93 vl~ 95 (428)
T TIGR00458 93 VIN 95 (428)
T ss_pred EEe
Confidence 544
No 54
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=96.32 E-value=0.03 Score=54.68 Aligned_cols=77 Identities=17% Similarity=0.141 Sum_probs=56.5
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeee-eCCccEEEEEEeeeC
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKA-FQDKRSLNAYSLRPI 144 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~-f~~~~~i~~~~i~~v 144 (265)
.|+|.|+|.+++.....+.+.|.|++|.|.|..-.+...+. .....+..|+.|.|.|.+.. -.+...|.+..+..+
T Consensus 67 ~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~~~ll 146 (505)
T PRK12445 67 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLL 146 (505)
T ss_pred EEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeEEEEE
Confidence 49999999999988888888999999999986643321111 12346889999999999864 346666766665544
Q ss_pred C
Q 024592 145 I 145 (265)
Q Consensus 145 ~ 145 (265)
.
T Consensus 147 s 147 (505)
T PRK12445 147 T 147 (505)
T ss_pred e
Confidence 3
No 55
>PRK14699 replication factor A; Provisional
Probab=96.29 E-value=0.015 Score=56.45 Aligned_cols=77 Identities=17% Similarity=0.209 Sum_probs=55.3
Q ss_pred eEEEEEEEEEEeee--------CC--CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEE
Q 024592 68 NTITVVGIVCDMQD--------KE--PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLN 137 (265)
Q Consensus 68 ~~V~iVG~V~~v~~--------~~--t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~ 137 (265)
..|+|.|+|.++.. .+ ....+.|.|.||+|.+..|.+.+. .-..-.|++|+.|+|.|.+|...+...|+
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 GPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMAD-LIKAGKIKAGQTLQISGYAKQGYSGVEVN 146 (484)
T ss_pred ceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccc-hhhhcCCCCCCEEEEcceeccCCCCceEE
Confidence 46888888888741 12 345679999999999999986431 01112599999999999998866667888
Q ss_pred EE---EeeeCC
Q 024592 138 AY---SLRPII 145 (265)
Q Consensus 138 ~~---~i~~v~ 145 (265)
+. .+++.+
T Consensus 147 ~~~~~~i~~~~ 157 (484)
T PRK14699 147 IGNNGVLTESE 157 (484)
T ss_pred eCCCceeeccC
Confidence 75 444443
No 56
>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=96.24 E-value=0.0062 Score=42.77 Aligned_cols=50 Identities=24% Similarity=0.247 Sum_probs=43.7
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+++....+||..|-. ..+++..+|++.++++...|..+|..|.+.|.|..
T Consensus 5 gLs~~E~~vy~~Ll~------~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 5 GLSENEAKVYLALLK------NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp CHHHHHHHHHHHHHH------HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred CcCHHHHHHHHHHHH------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 456778889888753 24789999999999999999999999999999987
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=96.23 E-value=0.025 Score=60.47 Aligned_cols=78 Identities=15% Similarity=0.286 Sum_probs=61.4
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee--eeCCccEEEEEE
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK--AFQDKRSLNAYS 140 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~--~f~~~~~i~~~~ 140 (265)
..|.|.|.|-.++.. ..-++|.|.|.|.+|.|+.|.....+.+....+++|++|+|.|++. .|..+..+.+..
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 678899999887642 2456899999999999999986554334457899999999999987 466777888877
Q ss_pred eeeCC
Q 024592 141 LRPII 145 (265)
Q Consensus 141 i~~v~ 145 (265)
|.++.
T Consensus 88 ~~~~~ 92 (1213)
T TIGR01405 88 IEEIP 92 (1213)
T ss_pred eeecC
Confidence 77653
No 58
>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=96.21 E-value=0.074 Score=42.84 Aligned_cols=69 Identities=12% Similarity=0.189 Sum_probs=54.1
Q ss_pred eEEEEEEEEEEeee------CCCeEEEEEEcCCC---e-EEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEE
Q 024592 68 NTITVVGIVCDMQD------KEPQFIFLIDDGTG---R-IECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~------~~t~~~y~LdDgTG---~-I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i 136 (265)
..|.++|+|+++.. ..-.++|+|-|.|+ . |.|.+|.+..+ ..+.+.+|+.|.+.+- |+.|+|+.+.
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 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEE---SLPIVKVGDIILLRRVKIQSYNGKPQG 91 (138)
T ss_pred CeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChh---hCCCCCCCCEEEEEEEEEEEECCceEE
Confidence 57889999999753 23468999999887 2 99999987653 4666799999999874 8889988666
Q ss_pred EEE
Q 024592 137 NAY 139 (265)
Q Consensus 137 ~~~ 139 (265)
...
T Consensus 92 ~~~ 94 (138)
T cd04497 92 ISN 94 (138)
T ss_pred EEC
Confidence 554
No 59
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=96.20 E-value=0.0038 Score=56.22 Aligned_cols=63 Identities=22% Similarity=0.420 Sum_probs=55.9
Q ss_pred eCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 81 DKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 81 ~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
....++.++++|.||.|+++.|..... ....+..|..|.+.|....+++.+|+.+..+|++++
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 345789999999999999999986543 356799999999999999999999999999999887
No 60
>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=96.18 E-value=0.017 Score=39.35 Aligned_cols=55 Identities=16% Similarity=0.193 Sum_probs=46.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
+++..+-.||.+|...+ +.+++..+|++.++++...|...|..|++.|.|.. -|.
T Consensus 2 glt~~q~~vL~~l~~~~----~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP----GEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp TSTHHHHHHHHHHHHST----TSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred ccCHHHHHHHHHHHHCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 46778889999998742 33599999999999999999999999999999998 654
No 61
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=96.17 E-value=0.029 Score=60.89 Aligned_cols=79 Identities=25% Similarity=0.431 Sum_probs=61.7
Q ss_pred eEEEEEEEEEEeeeCC-----CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEEE
Q 024592 68 NTITVVGIVCDMQDKE-----PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAYS 140 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~-----t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~~ 140 (265)
..|.|-|.|-.++... .-++|.|.|.|.+|.|+.|..+..+.+....++.|++|+|.|++.. |.....+.+..
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 5788999998876432 3568999999999999999865443344577999999999999975 66777777777
Q ss_pred eeeCCC
Q 024592 141 LRPIID 146 (265)
Q Consensus 141 i~~v~d 146 (265)
|.++..
T Consensus 317 ~~~~~~ 322 (1437)
T PRK00448 317 INEIKH 322 (1437)
T ss_pred eeecCC
Confidence 776644
No 62
>PRK08402 replication factor A; Reviewed
Probab=96.15 E-value=0.031 Score=52.14 Aligned_cols=70 Identities=20% Similarity=0.280 Sum_probs=53.1
Q ss_pred eEEEEEEEEEEeee--------CCC--eEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeee-CCccE
Q 024592 68 NTITVVGIVCDMQD--------KEP--QFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAF-QDKRS 135 (265)
Q Consensus 68 ~~V~iVG~V~~v~~--------~~t--~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f-~~~~~ 135 (265)
..|.++|+|.++.. .++ -...+|.|.||.|.+..|.+... ...+.+.+|+.|+|. +.++.| +|..+
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 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVA--KYYNKINVGDVIKVIDAQVRESLSGLPE 150 (355)
T ss_pred ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhh--hhcccCCCCCEEEEECCEEeecCCCcEE
Confidence 57899999988742 111 23479999999999999987542 123568999999987 889975 88878
Q ss_pred EEEE
Q 024592 136 LNAY 139 (265)
Q Consensus 136 i~~~ 139 (265)
|++.
T Consensus 151 Lsvg 154 (355)
T PRK08402 151 LHIN 154 (355)
T ss_pred EEEC
Confidence 8884
No 63
>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=96.13 E-value=0.012 Score=39.14 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=38.3
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-.||++|.+. ..++++.+|+++++++...+...|..|.+.|.|..
T Consensus 6 l~iL~~l~~~-----~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 6 LRILEALAES-----GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHCHHCT-----BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 3578888764 45789999999999999999999999999999864
No 64
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=96.12 E-value=0.039 Score=52.92 Aligned_cols=78 Identities=18% Similarity=0.265 Sum_probs=57.1
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeC---CccEEEEEEeee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLRP 143 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~~ 143 (265)
..|+|.|+|.+++.....+.+.|.|++|.|.|..=.+...+ .+....|..|+.|.|.|.+..-+ +...|.+..+..
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 45889999999998887788899999999998763322111 12345789999999999998754 445677666555
Q ss_pred CC
Q 024592 144 II 145 (265)
Q Consensus 144 v~ 145 (265)
+.
T Consensus 97 ls 98 (437)
T PRK05159 97 LN 98 (437)
T ss_pred Ee
Confidence 43
No 65
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.09 E-value=0.032 Score=43.97 Aligned_cols=82 Identities=22% Similarity=0.220 Sum_probs=59.0
Q ss_pred eeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEE
Q 024592 44 MTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRV 123 (265)
Q Consensus 44 vtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV 123 (265)
..||||..+... + .....|...|.++.-.+......+.+-|.||+|.+-.|.+. ...++.||.||.
T Consensus 5 i~ikdi~P~~kN----~----~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~------~~~~~PGDIirL 70 (134)
T KOG3416|consen 5 IFIKDIKPGLKN----I----NVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEE------GCLIQPGDIIRL 70 (134)
T ss_pred hhHhhcChhhhc----c----eEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCc------CcccCCccEEEe
Confidence 357777665321 1 12344556677776667778999999999999999999853 367899999999
Q ss_pred EEEeee-eCCccEEEEE
Q 024592 124 YGHLKA-FQDKRSLNAY 139 (265)
Q Consensus 124 ~G~i~~-f~~~~~i~~~ 139 (265)
.|...+ |++...|-+.
T Consensus 71 t~Gy~Si~qg~LtL~~G 87 (134)
T KOG3416|consen 71 TGGYASIFQGCLTLYVG 87 (134)
T ss_pred cccchhhhcCceEEEec
Confidence 988765 6776655553
No 66
>PRK14699 replication factor A; Provisional
Probab=96.06 E-value=0.027 Score=54.62 Aligned_cols=75 Identities=23% Similarity=0.304 Sum_probs=55.5
Q ss_pred EEEEEEEEEEeeeC-------C---CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-ee--eeCCccE
Q 024592 69 TITVVGIVCDMQDK-------E---PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LK--AFQDKRS 135 (265)
Q Consensus 69 ~V~iVG~V~~v~~~-------~---t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~--~f~~~~~ 135 (265)
.|+|.|+|.++..- . .-....|-|.||+|.+..|.+... ..+.|++|+.|+|.+. +| .|++...
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 48899999886431 1 244579999999999999987532 3457999999998744 44 5888888
Q ss_pred EEEEEeeeCCC
Q 024592 136 LNAYSLRPIID 146 (265)
Q Consensus 136 i~~~~i~~v~d 146 (265)
|++.....+..
T Consensus 255 l~~~~~s~i~~ 265 (484)
T PRK14699 255 LQVGNRSIIRK 265 (484)
T ss_pred EEecCceEeec
Confidence 88866555544
No 67
>PRK07211 replication factor A; Reviewed
Probab=96.05 E-value=0.034 Score=53.82 Aligned_cols=77 Identities=16% Similarity=0.276 Sum_probs=57.6
Q ss_pred eEEEEEEEEEEeee------C-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592 68 NTITVVGIVCDMQD------K-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i 136 (265)
..|+|.|+|.++.. . ..-..+.|-|.||.|.+..|.+... .....|++|+.++|.|+++...+...|
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 56888888877542 1 2457889999999999999986542 134679999999999998765555677
Q ss_pred EEEEeeeCCC
Q 024592 137 NAYSLRPIID 146 (265)
Q Consensus 137 ~~~~i~~v~d 146 (265)
++..+.+-.|
T Consensus 142 ~i~~ve~~~d 151 (485)
T PRK07211 142 SVDKVEPDPD 151 (485)
T ss_pred EEeeEEEccc
Confidence 7777666544
No 68
>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=96.01 E-value=0.041 Score=54.60 Aligned_cols=76 Identities=17% Similarity=0.158 Sum_probs=56.8
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee----------eCCccEEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA----------FQDKRSLN 137 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~----------f~~~~~i~ 137 (265)
..|+|.|||.+++....-+.+.|.|+||.|.|..-.+ ....+....+..|+.|.|.|.+.. -.+...|.
T Consensus 16 ~~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~-~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~ 94 (583)
T TIGR00459 16 QTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPD-ADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEIL 94 (583)
T ss_pred CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC-HHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEE
Confidence 3699999999999888888889999999999875333 111123457899999999999974 23456777
Q ss_pred EEEeeeC
Q 024592 138 AYSLRPI 144 (265)
Q Consensus 138 ~~~i~~v 144 (265)
+..+..+
T Consensus 95 ~~~i~iL 101 (583)
T TIGR00459 95 AESITLL 101 (583)
T ss_pred EeEEEEe
Confidence 7776554
No 69
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=95.98 E-value=0.045 Score=53.29 Aligned_cols=100 Identities=18% Similarity=0.152 Sum_probs=65.6
Q ss_pred eeeeHHHHhcCCCC-CCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCC
Q 024592 42 LPMTVKQLSELSSN-DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKG 118 (265)
Q Consensus 42 ~PvtIkqi~~a~~~-~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g 118 (265)
+..+|+++...-.. ......- .-..|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+ -.....+..|
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~---~~~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g 107 (491)
T PRK00484 31 RTHTAAELRAKYDDKEKEELEE---LEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLG 107 (491)
T ss_pred CccCHHHHHHHhccccchhhcc---cCcEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCC
Confidence 34678888765211 1111100 0156999999999998888888899999999998754332111 1123358999
Q ss_pred CEEEEEEEeee-eCCccEEEEEEeeeC
Q 024592 119 MYVRVYGHLKA-FQDKRSLNAYSLRPI 144 (265)
Q Consensus 119 ~yVrV~G~i~~-f~~~~~i~~~~i~~v 144 (265)
+.|.|.|.+.. -.+...|.+..++.+
T Consensus 108 ~~v~v~G~v~~t~~ge~el~~~~~~vl 134 (491)
T PRK00484 108 DIIGVEGTLFKTKTGELSVKATELTLL 134 (491)
T ss_pred CEEEEEEEEEEcCCCcEEEEEeEEEEE
Confidence 99999999875 345566666665543
No 70
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=95.94 E-value=0.025 Score=59.73 Aligned_cols=76 Identities=18% Similarity=0.246 Sum_probs=59.0
Q ss_pred EEEEEEEEEEeeeCCC---eEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCC
Q 024592 69 TITVVGIVCDMQDKEP---QFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPII 145 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t---~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~ 145 (265)
.|+++|+|..+....| ...++|+|.||.++|..|.+.-. .....++++..|.|.|+++.-++..++.+..|.++.
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 4889999988765422 57789999999999999976321 123568999999999999976666788888887764
Q ss_pred C
Q 024592 146 D 146 (265)
Q Consensus 146 d 146 (265)
+
T Consensus 1033 ~ 1033 (1046)
T PRK05672 1033 P 1033 (1046)
T ss_pred H
Confidence 4
No 71
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.94 E-value=0.019 Score=60.74 Aligned_cols=75 Identities=12% Similarity=0.148 Sum_probs=59.0
Q ss_pred EEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592 69 TITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 69 ~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~ 143 (265)
.|+++|.|.+++.. .....++|+|.||.+++..|.+.-. .....+.++..|.|.|++..-++..++.+..+.|
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 68999999988532 3467889999999999999976321 2245689999999999998756667888888876
Q ss_pred CC
Q 024592 144 II 145 (265)
Q Consensus 144 v~ 145 (265)
+.
T Consensus 1023 l~ 1024 (1107)
T PRK06920 1023 LE 1024 (1107)
T ss_pred HH
Confidence 64
No 72
>PRK12366 replication factor A; Reviewed
Probab=95.89 E-value=0.031 Score=56.14 Aligned_cols=73 Identities=23% Similarity=0.345 Sum_probs=58.4
Q ss_pred EEEEEEEEEEeeeC----------CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee-eCCccEEE
Q 024592 69 TITVVGIVCDMQDK----------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA-FQDKRSLN 137 (265)
Q Consensus 69 ~V~iVG~V~~v~~~----------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~-f~~~~~i~ 137 (265)
.|.|+|.|.++... .....+.|.|.||+|.+.+|.+.+. ..+..|+.|+|.|..+. |++...|.
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 79999999887531 2467899999999999999987652 35899999999998554 77888888
Q ss_pred EEEeeeCCC
Q 024592 138 AYSLRPIID 146 (265)
Q Consensus 138 ~~~i~~v~d 146 (265)
+.....|..
T Consensus 261 ~~~~~~i~~ 269 (637)
T PRK12366 261 ANNIEILEK 269 (637)
T ss_pred eCCceeecc
Confidence 877666654
No 73
>PLN02903 aminoacyl-tRNA ligase
Probab=95.88 E-value=0.056 Score=54.18 Aligned_cols=78 Identities=19% Similarity=0.181 Sum_probs=56.5
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeee----------CCccEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAF----------QDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i 136 (265)
..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+ ......+..++.|.|.|.|+.- .+...|
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 36999999999998887788899999999998764332111 1123578999999999999852 144566
Q ss_pred EEEEeeeCC
Q 024592 137 NAYSLRPII 145 (265)
Q Consensus 137 ~~~~i~~v~ 145 (265)
.+..+..+.
T Consensus 153 ~~~~i~VL~ 161 (652)
T PLN02903 153 VAESVDILN 161 (652)
T ss_pred EEeEEEEEe
Confidence 666655543
No 74
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=95.84 E-value=0.2 Score=39.46 Aligned_cols=81 Identities=15% Similarity=0.290 Sum_probs=57.2
Q ss_pred eeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEE----EecccccccccccccC
Q 024592 41 LLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECS----RWAHEQMEFNEVNQIS 116 (265)
Q Consensus 41 ~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~----~w~~~~~~~~~~~~~~ 116 (265)
..-.|+++-+++.. + ..|+|.|.|+..-... .|...|+||+|.+- .|.. ..+.
T Consensus 43 ~~~~TV~~Ak~~~D--d----------a~V~l~GnIv~qi~~D---~y~FrD~sGeI~VeIdd~~w~g--------~tv~ 99 (128)
T COG3111 43 AKVTTVDQAKTLHD--D----------AWVSLEGNIVRQIGDD---RYVFRDASGEINVDIDDKVWNG--------QTVT 99 (128)
T ss_pred cceeEHHHhhcccc--C----------CeEEEEeeEEEeeCCc---eEEEEcCCccEEEEecccccCC--------cccC
Confidence 44567888777632 3 6788999887754443 56889999987765 4543 3577
Q ss_pred CCCEEEEEEEeeeeCCccEEEEEEeeeC
Q 024592 117 KGMYVRVYGHLKAFQDKRSLNAYSLRPI 144 (265)
Q Consensus 117 ~g~yVrV~G~i~~f~~~~~i~~~~i~~v 144 (265)
+.+.|++.|.+..=-.+..|-+.+|+++
T Consensus 100 P~dkV~I~GevDk~~~~~eIdV~~I~k~ 127 (128)
T COG3111 100 PKDKVRIQGEVDKDWNSVEIDVKHIEKL 127 (128)
T ss_pred cccEEEEEeEEcCCCccceeEhhheEec
Confidence 8899999999976445566766666654
No 75
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=95.83 E-value=0.061 Score=53.49 Aligned_cols=76 Identities=17% Similarity=0.229 Sum_probs=55.1
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee----------CCccEEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF----------QDKRSLN 137 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i~ 137 (265)
..|+|.|||.+++.....+.+.|.|+||.|.|..-. .....+....+..++.|.|.|.+..- .+...|.
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 359999999999988888888999999999887532 11111234578999999999999862 2345565
Q ss_pred EEEeeeC
Q 024592 138 AYSLRPI 144 (265)
Q Consensus 138 ~~~i~~v 144 (265)
+..++.+
T Consensus 97 ~~~i~il 103 (588)
T PRK00476 97 ASELEVL 103 (588)
T ss_pred EeEEEEE
Confidence 5555443
No 76
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.81 E-value=0.03 Score=59.69 Aligned_cols=77 Identities=16% Similarity=0.239 Sum_probs=60.3
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
..|+++|.|.+++.. .....++|+|.||.++|..|.+.-. .....+.++..|.|.|++..-.+..++.+..+.
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 468999999988632 2357789999999999999975321 123568999999999999875567789998888
Q ss_pred eCCC
Q 024592 143 PIID 146 (265)
Q Consensus 143 ~v~d 146 (265)
++.+
T Consensus 1079 ~l~~ 1082 (1170)
T PRK07374 1079 EIDD 1082 (1170)
T ss_pred cHhh
Confidence 7754
No 77
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.79 E-value=0.033 Score=40.94 Aligned_cols=55 Identities=20% Similarity=0.217 Sum_probs=45.8
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA 262 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t 262 (265)
...|+++|... +.++++.+|++.++++...|...|..|.+.|.|.. -++..|..+
T Consensus 7 ~~~Il~~l~~~-----~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~ 62 (91)
T smart00346 7 GLAVLRALAEE-----PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLG 62 (91)
T ss_pred HHHHHHHHHhC-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeec
Confidence 34578888652 24799999999999999999999999999999998 566677654
No 78
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=95.75 E-value=0.06 Score=54.48 Aligned_cols=77 Identities=12% Similarity=0.170 Sum_probs=56.3
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeee----------CCccE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAF----------QDKRS 135 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f----------~~~~~ 135 (265)
..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+ ......+..++.|.|.|.++.- .+...
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 45999999999998888888899999999998764332111 1123578999999999998872 14456
Q ss_pred EEEEEeeeC
Q 024592 136 LNAYSLRPI 144 (265)
Q Consensus 136 i~~~~i~~v 144 (265)
|.+..+..+
T Consensus 99 l~~~~i~iL 107 (706)
T PRK12820 99 VFVRELSIL 107 (706)
T ss_pred EEeeEEEEE
Confidence 666655544
No 79
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.73 E-value=0.032 Score=36.27 Aligned_cols=45 Identities=20% Similarity=0.326 Sum_probs=39.4
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+..|+++|.+. .++++.+|++.++++...++..|..|.++|.|..
T Consensus 2 ~~~il~~l~~~------~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 2 QQQILELLAQQ------GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 45688888652 3699999999999999999999999999999986
No 80
>PLN02221 asparaginyl-tRNA synthetase
Probab=95.67 E-value=0.13 Score=51.07 Aligned_cols=94 Identities=15% Similarity=0.201 Sum_probs=62.3
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCC--eEEEEEEcCC--CeEEEEEecccccccccccccCC
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP--QFIFLIDDGT--GRIECSRWAHEQMEFNEVNQISK 117 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t--~~~y~LdDgT--G~I~~~~w~~~~~~~~~~~~~~~ 117 (265)
..++|+.|+..+.. + -...| ..|+|.|||.+++.... .+.+.|.|+| |.|.|..-.+.. .....+..
T Consensus 31 ~~~~~~~~~~~~~~-~--~~~~g---~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~---~~~~~L~~ 101 (572)
T PLN02221 31 DRVLIRSILDRPDG-G--AGLAG---QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLY---DLSTLVAT 101 (572)
T ss_pred CceEHHHHhccccC-C--hhcCC---CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchh---hHHhcCCC
Confidence 56689999855211 1 11122 46999999999998764 5677999999 899997632211 11125788
Q ss_pred CCEEEEEEEeeeeC------CccEEEEEEeeeC
Q 024592 118 GMYVRVYGHLKAFQ------DKRSLNAYSLRPI 144 (265)
Q Consensus 118 g~yVrV~G~i~~f~------~~~~i~~~~i~~v 144 (265)
++.|+|.|.|+.-. +...|.+..+..+
T Consensus 102 ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl 134 (572)
T PLN02221 102 GTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDV 134 (572)
T ss_pred ceEEEEEEEEEeCCccCCCCccEEEEEeEEEEE
Confidence 99999999998632 2345666555443
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=95.65 E-value=0.093 Score=51.18 Aligned_cols=75 Identities=13% Similarity=0.106 Sum_probs=53.2
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc--ccc-cccCCCCEEEEEEEeeeeC-CccEEEEEEeee
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF--NEV-NQISKGMYVRVYGHLKAFQ-DKRSLNAYSLRP 143 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~--~~~-~~~~~g~yVrV~G~i~~f~-~~~~i~~~~i~~ 143 (265)
.|+|.|+|.+++.......+.|.|+||.|.|..-.+...+. ... ..+..|+.|.|.|.+..-+ +...|.+..+..
T Consensus 55 ~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~i~i 133 (496)
T TIGR00499 55 EVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTELQI 133 (496)
T ss_pred EEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeEEEE
Confidence 48999999999987788888999999999987643321110 111 2379999999999987543 445565555443
No 82
>PRK06386 replication factor A; Reviewed
Probab=95.62 E-value=0.054 Score=50.55 Aligned_cols=70 Identities=16% Similarity=0.310 Sum_probs=53.6
Q ss_pred eEEEEEEEEEEeeeC--------CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEE
Q 024592 68 NTITVVGIVCDMQDK--------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNA 138 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~ 138 (265)
..|.+.|+|.++.+. ..-....|.|.||+|....|.+ .+.+|+.|+|.+- ++.|++..+|++
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 457888888876431 1245789999999999999964 3789999999886 667999999998
Q ss_pred EEeeeCCC
Q 024592 139 YSLRPIID 146 (265)
Q Consensus 139 ~~i~~v~d 146 (265)
.....|+.
T Consensus 189 ~~~t~I~~ 196 (358)
T PRK06386 189 GNKSVIKE 196 (358)
T ss_pred CCeEEEEE
Confidence 55544443
No 83
>PLN02502 lysyl-tRNA synthetase
Probab=95.62 E-value=0.099 Score=51.62 Aligned_cols=77 Identities=14% Similarity=0.130 Sum_probs=55.0
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc----ccc-cccCCCCEEEEEEEeee-eCCccEEEEEEe
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF----NEV-NQISKGMYVRVYGHLKA-FQDKRSLNAYSL 141 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~----~~~-~~~~~g~yVrV~G~i~~-f~~~~~i~~~~i 141 (265)
..|+|.|+|.+++.....+.+.|.|++|.|.|..-.+...+. ... ..+..|+.|.|.|.+.. -.+...|.+..+
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 359999999999988888889999999999987543321110 111 35889999999998764 235566666555
Q ss_pred eeC
Q 024592 142 RPI 144 (265)
Q Consensus 142 ~~v 144 (265)
..+
T Consensus 189 ~vL 191 (553)
T PLN02502 189 EVL 191 (553)
T ss_pred EEE
Confidence 443
No 84
>PRK15491 replication factor A; Provisional
Probab=95.60 E-value=0.05 Score=51.18 Aligned_cols=75 Identities=23% Similarity=0.346 Sum_probs=55.8
Q ss_pred EEEEEEEEEEeee-------CC---CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-ee--eeCCccE
Q 024592 69 TITVVGIVCDMQD-------KE---PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LK--AFQDKRS 135 (265)
Q Consensus 69 ~V~iVG~V~~v~~-------~~---t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~--~f~~~~~ 135 (265)
.|.|.|+|.++.. .. ......|.|.||.|.+..|.+.+. ..+.|++|+.|++... +| .|+++..
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 4888999988743 11 356689999999999999987542 3467999999999663 55 4667888
Q ss_pred EEEE---EeeeCCC
Q 024592 136 LNAY---SLRPIID 146 (265)
Q Consensus 136 i~~~---~i~~v~d 146 (265)
|++. .|.+..+
T Consensus 255 l~~~~~s~I~~~~~ 268 (374)
T PRK15491 255 IQIGNHGSLRKTDR 268 (374)
T ss_pred EEeCCCceEEECCc
Confidence 8863 5777655
No 85
>PRK07218 replication factor A; Provisional
Probab=95.59 E-value=0.06 Score=51.36 Aligned_cols=83 Identities=22% Similarity=0.339 Sum_probs=62.8
Q ss_pred eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeC--------CCeEEEEEEcCCCeEEEEEecccccccccccc
Q 024592 43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDK--------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQ 114 (265)
Q Consensus 43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~ 114 (265)
++.|++|.... ..|.|.|+|.++.+. ..-....|-|.||+|....|.+. .
T Consensus 58 ~~kI~Di~~~~--------------~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~--------~ 115 (423)
T PRK07218 58 SKDIKELSTDD--------------KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF--------G 115 (423)
T ss_pred CccHhhCCCCC--------------ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC--------C
Confidence 56688874321 578899999887521 24567799999999999999832 3
Q ss_pred cCCCCEEEEEE-EeeeeCCccEEEE---EEeeeCCCh
Q 024592 115 ISKGMYVRVYG-HLKAFQDKRSLNA---YSLRPIIDF 147 (265)
Q Consensus 115 ~~~g~yVrV~G-~i~~f~~~~~i~~---~~i~~v~d~ 147 (265)
+++|+.|+|.+ .++.|+++..|++ ..|..+++.
T Consensus 116 l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~ 152 (423)
T PRK07218 116 LSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDS 152 (423)
T ss_pred CCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcc
Confidence 99999999995 6899999989986 456655553
No 86
>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=95.59 E-value=0.014 Score=41.18 Aligned_cols=46 Identities=20% Similarity=0.359 Sum_probs=37.8
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID 255 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD 255 (265)
.+|.++|++. .-++..+|+++|+.+++.|+..|+.|+..|+|-.++
T Consensus 3 ~~i~~~l~~~------~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 3 QEIRDYLRER------GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHHS-------SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 3588888763 368999999999999999999999999999998833
No 87
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.54 E-value=0.046 Score=58.29 Aligned_cols=77 Identities=14% Similarity=0.256 Sum_probs=59.7
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSL 141 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i 141 (265)
..|+++|.|.+++.. .....++|+|.||.+++..|.+.-. .....+.++..|.|.|++... ++..++.+..+
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 368899999887642 2467889999999999999976321 123568999999999999864 46678999888
Q ss_pred eeCCC
Q 024592 142 RPIID 146 (265)
Q Consensus 142 ~~v~d 146 (265)
.++.+
T Consensus 1070 ~~l~~ 1074 (1151)
T PRK06826 1070 EPLVI 1074 (1151)
T ss_pred ecHhh
Confidence 87754
No 88
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=95.47 E-value=0.035 Score=45.99 Aligned_cols=51 Identities=18% Similarity=0.375 Sum_probs=45.5
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE--Ee
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV--YS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I--Ys 253 (265)
..+..+..+||++|+.+ .-++..+|++++++++..|+.-++.|.++|.| |.
T Consensus 10 ~~lD~~D~~IL~~Lq~d------~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~ 62 (164)
T PRK11169 10 KDLDRIDRNILNELQKD------GRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYT 62 (164)
T ss_pred hhHHHHHHHHHHHhccC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 34778999999999874 35789999999999999999999999999998 66
No 89
>PLN02603 asparaginyl-tRNA synthetase
Probab=95.45 E-value=0.11 Score=51.50 Aligned_cols=96 Identities=18% Similarity=0.309 Sum_probs=62.4
Q ss_pred eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCC--eEEEEEeccccccccccc--ccCC
Q 024592 42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTG--RIECSRWAHEQMEFNEVN--QISK 117 (265)
Q Consensus 42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~--~~~~ 117 (265)
..+.|++|+..+... .-.+ | ..|+|.|||++++.........|.|+|| .|.|..=.+ ........ .+..
T Consensus 88 ~~~~~~~~~~~~~~~--~~~~-g---~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~-~~~~~~l~~~~l~~ 160 (565)
T PLN02603 88 KKLRIADVKGGEDEG--LARV-G---KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPD-AEGYDQVESGLITT 160 (565)
T ss_pred CceEhhhcccccccc--cccC-C---CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECc-HHHHHHHhhcCCCC
Confidence 456788887431110 1111 2 4699999999999888888889999997 488876322 11111122 3889
Q ss_pred CCEEEEEEEeeeeCCc---cEEEEEEeeeC
Q 024592 118 GMYVRVYGHLKAFQDK---RSLNAYSLRPI 144 (265)
Q Consensus 118 g~yVrV~G~i~~f~~~---~~i~~~~i~~v 144 (265)
|+.|.|.|.++.-.+. ..|.+..+..+
T Consensus 161 gs~V~V~G~v~~~~~~~~~~EL~v~~i~vl 190 (565)
T PLN02603 161 GASVLVQGTVVSSQGGKQKVELKVSKIVVV 190 (565)
T ss_pred CCEEEEEEEEEecCCCCccEEEEEeEEEEE
Confidence 9999999999864332 46666665443
No 90
>PRK12366 replication factor A; Reviewed
Probab=95.44 E-value=0.11 Score=52.20 Aligned_cols=66 Identities=24% Similarity=0.317 Sum_probs=50.9
Q ss_pred eEEEEEEEEEEeeeCC----------CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEE
Q 024592 68 NTITVVGIVCDMQDKE----------PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~----------t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i 136 (265)
..|.|+|+|.++.+.. ..-...|.|.||+|.+.+|.+.+. ..+.+|+.|++.+- ++.|+|...|
T Consensus 409 ~~VdVig~V~~v~~~~~i~~k~G~~~~~r~i~l~D~TG~I~vtlWg~~a~-----~~~~~G~vi~i~~~~V~~~~g~~~L 483 (637)
T PRK12366 409 NDITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDAE-----IEIKEGDAIKILHPYVKENGDYLDL 483 (637)
T ss_pred cEEEEEEEEEEccCceEEEecCCCEeEEEEEEEEeCCCEEEEEEeccccc-----cCCCCCCEEEEEeeEEEeCCCeeEE
Confidence 5788999998764321 245678999999999999987542 25788999998764 7789988777
Q ss_pred EE
Q 024592 137 NA 138 (265)
Q Consensus 137 ~~ 138 (265)
++
T Consensus 484 s~ 485 (637)
T PRK12366 484 SI 485 (637)
T ss_pred Ee
Confidence 76
No 91
>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=95.43 E-value=0.046 Score=36.43 Aligned_cols=42 Identities=12% Similarity=0.294 Sum_probs=34.8
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENS 249 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG 249 (265)
+.+|+.+|.+. +..++.++|++.|+++...|+..|..|.+.|
T Consensus 2 ~~~il~~L~~~-----~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLES-----KEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHT-----TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHc-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 45688888542 2349999999999999999999999999999
No 92
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.43 E-value=0.046 Score=40.34 Aligned_cols=62 Identities=11% Similarity=0.109 Sum_probs=50.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeeccC
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAVN 264 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~~ 264 (265)
.+++..+-.||.+|... .+++..+|++.++++...|..+|..|.+.|.|+. -+.. +|+.|..
T Consensus 6 ~~l~~~~~~il~~l~~~------~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~ 73 (101)
T smart00347 6 LGLTPTQFLVLRILYEE------GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEE 73 (101)
T ss_pred cCCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHh
Confidence 35777888899999763 2689999999999999999999999999999998 5532 5655543
No 93
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=95.41 E-value=0.079 Score=53.66 Aligned_cols=66 Identities=23% Similarity=0.310 Sum_probs=50.8
Q ss_pred eEEEEEEEEEEeeeC---CCeEEEEEEcCCCeEEEEEec-ccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592 68 NTITVVGIVCDMQDK---EPQFIFLIDDGTGRIECSRWA-HEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~---~t~~~y~LdDgTG~I~~~~w~-~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i 136 (265)
..|+++|.|.++... ...+.+.+.|+||.|.+++|. +.. -....+++|..+.|+|+++.+++++++
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 478999999887533 357899999999999998773 221 123578999999999999998766554
No 94
>PLN02850 aspartate-tRNA ligase
Probab=95.36 E-value=0.13 Score=50.60 Aligned_cols=77 Identities=13% Similarity=0.200 Sum_probs=56.2
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc----ccccccCCCCEEEEEEEeeee-------CCccEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF----NEVNQISKGMYVRVYGHLKAF-------QDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~----~~~~~~~~g~yVrV~G~i~~f-------~~~~~i 136 (265)
..|+|.|+|.+++..+..+.+.|.|++|.|.|..-.....-+ +....|..|+.|.|.|.|+.- .+...|
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 469999999999988887888999999999998754422101 124578999999999999842 123556
Q ss_pred EEEEeeeC
Q 024592 137 NAYSLRPI 144 (265)
Q Consensus 137 ~~~~i~~v 144 (265)
.+..|..+
T Consensus 162 ~~~~i~vl 169 (530)
T PLN02850 162 QVRKIYCV 169 (530)
T ss_pred EEeEEEEE
Confidence 66665544
No 95
>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=95.34 E-value=0.073 Score=36.82 Aligned_cols=52 Identities=13% Similarity=0.196 Sum_probs=38.6
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI 254 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi 254 (265)
+-..|.+.|.... ....+=+ +..+|+++++.+...|++||..|.++|.|+..
T Consensus 5 i~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 5 IYDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 3455666666542 2334567 89999999999999999999999999999873
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.34 E-value=0.039 Score=42.06 Aligned_cols=47 Identities=15% Similarity=0.342 Sum_probs=42.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++++.+|+..|+.. ..++..+|++.+++++..++..+..|.++|.|.
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 46788999999873 368999999999999999999999999999987
No 97
>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=95.33 E-value=0.13 Score=34.95 Aligned_cols=39 Identities=18% Similarity=0.152 Sum_probs=33.5
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592 223 HRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS 261 (265)
Q Consensus 223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~ 261 (265)
+..+|++.++++.+.|+++|..|.++|.|......+|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~~~~~~l 65 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEe
Confidence 499999999999999999999999999987654445543
No 98
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.13 E-value=0.063 Score=56.52 Aligned_cols=75 Identities=5% Similarity=0.177 Sum_probs=57.2
Q ss_pred EEEEEEEEEEee----e--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 69 TITVVGIVCDMQ----D--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 69 ~V~iVG~V~~v~----~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
.+.++|+|.++. . ......++|+|.||.|+|..|.+.-. .....+.++..|.|.|++..-++..++.+..+.
T Consensus 886 ~~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~l~~~~i~ 963 (1034)
T PRK07279 886 EATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPETYR--QYKDELKEGKFYYLKGKIQERDGRLQMVLQQIQ 963 (1034)
T ss_pred cceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeeEEEEeeee
Confidence 356777776653 2 23468889999999999999976321 224568999999999999876677889998888
Q ss_pred eCC
Q 024592 143 PII 145 (265)
Q Consensus 143 ~v~ 145 (265)
++.
T Consensus 964 ~l~ 966 (1034)
T PRK07279 964 EAS 966 (1034)
T ss_pred ccc
Confidence 875
No 99
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=95.13 E-value=0.17 Score=49.88 Aligned_cols=77 Identities=13% Similarity=0.210 Sum_probs=56.1
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc---cccccccCCCCEEEEEEEeeee--------CCccEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME---FNEVNQISKGMYVRVYGHLKAF--------QDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~g~yVrV~G~i~~f--------~~~~~i 136 (265)
..|+|.|+|.+++.....+.+.|.|++|.|.|..-.....+ .+....|..++.|.|.|.|+.- .+...|
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 45999999999998888888899999999999874332111 1123568999999999998862 233556
Q ss_pred EEEEeeeC
Q 024592 137 NAYSLRPI 144 (265)
Q Consensus 137 ~~~~i~~v 144 (265)
.+..+..+
T Consensus 159 ~v~~i~vl 166 (550)
T PTZ00401 159 KVKKIHTV 166 (550)
T ss_pred EeeEEEEE
Confidence 66555443
No 100
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.10 E-value=0.06 Score=42.79 Aligned_cols=52 Identities=21% Similarity=0.191 Sum_probs=45.3
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-+++.+.-.||..|-+. +.++++++|++.|+.+.+.|..+|+.|++-|.|+-
T Consensus 23 ~GLs~~Dv~v~~~LL~~-----~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 23 YGLSELDVEVYKALLEE-----NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred hCCcHHHHHHHHHHHhh-----cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 36888888888877532 45889999999999999999999999999999987
No 101
>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=95.05 E-value=0.7 Score=35.17 Aligned_cols=64 Identities=17% Similarity=0.239 Sum_probs=45.4
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
+.|+|||+|.+++.. .+++.+.-| .++|+.-.+ .....+.||.|+|++.. ...|.+......-|
T Consensus 16 k~V~ivGkV~~~~~~----~~~~~~~Dg~~v~v~l~~~--------~~~~~~~~vEViG~V~~---~~~I~~~~~~~~g~ 80 (101)
T cd04479 16 KTVRIVGKVEKVDGD----SLTLISSDGVNVTVELNRP--------LDLPISGYVEVIGKVSP---DLTIRVLSYIDFGD 80 (101)
T ss_pred CEEEEEEEEEEecCC----eEEEEcCCCCEEEEEeCCC--------CCcccCCEEEEEEEECC---CCeEEEEEEEECCC
Confidence 689999999998643 355555554 788875432 24577899999999974 46677766665544
No 102
>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=95.01 E-value=0.1 Score=33.84 Aligned_cols=46 Identities=20% Similarity=0.285 Sum_probs=39.3
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.+|+.+|.+. -.++.+|++.++++.+.|..-|..|.+.|.|.+
T Consensus 2 ~~R~~Il~~L~~~-------~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 2 PTRLRILKLLSEG-------PLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHHTTS-------SEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHhC-------CCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 4677889888752 478999999999999999999999999999864
No 103
>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=94.98 E-value=0.056 Score=37.38 Aligned_cols=59 Identities=17% Similarity=0.255 Sum_probs=43.6
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC-----Cceeecc
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE-----FHYKSAV 263 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd-----~hyk~t~ 263 (265)
+.-+-.||.+|.. ....++..+|++.++++...+..+|+.|.+.|.|.. -|+ .+|..|.
T Consensus 2 t~~q~~vL~~l~~-----~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~ 66 (68)
T PF13463_consen 2 TRPQWQVLRALAH-----SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTP 66 (68)
T ss_dssp -HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-H
T ss_pred CHHHHHHHHHHHc-----cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCC
Confidence 4456778998872 246889999999999999999999999999999977 554 3566654
No 104
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.91 E-value=0.1 Score=49.51 Aligned_cols=75 Identities=23% Similarity=0.263 Sum_probs=58.2
Q ss_pred EEeEEEEEEEEEEe--eeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592 66 DVNTITVVGIVCDM--QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 66 ~v~~V~iVG~V~~v--~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~ 143 (265)
+.+..+++|+|... ......+.+.+.|++|.|.|..+............|..|+.|.++|.++... |++.+++.
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 34678999988774 3456789999999999999999976554334467899999999999999865 66655554
Q ss_pred C
Q 024592 144 I 144 (265)
Q Consensus 144 v 144 (265)
+
T Consensus 341 ~ 341 (421)
T COG1571 341 L 341 (421)
T ss_pred E
Confidence 3
No 105
>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=94.80 E-value=0.22 Score=37.53 Aligned_cols=64 Identities=19% Similarity=0.337 Sum_probs=43.2
Q ss_pred EEEEEEEEEeee-----------CCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccEE
Q 024592 70 ITVVGIVCDMQD-----------KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRSL 136 (265)
Q Consensus 70 V~iVG~V~~v~~-----------~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~i 136 (265)
|-|+|.|.++.. ......+.|.|.|| .|.|.+|.+.+.. ...+.|+.|.+.+ +++.|+ .+.+
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 567888876632 12578899999999 8999999875431 1112277777666 466787 4566
Q ss_pred EE
Q 024592 137 NA 138 (265)
Q Consensus 137 ~~ 138 (265)
+.
T Consensus 77 ~~ 78 (101)
T cd04475 77 ST 78 (101)
T ss_pred ee
Confidence 55
No 106
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.75 E-value=0.19 Score=33.42 Aligned_cols=39 Identities=21% Similarity=0.229 Sum_probs=33.4
Q ss_pred CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCc
Q 024592 220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH 258 (265)
Q Consensus 220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~h 258 (265)
.-+ +..+|++.++++...|+++|..|.++|.|.......
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence 356 899999999999999999999999999987644333
No 107
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.72 E-value=0.07 Score=56.07 Aligned_cols=78 Identities=17% Similarity=0.322 Sum_probs=60.6
Q ss_pred eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEEE
Q 024592 68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAYS 140 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~~ 140 (265)
..|.|.|.|-.++.. .+-+.|.+-|+|-++.|+.|..+..+.+....++.|++|||.|.|.. |....++.+..
T Consensus 240 ~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g~v~~d~f~~~l~m~i~~ 319 (1444)
T COG2176 240 TRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVKARGNVQLDTFTRDLTMIIND 319 (1444)
T ss_pred cceEEEEEEEEEeeeecccCcEEEEEEEecCchheeehhhccccccHHHHhhcccCcEEEEEEEEEecccccceEEEhhh
Confidence 459999999887643 24688999999999999999987666667788999999999999975 45555555555
Q ss_pred eeeCC
Q 024592 141 LRPII 145 (265)
Q Consensus 141 i~~v~ 145 (265)
|.+|.
T Consensus 320 I~ei~ 324 (1444)
T COG2176 320 INEIE 324 (1444)
T ss_pred hhhhh
Confidence 54443
No 108
>PRK15491 replication factor A; Provisional
Probab=94.68 E-value=0.18 Score=47.42 Aligned_cols=77 Identities=14% Similarity=0.193 Sum_probs=55.0
Q ss_pred eEEEEEEEEEEeee--------C--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee-eeCCccEE
Q 024592 68 NTITVVGIVCDMQD--------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK-AFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~--------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~-~f~~~~~i 136 (265)
..|+|.|+|.++.. . .....+.|-|.||+|.+..|.+.... -....|++|+.|+|.|..+ .|++ ..|
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 56889999987631 1 23455699999999999999865421 1124689999999999988 4555 677
Q ss_pred EEE---EeeeCCC
Q 024592 137 NAY---SLRPIID 146 (265)
Q Consensus 137 ~~~---~i~~v~d 146 (265)
++. .+.+.++
T Consensus 146 ~i~~~~~i~~~~~ 158 (374)
T PRK15491 146 NIGRYGGISESDE 158 (374)
T ss_pred EeCCCceeeeccc
Confidence 775 4555544
No 109
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=94.67 E-value=0.068 Score=43.20 Aligned_cols=49 Identities=14% Similarity=0.362 Sum_probs=44.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
.+..+..+||++|+..+ -++..+|++++++++..+...++.|.++|.|-
T Consensus 5 ~lD~~D~~IL~~L~~d~------r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 5 KLDDIDRRILRLLQEDA------RISNAELAERVGLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cccHHHHHHHHHHHHhC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcee
Confidence 47789999999999853 38999999999999999999999999999773
No 110
>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=94.65 E-value=0.23 Score=37.93 Aligned_cols=67 Identities=24% Similarity=0.449 Sum_probs=42.6
Q ss_pred EEEEEEEeee---------CCCeEEEEEEcCCC-eEEEEEeccccccccccc--ccCCCCEEEE--EEEeeeeCCccEEE
Q 024592 72 VVGIVCDMQD---------KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVN--QISKGMYVRV--YGHLKAFQDKRSLN 137 (265)
Q Consensus 72 iVG~V~~v~~---------~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~--~~~~g~yVrV--~G~i~~f~~~~~i~ 137 (265)
++|.|.++.. ......|+|.|.+| +|+|..|-+.+.+-.... ....+-.|-| ..+|+.|+|.+.+.
T Consensus 2 viG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls 81 (106)
T cd04481 2 VIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLS 81 (106)
T ss_pred eeEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEE
Confidence 4566655532 34589999999998 699999976443211110 2344555544 36899999876664
Q ss_pred E
Q 024592 138 A 138 (265)
Q Consensus 138 ~ 138 (265)
-
T Consensus 82 ~ 82 (106)
T cd04481 82 N 82 (106)
T ss_pred c
Confidence 3
No 111
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.64 E-value=0.072 Score=43.54 Aligned_cols=50 Identities=10% Similarity=0.210 Sum_probs=44.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE--Ee
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV--YS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I--Ys 253 (265)
.+..+..+||++|+.+ .=.+..+|++++++++..|+.-++.|.++|.| |.
T Consensus 6 ~lD~~D~~Il~~Lq~d------~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~ 57 (153)
T PRK11179 6 QIDNLDRGILEALMEN------ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTR 57 (153)
T ss_pred ccCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEE
Confidence 4678999999999874 24699999999999999999999999999999 65
No 112
>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=94.60 E-value=0.65 Score=35.73 Aligned_cols=70 Identities=21% Similarity=0.270 Sum_probs=40.0
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
..|+|||+|.++...+..++..-.|+ |.|.|..-.+ ..+..+.||.|+|++..-.+-..|....+.+..|
T Consensus 19 k~VrivGkv~~~~~~g~~~~l~~~d~-~~V~v~l~~~--------~~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~ 88 (109)
T PF08661_consen 19 KTVRIVGKVESVDPDGGSATLSTSDG-GQVTVSLNPP--------SDEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGD 88 (109)
T ss_dssp SEEEEEEEEEEE-TTSSEEEEE-TTS--EEEEEESS----------SS---SEEEEEEEE-TTS-EEEEEEEE---SSS
T ss_pred CeEEEEEEEeeEcCCCCEEEEEcCCC-CEEEEEeCCC--------CCCCCCCEEEEEEEEcCCCCceEEEEEEeccCCC
Confidence 58999999999985555444433343 3566654422 2345689999999998765545777777777665
No 113
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=94.58 E-value=0.24 Score=49.60 Aligned_cols=74 Identities=19% Similarity=0.248 Sum_probs=58.1
Q ss_pred eEEEEEEEEEEeeeC----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592 68 NTITVVGIVCDMQDK----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~ 143 (265)
..|+++|.|.++... .....+.+.|+||.|.+++|.-... -...+++|.-|.|+|+++.|++..++.--.+..
T Consensus 61 ~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~~---l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~ 137 (677)
T COG1200 61 EIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPAY---LKKKLKVGERVIVYGKVKRFKGGLQITHPEYIV 137 (677)
T ss_pred ceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccHH---HHhhCCCCCEEEEEEEEeeccCceEEEcceEEe
Confidence 578999999887644 3678999999999999998865421 346789999999999999999877666544444
Q ss_pred C
Q 024592 144 I 144 (265)
Q Consensus 144 v 144 (265)
.
T Consensus 138 ~ 138 (677)
T COG1200 138 N 138 (677)
T ss_pred c
Confidence 3
No 114
>PRK06386 replication factor A; Reviewed
Probab=94.55 E-value=0.23 Score=46.39 Aligned_cols=65 Identities=14% Similarity=0.250 Sum_probs=50.4
Q ss_pred eEEEEEEEEEEeee------C--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEE
Q 024592 68 NTITVVGIVCDMQD------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNA 138 (265)
Q Consensus 68 ~~V~iVG~V~~v~~------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~ 138 (265)
..|.|.|+|.++.. . .....=.|-|.||+|....|.. .+.+++|+.|++..- ++.|+|+..|++
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 QNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEF-------PDAVKSGDVIEIKYCYSKEYNGKIRIYF 85 (358)
T ss_pred CcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCC-------cccCCCCCEEEEEeEEEeeECCEEEEEE
Confidence 46788888876642 1 2344447999999999999973 246899999999876 679999988888
Q ss_pred E
Q 024592 139 Y 139 (265)
Q Consensus 139 ~ 139 (265)
.
T Consensus 86 ~ 86 (358)
T PRK06386 86 D 86 (358)
T ss_pred c
Confidence 4
No 115
>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=94.52 E-value=0.51 Score=38.28 Aligned_cols=71 Identities=14% Similarity=0.237 Sum_probs=55.0
Q ss_pred eEEEEEEEEEEeeeC--------CCeEEEEEEcCCC--------eEEEEEecccccccccccccCC-CCEEEEE-EEeee
Q 024592 68 NTITVVGIVCDMQDK--------EPQFIFLIDDGTG--------RIECSRWAHEQMEFNEVNQISK-GMYVRVY-GHLKA 129 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG--------~I~~~~w~~~~~~~~~~~~~~~-g~yVrV~-G~i~~ 129 (265)
..|.|+|+|++...- .-.++++|-|.|- .|.|.+|.+..+ ..+.+.. ||.|++. -+|+.
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 KFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKE---SLPNVKSVGDIIRLRRVKVQS 89 (146)
T ss_dssp EEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHH---HSCTTCSTTHEEEEEEEEEEE
T ss_pred CEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHH---HCCCCCCCCCEEEEEEEEEEE
Confidence 678999999887532 2268899999883 599999976542 4677777 9999998 78999
Q ss_pred eCCccEEEEEEe
Q 024592 130 FQDKRSLNAYSL 141 (265)
Q Consensus 130 f~~~~~i~~~~i 141 (265)
|+++.++....-
T Consensus 90 ~~~~~~~~~~~~ 101 (146)
T PF02765_consen 90 YNGKPQGLSNST 101 (146)
T ss_dssp ETTEEEEEEECE
T ss_pred ECCEEEEEecCC
Confidence 999988766433
No 116
>PRK08402 replication factor A; Reviewed
Probab=94.45 E-value=0.14 Score=47.86 Aligned_cols=75 Identities=23% Similarity=0.250 Sum_probs=53.9
Q ss_pred eEEEEEEcCCCeEEEEEecccccc-----------c-c---c----ccc-----------cCCCCEEEEEEEee--eeCC
Q 024592 85 QFIFLIDDGTGRIECSRWAHEQME-----------F-N---E----VNQ-----------ISKGMYVRVYGHLK--AFQD 132 (265)
Q Consensus 85 ~~~y~LdDgTG~I~~~~w~~~~~~-----------~-~---~----~~~-----------~~~g~yVrV~G~i~--~f~~ 132 (265)
.+.+.|+|+||.+.|..|.+.... . . + .+. -..|.+..+.|+++ .|++
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 467789999999999999764321 0 0 0 011 23489999999998 4777
Q ss_pred ccEEEEEEeeeCCChhHHHHHHHHHHHHH
Q 024592 133 KRSLNAYSLRPIIDFNEITSHFVECIYVQ 161 (265)
Q Consensus 133 ~~~i~~~~i~~v~d~Nei~~H~Levi~~~ 161 (265)
.. +.+..+.|| |+....-|+++-|...
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 55 888889888 6777778888877543
No 117
>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=94.44 E-value=0.67 Score=37.00 Aligned_cols=65 Identities=23% Similarity=0.278 Sum_probs=44.6
Q ss_pred eEEEEEEEEE--Eeee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEe
Q 024592 68 NTITVVGIVC--DMQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSL 141 (265)
Q Consensus 68 ~~V~iVG~V~--~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i 141 (265)
..|++-|.|. +++. ....++|.|.|+...|.|.+--. .++.|++|.-|-|.|++. ....+.|..|
T Consensus 51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~------~Pd~F~eg~~VVv~G~~~---~~g~F~A~~l 119 (131)
T PF03100_consen 51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGP------LPDLFREGQGVVVEGRLG---EDGVFEATEL 119 (131)
T ss_dssp SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--------CTT--TTSEEEEEEEEC---CTSEEEEEEE
T ss_pred ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCC------CCccccCCCeEEEEEEEC---CCCEEEEEEE
Confidence 6788899998 5655 46899999999988898886532 467899999999999882 2334555443
No 118
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=94.40 E-value=0.33 Score=48.84 Aligned_cols=77 Identities=14% Similarity=0.152 Sum_probs=56.8
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccc-cc--ccc-ccccCCCCEEEEEEEeeee-CCccEEEEEEeee
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQ-ME--FNE-VNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRP 143 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~-~~--~~~-~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~ 143 (265)
.|+|.|+|.+++..+.-+.+.|.|.||.|.|..-.++. .+ ... ...+..|+.|.|.|.+..- .+...|.+..+..
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 49999999999988877888999999999998865431 11 111 2358899999999988764 4666776666554
Q ss_pred CC
Q 024592 144 II 145 (265)
Q Consensus 144 v~ 145 (265)
++
T Consensus 189 Ls 190 (659)
T PTZ00385 189 LS 190 (659)
T ss_pred ec
Confidence 43
No 119
>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=94.39 E-value=0.11 Score=34.93 Aligned_cols=52 Identities=13% Similarity=0.271 Sum_probs=43.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
+..+-.||.+|.+. .|++..+|++.++++...+...++.|...|.|.. .|.+
T Consensus 2 t~~q~~iL~~l~~~------~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 2 TPSQFRILRILYEN------GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp THHHHHHHHHHHHH------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CHHHHHHHHHHHHc------CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 34566788888764 4799999999999999999999999999999998 6654
No 120
>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=94.36 E-value=0.19 Score=34.59 Aligned_cols=55 Identities=20% Similarity=0.260 Sum_probs=44.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC--Cceeec
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE--FHYKSA 262 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd--~hyk~t 262 (265)
..+..|+.++... +++..+|++.++++...++.+|+.|.+.|.|.. -+. .+|..|
T Consensus 7 ~~~~~il~~l~~~-------~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 7 PTRLRILRLLLEG-------PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT 64 (78)
T ss_pred hHHHHHHHHHHHC-------CcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeC
Confidence 5677888887652 289999999999999999999999999999998 544 344444
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=94.30 E-value=0.1 Score=35.73 Aligned_cols=48 Identities=17% Similarity=0.268 Sum_probs=41.1
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++....||..|.. ..++++.+|++.++++...+..-|..|.+.|.|=.
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 3678889999933 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=94.25 E-value=0.28 Score=33.56 Aligned_cols=44 Identities=20% Similarity=0.299 Sum_probs=38.1
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA 262 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t 262 (265)
...++..+|++.++++...|..+|..|.++|.|......+|..+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~ 66 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVN 66 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 45689999999999999999999999999999988445577654
No 123
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=94.23 E-value=0.28 Score=49.28 Aligned_cols=65 Identities=23% Similarity=0.258 Sum_probs=48.5
Q ss_pred eEEEEEEEEEEeee----CCCeEEEEEEc-CCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592 68 NTITVVGIVCDMQD----KEPQFIFLIDD-GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~----~~t~~~y~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i 136 (265)
..|++.|.|.+... ....+.+.+.| +||.|.+++|.. . -....++.|+.|.|+|+++.++++.++
T Consensus 33 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~-~---~~~~~~~~g~~~~~~Gk~~~~~~~~~~ 102 (630)
T TIGR00643 33 ERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNR-A---FLKKKFKVGSKVVVYGKVKSSKFKAYL 102 (630)
T ss_pred CEEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECC-H---HHHhhCCCCCEEEEEEEEEeeCCEEEE
Confidence 35777888776432 12468999999 999999998852 1 123578999999999999998876543
No 124
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=94.13 E-value=0.1 Score=37.67 Aligned_cols=55 Identities=24% Similarity=0.323 Sum_probs=40.3
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
.+--+||++++ +.+.++.+|+..++++...+.+.|++|.+.|.| .-++..|..|.
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 34455666664 347889999999999999999999999999999 64677898885
No 125
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=93.95 E-value=0.17 Score=50.25 Aligned_cols=61 Identities=16% Similarity=0.213 Sum_probs=44.7
Q ss_pred eEEEEEEEEEEeeeCCC--eEEEEEEcCCC--eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 68 NTITVVGIVCDMQDKEP--QFIFLIDDGTG--RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t--~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
..|+|.|||.+++.... .+...|.|||| .|.|..- ...........+..|+-|+|.|.+..
T Consensus 82 ~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~-~~~~~~~~l~~l~~gs~v~v~G~v~~ 146 (586)
T PTZ00425 82 QIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIENYEKLLKCGVGCCFRFTGKLII 146 (586)
T ss_pred CEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEEC-CchHHHHHHhcCCCccEEEEEEEEEc
Confidence 46999999999998663 67779999998 4777542 21111112346889999999999975
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=93.79 E-value=0.27 Score=35.69 Aligned_cols=64 Identities=25% Similarity=0.215 Sum_probs=41.7
Q ss_pred EEEEEEEeeeCCCeEEEEEEcCCCe-----EEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEE
Q 024592 72 VVGIVCDMQDKEPQFIFLIDDGTGR-----IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYS 140 (265)
Q Consensus 72 iVG~V~~v~~~~t~~~y~LdDgTG~-----I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~ 140 (265)
+-|+|..+......--|-|.|.++- -+.++-... . ...+++|+.|+|.|++.+|++..+|....
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 4578887766543445668886432 112111111 1 46789999999999999999988877643
No 127
>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=93.69 E-value=0.097 Score=44.50 Aligned_cols=55 Identities=18% Similarity=0.146 Sum_probs=45.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCC-HHHHHHHHHHHhhCCeEEe
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLP-MDKLMEALESLNENSLVYS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~-~~~v~~al~~L~~eG~IYs 253 (265)
+|++.|.+||++|++... ......++.+|++.++++ ...|...|+.|...|.|-.
T Consensus 3 ~lt~~q~~iL~~l~~~~~-~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~ 58 (199)
T TIGR00498 3 PLTARQQEVLDLIRAHIE-STGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIER 58 (199)
T ss_pred ccCHHHHHHHHHHHHHHH-hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEec
Confidence 478899999999985411 223457888999999998 9999999999999999977
No 128
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=93.69 E-value=0.18 Score=44.89 Aligned_cols=54 Identities=22% Similarity=0.318 Sum_probs=46.3
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA 262 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t 262 (265)
-.||++|.+. +.+++..||++.++++.+.+...|..|.++|.|.. -++..|..+
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 3477888642 34699999999999999999999999999999999 778888765
No 129
>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=93.64 E-value=0.19 Score=38.33 Aligned_cols=62 Identities=18% Similarity=0.176 Sum_probs=43.2
Q ss_pred eEEEEEEEEEEeee---------CCCeEEEEEEcC-CCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeC
Q 024592 68 NTITVVGIVCDMQD---------KEPQFIFLIDDG-TGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQ 131 (265)
Q Consensus 68 ~~V~iVG~V~~v~~---------~~t~~~y~LdDg-TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~ 131 (265)
..++|+|+|..+.+ ....+.+.|-|. +|.|.|.+|.+... ...+.|++|+.+.+.+ +|+..+
T Consensus 10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~--~f~~~l~eG~vy~i~~~~V~~a~ 82 (104)
T cd04474 10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVD--KFYDLLEVGKVYYISKGSVKVAN 82 (104)
T ss_pred CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHH--HhhcccccccEEEEeccEEeecc
Confidence 46788888876421 134578999999 89999999986432 2346789998777764 455443
No 130
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=93.57 E-value=0.55 Score=50.13 Aligned_cols=73 Identities=19% Similarity=0.130 Sum_probs=52.8
Q ss_pred EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592 69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSL 141 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i 141 (265)
.|+|.|+|.+++.......+.|.|+||.|.|..=.+...+. .....+..|+.|.|.|.+..- .+...|.+..+
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 59999999999998888888999999999997643321110 012357899999999998643 34455555444
No 131
>PRK12423 LexA repressor; Provisional
Probab=93.49 E-value=0.094 Score=44.95 Aligned_cols=52 Identities=17% Similarity=0.211 Sum_probs=44.4
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCc--CHHHHHHhcC-CCHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGV--HRNVISQQLN-LPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv--~~~~I~~~l~-~~~~~v~~al~~L~~eG~IYs 253 (265)
|++-|++||++|++. -.+.|+ ++.||++.|+ .+...|+++|+.|...|+|-.
T Consensus 4 lt~~q~~il~~l~~~---i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 4 LTPKRAAILAFIRER---IAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV 58 (202)
T ss_pred CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 678899999999864 224455 9999999999 589999999999999999976
No 132
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=93.45 E-value=0.26 Score=31.34 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=34.6
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS 261 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~ 261 (265)
..++..+|++.++++...+.++|..|.++|.|.... .+|..
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~~i 47 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRIVI 47 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEEEE
Confidence 357899999999999999999999999999997632 45543
No 133
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=93.33 E-value=0.98 Score=36.97 Aligned_cols=55 Identities=18% Similarity=0.235 Sum_probs=43.6
Q ss_pred eEEEEEEEEEE--eee-CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592 68 NTITVVGIVCD--MQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK 128 (265)
Q Consensus 68 ~~V~iVG~V~~--v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~ 128 (265)
..|++-|.|.. +.. ....+.|.|.|+...|.|.+--. .++.|++|.-|-|.|++.
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 57888888864 444 56789999999988888876432 367799999999999985
No 134
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=93.21 E-value=0.24 Score=44.32 Aligned_cols=54 Identities=20% Similarity=0.348 Sum_probs=45.6
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA 262 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t 262 (265)
-.||++|... +.++++.||++.++++.+.+...|..|++.|.|+. -+...|...
T Consensus 28 l~IL~~~~~~-----~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG 82 (271)
T PRK10163 28 IAILQYLEKS-----GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG 82 (271)
T ss_pred HHHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence 3478888642 45799999999999999999999999999999998 667778643
No 135
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.18 E-value=0.29 Score=39.34 Aligned_cols=53 Identities=15% Similarity=0.111 Sum_probs=46.8
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
+++..|-.||..|.. +.|++..+|++.++++...|-.+|+.|+..|.|+. .|.
T Consensus 37 glt~~q~~vL~~l~~------~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~ 90 (144)
T PRK11512 37 DITAAQFKVLCSIRC------AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP 90 (144)
T ss_pred CCCHHHHHHHHHHHH------cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence 577788889998854 34899999999999999999999999999999998 664
No 136
>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=93.07 E-value=0.38 Score=41.15 Aligned_cols=63 Identities=16% Similarity=0.151 Sum_probs=52.4
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-e-cCCceeeccCC
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-I-DEFHYKSAVNA 265 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-i-Dd~hyk~t~~~ 265 (265)
..++..+..||.+|.+. .++++.+|++.++++.+.+...|..|.+.|.|.. - ....|+.|.-|
T Consensus 139 ~~ls~~~~~IL~~l~~~------g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 139 AGLSREELKVLEVLKAE------GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred cCCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 35677888999999753 3689999999999999999999999999999999 4 45567777543
No 137
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=92.86 E-value=0.74 Score=38.99 Aligned_cols=78 Identities=18% Similarity=0.209 Sum_probs=48.2
Q ss_pred EeEEEEEEEEEE-ee--e---CCCeEEEEEE--------c-----CCCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592 67 VNTITVVGIVCD-MQ--D---KEPQFIFLID--------D-----GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL 127 (265)
Q Consensus 67 v~~V~iVG~V~~-v~--~---~~t~~~y~Ld--------D-----gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i 127 (265)
++.|.|+|+|.. .+ . ....+.|+|. | .|--|.|..|...++ .....|+.|+.|-|.|+|
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 467888888854 11 1 2235566662 2 244588999975432 123568999999999999
Q ss_pred ee--eCCc-------cEEEEEEeeeCCC
Q 024592 128 KA--FQDK-------RSLNAYSLRPIID 146 (265)
Q Consensus 128 ~~--f~~~-------~~i~~~~i~~v~d 146 (265)
+. |.++ ..|.+..|..+..
T Consensus 80 ~~~~y~dkdG~~r~~~eI~a~~v~~L~~ 107 (182)
T PRK08486 80 TFESWMDQNGQKRSKHTITAESMQMLDS 107 (182)
T ss_pred EeCcEECCCCcEEEEEEEEEeEEEECCC
Confidence 74 6433 3455555655543
No 138
>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=92.85 E-value=0.22 Score=31.76 Aligned_cols=41 Identities=15% Similarity=0.310 Sum_probs=32.7
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
..+..+|++.|+.. .-.+..+|++.+++++..|..-+..|.
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 46888999999874 357999999999999999999998873
No 139
>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=92.85 E-value=0.32 Score=35.42 Aligned_cols=49 Identities=22% Similarity=0.328 Sum_probs=37.5
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..-.+|-+|... ..+.-++.++|+++++.++..+++.++.|...|.|-+
T Consensus 9 ~Al~~l~~la~~---~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s 57 (83)
T PF02082_consen 9 YALRILLYLARH---PDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES 57 (83)
T ss_dssp HHHHHHHHHHCT---TTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhC---CCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence 334556666553 2222399999999999999999999999999999977
No 140
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=92.81 E-value=0.28 Score=41.40 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=45.7
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF 257 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~ 257 (265)
+...+|+++|+.. ..+++..+|+++|++.-.+|+..|-.|..+|.||.+|+.
T Consensus 4 ~~~~~i~~~l~~~-----~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~~ 55 (183)
T PHA02701 4 DCASLILTLLSSS-----GDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDGC 55 (183)
T ss_pred hHHHHHHHHHHhc-----CCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCCC
Confidence 4678899999974 335999999999999999999999999999999987664
No 141
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.73 E-value=0.28 Score=38.87 Aligned_cols=48 Identities=8% Similarity=0.205 Sum_probs=43.8
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..|+.+|++++|+.+ =+++.++...++.+...++..+.+|+..|+||-
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 468999999999853 479999999999999999999999999999996
No 142
>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=92.70 E-value=0.24 Score=29.76 Aligned_cols=30 Identities=23% Similarity=0.407 Sum_probs=26.0
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
++.+||++.++.+.+.|-.+|..|..+|.|
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 143
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.64 E-value=0.25 Score=42.95 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=41.5
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-++.|+.++++. -+++.++|+++|+++...+|.-|+.|+.+|.|=.
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 5678899999864 3889999999999999999999999999997654
No 144
>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=92.62 E-value=0.38 Score=41.69 Aligned_cols=51 Identities=12% Similarity=0.182 Sum_probs=37.9
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus 13 i~~~l~~~I~~g~-~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r 64 (238)
T TIGR02325 13 IADKIEQEIAAGH-LRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRA 64 (238)
T ss_pred HHHHHHHHHHcCC-CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4455555555421 1112223 7789999999999999999999999999997
No 145
>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=92.57 E-value=0.38 Score=41.72 Aligned_cols=51 Identities=14% Similarity=0.186 Sum_probs=38.3
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.|.+-|.+..- ....=+ +..+++++++.+...||+||+.|.+||.|+.
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 45566666654321 111123 6899999999999999999999999999997
No 146
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=92.53 E-value=0.29 Score=36.77 Aligned_cols=52 Identities=25% Similarity=0.487 Sum_probs=42.3
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE 256 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd 256 (265)
++++...||..|+.. ..| +..-|++.++++.++|+.+|+.|.+.|.|=.++.
T Consensus 5 ~~~l~~~IL~hl~~~---~~D---y~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 5 LDPLDLKILQHLKKA---GPD---YAKSIARRLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred cChhHHHHHHHHHHH---CCC---cHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 356788899999875 233 5677899999999999999999999999865443
No 147
>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=92.40 E-value=0.38 Score=42.28 Aligned_cols=51 Identities=16% Similarity=0.070 Sum_probs=43.1
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS 261 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~ 261 (265)
.||++|.+. ..++++.||++.++++.+.+...|..|.+.|.+.. |+..|..
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 477777642 46899999999999999999999999999999986 4567764
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=92.35 E-value=0.25 Score=34.03 Aligned_cols=35 Identities=26% Similarity=0.318 Sum_probs=31.3
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
...+...+|++.|+++++.+.+.|..|.++|.|-.
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 46899999999999999999999999999999853
No 149
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=92.33 E-value=0.69 Score=46.04 Aligned_cols=75 Identities=15% Similarity=0.124 Sum_probs=51.9
Q ss_pred EEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc---cc-ccc-ccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592 69 TITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ---ME-FNE-VNQISKGMYVRVYGHLKAF-QDKRSLNAYSL 141 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~---~~-~~~-~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i 141 (265)
.|+|.|||.+++... .-..+.|.|.+|.|.|..-.+.. .+ -.. ...+..|+.|.|.|.+..- .+...|.+..+
T Consensus 134 ~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~~gel~i~~~~i 213 (585)
T PTZ00417 134 ILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKET 213 (585)
T ss_pred eEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCCCceEEEEEEEE
Confidence 389999999999887 45667887888898888753321 11 011 2468999999999996543 45566666555
Q ss_pred ee
Q 024592 142 RP 143 (265)
Q Consensus 142 ~~ 143 (265)
..
T Consensus 214 ~l 215 (585)
T PTZ00417 214 II 215 (585)
T ss_pred EE
Confidence 43
No 150
>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=92.30 E-value=0.43 Score=41.36 Aligned_cols=51 Identities=20% Similarity=0.251 Sum_probs=38.4
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.||.
T Consensus 6 i~~~l~~~I~~g~-~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 57 (230)
T TIGR02018 6 IKQDILERIRSGE-WPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLER 57 (230)
T ss_pred HHHHHHHHHHhCC-CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4555666665421 1112224 7799999999999999999999999999997
No 151
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=92.24 E-value=0.46 Score=41.56 Aligned_cols=51 Identities=18% Similarity=0.299 Sum_probs=38.2
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus 10 i~~~L~~~I~~g~-~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r 61 (240)
T PRK09764 10 IADRIREQIARGE-LKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILES 61 (240)
T ss_pred HHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4555656555432 1112234 6799999999999999999999999999996
No 152
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=92.23 E-value=1.7 Score=37.91 Aligned_cols=79 Identities=16% Similarity=0.193 Sum_probs=53.5
Q ss_pred EeEEEEEEEEEEe-----e-eCCCeEEEEEE-----cCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC----
Q 024592 67 VNTITVVGIVCDM-----Q-DKEPQFIFLID-----DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ---- 131 (265)
Q Consensus 67 v~~V~iVG~V~~v-----~-~~~t~~~y~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~---- 131 (265)
-+.|.|+|.+.+= + ....+.+|+|. |.|-.|+|..|..-.+ ...+..|+.|.|.|+|++|+
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae----~~~l~kG~~v~VeGqlrsy~~~~~ 83 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLA----GMDLKVGTLVIVEGQLRSYNKFID 83 (219)
T ss_pred cCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhh----hhcccCCCEEEEEEEEEEeccCCC
Confidence 4688889988551 1 12345556554 7788899999976542 22389999999999999884
Q ss_pred Ccc----EEEEEEeeeCCChhH
Q 024592 132 DKR----SLNAYSLRPIIDFNE 149 (265)
Q Consensus 132 ~~~----~i~~~~i~~v~d~Ne 149 (265)
+++ .|.|-.|+.+...++
T Consensus 84 G~~R~vl~V~a~~i~~l~~~~~ 105 (219)
T PRK05813 84 GKNRLILTVFARNIEYCDERSD 105 (219)
T ss_pred CcEEEEEEEEEEEEEEccCCCc
Confidence 332 345555666665433
No 153
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=92.23 E-value=0.48 Score=31.45 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=37.0
Q ss_pred HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
|+++|. . ..++..+|++.++++...+.++|+.|.++|.|.. -+.
T Consensus 2 il~~l~-~------~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 2 ILKLLA-E------GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred HHHHhh-c------CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence 566664 2 3579999999999999999999999999999987 544
No 154
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=92.22 E-value=0.21 Score=44.39 Aligned_cols=46 Identities=17% Similarity=0.311 Sum_probs=40.4
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
.=+++|+++|++. .=++++++++.|+.++..||.-|.+|.++|.+=
T Consensus 5 eR~~~Il~~l~~~------g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 5 ERHQKILELLKEK------GKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHc------CcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 3567899999874 257999999999999999999999999999874
No 155
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=92.22 E-value=0.38 Score=33.76 Aligned_cols=49 Identities=10% Similarity=0.014 Sum_probs=40.6
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
.-.|+.+|.+. ..+++.+|.+..+++..++.-||-.|..|+.|+- -.+.
T Consensus 10 AG~Vw~~L~~~------~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~ 59 (65)
T PF10771_consen 10 AGKVWQLLNEN------GEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNG 59 (65)
T ss_dssp HHHHHHHHCCS------SSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETT
T ss_pred HHHHHHHHhhC------CCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCC
Confidence 34688999763 3689999999999999999999999999999998 4443
No 156
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=92.20 E-value=0.22 Score=44.26 Aligned_cols=47 Identities=13% Similarity=0.216 Sum_probs=40.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.=+++|+++|++. .-+++.++++.|+.++..||.-|..|.++|.|.-
T Consensus 5 eR~~~Il~~L~~~------~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r 51 (256)
T PRK10434 5 QRQAAILEYLQKQ------GKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR 51 (256)
T ss_pred HHHHHHHHHHHHc------CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3567799999874 2489999999999999999999999999997643
No 157
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=92.16 E-value=0.96 Score=43.83 Aligned_cols=76 Identities=20% Similarity=0.224 Sum_probs=57.2
Q ss_pred EEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeeeeC-CccEEEEEEeeeCC
Q 024592 70 ITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKAFQ-DKRSLNAYSLRPII 145 (265)
Q Consensus 70 V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~f~-~~~~i~~~~i~~v~ 145 (265)
|.+.|+|..++.......+.|.|.+|.|.+..-.+...+. .....+..||+|-|.|.+-.-+ |..+|.+..++.++
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLs 143 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLS 143 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeec
Confidence 9999999999988888888999999999988765532211 1234567899999999976544 77777776655443
No 158
>PRK14999 histidine utilization repressor; Provisional
Probab=92.07 E-value=0.49 Score=41.36 Aligned_cols=52 Identities=10% Similarity=0.142 Sum_probs=39.2
Q ss_pred hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+...|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus 16 qi~~~i~~~I~~g~-~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 68 (241)
T PRK14999 16 TVKQDICKKIAGGV-WQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVR 68 (241)
T ss_pred HHHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 35555666665431 1222235 7899999999999999999999999999996
No 159
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=92.05 E-value=0.45 Score=42.10 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=44.1
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA 262 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t 262 (265)
.||++|.+ ..++++.||+++++++.+.+...|..|.+.|.|+. -++..|...
T Consensus 18 ~IL~~l~~------~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG 70 (257)
T PRK15090 18 GILQALGE------EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLT 70 (257)
T ss_pred HHHHHhhc------CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence 47777754 23689999999999999999999999999999998 677778653
No 160
>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=92.01 E-value=0.27 Score=35.71 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=41.6
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
|++-|+.||..|=+. .....+-|.-.+|++.++.++..||+.+..|.+.|.|.+
T Consensus 2 Lt~rq~~IL~alV~~-Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 2 LTERQREILKALVEL-YIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred CCHHHHHHHHHHHHH-HHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 456777777754322 113345677799999999999999999999999999985
No 161
>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=91.99 E-value=0.17 Score=36.35 Aligned_cols=49 Identities=12% Similarity=0.129 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
..+.+..+.++.+.+. .+|++..||++.+++++..|+..+..+.++|.+
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 3567788888887754 259999999999999999999999999888865
No 162
>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=91.94 E-value=0.61 Score=35.74 Aligned_cols=54 Identities=13% Similarity=0.236 Sum_probs=45.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+++..+-.||.+|.... ..+.+++..+|++.++++...|-..++.|...|.|.-
T Consensus 22 ~ls~~q~~vL~~l~~~~--~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r 75 (109)
T TIGR01889 22 NLSLEELLILYYLGKLE--NNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSK 75 (109)
T ss_pred CCCHHHHHHHHHHHhhh--ccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEec
Confidence 46677888998887210 1245899999999999999999999999999999997
No 163
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=91.93 E-value=0.28 Score=43.54 Aligned_cols=47 Identities=9% Similarity=0.270 Sum_probs=41.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-++.|+++|++. .-+++.+|+++|+.++..||.-|..|.++|.|.-
T Consensus 5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r 51 (252)
T PRK10906 5 QRHDAIIELVKQQ------GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHHHHHHHc------CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 4567899999764 2589999999999999999999999999999854
No 164
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=91.93 E-value=0.5 Score=41.30 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=29.8
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 223 HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+-.+++++++.+...||+||+.|++||.||.
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 67 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQR 67 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 6799999999999999999999999999997
No 165
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=91.83 E-value=0.45 Score=42.04 Aligned_cols=54 Identities=22% Similarity=0.353 Sum_probs=46.2
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA 262 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t 262 (265)
-.||++|.+. +.++++.+|+++++++.+.+...|..|.+.|.+.. -++.+|..+
T Consensus 7 l~iL~~l~~~-----~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg 61 (246)
T COG1414 7 LAILDLLAEG-----PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHhC-----CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeeh
Confidence 4588888763 45789999999999999999999999999999999 555688754
No 166
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=91.67 E-value=0.58 Score=40.86 Aligned_cols=31 Identities=16% Similarity=0.254 Sum_probs=29.8
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 223 HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+-.+++++++.+...||+||+.|.+||.|+.
T Consensus 35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r 65 (241)
T PRK11402 35 TENELCTQYNVSRITIRKAISDLVADGVLIR 65 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7799999999999999999999999999997
No 167
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=91.48 E-value=0.58 Score=41.01 Aligned_cols=52 Identities=17% Similarity=0.277 Sum_probs=38.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+.+.|.+-|.+.. -....=+ +-.+++++++.+...||+||+.|.++|.|+.
T Consensus 11 qI~~~i~~~I~~G~-~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r 63 (236)
T COG2188 11 QIAEDIRQRIESGE-LPPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVR 63 (236)
T ss_pred HHHHHHHHHHHhCC-CCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEE
Confidence 35566666665432 1111223 6789999999999999999999999999996
No 168
>PRK11569 transcriptional repressor IclR; Provisional
Probab=91.36 E-value=0.51 Score=42.26 Aligned_cols=52 Identities=19% Similarity=0.296 Sum_probs=44.5
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS 261 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~ 261 (265)
.||++|.+. +.++++.||++.++++.+.+...|..|+++|.+.. -+...|..
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 477777652 45799999999999999999999999999999988 66778864
No 169
>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=91.35 E-value=0.64 Score=35.93 Aligned_cols=53 Identities=15% Similarity=0.120 Sum_probs=46.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
+++..+-.||.+|... .+++..+|++.++++...|...|+.|...|.|.. -|.
T Consensus 25 ~lt~~q~~iL~~l~~~------~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~ 78 (118)
T TIGR02337 25 GLTEQQWRILRILAEQ------GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKAS 78 (118)
T ss_pred CCCHHHHHHHHHHHHc------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCC
Confidence 5677888899998753 4789999999999999999999999999999998 544
No 170
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=91.27 E-value=0.67 Score=37.09 Aligned_cols=55 Identities=13% Similarity=0.158 Sum_probs=46.6
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
+++.-|-.||..|... +.|++..+|++.++++...|...++.|+..|.|.. .|+.
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 5667787888888642 34789999999999999999999999999999999 6653
No 171
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=91.26 E-value=0.82 Score=36.02 Aligned_cols=61 Identities=18% Similarity=0.320 Sum_probs=42.5
Q ss_pred EeEEEEEEEEEE---ee---eCCCeEEEEEE-------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 67 VNTITVVGIVCD---MQ---DKEPQFIFLID-------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 67 v~~V~iVG~V~~---v~---~~~t~~~y~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
++.|.|+|++.. ++ .....+.|.|- +.|-=+.|..|...+. .....++.|+.|.|.|+|+.
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 467888998865 22 12246677776 4465699999976432 22456899999999999985
No 172
>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=91.14 E-value=0.47 Score=32.74 Aligned_cols=57 Identities=21% Similarity=0.364 Sum_probs=41.2
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHH-HHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDK-LMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~-v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
+.+.|+.-|+- ..|++.+++.++++.+..+ +.+.|+.|.++|.| .+++++++.|.-|
T Consensus 7 ~~e~i~~~LR~------~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll-~~~~~~l~lT~~G 64 (66)
T PF06969_consen 7 LREYIMLGLRC------NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL-EIDGGRLRLTEKG 64 (66)
T ss_dssp HHHHHHHHHHH------HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE-EE-SSEEEE-TTT
T ss_pred HHHHHHHHHHh------HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE-EEeCCEEEECccc
Confidence 44555555654 3699999999999977555 58889999999998 5778899988754
No 173
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=91.12 E-value=0.9 Score=38.16 Aligned_cols=61 Identities=25% Similarity=0.413 Sum_probs=40.3
Q ss_pred EeEEEEEEEEEE-ee--e---CCCeEEEEEE------cCCC-----eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 67 VNTITVVGIVCD-MQ--D---KEPQFIFLID------DGTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 67 v~~V~iVG~V~~-v~--~---~~t~~~y~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
+..|.|+|+|.. .+ . ....+.|.|- +..| -|.|..|...+. .....++.|+.|.|.|+|+.
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 367888888854 22 1 1245667662 2223 488899976432 23456899999999999986
No 174
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=91.02 E-value=1.4 Score=36.54 Aligned_cols=61 Identities=21% Similarity=0.396 Sum_probs=40.1
Q ss_pred EeEEEEEEEEEE-e--ee---CCCeEEEEEE------cC-----CCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 67 VNTITVVGIVCD-M--QD---KEPQFIFLID------DG-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 67 v~~V~iVG~V~~-v--~~---~~t~~~y~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
++.|.|+|++.. . +. ....+.|+|- +. |--|.|..|...+. ....-++.|+.|-|.|+|+.
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 2 21 2245566663 22 33489999976432 12456899999999999974
No 175
>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=90.88 E-value=0.62 Score=36.76 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=39.1
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-.+|..|... .+..+++.+|+++++++..-+++.|+.|...|.|.+
T Consensus 11 al~~l~~la~~----~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 11 ATLVLTTLAQN----DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred HHHHHHHHHhC----CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 34466666542 245799999999999999999999999999999987
No 176
>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=90.80 E-value=0.64 Score=35.69 Aligned_cols=47 Identities=21% Similarity=0.339 Sum_probs=40.6
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+..||++|.+. +.-++.++|.+++ +++...|-.+|+.|.+.|.|-.
T Consensus 2 qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 2 QRLAILEVLLES-----DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHHhC-----CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 356799999863 4568999999998 4899999999999999999988
No 177
>PRK02801 primosomal replication protein N; Provisional
Probab=90.74 E-value=2.3 Score=32.28 Aligned_cols=33 Identities=15% Similarity=0.170 Sum_probs=25.3
Q ss_pred EEEEEecccccccccccccCCCCEEEEEEEeeeeC
Q 024592 97 IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ 131 (265)
Q Consensus 97 I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~ 131 (265)
|+|..|-+.++ .....+..|+.|.|.|+|+.+.
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 89999976442 1233689999999999999854
No 178
>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=90.67 E-value=0.79 Score=36.02 Aligned_cols=46 Identities=22% Similarity=0.177 Sum_probs=38.8
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-e-cCCceeeccC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-I-DEFHYKSAVN 264 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-i-Dd~hyk~t~~ 264 (265)
+..++.++|++.++++...+++.|+.|...|.|-+ - .+..|+.+.+
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~ 70 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARP 70 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCC
Confidence 44899999999999999999999999999999987 3 3347776543
No 179
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=90.58 E-value=1.9 Score=36.00 Aligned_cols=80 Identities=23% Similarity=0.287 Sum_probs=48.3
Q ss_pred EeEEEEEEEEEE---eee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592 67 VNTITVVGIVCD---MQD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH 126 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~ 126 (265)
+++|.|+|+|.. ++. ....+.|+|- | .+| -+.|..|..... .....|+.|+.|.|.|+
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 678889998865 222 1234555554 1 122 377778865322 23456899999999999
Q ss_pred eee--eCCc-------cEEEEEEeeeCCChh
Q 024592 127 LKA--FQDK-------RSLNAYSLRPIIDFN 148 (265)
Q Consensus 127 i~~--f~~~-------~~i~~~~i~~v~d~N 148 (265)
|+. |.++ ..|.+..|..+...+
T Consensus 82 L~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~ 112 (168)
T PRK06863 82 LKTRKWQDQNGQDRYTTEIQGDVLQMLGGRN 112 (168)
T ss_pred EEeCCccCCCCCEEEEEEEEEeEEEECCCCC
Confidence 986 4332 345555565555443
No 180
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=90.57 E-value=0.6 Score=37.50 Aligned_cols=59 Identities=5% Similarity=0.041 Sum_probs=45.0
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
+.-+.|+.++.. ...+++.+|++.|+++...|...|..|...|.|.......|..|..|
T Consensus 8 dyL~~I~~l~~~------~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G 66 (142)
T PRK03902 8 DYIEQIYLLIEE------KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKG 66 (142)
T ss_pred HHHHHHHHHHhc------CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEecCceEEECHHH
Confidence 344556666544 23569999999999999999999999999999975444567777654
No 181
>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=90.41 E-value=1 Score=32.94 Aligned_cols=63 Identities=11% Similarity=0.150 Sum_probs=47.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--------CCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN--------LPMDKLMEALESLNENSLVYSIDEFHYKSA 262 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--------~~~~~v~~al~~L~~eG~IYsiDd~hyk~t 262 (265)
.+.+|-+.|..+|-+.. .+...++.+.|.+.|. =+.+-|+++|..|+.|+.||...+-.|-.|
T Consensus 8 qfiPL~EvlC~~I~dln--~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivt 78 (80)
T PF10264_consen 8 QFIPLPEVLCWVISDLN--AAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVT 78 (80)
T ss_pred cceeHHHHHHHHHHHHh--ccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeCCCceEeeC
Confidence 45678888888877652 4567788999988882 244559999999999999999777666554
No 182
>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=90.35 E-value=0.53 Score=33.07 Aligned_cols=51 Identities=18% Similarity=0.295 Sum_probs=39.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI 254 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi 254 (265)
.+++++|+++|++.+ ......-+++..|+.+..+|+..|-.|..+|.|+..
T Consensus 3 ~~~ee~Il~~L~~~g----~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 3 QDLEEKILDFLKELG----GSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHHHT----SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hhHHHHHHHHHHhcC----CccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeC
Confidence 368899999999852 345555555666778899999999999999999763
No 183
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=90.32 E-value=0.53 Score=41.74 Aligned_cols=47 Identities=15% Similarity=0.224 Sum_probs=41.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-+.+|+++|++. .-+++.+|++.|+.++..||.-|..|.++|.|-.
T Consensus 5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 5 QRHQILLELLAQL------GFVTVEKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4567799999863 3689999999999999999999999999999853
No 184
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=90.30 E-value=0.29 Score=41.43 Aligned_cols=45 Identities=4% Similarity=0.111 Sum_probs=39.2
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
.-++.|+++|++. .=+++.++++.|+.++..||.-|..|.++|++
T Consensus 7 ~R~~~Il~~l~~~------~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 7 ERQKALQELIEEN------PFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHHC------CCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 3567799999874 24799999999999999999999999999976
No 185
>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=90.23 E-value=0.48 Score=44.63 Aligned_cols=67 Identities=22% Similarity=0.368 Sum_probs=49.9
Q ss_pred EEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee-CCc
Q 024592 66 DVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF-QDK 133 (265)
Q Consensus 66 ~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f-~~~ 133 (265)
.=.+|++-|||-+++.+.+-+...|-||||.+.|.+-..-.. +.+.-.+..-.-|.|+|.|+.. .||
T Consensus 122 r~qrVkv~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~-~yd~~~Ls~essv~vYG~i~~~p~GK 189 (545)
T KOG0555|consen 122 RGQRVKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQ-SYDALTLSTESSVTVYGTIKKLPEGK 189 (545)
T ss_pred cCceEEeehhhHhhhhcCceEEEEEecCCceEEEEEcchhhh-hhccccccccceEEEEEEEecCcCCC
Confidence 336899999999998888888889999999999997654221 1223345566788999998876 443
No 186
>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=90.01 E-value=0.93 Score=31.81 Aligned_cols=49 Identities=10% Similarity=0.150 Sum_probs=35.9
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY 252 (265)
+++.|+++|+... .+-.=.=+.++++.+ ...+.+|.+++..|++||.+-
T Consensus 2 ~K~~Ile~L~~k~--~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~ 51 (67)
T PF08679_consen 2 AKQKILEFLEAKK--KKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLE 51 (67)
T ss_dssp HHHHHHHHHSSCC--CHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcc--CCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEE
Confidence 6788999998432 112234578888866 699999999999999999874
No 187
>PRK09954 putative kinase; Provisional
Probab=89.99 E-value=0.56 Score=43.45 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=40.7
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
+....+||++|++++ =++..+|+++|+++...|+..|..|.++|.|
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 456778999999742 5899999999999999999999999999877
No 188
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=89.88 E-value=0.6 Score=41.15 Aligned_cols=45 Identities=18% Similarity=0.372 Sum_probs=39.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
.-+.+|+++|++. ..+++++|++.|++++..||.-|.+|.++|.|
T Consensus 4 ~R~~~Il~~l~~~------~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l 48 (240)
T PRK10411 4 ARQQAIVDLLLNH------TSLTTEALAEQLNVSKETIRRDLNELQTQGKI 48 (240)
T ss_pred HHHHHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 3567799999863 37899999999999999999999999999876
No 189
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=89.78 E-value=6.7 Score=32.32 Aligned_cols=84 Identities=13% Similarity=0.082 Sum_probs=54.5
Q ss_pred eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEE--EeeeC--CCeEEEEEEcCCCeEEEEEecccccccccccccCCC
Q 024592 43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVC--DMQDK--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKG 118 (265)
Q Consensus 43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~--~v~~~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g 118 (265)
=.|.+++.......+ ..+++=|.|. ++... ...+.|.|.|+...|.|.+--- -++-|++|
T Consensus 37 F~tpsEv~~~~~~~~----------~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG 100 (155)
T PRK13159 37 LFTPSQVRAGAAAGY----------QQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGI------LPDLFRDN 100 (155)
T ss_pred EECHHHHhcCCcccC----------CeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccC------CCccccCC
Confidence 356666665422222 4555556665 45544 3479999999999998875421 35678999
Q ss_pred CEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592 119 MYVRVYGHLKAFQDKRSLNAYSLRPIID 146 (265)
Q Consensus 119 ~yVrV~G~i~~f~~~~~i~~~~i~~v~d 146 (265)
.=|-+.|++. + -.+.+..|--=.|
T Consensus 101 qgVVaeG~~~--~--g~F~A~~vLAKHd 124 (155)
T PRK13159 101 QSVIANGRMQ--G--GRFVANEVLAKHD 124 (155)
T ss_pred CeEEEEEEEc--C--CEEEEeEEEecCC
Confidence 9999999986 2 3555555543334
No 190
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=89.73 E-value=3 Score=32.17 Aligned_cols=77 Identities=17% Similarity=0.319 Sum_probs=45.8
Q ss_pred eEEEEEEEEEE---ee---eCCCeEEEEEE------cC-----CCeEEEEEecccccccccccccCCCCEEEEEEEeee-
Q 024592 68 NTITVVGIVCD---MQ---DKEPQFIFLID------DG-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA- 129 (265)
Q Consensus 68 ~~V~iVG~V~~---v~---~~~t~~~y~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~- 129 (265)
+.|.|+|++.. +. .....+.|+|- |. |--|.|..|...+. .....+..|+.|.|.|+|+.
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 56777777754 11 11234555554 22 23488888875332 12346899999999999986
Q ss_pred -eCC---c----cEEEEEEeeeCCC
Q 024592 130 -FQD---K----RSLNAYSLRPIID 146 (265)
Q Consensus 130 -f~~---~----~~i~~~~i~~v~d 146 (265)
|.+ + ..|.+..|..++.
T Consensus 81 ~~~~~~G~~~~~~ei~a~~i~~l~~ 105 (112)
T PRK06752 81 NYEDDQGKRIYITEVVIESITFLER 105 (112)
T ss_pred ccCCCCCcEEEEEEEEEEEEEECCC
Confidence 443 2 2466666665543
No 191
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=89.72 E-value=1.8 Score=35.98 Aligned_cols=61 Identities=13% Similarity=0.149 Sum_probs=40.5
Q ss_pred EeEEEEEEEEEE---eee---CCCeEEEEEE------cCCC-------eEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592 67 VNTITVVGIVCD---MQD---KEPQFIFLID------DGTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGHL 127 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i 127 (265)
++.|.|+|.|.+ ++. ....+.|+|- |..| -+.|..|..-+. .....++.|+.|.|.|+|
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 788999999966 221 2245666664 2222 388888864321 223558999999999999
Q ss_pred ee
Q 024592 128 KA 129 (265)
Q Consensus 128 ~~ 129 (265)
+.
T Consensus 83 ~~ 84 (164)
T PRK08763 83 RY 84 (164)
T ss_pred Ee
Confidence 86
No 192
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=89.71 E-value=0.55 Score=42.09 Aligned_cols=47 Identities=15% Similarity=0.208 Sum_probs=40.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-+..|+++|++.+ -+++.+|++.|+.++..||.-|..|.++|.+.-
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 45677899998742 399999999999999999999999999999854
No 193
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=89.70 E-value=1.4 Score=34.95 Aligned_cols=32 Identities=13% Similarity=0.241 Sum_probs=31.0
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-|+.++|..++.++..|++|.++|..+|.||+
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t 67 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELEREGIVET 67 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 48999999999999999999999999999998
No 194
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=89.65 E-value=1.4 Score=35.81 Aligned_cols=54 Identities=19% Similarity=0.205 Sum_probs=45.2
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
+++-+..||++|.+.. + .++.++|.+.+ +++...|..+|+.|.+.|.|.. -.++
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 5678889999998742 3 49999999988 3999999999999999999988 4433
No 195
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=89.58 E-value=3 Score=34.61 Aligned_cols=61 Identities=18% Similarity=0.214 Sum_probs=40.3
Q ss_pred eEEEEEEEEEE-e--e---eCCCeEEEEEE--------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee
Q 024592 68 NTITVVGIVCD-M--Q---DKEPQFIFLID--------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF 130 (265)
Q Consensus 68 ~~V~iVG~V~~-v--~---~~~t~~~y~Ld--------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f 130 (265)
+.|.|+|++.. . + .....+.|+|- +.|-=|.|..|...+. .....++.|+.|-|.|+|+.-
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 56888888854 2 1 12245666665 2344588999975432 124558999999999999863
No 196
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=89.47 E-value=1.5 Score=36.73 Aligned_cols=56 Identities=14% Similarity=0.179 Sum_probs=43.8
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQL--NLPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
....|++++.-. .|. ...+|+++| +++.++|+++|++|..-|.|=-..+..|+.|.
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 YHPAIRELLPLM------PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTD 83 (171)
T ss_pred HHHHHHHHhhcC------CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEec
Confidence 445566666543 233 899999999 89999999999999999999774446787765
No 197
>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=89.41 E-value=1.8 Score=30.14 Aligned_cols=50 Identities=12% Similarity=0.172 Sum_probs=40.5
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS 261 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~ 261 (265)
.+|++++++. -++..+|+++++++...|+..+..|.++|.... . ...|..
T Consensus 3 ~~il~~L~~~-------~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~-~~g~~l 53 (69)
T TIGR00122 3 LRLLALLADN-------PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV-GKGYRL 53 (69)
T ss_pred HHHHHHHHcC-------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec-CCceEe
Confidence 4677777642 367999999999999999999999999999776 5 555543
No 198
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=89.37 E-value=1.2 Score=40.85 Aligned_cols=52 Identities=15% Similarity=0.307 Sum_probs=43.4
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe-EEeecCCcee
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL-VYSIDEFHYK 260 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~-IYsiDd~hyk 260 (265)
..+||++|++ +..++.++|+++|+++...|.++|..|.++|. |+++....|.
T Consensus 6 ~~~il~~L~~------~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~ 58 (319)
T PRK11886 6 MLQLLSLLAD------GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYR 58 (319)
T ss_pred HHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEE
Confidence 4568888875 35789999999999999999999999999999 8775544564
No 199
>PHA02943 hypothetical protein; Provisional
Probab=89.30 E-value=1.1 Score=36.68 Aligned_cols=46 Identities=17% Similarity=0.167 Sum_probs=38.3
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-..+||++|+. -..+..+|++.|+++-.+++-+|.-|..||.|-+
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 345668888832 1457999999999999999999999999999865
No 200
>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=89.29 E-value=2.8 Score=42.06 Aligned_cols=65 Identities=20% Similarity=0.419 Sum_probs=46.1
Q ss_pred EEEEEEEEEEeee------C-----CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccE
Q 024592 69 TITVVGIVCDMQD------K-----EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRS 135 (265)
Q Consensus 69 ~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~ 135 (265)
.|.|+|+|.++.. . .....++|.|.|| +|++.+|.+.+.. ....++..|.+.| +++.|++ +.
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----FDVSVQPVIAIKGVRVSDFGG-KS 386 (608)
T ss_pred CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh----cCCCCCCEEEEEeEEEEecCC-ce
Confidence 6788888887632 1 1357899999999 5999999876531 1256778877774 5788965 46
Q ss_pred EEE
Q 024592 136 LNA 138 (265)
Q Consensus 136 i~~ 138 (265)
|..
T Consensus 387 Ls~ 389 (608)
T TIGR00617 387 LST 389 (608)
T ss_pred Eec
Confidence 654
No 201
>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=89.26 E-value=0.8 Score=35.53 Aligned_cols=49 Identities=16% Similarity=0.339 Sum_probs=40.8
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs 253 (265)
+..+..||++|.+. +.-++.++|.+.| +++...|-.+|+.|.+.|.|-.
T Consensus 7 T~~R~~Il~~l~~~-----~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 7 TPQRLAILELLKES-----PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp HHHHHHHHHHHHHH-----SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHcC-----CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence 56788899999975 2378999999988 3888999999999999999988
No 202
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=89.06 E-value=2.9 Score=35.37 Aligned_cols=61 Identities=16% Similarity=0.159 Sum_probs=39.6
Q ss_pred EeEEEEEEEEEEe---ee--C-CCeEEEEEE------c--------CCCeEEEEEecccccccccccccCCCCEEEEEEE
Q 024592 67 VNTITVVGIVCDM---QD--K-EPQFIFLID------D--------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH 126 (265)
Q Consensus 67 v~~V~iVG~V~~v---~~--~-~t~~~y~Ld------D--------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~ 126 (265)
++.|.|+|+|..- .. . ...+.|+|- | .|--+.|..|...+. .....|+.|+.|.|.|+
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 6788999998652 11 1 235667663 1 233477777764321 22456899999999999
Q ss_pred eee
Q 024592 127 LKA 129 (265)
Q Consensus 127 i~~ 129 (265)
|+.
T Consensus 82 L~~ 84 (182)
T PRK06958 82 IRT 84 (182)
T ss_pred EEe
Confidence 996
No 203
>PF14502 HTH_41: Helix-turn-helix domain
Probab=88.89 E-value=0.84 Score=30.01 Aligned_cols=32 Identities=19% Similarity=0.212 Sum_probs=29.7
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-+++|.+++|+.+.-.|+.||.+|.++|.|.-
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 47899999999999999999999999999875
No 204
>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=88.73 E-value=1.5 Score=37.74 Aligned_cols=51 Identities=18% Similarity=0.295 Sum_probs=38.7
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.+.+.|++..- ....=+ +..+++++|+.+...||+||+.|.++|.||.
T Consensus 6 i~~~l~~~I~~g~~-~~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~ 57 (231)
T TIGR03337 6 IKDHLSYQIRAGAL-LPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYR 57 (231)
T ss_pred HHHHHHHHHHcCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEE
Confidence 55666676765321 111123 6799999999999999999999999999997
No 205
>PRK00215 LexA repressor; Validated
Probab=88.57 E-value=0.66 Score=39.54 Aligned_cols=54 Identities=22% Similarity=0.272 Sum_probs=44.6
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCC-CHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNL-PMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~-~~~~v~~al~~L~~eG~IYs 253 (265)
++..|..||++|++... ......+..+|++.+++ +...+...|..|.+.|.|-.
T Consensus 2 lt~~q~~il~~i~~~~~-~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~ 56 (205)
T PRK00215 2 LTKRQQEILDFIRDHIE-ETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRR 56 (205)
T ss_pred CCHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 46789999999975210 22456799999999999 99999999999999999966
No 206
>PRK09462 fur ferric uptake regulator; Provisional
Probab=88.23 E-value=1.9 Score=34.91 Aligned_cols=51 Identities=16% Similarity=0.325 Sum_probs=43.3
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs 253 (265)
++.-+..||++|.+. .+.-++.++|.++| +++...|-.+|+.|.+.|.|-.
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 567888999999863 23478999999988 3789999999999999999976
No 207
>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=87.96 E-value=1.9 Score=34.76 Aligned_cols=62 Identities=21% Similarity=0.357 Sum_probs=35.3
Q ss_pred eEEEEEEcCCCeEEEEEecccccc-----c-----------cc----cccc-CCCCEEEEEEEeeeeCCc--cEEEEEEe
Q 024592 85 QFIFLIDDGTGRIECSRWAHEQME-----F-----------NE----VNQI-SKGMYVRVYGHLKAFQDK--RSLNAYSL 141 (265)
Q Consensus 85 ~~~y~LdDgTG~I~~~~w~~~~~~-----~-----------~~----~~~~-~~g~yVrV~G~i~~f~~~--~~i~~~~i 141 (265)
.+.+.|.|+||.+.+..|.+.... . .. ...+ -..-.++|.++...|+++ ..+++..|
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 367789999999999999764320 0 00 0111 222356888899999865 45788888
Q ss_pred eeCCC
Q 024592 142 RPIID 146 (265)
Q Consensus 142 ~~v~d 146 (265)
.||+-
T Consensus 135 ~~vd~ 139 (146)
T PF08646_consen 135 EPVDY 139 (146)
T ss_dssp EE--H
T ss_pred EeCCH
Confidence 88853
No 208
>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=87.93 E-value=1 Score=32.73 Aligned_cols=38 Identities=11% Similarity=0.226 Sum_probs=35.3
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
.=+++++|++.++++.+++...|..++.+|.|.- ||..
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00088 23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 4689999999999999999999999999999999 9864
No 209
>smart00753 PAM PCI/PINT associated module.
Probab=87.93 E-value=1 Score=32.73 Aligned_cols=38 Identities=11% Similarity=0.226 Sum_probs=35.3
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
.=+++++|++.++++.+++...|..++.+|.|.- ||..
T Consensus 23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00753 23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 4689999999999999999999999999999999 9864
No 210
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=87.93 E-value=2.8 Score=35.35 Aligned_cols=66 Identities=20% Similarity=0.230 Sum_probs=41.5
Q ss_pred EEeEEEEEEEEEEe---ee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEE
Q 024592 66 DVNTITVVGIVCDM---QD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYG 125 (265)
Q Consensus 66 ~v~~V~iVG~V~~v---~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G 125 (265)
-++.|.|||+|..- +. ....+.|+|- | .+| -+.|..|...+. .....|+.|+.|.|.|
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 36888999988552 21 2234555554 2 133 367888865322 1245689999999999
Q ss_pred Eeee--eCCc
Q 024592 126 HLKA--FQDK 133 (265)
Q Consensus 126 ~i~~--f~~~ 133 (265)
+|+. |.++
T Consensus 83 rL~~~~yedk 92 (177)
T PRK09010 83 QLRTRKWTDQ 92 (177)
T ss_pred EEEeccccCC
Confidence 9975 5443
No 211
>PRK10870 transcriptional repressor MprA; Provisional
Probab=87.92 E-value=2.2 Score=35.68 Aligned_cols=57 Identities=12% Similarity=0.072 Sum_probs=47.8
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
.+++..|-.||..|... .+.+++..+|++.++++...+...|+.|...|.|.- -|.+
T Consensus 51 ~gLt~~q~~iL~~L~~~----~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~ 108 (176)
T PRK10870 51 QGINETLFMALITLESQ----ENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN 108 (176)
T ss_pred CCCCHHHHHHHHHHhcC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 35677788899888752 245799999999999999999999999999999998 5544
No 212
>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=87.86 E-value=2 Score=35.61 Aligned_cols=61 Identities=20% Similarity=0.260 Sum_probs=38.6
Q ss_pred EeEEEEEEEEEE---eeeC---CCeEEEEEE-------------cCCCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592 67 VNTITVVGIVCD---MQDK---EPQFIFLID-------------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL 127 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~~---~t~~~y~Ld-------------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i 127 (265)
++.|.|+|.|.. ++.. ...+.|+|. |.|--|.|..|...+. .....++.|+.|.|.|+|
T Consensus 4 ~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L 81 (164)
T TIGR00621 4 VNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAE--VAAQYLKKGSLVYVEGRL 81 (164)
T ss_pred ccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHH--HHHHhCCCCCEEEEEEEE
Confidence 466777777755 2211 123334432 2244688999976432 234578999999999999
Q ss_pred ee
Q 024592 128 KA 129 (265)
Q Consensus 128 ~~ 129 (265)
+.
T Consensus 82 ~~ 83 (164)
T TIGR00621 82 RT 83 (164)
T ss_pred Ee
Confidence 85
No 213
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=87.64 E-value=0.72 Score=33.56 Aligned_cols=45 Identities=20% Similarity=0.238 Sum_probs=37.1
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+-.|+.+|... ..++..+|.+.++++...+...|..|.++|.|=.
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 45678887653 4799999999999999999999999999999865
No 214
>PRK11050 manganese transport regulator MntR; Provisional
Probab=87.56 E-value=2 Score=35.11 Aligned_cols=44 Identities=14% Similarity=0.052 Sum_probs=36.9
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
.+++..+|++.|+++.+.|..+|..|...|.|.......+..|.
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~LT~ 93 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTP 93 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEECc
Confidence 47899999999999999999999999999999873334555554
No 215
>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=87.38 E-value=2.3 Score=31.82 Aligned_cols=36 Identities=19% Similarity=0.403 Sum_probs=33.4
Q ss_pred CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
....++..+|++.++++.+.|..+|..|...|.|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 356899999999999999999999999999999985
No 216
>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=87.28 E-value=1.2 Score=37.84 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=31.9
Q ss_pred CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
...=++..+++++|+++..-||+||..|..+|.|-.
T Consensus 31 pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 344578899999999999999999999999999865
No 217
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=87.15 E-value=4.6 Score=33.44 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=43.0
Q ss_pred eEEEEEEEEE--EeeeCC--CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592 68 NTITVVGIVC--DMQDKE--PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK 128 (265)
Q Consensus 68 ~~V~iVG~V~--~v~~~~--t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~ 128 (265)
..|++=|.|. ++.... ..+.|+|.|+...|.|.+--. -++.|++|.=|-|.|++.
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 5677888887 565543 379999999999998876422 356789999999999985
No 218
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.05 E-value=1.4 Score=37.22 Aligned_cols=47 Identities=19% Similarity=0.176 Sum_probs=40.0
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.....||+.|...+ -++.++|+..|+++..+||+.|..|.++|.|-.
T Consensus 22 ~~~~~Vl~~L~~~g------~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 22 EEGFEVLKALIKKG------EVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred ccHhHHHHHHHHcC------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 45567888887531 379999999999999999999999999999974
No 219
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=86.97 E-value=1.9 Score=31.91 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=37.5
Q ss_pred EEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592 71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV 121 (265)
Q Consensus 71 ~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV 121 (265)
++++.|+++..........|.|.||+|.|..-.+--. +....+..|..+
T Consensus 6 ~l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~v~~--~y~~~l~~GavL 54 (86)
T PF15072_consen 6 CLVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRKVLE--EYGDELSPGAVL 54 (86)
T ss_pred EEEEEEEEeeccCCCeEEEEECCCCcEEEEEeHHHHh--hcCCccccCEEE
Confidence 5789999998877789999999999999998754322 234567777644
No 220
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=86.89 E-value=2.1 Score=37.16 Aligned_cols=51 Identities=10% Similarity=0.190 Sum_probs=37.8
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+...|.+.|.+. ......=+ +..+|+++|+.+..-||+||..|..+|.|..
T Consensus 12 ~~~~l~~~I~~g-~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~ 63 (239)
T PRK04984 12 AEEYIIESIWNN-RFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI 63 (239)
T ss_pred HHHHHHHHHHcC-CCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 334444444432 12333456 5889999999999999999999999999986
No 221
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=86.89 E-value=2.7 Score=35.24 Aligned_cols=62 Identities=19% Similarity=0.191 Sum_probs=40.2
Q ss_pred EeEEEEEEEEEEe---ee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592 67 VNTITVVGIVCDM---QD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH 126 (265)
Q Consensus 67 v~~V~iVG~V~~v---~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~ 126 (265)
++.|.|+|+|..- +. ....+.|.|- | .+| =+.|..|...+. .....++.|+.|.|.|+
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 6788999998652 11 2234555543 1 233 288888865332 23456899999999999
Q ss_pred eeee
Q 024592 127 LKAF 130 (265)
Q Consensus 127 i~~f 130 (265)
|+.-
T Consensus 83 Lr~~ 86 (172)
T PRK05733 83 LQTR 86 (172)
T ss_pred EEeC
Confidence 9863
No 222
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=86.64 E-value=1.2 Score=35.83 Aligned_cols=33 Identities=6% Similarity=0.185 Sum_probs=31.5
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
=++.++|+++++++..-|+++|..|..+|.|.+
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s 57 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVTA 57 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEE
Confidence 478999999999999999999999999999987
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=86.63 E-value=1.8 Score=30.97 Aligned_cols=49 Identities=20% Similarity=0.379 Sum_probs=44.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+++-.||+.|... .+.|+...++.+.++.+...+--.+..|.+.|.|.-
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 5678899999764 478999999999999999999999999999999976
No 224
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=86.62 E-value=1.4 Score=38.40 Aligned_cols=41 Identities=10% Similarity=0.118 Sum_probs=36.3
Q ss_pred CCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 217 ANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 217 ~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
....+++..+|++.++++...+...|..|.++|.|.- .+..
T Consensus 17 ~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r 58 (217)
T PRK14165 17 NNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPR 58 (217)
T ss_pred CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCC
Confidence 3356899999999999999999999999999999988 6543
No 225
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=86.39 E-value=1.4 Score=39.07 Aligned_cols=47 Identities=13% Similarity=0.153 Sum_probs=40.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-+.+|+++|++. .-+++.++++.|+.++..||.-|.+|...+.+|=
T Consensus 7 eR~~~I~~~l~~~------~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~g 53 (252)
T PRK10681 7 ERIGQLLQALKRS------DKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLLG 53 (252)
T ss_pred HHHHHHHHHHHHc------CCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEEC
Confidence 3567799999874 3589999999999999999999999998887553
No 226
>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=86.35 E-value=0.87 Score=42.11 Aligned_cols=54 Identities=22% Similarity=0.387 Sum_probs=45.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI 254 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi 254 (265)
.++++-...||.+|++. .+.||-..+|..+.+++...|.++|..|++.++|=++
T Consensus 80 ~~l~~~e~lvy~~I~~a----g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~v 133 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEA----GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSV 133 (327)
T ss_dssp -SSSCCHHHHHHHHHHH----TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE
T ss_pred cCCCHHHHHHHHHHHHh----CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEe
Confidence 56788889999999985 4689999999999999999999999999999999873
No 227
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=86.35 E-value=2.3 Score=35.42 Aligned_cols=57 Identities=16% Similarity=0.092 Sum_probs=46.2
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
.+..+..||++|.+. +.-++.++|.++| +++...|...|+.|.+.|.|-. -..+.|.
T Consensus 24 ~T~qR~~IL~~l~~~-----~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~~~~ 86 (169)
T PRK11639 24 LTPQRLEVLRLMSLQ-----PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYV 86 (169)
T ss_pred CCHHHHHHHHHHHhc-----CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCCcEE
Confidence 457888899999863 3578999999988 3789999999999999999987 3444453
No 228
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=86.29 E-value=5.5 Score=32.96 Aligned_cols=65 Identities=20% Similarity=0.222 Sum_probs=47.4
Q ss_pred eEEEEEEEEE--EeeeC--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEe
Q 024592 68 NTITVVGIVC--DMQDK--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSL 141 (265)
Q Consensus 68 ~~V~iVG~V~--~v~~~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i 141 (265)
..+++=|.|. ++... ...+.|.|.|+...|.|.+--. -++.|++|.=|-|.|++.. .-.+.|..|
T Consensus 58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~~---~g~F~A~ev 126 (159)
T PRK13150 58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI------LPDLFREGQGVVVQGTLEK---GNHVLAHEV 126 (159)
T ss_pred CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc------CCccccCCCeEEEEEEECC---CCEEEEeEE
Confidence 6778888887 56553 3579999999999998875432 3567899999999999853 234555444
No 229
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=86.15 E-value=2.4 Score=35.95 Aligned_cols=54 Identities=11% Similarity=0.028 Sum_probs=46.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
-+++.-|-.||.+|... .|++..+|++.+.++.+.|...|+.|...|.|.- .|.
T Consensus 41 ~gLt~~q~~iL~~L~~~------~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~ 95 (185)
T PRK13777 41 YDLNINEHHILWIAYHL------KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE 95 (185)
T ss_pred CCCCHHHHHHHHHHHhC------CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence 35777888899998753 4899999999999999999999999999999997 554
No 230
>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=86.14 E-value=1.9 Score=38.02 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=38.1
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..||+.|+.. +.-++..+|+++++++..-|++++..|...|.|.+
T Consensus 186 ~~IL~~L~~~-----egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~ 230 (251)
T TIGR02787 186 EHIFEELDGN-----EGLLVASKIADRVGITRSVIVNALRKLESAGVIES 230 (251)
T ss_pred HHHHHHhccc-----cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4477777542 34579999999999999999999999999999987
No 231
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=85.87 E-value=3.4 Score=32.89 Aligned_cols=61 Identities=16% Similarity=0.288 Sum_probs=39.0
Q ss_pred EeEEEEEEEEEEe---ee---CCCeEEEEEE------cCCC-----eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 67 VNTITVVGIVCDM---QD---KEPQFIFLID------DGTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 67 v~~V~iVG~V~~v---~~---~~t~~~y~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
++.|.|+|++..- .. ....+.|+|- |..| -+.|..|...+. .-...++.|+.|.|.|+|+.
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 4678888888652 11 1235666665 3233 377888864321 12455899999999999886
No 232
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=85.78 E-value=2.4 Score=35.94 Aligned_cols=50 Identities=22% Similarity=0.296 Sum_probs=41.2
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF 257 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~ 257 (265)
|=.++++.|.. .++++..+|+++|+++-.+|+..|-.|..+|.||..|+.
T Consensus 14 lv~~~~~~l~~------~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~ 63 (183)
T PHA03103 14 LVKKEVKNLGL------GEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSN 63 (183)
T ss_pred HHHHHHHHhcc------CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCC
Confidence 44444555543 469999999999999999999999999999999987764
No 233
>PRK07217 replication factor A; Reviewed
Probab=85.68 E-value=2.2 Score=39.01 Aligned_cols=57 Identities=28% Similarity=0.290 Sum_probs=41.0
Q ss_pred eEEEEEEcCCCeEEEEEeccccc--------cc--------------ccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592 85 QFIFLIDDGTGRIECSRWAHEQM--------EF--------------NEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142 (265)
Q Consensus 85 ~~~y~LdDgTG~I~~~~w~~~~~--------~~--------------~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~ 142 (265)
++.+.||||||.++|++..+... +. ......-.|.|++|+|.+ | -+++.+..+.
T Consensus 218 rik~vlDDGt~~~~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~--~--g~~l~~~~~~ 293 (311)
T PRK07217 218 RIKGVLDDGEEVQEVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT--L--GRYLLADSVE 293 (311)
T ss_pred EEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc--C--CcEEEeeEee
Confidence 89999999999999998864221 00 011124689999999976 3 3688888887
Q ss_pred eCC
Q 024592 143 PII 145 (265)
Q Consensus 143 ~v~ 145 (265)
+.+
T Consensus 294 ~~~ 296 (311)
T PRK07217 294 PLT 296 (311)
T ss_pred ccc
Confidence 774
No 234
>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=85.65 E-value=0.71 Score=35.10 Aligned_cols=45 Identities=24% Similarity=0.300 Sum_probs=33.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
+-.-.|+++|-.. ..++-++|++.++++..++|++|..|.++|.|
T Consensus 13 ~~~~~Il~~L~~~------~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv 57 (105)
T PF02002_consen 13 EEAVRILDALLRK------GELTDEDLAKKLGLKPKEVRKILYKLYEDGLV 57 (105)
T ss_dssp STTHHHHHHHHHH--------B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-
T ss_pred chHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence 3456788888653 25788999999999999999999999999999
No 235
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=85.61 E-value=3.1 Score=26.79 Aligned_cols=41 Identities=17% Similarity=0.300 Sum_probs=32.3
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
+++.+..|+..+. .|++..+|++.++++...|+..+..+..
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 5566666776652 3789999999999999999998887643
No 236
>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=85.61 E-value=2.3 Score=31.21 Aligned_cols=65 Identities=18% Similarity=0.065 Sum_probs=46.9
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA 265 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~ 265 (265)
+++..=+||..|...- ..-+=|+.+.|.+..+++..++...|..|...+.|.. ..-+-|+.|..|
T Consensus 4 L~~~d~rvL~aiE~gm--k~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~G 70 (82)
T PF09202_consen 4 LSKEDFRVLRAIEMGM--KNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLG 70 (82)
T ss_dssp --HHHHHHHHHHHTTT--TT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHH
T ss_pred CCHHHHHHHHHHHHcc--cCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecc
Confidence 4556667888886642 4457899999999999999999999999999999988 333578877643
No 237
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=85.58 E-value=2.5 Score=30.83 Aligned_cols=56 Identities=18% Similarity=0.217 Sum_probs=41.6
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS 261 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~ 261 (265)
....++.++... ++.-++=++|++.|+++...|-+.++.|-++|.=.. +-..-|+.
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 445566665543 345789999999999999999999999999996444 44445543
No 238
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=85.58 E-value=3.8 Score=33.44 Aligned_cols=60 Identities=15% Similarity=0.188 Sum_probs=38.9
Q ss_pred eEEEEEEEEEE---ee--eCCC-----eEEEEEE------cCCC--------eEEEEEecccccccccccccCCCCEEEE
Q 024592 68 NTITVVGIVCD---MQ--DKEP-----QFIFLID------DGTG--------RIECSRWAHEQMEFNEVNQISKGMYVRV 123 (265)
Q Consensus 68 ~~V~iVG~V~~---v~--~~~t-----~~~y~Ld------DgTG--------~I~~~~w~~~~~~~~~~~~~~~g~yVrV 123 (265)
+.|.|+|.+.. +. ...+ .+.|.|- +.+| -|.|..|...+. .....|+.|+.|-|
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 57888888855 11 1222 5677772 2233 378889975332 12456899999999
Q ss_pred EEEeee
Q 024592 124 YGHLKA 129 (265)
Q Consensus 124 ~G~i~~ 129 (265)
.|+|+.
T Consensus 81 ~GrL~~ 86 (148)
T PRK08182 81 EGRMER 86 (148)
T ss_pred EEEEEe
Confidence 999975
No 239
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=85.13 E-value=1.9 Score=38.63 Aligned_cols=49 Identities=22% Similarity=0.414 Sum_probs=43.8
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.++++|+..|+.. .++|+..-||-+..+++.+.+-++|..|.++|.|--
T Consensus 4 ~~reklir~Lk~a----~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~R 52 (321)
T COG3888 4 SLREKLIRELKRA----GPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKR 52 (321)
T ss_pred cHHHHHHHHHHhc----CCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeee
Confidence 4788899999984 478999999999999999999999999999998754
No 240
>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=85.13 E-value=1.9 Score=32.12 Aligned_cols=62 Identities=26% Similarity=0.397 Sum_probs=35.1
Q ss_pred EeEEEEEEEEEE---eeeC--C-CeEEEEEE--c------C-----CCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592 67 VNTITVVGIVCD---MQDK--E-PQFIFLID--D------G-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL 127 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~~--~-t~~~y~Ld--D------g-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i 127 (265)
++.|.|+|.|.. +... . ..+.|.|. + + |--+.|..|.+.+. .-...++.|+.|.|.|++
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 467888998844 2221 1 23444432 2 1 12377888865332 223458999999999999
Q ss_pred eee
Q 024592 128 KAF 130 (265)
Q Consensus 128 ~~f 130 (265)
+..
T Consensus 79 ~~~ 81 (104)
T PF00436_consen 79 RTR 81 (104)
T ss_dssp EEE
T ss_pred Eee
Confidence 875
No 241
>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=85.03 E-value=3.7 Score=33.77 Aligned_cols=72 Identities=13% Similarity=0.238 Sum_probs=43.4
Q ss_pred eEEEEEEcCCCeEEEEEecccccc-------------ccc-------ccccCCCC--EEEEEEEeeeeCC--ccEEEEEE
Q 024592 85 QFIFLIDDGTGRIECSRWAHEQME-------------FNE-------VNQISKGM--YVRVYGHLKAFQD--KRSLNAYS 140 (265)
Q Consensus 85 ~~~y~LdDgTG~I~~~~w~~~~~~-------------~~~-------~~~~~~g~--yVrV~G~i~~f~~--~~~i~~~~ 140 (265)
.+.+.|.|+||.+.+..|.+.... ... ... ..|. .++|..+...|++ +...++..
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 ILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQD-LVGKTFLFRVSVKEETYNDEGRIRYTVVK 147 (166)
T ss_pred EEEEEEEeCCCCEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHH-hhCceEEEEEEEEehhcCCcceEEEEEEE
Confidence 477899999999999999753320 000 111 1233 4555566667887 55666666
Q ss_pred eeeCCChhHHHHHHHHHH
Q 024592 141 LRPIIDFNEITSHFVECI 158 (265)
Q Consensus 141 i~~v~d~Nei~~H~Levi 158 (265)
+.|+. +.....++|+-+
T Consensus 148 i~~~~-~~~~~~~l~~~i 164 (166)
T cd04476 148 VAPVD-YKKESKRLIQSI 164 (166)
T ss_pred cccCC-HHHHHHHHHHHh
Confidence 66664 334566666544
No 242
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=85.01 E-value=3.5 Score=34.70 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=40.8
Q ss_pred EeEEEEEEEEEE---eee---CCCeEEEEEEc-------CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592 67 VNTITVVGIVCD---MQD---KEPQFIFLIDD-------GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH 126 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~---~~t~~~y~LdD-------gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~ 126 (265)
++.|.|+|+|.. +.. ....+.|+|-- .+| -+.|..|..-+. .....++.|+.|.|.|+
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 688999999965 221 22456666642 234 367888865322 22355899999999999
Q ss_pred eee
Q 024592 127 LKA 129 (265)
Q Consensus 127 i~~ 129 (265)
|+.
T Consensus 84 L~~ 86 (175)
T PRK13732 84 LRT 86 (175)
T ss_pred EEe
Confidence 986
No 243
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=85.00 E-value=2.2 Score=41.94 Aligned_cols=63 Identities=17% Similarity=0.271 Sum_probs=48.7
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-ccccccccCCCCEEEEEEEeeee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-EFNEVNQISKGMYVRVYGHLKAF 130 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~g~yVrV~G~i~~f 130 (265)
..|+|.|||-.+++...-+...|-|.+|.+.+..-.++.. --+....++.-..|+|.|.++.=
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 5799999999999888888889999999877775543211 11345678888899999988764
No 244
>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=84.89 E-value=1.7 Score=30.50 Aligned_cols=33 Identities=12% Similarity=0.275 Sum_probs=30.3
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
..++.++|+..++.+...|...|..|.++|.|=
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 457899999999999999999999999999773
No 245
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=84.71 E-value=3.3 Score=35.20 Aligned_cols=32 Identities=38% Similarity=0.629 Sum_probs=24.6
Q ss_pred eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 96 RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 96 ~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
-|+|..|...+. .....|+.|+.|.|.|+|+.
T Consensus 54 fi~V~~Wg~~Ae--~va~~L~KGd~V~V~GrL~~ 85 (186)
T PRK07772 54 FLRCSIWRQAAE--NVAESLTKGMRVIVTGRLKQ 85 (186)
T ss_pred EEEEEEecHHHH--HHHHhcCCCCEEEEEEEEEc
Confidence 478999976432 23456899999999999985
No 246
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=84.59 E-value=1.9 Score=41.96 Aligned_cols=61 Identities=26% Similarity=0.294 Sum_probs=50.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec--CCceeeccC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID--EFHYKSAVN 264 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD--d~hyk~t~~ 264 (265)
+++..+..||..|... .+++..+|++.++++.+.|..+++.|...|.|-..| ...|..|..
T Consensus 3 ~Lt~~e~~vL~~L~~~------~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTee 65 (489)
T PRK04172 3 ELHPNEKKVLKALKEL------KEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEE 65 (489)
T ss_pred CCCHHHHHHHHHHHhC------CCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHH
Confidence 4678899999999642 378999999999999999999999999999988733 346666654
No 247
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=84.45 E-value=1.8 Score=38.65 Aligned_cols=50 Identities=18% Similarity=0.337 Sum_probs=44.4
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCC-cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNG-VHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~G-v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
..|++..+.|+++|++.+ | +...||.+.+++|...|-.+|..|+..|.|=
T Consensus 191 ~~L~~~e~~il~~i~~~G------Gri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe 241 (258)
T COG2512 191 YDLNEDEKEILDLIRERG------GRITQAELRRALGLSKTTVSRILRRLEKRGLIE 241 (258)
T ss_pred CCCCHHHHHHHHHHHHhC------CEEeHHHHHHhhCCChHHHHHHHHHHHhCCceE
Confidence 357888899999999853 5 7889999999999999999999999999873
No 248
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.13 E-value=2.8 Score=35.85 Aligned_cols=45 Identities=16% Similarity=0.234 Sum_probs=39.4
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++|+.++.+. ..|.+..||+++|++++..|+.-+.+|...|.+-.
T Consensus 165 r~Vl~~~~~g-----~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 165 NAVRKLFKEP-----GVQHTAETVAQALTISRTTARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHHHcC-----CCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEE
Confidence 4788888642 34899999999999999999999999999999866
No 249
>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=84.03 E-value=2.3 Score=28.54 Aligned_cols=42 Identities=14% Similarity=0.226 Sum_probs=34.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.|++.+..|+.++.. |.+..+|++.+++++..|+.-+..+..
T Consensus 3 ~LT~~E~~vl~~l~~--------G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--------GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp SS-HHHHHHHHHHHT--------TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--------cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 477888889999864 899999999999999999988877653
No 250
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=83.87 E-value=2.1 Score=31.46 Aligned_cols=39 Identities=18% Similarity=0.165 Sum_probs=33.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592 224 RNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAV 263 (265)
Q Consensus 224 ~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~ 263 (265)
+.+|++.++++...|..+|+.|.+.|.|.. -+ --|..|.
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~-~~~~lT~ 41 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY-RGITLTE 41 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC-CceEech
Confidence 468999999999999999999999999999 54 3565554
No 251
>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=83.86 E-value=4.5 Score=26.14 Aligned_cols=41 Identities=12% Similarity=0.179 Sum_probs=31.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.|++-++.|+...- -+|.+..+|++.++++...|+.....-
T Consensus 4 ~L~~~er~vi~~~y-------~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRY-------FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHH-------TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-------cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 57788888887653 248899999999999999998876654
No 252
>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=83.51 E-value=4.6 Score=32.11 Aligned_cols=43 Identities=21% Similarity=0.194 Sum_probs=35.9
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec-CCceeec
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID-EFHYKSA 262 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD-d~hyk~t 262 (265)
.-++.++|++++++|..-++++|+.|...|.|-+ -- ..-|..+
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~ 68 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLG 68 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEecc
Confidence 4689999999999999999999999999999977 22 2356544
No 253
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=83.17 E-value=3.6 Score=43.47 Aligned_cols=58 Identities=9% Similarity=0.013 Sum_probs=43.7
Q ss_pred EEEEEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 69 TITVVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 69 ~V~iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
.|+++|.|.+++. ......++|+|.||.|+|..|.+.-. ....+.+++++.|.|+.+.
T Consensus 899 ~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~~~~---~~~~l~~~~~~~~~~~~~~ 960 (973)
T PRK07135 899 EYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDNDYL---LFETLKKGDIYEFLISKSK 960 (973)
T ss_pred eEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHHHHH---HHHHhhcCCEEEEEEEEcC
Confidence 4678888877542 34677889999999999999975321 2234888899999998766
No 254
>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=83.16 E-value=3 Score=27.30 Aligned_cols=40 Identities=10% Similarity=0.094 Sum_probs=28.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+....- .|.+..+|++.++++++.|+..+..
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 467788888877543 4999999999999999999887753
No 255
>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=83.07 E-value=2.4 Score=34.93 Aligned_cols=42 Identities=24% Similarity=0.277 Sum_probs=35.3
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
-.|++.|-.. .-++.++|++.|+++..+||++|..|.++|.|
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 256
>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=83.02 E-value=6 Score=32.71 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=27.2
Q ss_pred EEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE
Q 024592 77 CDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY 124 (265)
Q Consensus 77 ~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~ 124 (265)
........++.|.|.|.||.++|..+-.-. .-..++||-+|.+
T Consensus 123 ~KK~v~~~~~~YeI~DnTG~MeVvv~G~~~-----ni~CEeGDKLrL~ 165 (170)
T PF02760_consen 123 HKKTVNKKNTIYEIQDNTGKMEVVVYGKWH-----NIKCEEGDKLRLF 165 (170)
T ss_dssp EEEEEESSEEEEEEEETTEEEEEEEEGGGC-----GCC--TT-EEEEE
T ss_pred EEEEEcCCeEEEEEecCCCcEEEEEeccCc-----ccccCCCCeEEEE
Confidence 334455678999999999999999764321 1345677755543
No 257
>PRK04036 DNA polymerase II small subunit; Validated
Probab=82.98 E-value=4.5 Score=39.62 Aligned_cols=61 Identities=16% Similarity=0.276 Sum_probs=42.4
Q ss_pred eEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592 68 NTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK 128 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~ 128 (265)
..|.|||.|.++.... ....+.|+|.||+|.+..-.+...-......+-.|..|-|.|++.
T Consensus 154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v~G~~~ 215 (504)
T PRK04036 154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGVEGTLS 215 (504)
T ss_pred ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEEEEEEc
Confidence 4689999999886443 344789999999999876322100001134688899999999875
No 258
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=82.96 E-value=3.4 Score=35.43 Aligned_cols=37 Identities=16% Similarity=0.174 Sum_probs=33.0
Q ss_pred CCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 217 ANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 217 ~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
....=++..+|+++|+++..-||+||..|..+|.|..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~ 66 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSVNALSV 66 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe
Confidence 3345678899999999999999999999999999976
No 259
>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=82.86 E-value=2.5 Score=27.05 Aligned_cols=33 Identities=12% Similarity=0.232 Sum_probs=24.0
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
...|+++++ .|+++.+|++.++++...|...|.
T Consensus 11 ~~~i~~l~~--------~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA--------EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH--------TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH--------CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 456777764 389999999999999999987763
No 260
>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=82.77 E-value=4.4 Score=36.51 Aligned_cols=43 Identities=14% Similarity=0.204 Sum_probs=36.0
Q ss_pred Cc-CHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 221 GV-HRNVISQQLN--LPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 221 Gv-~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
|- ...+|+++|+ ++.++|+++|++|..-|.|=-..|..|+.|.
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~ 181 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTD 181 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeec
Confidence 44 6889999997 9999999999999999999764445677764
No 261
>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=82.69 E-value=3.6 Score=30.23 Aligned_cols=36 Identities=25% Similarity=0.270 Sum_probs=26.6
Q ss_pred CCCeEEEEEecccccccccccccCCCCEEEEEEEeeee
Q 024592 93 GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF 130 (265)
Q Consensus 93 gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f 130 (265)
.+--+.|..|.+.+. .-...++.|++|.|.|+++..
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 344589999976332 223468999999999999875
No 262
>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=82.62 E-value=3.4 Score=32.27 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=43.8
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.++..-++.|+++.+. -.++.||+..+++|..-++--+..|.+.|+|--
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 4678899999998764 569999999999999999999999999999864
No 263
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=82.41 E-value=2.2 Score=37.53 Aligned_cols=47 Identities=21% Similarity=0.429 Sum_probs=41.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..+-+||++|+.. .++++.||++.+++|-+.+..-+..|.+.|.|-+
T Consensus 23 ~vRv~Il~lL~~k------~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 23 KVRVAILQLLHRK------GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHh------CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence 4667789999874 3699999999999999999999999999999876
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=82.40 E-value=2.5 Score=35.01 Aligned_cols=46 Identities=20% Similarity=0.352 Sum_probs=39.7
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLN--LPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs 253 (265)
...|+++|+.. +.-.++.+|..-|+ ++-..|.++|+.|.++|.|-.
T Consensus 3 e~~Il~y~~~q-----NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 3 EDAILEYMKEQ-----NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHHHHc-----CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee
Confidence 46799999874 46789999999994 999999999999999998744
No 265
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=82.37 E-value=3 Score=43.62 Aligned_cols=42 Identities=12% Similarity=0.086 Sum_probs=36.2
Q ss_pred CCCcCHHHHHHhc------------CCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592 219 NNGVHRNVISQQL------------NLPMDKLMEALESLNENSLVYSIDEFHYK 260 (265)
Q Consensus 219 ~~Gv~~~~I~~~l------------~~~~~~v~~al~~L~~eG~IYsiDd~hyk 260 (265)
..++++++|.+.+ ++++++++++|+.|..+|.||.....+||
T Consensus 857 ~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i~~~~~g~y~ 910 (915)
T PTZ00111 857 NKSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTAVRENNSYYL 910 (915)
T ss_pred CCceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeEeeeCCCchh
Confidence 3589999998654 59999999999999999999996666787
No 266
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=82.21 E-value=3.7 Score=32.19 Aligned_cols=47 Identities=17% Similarity=0.198 Sum_probs=41.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+...+||.+|... ..+++.+|++.++++.+.|-.-|..|.+.|.|-+
T Consensus 16 ptRl~IL~~L~~~------~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~ 62 (117)
T PRK10141 16 ETRLGIVLLLRES------GELCVCDLCTALDQSQPKISRHLALLRESGLLLD 62 (117)
T ss_pred HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 5777899998642 2589999999999999999999999999999955
No 267
>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=82.02 E-value=5 Score=30.03 Aligned_cols=61 Identities=18% Similarity=0.183 Sum_probs=47.1
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH----------HHhhCCeE-Ee-ecC--CceeeccC
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE----------SLNENSLV-YS-IDE--FHYKSAVN 264 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~----------~L~~eG~I-Ys-iDd--~hyk~t~~ 264 (265)
+.+..+||.+|.+. -.+.....+|++..+.+.++|.-||. .|+.-|.+ .. .+. ..|+.|.-
T Consensus 8 S~~R~~vl~~L~~~----yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~ 82 (90)
T PF07381_consen 8 SKVRKKVLEYLCSI----YPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEK 82 (90)
T ss_pred HHHHHHHHHHHHHc----CCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChh
Confidence 46889999999875 24688999999999999999999995 58888998 44 322 25555543
No 268
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=81.67 E-value=5.7 Score=34.64 Aligned_cols=81 Identities=17% Similarity=0.350 Sum_probs=54.0
Q ss_pred eEEeEEEEEEEEEEe---ee---CCCeEEEEEEc-----CCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eC
Q 024592 65 ADVNTITVVGIVCDM---QD---KEPQFIFLIDD-----GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQ 131 (265)
Q Consensus 65 ~~v~~V~iVG~V~~v---~~---~~t~~~y~LdD-----gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~ 131 (265)
...+.|.|+|.+..- +. ....+.|+|-= .|--|+|..|...+. ....++.|+.|.|.|+|+. |.
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 447899999999652 21 22456666652 244699999976442 2345999999999999986 43
Q ss_pred Cc-----------cEEEEEEeeeCCChh
Q 024592 132 DK-----------RSLNAYSLRPIIDFN 148 (265)
Q Consensus 132 ~~-----------~~i~~~~i~~v~d~N 148 (265)
++ -.|.+..+..++...
T Consensus 184 ~k~g~~~g~kr~~~eV~v~~i~~l~~~~ 211 (219)
T PRK05813 184 KKLSEGEVVTKVAYEVSISKMEKVEKEE 211 (219)
T ss_pred cCCCCccceEEEEEEEEEEEEEEcCChh
Confidence 21 246666776665533
No 269
>PRK03837 transcriptional regulator NanR; Provisional
Probab=81.65 E-value=4.9 Score=34.74 Aligned_cols=35 Identities=17% Similarity=0.227 Sum_probs=31.6
Q ss_pred CCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+=+ +..+|+++|+.+..-||+||..|..+|.|..
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 3446 7899999999999999999999999999976
No 270
>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=81.60 E-value=2.1 Score=31.57 Aligned_cols=39 Identities=23% Similarity=0.343 Sum_probs=35.7
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
..-+++++|++.|++++++++..|..|+.+|.|-- ||..
T Consensus 58 y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~ 97 (105)
T PF01399_consen 58 YSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQV 97 (105)
T ss_dssp -SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETT
T ss_pred hcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECC
Confidence 45799999999999999999999999999999998 8864
No 271
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=81.58 E-value=3.8 Score=36.21 Aligned_cols=59 Identities=14% Similarity=0.211 Sum_probs=45.4
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
..-+||..|... ..-++..||++.++++.+-|-+-+.+|.+||+|=+----+|..|.-|
T Consensus 11 t~fqIL~ei~~~-----qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG 69 (260)
T COG1497 11 TRFQILSEIAVR-----QPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEITKKG 69 (260)
T ss_pred hHHHHHHHHHHh-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEEehhH
Confidence 445577666432 23578999999999999999999999999999988333478877543
No 272
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=81.52 E-value=5.3 Score=35.90 Aligned_cols=62 Identities=15% Similarity=0.113 Sum_probs=48.9
Q ss_pred CCChhHHHHHHHhcCcCCCC-CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592 198 EGKSIDQMVLDFLRRPEFLA-NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYK 260 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~-~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk 260 (265)
.+....++||..|++...-+ =..=-+.++|-+.|+++-.+.++||-.|..+|.||. |-+.|+
T Consensus 222 ~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q-~g~~t~ 284 (287)
T COG2996 222 MLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ-DGDGTE 284 (287)
T ss_pred hhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE-cCceEE
Confidence 46678899999998764211 122347899999999999999999999999999998 555554
No 273
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=81.52 E-value=6.1 Score=32.39 Aligned_cols=61 Identities=15% Similarity=0.198 Sum_probs=41.1
Q ss_pred EeEEEEEEEEEE---eee---CCCeEEEEEE------cC-CC-------eEEEEEecc-cccccccccccCCCCEEEEEE
Q 024592 67 VNTITVVGIVCD---MQD---KEPQFIFLID------DG-TG-------RIECSRWAH-EQMEFNEVNQISKGMYVRVYG 125 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------Dg-TG-------~I~~~~w~~-~~~~~~~~~~~~~g~yVrV~G 125 (265)
++.|.|+|+|.. ++. ....+.|+|- |. +| =+.|..|.. .+. .....++.|+.|.|.|
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 222 2246777776 21 22 377888874 221 1234589999999999
Q ss_pred Eeee
Q 024592 126 HLKA 129 (265)
Q Consensus 126 ~i~~ 129 (265)
+|+.
T Consensus 83 rL~~ 86 (152)
T PRK06642 83 SLQT 86 (152)
T ss_pred EEEe
Confidence 9986
No 274
>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=81.45 E-value=5.2 Score=25.78 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=31.1
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
+..+..|+.++. .|++..+|++.++++...|+..+..+..
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 3789999999999999999998887654
No 275
>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=81.39 E-value=3.5 Score=28.41 Aligned_cols=47 Identities=21% Similarity=0.160 Sum_probs=36.8
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++-.+|.++|-.. -..+..+|.+..+++.++|+++|--|+..+.++-
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 4667788877553 2468999999999999999999999999988763
No 276
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=81.20 E-value=6.3 Score=30.01 Aligned_cols=57 Identities=14% Similarity=0.216 Sum_probs=42.9
Q ss_pred CCCChhHHHHHH-HhcCcC-CCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 197 DEGKSIDQMVLD-FLRRPE-FLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~-~i~~~~-~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+++.-+-+|+. ++|.+- ..+...-|+..+|++..+++.+.|.+++.+|++.|.|..
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 356655556554 455432 224456899999999999999999999999999999954
No 277
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=81.06 E-value=4 Score=35.81 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=31.4
Q ss_pred CCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~ 58 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLS 58 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 3457 5789999999999999999999999999976
No 278
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=81.04 E-value=4.5 Score=35.33 Aligned_cols=37 Identities=14% Similarity=0.261 Sum_probs=32.5
Q ss_pred CCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 217 ANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 217 ~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
....-+ +..+|+++|+.+..-||+||..|..+|.|-.
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~ 63 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIET 63 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 344567 6889999999999999999999999999965
No 279
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=80.91 E-value=3.3 Score=39.43 Aligned_cols=57 Identities=18% Similarity=0.152 Sum_probs=44.2
Q ss_pred HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccC
Q 024592 206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVN 264 (265)
Q Consensus 206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~ 264 (265)
|+..+.+.. ..+++++.++|+++++.+++.+++.++.|.+.|.|-..+++.|..+.|
T Consensus 297 iL~~l~~~~--~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~l~rd 353 (412)
T PRK04214 297 LLGRLDQAR--KHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWVLARD 353 (412)
T ss_pred HHHHHHHHH--hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceEecCC
Confidence 555553211 234699999999999999999999999999999997666567876544
No 280
>PHA00738 putative HTH transcription regulator
Probab=80.62 E-value=4.7 Score=31.13 Aligned_cols=48 Identities=21% Similarity=0.324 Sum_probs=42.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+.+++||++|... +.+.+.+|++.++++-+.|-.-|.-|.+.|.|-+
T Consensus 11 dptRr~IL~lL~~~------e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~s 58 (108)
T PHA00738 11 KILRRKILELIAEN------YILSASLISHTLLLSYTTVLRHLKILNEQGYIEL 58 (108)
T ss_pred CHHHHHHHHHHHHc------CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEE
Confidence 47899999999752 2589999999999999999999999999998855
No 281
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=80.57 E-value=3 Score=26.59 Aligned_cols=38 Identities=13% Similarity=0.174 Sum_probs=20.3
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
|+.-++..+..+.+ .|.++.+||+.|+.+.+.|...|.
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 44445555555443 599999999999999999988775
No 282
>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=80.29 E-value=2.1 Score=29.10 Aligned_cols=36 Identities=19% Similarity=0.264 Sum_probs=30.8
Q ss_pred CCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeEEe
Q 024592 218 NNNGVHRNVISQQL---NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 218 ~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~IYs 253 (265)
-..|++.+++.+++ +++...+...|+.|+.+|.|-.
T Consensus 14 lr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~ 52 (59)
T PF09106_consen 14 LRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKV 52 (59)
T ss_dssp TSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEE
T ss_pred CccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeee
Confidence 46899999999988 6899999999999999999875
No 283
>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=79.88 E-value=6 Score=34.17 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=32.1
Q ss_pred CCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 218 NNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 218 ~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
...=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~ 62 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI 62 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34457 6899999999999999999999999999976
No 284
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=79.85 E-value=5 Score=34.58 Aligned_cols=54 Identities=7% Similarity=0.110 Sum_probs=43.3
Q ss_pred CChhH-HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 199 GKSID-QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 199 l~~~~-~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
+++.. +.++.++.+. ...|.+.++|+++|++++..|+.-+.+|.+-|.+.. ++.
T Consensus 159 Lt~re~~~l~~~i~~~----~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 214 (239)
T PRK10430 159 LTPQTLRTLCQWIDAH----QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHY 214 (239)
T ss_pred CCHHHHHHHHHHHHhC----CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeec
Confidence 55444 3456677553 357999999999999999999999999999999977 654
No 285
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=79.77 E-value=6 Score=32.49 Aligned_cols=46 Identities=15% Similarity=0.036 Sum_probs=39.4
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
.-+...+|++.|+.+++.|.+.+..|.+.|.|=-+....++.|..|
T Consensus 23 ~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G 68 (154)
T COG1321 23 GFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKG 68 (154)
T ss_pred CcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhh
Confidence 3578999999999999999999999999999966677777777544
No 286
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=79.31 E-value=3.6 Score=44.13 Aligned_cols=63 Identities=16% Similarity=0.277 Sum_probs=46.0
Q ss_pred EEEEEEEEEEeeeC------CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc
Q 024592 69 TITVVGIVCDMQDK------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK 133 (265)
Q Consensus 69 ~V~iVG~V~~v~~~------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~ 133 (265)
.+.++|.|+.++.. ......+|+|.||.++|..|...-. .....+.++..+.|.|+++.-+..
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 47777888776532 1267789999999999999965322 234567778999999999884433
No 287
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=79.24 E-value=6.3 Score=34.59 Aligned_cols=37 Identities=22% Similarity=0.202 Sum_probs=32.3
Q ss_pred CCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 217 ANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 217 ~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
...+=+ +..+++++|+++..-||+||..|..+|.|..
T Consensus 28 ~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~ 65 (257)
T PRK10225 28 NPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEV 65 (257)
T ss_pred CCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 334567 5889999999999999999999999999975
No 288
>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=79.15 E-value=3.8 Score=28.66 Aligned_cols=41 Identities=17% Similarity=0.426 Sum_probs=34.0
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcC-----CCHHHHHHHHHHHhhCCe
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLN-----LPMDKLMEALESLNENSL 250 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-----~~~~~v~~al~~L~~eG~ 250 (265)
.||++|++. +.-+...+|++.|. +++..|+.-|..|..+|.
T Consensus 2 ~IL~~L~~~-----~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Gl 47 (66)
T PF08461_consen 2 FILRILAES-----DKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGL 47 (66)
T ss_pred HHHHHHHHc-----CCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCC
Confidence 488999874 34688999999883 777999999999999993
No 289
>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=79.10 E-value=4.2 Score=29.41 Aligned_cols=53 Identities=13% Similarity=0.109 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH-HHhhCCeEE
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE-SLNENSLVY 252 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~-~L~~eG~IY 252 (265)
.+|..+++++|++|.+.- ..--+.++-|+..++.+.+.|.+.++ +|+..|.|-
T Consensus 4 ~GLd~~D~~yL~~l~~~f---~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~ 57 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENF---KGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQ 57 (76)
T ss_dssp TS-BHHHHHHHHHHHHCS---TTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEE
T ss_pred ccCCHHHHHHHHHHHHHc---CCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHh
Confidence 468899999999997742 23347889999999999999998887 788888874
No 290
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=79.10 E-value=4.1 Score=27.42 Aligned_cols=32 Identities=25% Similarity=0.407 Sum_probs=23.0
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHHHHHHHHH
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDKLMEALES 244 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~v~~al~~ 244 (265)
.|++.++ .|.+.++|++.+. ++.++|+.||.+
T Consensus 23 ~i~~~~~--------~G~s~eeI~~~yp~Lt~~~i~aAl~y 55 (56)
T PF04255_consen 23 DILDLLA--------AGESPEEIAEDYPSLTLEDIRAALAY 55 (56)
T ss_dssp HHHHHHH--------TT--HHHHHHHSTT--HHHHHHHHHH
T ss_pred HHHHHHH--------cCCCHHHHHHHCCCCCHHHHHHHHHh
Confidence 4666663 3899999999996 999999999986
No 291
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=79.04 E-value=3.6 Score=35.24 Aligned_cols=58 Identities=12% Similarity=0.117 Sum_probs=42.5
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-e--cCCceeecc
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-I--DEFHYKSAV 263 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-i--Dd~hyk~t~ 263 (265)
.+|.-|...+.... .+++..+++++++.+.+..-..|.+|.++|+|+- + +-.--+.|.
T Consensus 4 ~~lk~l~~~~a~~~-~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTe 64 (214)
T COG1339 4 RLLKKLALRGAVRG-VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITE 64 (214)
T ss_pred HHHHHHHHhhhhcC-ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehH
Confidence 45555544432222 6799999999999999999999999999999997 5 333444443
No 292
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=79.01 E-value=5.7 Score=34.05 Aligned_cols=35 Identities=23% Similarity=0.328 Sum_probs=31.5
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..=++..+++++|+++..-||+||..|..+|.|-.
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~ 62 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAERLVTV 62 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEE
Confidence 44578899999999999999999999999999865
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=78.79 E-value=8.1 Score=25.89 Aligned_cols=45 Identities=9% Similarity=0.136 Sum_probs=32.6
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
|++-|.++|..--+.+--....+++..+|++.|+++.+.+.+-|.
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 456777887765554433556799999999999998887655544
No 294
>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=78.54 E-value=6.2 Score=31.33 Aligned_cols=85 Identities=18% Similarity=0.338 Sum_probs=40.2
Q ss_pred eeeHHHHhcC-CCC-CCCCeEECCeEEeEEEEEEEEEEeeeCC-CeEEEEEEcCCC--eEEEEEecccccccccccccCC
Q 024592 43 PMTVKQLSEL-SSN-DESSASIDGADVNTITVVGIVCDMQDKE-PQFIFLIDDGTG--RIECSRWAHEQMEFNEVNQISK 117 (265)
Q Consensus 43 PvtIkqi~~a-~~~-~~~~f~i~g~~v~~V~iVG~V~~v~~~~-t~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~ 117 (265)
+++..+|.+. ... ....=.+.| ..|.+-|.|.++.... ........+..+ .|.|.+-.++.. ......++.
T Consensus 44 ~~sa~~L~~~y~~N~~~A~~kY~g---K~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~-~~~~~~l~~ 119 (144)
T PF12869_consen 44 SVSAEELYKDYKDNEVAADKKYKG---KIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEK-RASVAKLKK 119 (144)
T ss_dssp EEEHHHHHHHHHH-HHHHHHHHTT----EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGG-HHHHHH--T
T ss_pred eecHHHHHHHHHhCHHHHHhhcCC---CEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhh-hhhHhcCCC
Confidence 8899999886 111 000112234 4677789999997633 333333333233 455554433311 112345999
Q ss_pred CCEEEEEEEeeeeC
Q 024592 118 GMYVRVYGHLKAFQ 131 (265)
Q Consensus 118 g~yVrV~G~i~~f~ 131 (265)
|+.|.|.|++..+.
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 99999999999885
No 295
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=77.83 E-value=6.6 Score=34.35 Aligned_cols=35 Identities=17% Similarity=0.346 Sum_probs=31.2
Q ss_pred CCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+=+ +..+|+++|+.+..-||+||..|..+|.|-.
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~ 66 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLR 66 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 3345 6889999999999999999999999999975
No 296
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.60 E-value=6.5 Score=32.61 Aligned_cols=44 Identities=23% Similarity=0.164 Sum_probs=36.6
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeec
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSA 262 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t 262 (265)
+.-++.++|++++++|..-++++|..|...|.|-+ =...-|...
T Consensus 23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~La 68 (164)
T PRK10857 23 AGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLG 68 (164)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeecc
Confidence 34699999999999999999999999999999987 233355543
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=77.52 E-value=6.6 Score=28.08 Aligned_cols=50 Identities=18% Similarity=0.268 Sum_probs=39.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc--C----CCH----HHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL--N----LPM----DKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l--~----~~~----~~v~~al~~L~~eG~IYs 253 (265)
+..++|++.|++. ....|.+...|.+-+ + .++ ..++.+|..++++|.+-.
T Consensus 4 ~y~~mI~eAI~~l---~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~ 63 (77)
T PF00538_consen 4 PYSDMILEAIKAL---KERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQ 63 (77)
T ss_dssp CHHHHHHHHHHHC---CSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEE
T ss_pred CHHHHHHHHHHHc---CCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEe
Confidence 5678899999875 345799999998776 2 333 459999999999999876
No 298
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=77.50 E-value=6.7 Score=37.11 Aligned_cols=34 Identities=15% Similarity=0.220 Sum_probs=31.1
Q ss_pred CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.=+ +..+++++|+.+...|++|++.|..||.|++
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 6899999999999999999999999999997
No 299
>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=77.37 E-value=4.1 Score=27.59 Aligned_cols=39 Identities=21% Similarity=0.394 Sum_probs=31.7
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
+-.++++|-+ +.-++.++|++.++.++..|+..|.+|.+
T Consensus 7 q~~Ll~~L~~------~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLK------NKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHH------HTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHc------CCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3457887754 24789999999999999999999999985
No 300
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=77.15 E-value=7.3 Score=29.19 Aligned_cols=52 Identities=19% Similarity=0.227 Sum_probs=43.0
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
++..+-.||.+|...+ +++..+|++.++++...|...|+.|+..|.|.. .|.
T Consensus 20 lt~~q~~~L~~l~~~~------~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 20 LTPPQYQVLLALYEAG------GITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred CCHHHHHHHHHHHHhC------CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 6677888888887642 222299999999999999999999999999999 664
No 301
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=76.49 E-value=8.9 Score=33.58 Aligned_cols=37 Identities=16% Similarity=0.152 Sum_probs=32.0
Q ss_pred CCCCCcC-HHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 217 ANNNGVH-RNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 217 ~~~~Gv~-~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
....=++ ..+|+++|+.+..-||+||..|..+|.|..
T Consensus 27 ~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~ 64 (253)
T PRK11523 27 LVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEV 64 (253)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3345674 789999999999999999999999999965
No 302
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=76.47 E-value=6.9 Score=31.96 Aligned_cols=34 Identities=21% Similarity=0.142 Sum_probs=31.9
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-++.++|++++++|..-+++++..|...|.|-|
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S 56 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVET 56 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3589999999999999999999999999999987
No 303
>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=76.39 E-value=9.4 Score=27.31 Aligned_cols=45 Identities=13% Similarity=0.250 Sum_probs=39.2
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+.+.|+.++... .++.+++.+..+++.+++--.|..|.++|.|+.
T Consensus 6 ~~~~IL~~ls~~-------c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 6 VTQKILIILSKR-------CCTLEELEEKTGISKNTLLVYLSRLAKRGIIER 50 (72)
T ss_pred HHHHHHHHHHhc-------cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 456677777641 679999999999999999999999999999986
No 304
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=75.93 E-value=8.1 Score=30.99 Aligned_cols=50 Identities=10% Similarity=0.198 Sum_probs=43.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-|++-...+|+.|+.. .-.++.|+++..+...++|-..|..|.+-|.|.-
T Consensus 61 vLsp~nleLl~~Ia~~------~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~f 110 (144)
T COG4190 61 VLSPRNLELLELIAQE------EPASINELAELVGRDVKNVHRTLSTLADLGLIFF 110 (144)
T ss_pred HhChhHHHHHHHHHhc------CcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEE
Confidence 3667777888888764 3569999999999999999999999999999976
No 305
>PRK06474 hypothetical protein; Provisional
Probab=75.14 E-value=7.9 Score=32.47 Aligned_cols=51 Identities=14% Similarity=0.329 Sum_probs=43.5
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEeec
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYSID 255 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYsiD 255 (265)
++.+.+|+++|... ...+++.+|++.+ +++...|-..|..|.+.|.|-.+.
T Consensus 10 ~p~R~~Il~~L~~~-----~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 10 HPVRMKICQVLMRN-----KEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred CHHHHHHHHHHHhC-----CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 46788899999763 2249999999999 699999999999999999998744
No 306
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=74.77 E-value=21 Score=29.16 Aligned_cols=55 Identities=20% Similarity=0.264 Sum_probs=43.9
Q ss_pred eEEEEEEEEEE--eee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592 68 NTITVVGIVCD--MQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK 128 (265)
Q Consensus 68 ~~V~iVG~V~~--v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~ 128 (265)
.++++.|.|.. ++. ....+.|.+.|+-..|+|.+--. -++-|++|+=|-+.|.+.
T Consensus 52 ~rlR~GGlV~~GSv~R~~~~~~v~F~vtD~~~~v~V~Y~Gi------LPDLFREGQgVVa~G~~~ 110 (153)
T COG2332 52 QRLRLGGLVEAGSVQRDPGSLKVSFVVTDGNKSVTVSYEGI------LPDLFREGQGVVAEGQLQ 110 (153)
T ss_pred cEEEEeeeEeeceEEecCCCcEEEEEEecCCceEEEEEecc------CchhhhcCCeEEEEEEec
Confidence 67888999965 344 56899999999999999886432 356789999999999984
No 307
>KOG2411 consensus Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]
Probab=74.54 E-value=9.5 Score=37.20 Aligned_cols=63 Identities=13% Similarity=0.033 Sum_probs=48.2
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAF 130 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f 130 (265)
..|.|+||+.-...+.....|.|-|.+|.|.+..-.+.-.. ......+..-+.|+|.|++..-
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 57999999998887788888999999999999876553211 1223456777899999998764
No 308
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=74.42 E-value=8.2 Score=37.32 Aligned_cols=73 Identities=10% Similarity=0.113 Sum_probs=50.5
Q ss_pred EEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc-c--c-cccccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592 69 TITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ-M--E-FNEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSL 141 (265)
Q Consensus 69 ~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~-~--~-~~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i 141 (265)
.|+|.|+|.+++... .-+.|.|.++-..|.+..-...- . + ......++.||+|.|.|....- .+..+|.+..+
T Consensus 106 ~~svaGRI~s~R~sGsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~pgrt~~gELSi~~~~~ 184 (560)
T KOG1885|consen 106 IVSVAGRIHSKRESGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGYPGRTKSGELSIIPNEI 184 (560)
T ss_pred eeeeeeeEeeeeccCCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecCCCcCCCceEEEeecch
Confidence 499999999998776 56778998887778777543321 1 1 1234568999999999997643 34455555444
No 309
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=73.95 E-value=9.3 Score=33.25 Aligned_cols=52 Identities=19% Similarity=0.246 Sum_probs=43.2
Q ss_pred CCCChhH-HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 197 DEGKSID-QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~-~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+++... +.|.+.|+.+ +.+.+.+++++.++++.-.+|.-|++|++.|.|-.
T Consensus 153 kGi~~~Tl~~i~~~~~~~-----~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a 205 (224)
T COG4565 153 KGLDELTLQKVREALKEP-----DQELTAEELAQALGISRVTARRYLEYLVSNGILEA 205 (224)
T ss_pred CCcCHHHHHHHHHHHhCc-----CCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeE
Confidence 4554433 4588888842 57899999999999999999999999999999876
No 310
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=73.64 E-value=7.1 Score=38.08 Aligned_cols=60 Identities=12% Similarity=0.127 Sum_probs=49.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA 265 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~ 265 (265)
+++..||..+.+. +..++.+++++.++++.++|..++..|...|.|=. .....|..|..|
T Consensus 3 ~~e~~iL~~l~~~-----~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG 64 (492)
T PLN02853 3 MAEEALLGALSNN-----EEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIKRETWVLTEEG 64 (492)
T ss_pred hHHHHHHHHHHhc-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHH
Confidence 5778899988752 22378999999999999999999999999998766 777788888754
No 311
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=73.64 E-value=14 Score=30.86 Aligned_cols=65 Identities=18% Similarity=0.287 Sum_probs=40.8
Q ss_pred EeEEEEEEEEEE---eeeC---CCeEEEEEEc-------CCC-------eEEEEEecc-cccccccccccCCCCEEEEEE
Q 024592 67 VNTITVVGIVCD---MQDK---EPQFIFLIDD-------GTG-------RIECSRWAH-EQMEFNEVNQISKGMYVRVYG 125 (265)
Q Consensus 67 v~~V~iVG~V~~---v~~~---~t~~~y~LdD-------gTG-------~I~~~~w~~-~~~~~~~~~~~~~g~yVrV~G 125 (265)
+++|.|+|+|.. ++.. ...+.|.|-= .+| =+.|..|.+ .+. .....++.|+.|.|.|
T Consensus 5 mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae--~~~~~LkKG~~V~VeG 82 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCK--VAEQYLKKGAKVYIEG 82 (166)
T ss_pred ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHH--HHHHhcCCCCEEEEEE
Confidence 688999999865 2221 2345555532 133 367888864 221 1235689999999999
Q ss_pred Eeee--eCCc
Q 024592 126 HLKA--FQDK 133 (265)
Q Consensus 126 ~i~~--f~~~ 133 (265)
+|+. |.++
T Consensus 83 rL~~r~w~dk 92 (166)
T PRK06341 83 QLQTRKWTDQ 92 (166)
T ss_pred EEEeCcEECC
Confidence 9975 5443
No 312
>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=73.57 E-value=48 Score=32.75 Aligned_cols=73 Identities=18% Similarity=0.279 Sum_probs=50.8
Q ss_pred CCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee--eeC
Q 024592 54 SNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK--AFQ 131 (265)
Q Consensus 54 ~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~--~f~ 131 (265)
..+.-.|.+.+..+..++.+| ...+.+.+.++-..++|+.|.... ....+..+.++.+.+++. .|+
T Consensus 460 gnp~P~F~~~~~~i~~~~~~g--------~~h~kl~~~~~~~~~~ai~F~~~~----~~~~~~~~~~~~ii~~l~~n~~~ 527 (539)
T TIGR00644 460 GNPEPLFLLKNLRVEDIKLLG--------ENHLKLSLKSGGKNIEAIAFNAGD----LELELNLGRPLDVAGKLSINEWR 527 (539)
T ss_pred CCCCCEEEecCeEEEEEEEcC--------CCEEEEEEecCCEEEEEEEEcCcc----ccccccCCCEEEEEEEEEEEeeC
Confidence 344556777788777777765 456788887762259999996432 123455678999999988 499
Q ss_pred CccEEEE
Q 024592 132 DKRSLNA 138 (265)
Q Consensus 132 ~~~~i~~ 138 (265)
|+..+.+
T Consensus 528 g~~~~ql 534 (539)
T TIGR00644 528 GRETPQL 534 (539)
T ss_pred CcceEEE
Confidence 9876665
No 313
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=73.51 E-value=7.1 Score=38.14 Aligned_cols=61 Identities=16% Similarity=0.244 Sum_probs=51.0
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA 265 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~ 265 (265)
..++..||..|.+. ...++.+++++.++++.++|..++..|...|.|=. .....|..|..|
T Consensus 5 ~~~e~~iL~~l~~~-----~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG 67 (494)
T PTZ00326 5 ELEENTILSKLESE-----NEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKSNTWTLTEEG 67 (494)
T ss_pred hHHHHHHHHHHHhc-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHH
Confidence 36788999999762 13478999999999999999999999999998866 777788888754
No 314
>PF13518 HTH_28: Helix-turn-helix domain
Probab=73.36 E-value=11 Score=24.07 Aligned_cols=30 Identities=10% Similarity=0.262 Sum_probs=27.4
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCe
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSL 250 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~ 250 (265)
|.++.+|++.++++...|..-+......|.
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 569999999999999999999999988883
No 315
>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=72.99 E-value=9.2 Score=30.11 Aligned_cols=41 Identities=10% Similarity=0.109 Sum_probs=34.9
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA 262 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t 262 (265)
...+.|+..++.+.+.|+.||..|..-|.|.-.||..|..+
T Consensus 52 y~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~g~i~i~ 92 (119)
T TIGR01714 52 YNAEMLATMFNRNVGDIRITLQTLESLGLIEKKNNGDIFLE 92 (119)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCcEEeh
Confidence 46788888899999999999999999999998766666543
No 316
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=72.85 E-value=3.5 Score=26.51 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=19.5
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENS 249 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG 249 (265)
|.+..+|++.|+++...|...+....++|
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 99999999999999999999998887777
No 317
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=72.76 E-value=9.1 Score=29.26 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=41.7
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCc
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH 258 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~h 258 (265)
+...+++-++.+- ..+.=|+.-.|++++++..+=-|.+|..|.++|.|-.++-+|
T Consensus 42 vdee~~~ki~KEV--~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsknr 96 (107)
T COG4901 42 VDEELLDKIRKEV--PRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSKNR 96 (107)
T ss_pred ccHHHHHHHHHhc--ccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeeccCc
Confidence 4455555443321 346678999999999999999999999999999987655544
No 318
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=72.73 E-value=7.9 Score=28.19 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=28.7
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHHHHHHHHHHhh
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDKLMEALESLNE 247 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~v~~al~~L~~ 247 (265)
.|++.++ .|.+.+||+.-+. ++.++|++||++=.+
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 3666664 4999999999996 999999999997544
No 319
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=72.60 E-value=8.2 Score=32.92 Aligned_cols=42 Identities=14% Similarity=0.161 Sum_probs=36.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.|++-+.+||.++.+ |.+..+|+++|++++..|+.-+..+..
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 488999999999953 999999999999999999988776653
No 320
>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=72.60 E-value=7.5 Score=33.71 Aligned_cols=50 Identities=22% Similarity=0.407 Sum_probs=40.8
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++..+..|++++... ...+++..++++.++.+..-.+++|+.|+.+|.+.
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 24599999999999999999999999999999874
No 321
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=72.29 E-value=6.1 Score=29.29 Aligned_cols=36 Identities=8% Similarity=0.162 Sum_probs=32.7
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI 254 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi 254 (265)
..=|+...|+++|++..+=-|.+|++|+++|.|=.+
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 457899999999999999999999999999999553
No 322
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=72.19 E-value=8.1 Score=32.34 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=33.7
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA 262 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t 262 (265)
++..+|++.++++...|..+|..|.++|.| .++..++..+
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii-~~~~~~i~i~ 208 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLI-SAHGKTIVVY 208 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCE-EecCCEEEEe
Confidence 567999999999999999999999999977 4555566544
No 323
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=72.05 E-value=11 Score=32.06 Aligned_cols=82 Identities=13% Similarity=0.106 Sum_probs=55.2
Q ss_pred EEeeeCCChhHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCccccccccCCCCCCCCCChhHHHHHHHhcCcCCCCC
Q 024592 139 YSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLAN 218 (265)
Q Consensus 139 ~~i~~v~d~Nei~~H~Levi~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~~~~~Vl~~i~~~~~~~~ 218 (265)
..|..-+|.|||+.-+.-+++-. .+++.-+ . +.- -|.. | ..|++-..+||.++.+
T Consensus 93 ~~iyr~d~v~~i~~k~~~il~~~-al~~~~~---~----~~~----~~~~-~------~~LSpRErEVLrLLAq------ 147 (198)
T PRK15201 93 PHIYREDDVEEITRKMILILHKR-ALRHSVP---S----GIC----HYCT-T------RHFSVTERHLLKLIAS------ 147 (198)
T ss_pred chhhccccHHHHHHHHHHHHHHH-HHHhhCC---c----hhc----cccC-C------CCCCHHHHHHHHHHHC------
Confidence 44566688999998887776332 1222111 0 000 0111 1 3478899999999853
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
|.+..||++.|++++..|+.-+..+..
T Consensus 148 --GkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 148 --GYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred --CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 999999999999999999887776654
No 324
>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=71.90 E-value=21 Score=29.02 Aligned_cols=73 Identities=11% Similarity=0.169 Sum_probs=36.1
Q ss_pred eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEE-EEEEcCCC-eEEEEEecccccccccccccCCCCE
Q 024592 43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFI-FLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMY 120 (265)
Q Consensus 43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~-y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~y 120 (265)
++.+++|++.. |+ -++..|-+||.|+.|.....+.. .-|.|.-- -+-++.|.+-.. -...+-+++|.+
T Consensus 3 ~~~f~~l~~p~------f~---pp~~EvD~VG~VvsV~~~~~f~~~vYLsD~~~Nll~Ikfw~~l~~-~~~eDilk~~~l 72 (143)
T PF09104_consen 3 CTHFSDLQDPD------FQ---PPYGEVDTVGFVVSVSKKQGFQPLVYLSDECHNLLAIKFWTGLNQ-YGYEDILKPGSL 72 (143)
T ss_dssp B--CGGGGSTT-----------TCCCEEEEEEEEEEEE--TTS--EEEEE-TTS-EEEEEESS--------SS---TT-E
T ss_pred eechhhhcCcc------cC---CCccccceEEEEEEEEecCCCceeEEeecCCccEEEEEeccCccc-cchhhhcCcceE
Confidence 44566666651 11 23578999999999976655533 55677766 577777865321 111244688888
Q ss_pred EEEEE
Q 024592 121 VRVYG 125 (265)
Q Consensus 121 VrV~G 125 (265)
|-+.=
T Consensus 73 iA~SN 77 (143)
T PF09104_consen 73 IAASN 77 (143)
T ss_dssp EEEEE
T ss_pred EEEee
Confidence 76653
No 325
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=71.77 E-value=8.5 Score=35.72 Aligned_cols=49 Identities=14% Similarity=0.258 Sum_probs=40.6
Q ss_pred CChhHHHHHH-----HhcCcCCCCCCCCcCHHHHHHh--cCCCHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLD-----FLRRPEFLANNNGVHRNVISQQ--LNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~-----~i~~~~~~~~~~Gv~~~~I~~~--l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++.-+++||. +++. ..-++..+|++. +++++..||..+..|.++|.|..
T Consensus 4 l~~R~~~Il~~IV~~yi~~------~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~ 59 (339)
T PRK00082 4 LDERQREILRAIVEDYIAT------GEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEK 59 (339)
T ss_pred cCHHHHHHHHHHHHHHHhc------CCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCC
Confidence 5567788887 5654 346889999977 89999999999999999999864
No 326
>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=71.67 E-value=11 Score=38.49 Aligned_cols=56 Identities=18% Similarity=0.371 Sum_probs=43.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCC----HHHHHHHHHHHhhCCeEEeecCCcee
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLP----MDKLMEALESLNENSLVYSIDEFHYK 260 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~----~~~v~~al~~L~~eG~IYsiDd~hyk 260 (265)
+.+.+||++|++. ...++++.+|++.|+++ ..+++.+|+.|..+|.|-....+.|.
T Consensus 2 ~~~~~il~~l~~~----~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~ 61 (709)
T TIGR02063 2 PLRELILEFLKSK----KGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYA 61 (709)
T ss_pred CcHHHHHHHHHhC----CCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 3567799999863 35799999999999865 34599999999999999664444553
No 327
>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=71.44 E-value=6.5 Score=28.90 Aligned_cols=54 Identities=19% Similarity=0.235 Sum_probs=40.1
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeecc
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAV 263 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~ 263 (265)
.-.||..|.. .-....+|.+.+ +++..-+.+.|.+|.++|.|-. +... .|..|.
T Consensus 7 ~~~IL~~l~~-------g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~ 67 (90)
T PF01638_consen 7 TLLILRALFQ-------GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE 67 (90)
T ss_dssp HHHHHHHHTT-------SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred HHHHHHHHHh-------CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence 4456666643 245899999999 7999999999999999999988 5543 266654
No 328
>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=71.13 E-value=3.4 Score=38.21 Aligned_cols=53 Identities=17% Similarity=0.352 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+..+.++||+++++. ....|++.++|.+.+ +.+..++..+|+.|+++|.|=-
T Consensus 6 ~~~~~~~~l~~~~~~~---~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~ 59 (327)
T PF05158_consen 6 KLSELEKKLLELCREN---PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKL 59 (327)
T ss_dssp -HHHHHHHHHHHHHH------SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEE
T ss_pred hHHHHHHHHHHHHHHh---cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEE
Confidence 4678999999999875 246799999999996 7999999999999999887654
No 329
>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]
Probab=70.96 E-value=9.9 Score=36.01 Aligned_cols=70 Identities=20% Similarity=0.278 Sum_probs=52.6
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcCCC--eEEEEEecccccccccccccCCCCEEEEEEEeeeeCC---ccEEEEEEee
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDGTG--RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLR 142 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~ 142 (265)
..+.|-|||++++.......+.|+|||- .+.|..=.+ ....+..|.-|.|.|.++.-++ +..+.+.+|.
T Consensus 21 ~~~~i~GWvKsvr~~~~~~Fl~i~DGs~~~~lQvVv~~~------~~q~la~Gt~i~~~g~l~~~~~~~q~iel~~eki~ 94 (446)
T KOG0554|consen 21 DTISIGGWVKSVRKLKKVTFLDINDGSCPSPLQVVVDSE------QSQLLATGTCISAEGVLKVSKGAKQQIELNAEKIK 94 (446)
T ss_pred CceeecchhhhcccccceEEEEecCCCCCcceEEEechH------HhhhccccceEEEEeeEEeccchheeeeeeeeEEE
Confidence 5788899999999999999999999995 376665431 3456889999999999987653 2345555544
Q ss_pred e
Q 024592 143 P 143 (265)
Q Consensus 143 ~ 143 (265)
.
T Consensus 95 ~ 95 (446)
T KOG0554|consen 95 V 95 (446)
T ss_pred E
Confidence 3
No 330
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=70.74 E-value=11 Score=33.62 Aligned_cols=57 Identities=16% Similarity=0.190 Sum_probs=49.3
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
+++.++.||-+|++. ..+++||...++.+...|.-.|..|.+.|.|-.- ++.|+.|.
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 3589999999999999999999999999999875 66888775
No 331
>smart00526 H15 Domain in histone families 1 and 5.
Probab=70.55 E-value=17 Score=25.00 Aligned_cols=50 Identities=16% Similarity=0.195 Sum_probs=38.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc--CCC--H----HHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL--NLP--M----DKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l--~~~--~----~~v~~al~~L~~eG~IYs 253 (265)
....+|++.|... ....|.++..|.+-+ ++. . .-++.+|..+++.|.+..
T Consensus 6 ~~~~mI~eAI~~l---~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q 63 (66)
T smart00526 6 PYSEMITEAISAL---KERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQ 63 (66)
T ss_pred CHHHHHHHHHHHc---CCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceee
Confidence 5678899999886 446899999998776 232 2 338889999999998864
No 332
>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=70.42 E-value=19 Score=25.76 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=40.3
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH--hhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL--NENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L--~~eG~IYs 253 (265)
..|..|+.+|+.+ +|.++++|++.++-....||-+|.-| -.-|+-.+
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 5788999999874 69999999999999999999999999 55566554
No 333
>PHA02591 hypothetical protein; Provisional
Probab=70.04 E-value=5.1 Score=29.08 Aligned_cols=26 Identities=27% Similarity=0.355 Sum_probs=23.3
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
+.|+++++||+.|+++.+.|++.|+.
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 46999999999999999999998763
No 334
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=69.89 E-value=11 Score=32.37 Aligned_cols=51 Identities=8% Similarity=0.148 Sum_probs=38.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++..+|..+|..... ......+.++||+.++.+.+.|..+|..|.++|.|-
T Consensus 150 ~~~~Rla~~L~~~~~-~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 150 PLENRLAAFILLTQE-GDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred hHHHHHHHHHHhccc-CCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 467777777654321 112235789999999999999999999999999874
No 335
>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=69.65 E-value=12 Score=29.44 Aligned_cols=42 Identities=12% Similarity=0.126 Sum_probs=35.8
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA 262 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t 262 (265)
-...++||..++.+.+.|+.||..|.+-|.|.-.||.-|..+
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~ed~~i~i~ 94 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDEDGVIYIP 94 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeEEee
Confidence 457899999999999999999999999999988666666543
No 336
>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=69.16 E-value=15 Score=29.06 Aligned_cols=57 Identities=11% Similarity=0.066 Sum_probs=43.8
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc----CCCHHHHHHHHHHHhhCCeEEe-ecCC--ceee
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL----NLPMDKLMEALESLNENSLVYS-IDEF--HYKS 261 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l----~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~ 261 (265)
+++.+..||++|=.. .++++.+|.+.| +.....|...|..|.+.|.|-. -+.. .|.+
T Consensus 2 Lt~~E~~VM~vlW~~------~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p 65 (130)
T TIGR02698 2 ISDAEWEVMRVVWTL------GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTA 65 (130)
T ss_pred CCHHHHHHHHHHHcC------CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEe
Confidence 567788899999642 257899988887 4788999999999999999865 4443 4443
No 337
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=68.72 E-value=13 Score=32.35 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=36.4
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..|++-+.+||.++.+ |.+..+|+++|++++..|+.-+..+..
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 4578889999999853 999999999999999999887776543
No 338
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.71 E-value=6.5 Score=31.89 Aligned_cols=31 Identities=19% Similarity=0.285 Sum_probs=28.6
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
-++-++|++.++++..+||++|..|-+++++
T Consensus 15 ~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcc
Confidence 3789999999999999999999999997775
No 339
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=68.57 E-value=11 Score=31.61 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=36.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..|++-+.+||.++. .|.+..+|+++|++++..|+.-+..+..
T Consensus 149 ~~Lt~rE~evl~~~~--------~G~s~~eIA~~l~iS~~TV~~h~~~i~~ 191 (216)
T PRK10840 149 KRLSPKESEVLRLFA--------EGFLVTEIAKKLNRSIKTISSQKKSAMM 191 (216)
T ss_pred ccCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 358889999999985 3999999999999999999988776654
No 340
>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=68.37 E-value=13 Score=37.47 Aligned_cols=61 Identities=18% Similarity=0.219 Sum_probs=42.7
Q ss_pred EEEEEEEEEEee------eC---CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEE-EEEeeeeC
Q 024592 69 TITVVGIVCDMQ------DK---EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRV-YGHLKAFQ 131 (265)
Q Consensus 69 ~V~iVG~V~~v~------~~---~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV-~G~i~~f~ 131 (265)
..+|.|+|..+. .. ...+.+.|-|.+|.|.|..|.+..+ +..+.|++|+.+.+ .|+|+..+
T Consensus 192 ~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Degg~Irat~f~~~~d--kf~~~l~eG~VY~Is~~~Vk~an 262 (608)
T TIGR00617 192 KWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRATAFNEQAD--KFYDIIQEGKVYYISKGSLKPAN 262 (608)
T ss_pred ceEEEEEEEeccccceecCCCCCceeeEEEEecCCCeEEEEECchHHH--HHhhhcccCCEEEECceEEEEcc
Confidence 466677776532 11 2468888999999999999987432 23467899998877 56777654
No 341
>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=68.20 E-value=13 Score=29.96 Aligned_cols=39 Identities=13% Similarity=0.135 Sum_probs=31.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.-|++.++.|+.+.. .|++.++|++.|+++...|...+.
T Consensus 5 ~~Lte~qr~VL~Lr~--------~GlTq~EIAe~LgiS~stV~~~e~ 43 (137)
T TIGR00721 5 TFLTERQIKVLELRE--------KGLSQKEIAKELKTTRANVSAIEK 43 (137)
T ss_pred CCCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 347889999998852 489999999999999998884443
No 342
>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=68.15 E-value=4.7 Score=34.31 Aligned_cols=50 Identities=12% Similarity=0.308 Sum_probs=38.6
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF 257 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~ 257 (265)
+-...+++|+.. .=|++++|+..|++...++.+.|..|..+|.|-= +||-
T Consensus 100 lL~~Fi~yIK~~------Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Ddr 150 (188)
T PF09756_consen 100 LLQEFINYIKEH------KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDR 150 (188)
T ss_dssp HHHHHHHHHHH-------SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT
T ss_pred HHHHHHHHHHHc------ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCC
Confidence 556677899874 3579999999999999999999999999999999 8884
No 343
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=68.02 E-value=12 Score=32.06 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.|++-+.+||+++.+ |.+..+|+++|++++..|+.-+..+..
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 588999999999963 999999999999999999988776654
No 344
>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=67.91 E-value=8.6 Score=34.44 Aligned_cols=53 Identities=15% Similarity=0.172 Sum_probs=41.0
Q ss_pred CCCChhHHHHHH-HhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH-HHhhCCeEEe
Q 024592 197 DEGKSIDQMVLD-FLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE-SLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~-~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~-~L~~eG~IYs 253 (265)
.++...++..|. +++... ....++++|++.|+.+...++..++ .|++.|.||.
T Consensus 234 ~~l~~~~~~~L~al~~~~~----~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~ 288 (305)
T TIGR00635 234 LGLDEIDRKLLSVLIEQFQ----GGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQR 288 (305)
T ss_pred CCCCHHHHHHHHHHHHHhC----CCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCccc
Confidence 345566666777 445431 2247899999999999999999999 7999999986
No 345
>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=67.49 E-value=12 Score=25.54 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=26.2
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 223 HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-..|+.+++++.+-|-.||+.|.+.|.|-+
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 4578999999999999999999999999977
No 346
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=67.21 E-value=6.1 Score=29.87 Aligned_cols=59 Identities=20% Similarity=0.271 Sum_probs=44.5
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC---ceeeccCC
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF---HYKSAVNA 265 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~---hyk~t~~~ 265 (265)
-..|+++|+.. ++.|+.+.-|+-.++++-.-.++.++.|++.|.|-.-++. .|..|.-|
T Consensus 17 ~eIi~dIL~~~----~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG 78 (95)
T COG3432 17 LEIIFDILKAI----SEGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKG 78 (95)
T ss_pred HHHHHHHHHHh----cCCCCCceeeeeecCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhH
Confidence 34577777742 2568888889999999999999999999999944445544 58887643
No 347
>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=67.20 E-value=14 Score=28.30 Aligned_cols=58 Identities=12% Similarity=0.133 Sum_probs=43.7
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEF--HYKSA 262 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t 262 (265)
+++....||++|=+. + .+++.+|.+.|. .....|+..|..|.+-|.|-. -+.. +|.++
T Consensus 1 Ls~~E~~IM~~lW~~-----~-~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~ 65 (115)
T PF03965_consen 1 LSDLELEIMEILWES-----G-EATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPL 65 (115)
T ss_dssp --HHHHHHHHHHHHH-----S-SEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEES
T ss_pred CCHHHHHHHHHHHhC-----C-CCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCceEEEeC
Confidence 356788999999764 2 399999999994 668999999999999999988 5443 44443
No 348
>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=67.19 E-value=8 Score=31.80 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=29.9
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++.++|++.++.+.+.|..+|..|.++|.|-.
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 68899999999999999999999999999853
No 349
>PRK11642 exoribonuclease R; Provisional
Probab=67.18 E-value=14 Score=38.43 Aligned_cols=53 Identities=15% Similarity=0.307 Sum_probs=42.9
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCH----HHHHHHHHHHhhCCeEEeecCCcee
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPM----DKLMEALESLNENSLVYSIDEFHYK 260 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~----~~v~~al~~L~~eG~IYsiDd~hyk 260 (265)
...||++|++. +.++++.+|++.|+++. ..++.+|+.|..+|.|.....+.|.
T Consensus 21 ~~~Il~~l~~~-----~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 21 REFILEHLTKR-----EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHHHHhc-----CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 56799999752 36899999999998763 4499999999999999775555664
No 350
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=67.03 E-value=7.9 Score=32.21 Aligned_cols=31 Identities=3% Similarity=0.176 Sum_probs=29.5
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++.++||+.++.+.+.|..+|..|.++|.|-
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 5789999999999999999999999999995
No 351
>PF14493 HTH_40: Helix-turn-helix domain
Probab=67.02 E-value=9.2 Score=28.18 Aligned_cols=31 Identities=19% Similarity=0.206 Sum_probs=29.4
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSL 250 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~ 250 (265)
.|.++++|++.-++.++.|..-|..++..|.
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 3999999999999999999999999999998
No 352
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 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 1". 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 []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=66.74 E-value=32 Score=22.67 Aligned_cols=51 Identities=12% Similarity=0.244 Sum_probs=39.5
Q ss_pred HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceee
Q 024592 206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKS 261 (265)
Q Consensus 206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~ 261 (265)
+-.+|++. .+|+.-++-+.+-.++.++-|+.|+.+...|.+-- +..|-|..
T Consensus 7 laqiiqeh-----regldwqeaatraslsleetrkllqsmaaagqvtllrvendlyai 59 (61)
T PF09105_consen 7 LAQIIQEH-----REGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVENDLYAI 59 (61)
T ss_dssp HHHHHHC------TT-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEEETTEEEEE
T ss_pred HHHHHHHH-----HccCcHHHHHHHhhccHHHHHHHHHHHHhcCceEEEEecccceec
Confidence 33466664 46999999999999999999999999999999877 77777764
No 353
>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=66.65 E-value=10 Score=26.42 Aligned_cols=47 Identities=13% Similarity=0.313 Sum_probs=34.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc--------CCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL--------NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l--------~~~~~~v~~al~~L~~eG~IYs 253 (265)
.++..|..++|.. .=++.++|...+ ..+..+|+++|+.|++.+.|=-
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 4677888888874 246777775433 3778889999999999999866
No 354
>cd00131 PAX Paired Box domain
Probab=66.39 E-value=14 Score=29.24 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=38.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++..+|+.+++ +|++..+|+++|+++...|...+....+.|.+-.
T Consensus 21 d~R~rIv~~~~--------~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 21 SIRQRIVELAQ--------SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred HHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 57788887764 3899999999999999999999999999997643
No 355
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=66.01 E-value=22 Score=25.81 Aligned_cols=49 Identities=22% Similarity=0.366 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENS 249 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG 249 (265)
+|++.+..||+|=+.- ..-.|..-+.|...|++++-..-+.|..|+++-
T Consensus 2 ~Ls~~d~~iL~fE~~w---w~~~GaKe~aIre~fGls~~rYyq~Ln~LiD~p 50 (77)
T PF11662_consen 2 GLSDRDRAILDFERRW---WRHGGAKEEAIREEFGLSPTRYYQRLNALIDDP 50 (77)
T ss_pred CCCHHHHHHHHHHHHh---CcCCCCcHHHHHHHHCCCHHHHHHHHHHHhCCh
Confidence 5788999999998765 234577888999999999999999999999864
No 356
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=65.84 E-value=12 Score=32.14 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=38.7
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL 250 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~ 250 (265)
+.+..|++.|++. ..+=++.+++++.++.++.+||.-|.+|...|.
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 234689999999999999999999999988874
No 357
>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=65.64 E-value=13 Score=39.82 Aligned_cols=35 Identities=23% Similarity=0.462 Sum_probs=27.8
Q ss_pred eEEEEEEEEEEeeeC------CCeEEEEEEcCCCeEEEEEe
Q 024592 68 NTITVVGIVCDMQDK------EPQFIFLIDDGTGRIECSRW 102 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~------~t~~~y~LdDgTG~I~~~~w 102 (265)
..|+++|.|.+++.. .....++|+|.||.|+|..|
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 368899999876542 13577899999999999987
No 358
>PRK10736 hypothetical protein; Provisional
Probab=65.62 E-value=21 Score=33.67 Aligned_cols=51 Identities=10% Similarity=0.131 Sum_probs=41.0
Q ss_pred HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592 204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS 261 (265)
Q Consensus 204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~ 261 (265)
..||+.+. ...+|+|+|+.+++++..++..+|-+|.-.|.|...-...|+.
T Consensus 311 ~~v~~~l~-------~~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~g~~~~~ 361 (374)
T PRK10736 311 PELLANVG-------DEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGGYVRL 361 (374)
T ss_pred HHHHHhcC-------CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcCCcEEEE
Confidence 45666553 2468999999999999999999999999999999844446653
No 359
>PRK05638 threonine synthase; Validated
Probab=65.61 E-value=13 Score=35.61 Aligned_cols=59 Identities=17% Similarity=0.178 Sum_probs=46.8
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe-ecC---CceeeccC
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN--LPMDKLMEALESLNENSLVYS-IDE---FHYKSAVN 264 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs-iDd---~hyk~t~~ 264 (265)
+.+.+..||.+|++. -++..+|++.|+ ++...|...|..|.++|.|-+ ..+ -.|..|..
T Consensus 369 ~~~~r~~IL~~L~~~-------~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~ 433 (442)
T PRK05638 369 IGGTKLEILKILSER-------EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEK 433 (442)
T ss_pred ccchHHHHHHHHhhC-------CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcH
Confidence 457889999999852 378999999997 889999999999999999965 333 24666543
No 360
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=65.13 E-value=18 Score=29.40 Aligned_cols=33 Identities=24% Similarity=0.257 Sum_probs=31.2
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-++.++|+++.++++.-+++.+..|...|.|-|
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S 57 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKS 57 (150)
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEe
Confidence 478999999999999999999999999999987
No 361
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=65.01 E-value=9.9 Score=34.99 Aligned_cols=53 Identities=11% Similarity=0.238 Sum_probs=39.9
Q ss_pred CChhHHHHHH----HhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 199 GKSIDQMVLD----FLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 199 l~~~~~~Vl~----~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
.++++.+|.+ +|.+- -.-+|+.+|-.-+.+|++++.+-+.+|++.|++|. |.-
T Consensus 332 w~DL~krviEHN~RvI~~y-----YSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNr 389 (439)
T COG5071 332 WSDLRKRVIEHNIRVIANY-----YSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINR 389 (439)
T ss_pred HHHHHHHHHHhhHhHHHHH-----hhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecC
Confidence 4566666644 33221 13578888888888999999999999999999998 764
No 362
>PRK04217 hypothetical protein; Provisional
Probab=64.84 E-value=16 Score=28.34 Aligned_cols=40 Identities=10% Similarity=0.097 Sum_probs=30.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..++.-+..++.++.. +|++.++|++.++++...|...|.
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 4566677777766542 589999999999999988877654
No 363
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=64.74 E-value=14 Score=31.64 Aligned_cols=42 Identities=19% Similarity=0.257 Sum_probs=36.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.|++-+..||.+|.+ |.+..+|+.+|++++..|+.-+..+..
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 578888999999963 999999999999999999887776654
No 364
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=64.59 E-value=6.3 Score=34.02 Aligned_cols=53 Identities=23% Similarity=0.295 Sum_probs=39.1
Q ss_pred hhHHHHHHHhcCcC---CCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPE---FLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~---~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+...|++.|++.- ...+..=++..+|+++|+.+..=||+||..|..||.|-.
T Consensus 16 ~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~ 71 (230)
T COG1802 16 TLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEI 71 (230)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEe
Confidence 34555555444311 123345689999999999999999999999999999865
No 365
>PRK15320 transcriptional activator SprB; Provisional
Probab=64.58 E-value=16 Score=31.65 Aligned_cols=43 Identities=9% Similarity=0.016 Sum_probs=37.9
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..+++-...||++|.+ |.+-++|+++|+++.+.|.+-+..|.+
T Consensus 163 ~~LSdREIEVL~LLAk--------G~SNKEIAekL~LS~KTVSTYKnRLLe 205 (251)
T PRK15320 163 PGVTQAKYALLILLSS--------GHPAIELAKKFGLGTKTVSIYRKKVMY 205 (251)
T ss_pred CCCCHHHHHHHHHHHc--------CCCHHHHHHHhccchhhHHHHHHHHHH
Confidence 5788899999999964 999999999999999999988887765
No 366
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=63.21 E-value=14 Score=26.90 Aligned_cols=45 Identities=27% Similarity=0.265 Sum_probs=37.6
Q ss_pred HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592 205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID 255 (265)
Q Consensus 205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD 255 (265)
+|-++|+..+ =++..+|+.+|+.|++-|+.-|+.|+.-|.|-.++
T Consensus 6 qlRd~l~~~g------r~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRG------RMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcC------cccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 3666776542 36899999999999999999999999999998754
No 367
>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=63.11 E-value=16 Score=33.93 Aligned_cols=35 Identities=11% Similarity=0.247 Sum_probs=31.9
Q ss_pred CCCcCHHHHHHh--cCCCHHHHHHHHHHHhhCCeEEe
Q 024592 219 NNGVHRNVISQQ--LNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 219 ~~Gv~~~~I~~~--l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..-++..+|++. +++++..||..+..|.++|.|..
T Consensus 19 ~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~ 55 (337)
T TIGR00331 19 GQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEK 55 (337)
T ss_pred CCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccC
Confidence 457899999999 89999999999999999999864
No 368
>smart00351 PAX Paired Box domain.
Probab=62.87 E-value=18 Score=28.36 Aligned_cols=44 Identities=23% Similarity=0.258 Sum_probs=37.3
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++..+|+.+++ +|.+..+|+++|+++...|.+.+....+.|.+-
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 57777887764 378999999999999999999999998888654
No 369
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=62.84 E-value=40 Score=26.48 Aligned_cols=60 Identities=20% Similarity=0.259 Sum_probs=34.9
Q ss_pred eEEEEEEEEEEeeeCC-CeEEEEEE----cCCC---eEEEEE---ecccccccccccccCCCCEEEEEEEeeeeCC
Q 024592 68 NTITVVGIVCDMQDKE-PQFIFLID----DGTG---RIECSR---WAHEQMEFNEVNQISKGMYVRVYGHLKAFQD 132 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~-t~~~y~Ld----DgTG---~I~~~~---w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~ 132 (265)
..+++.|+|.+..... ....|.+. ...+ ....+. |..+. ...++.|+.+++.|+++...+
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 4566888888875433 44456664 1111 122222 22211 126899999999999987643
No 370
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=62.79 E-value=10 Score=31.43 Aligned_cols=46 Identities=20% Similarity=0.336 Sum_probs=38.8
Q ss_pred HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
.+.+|..|.+. ..|++.-|++.+|+.+.++-|.+|+.|.++|.+--
T Consensus 111 ~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (166)
T PRK15466 111 ADELLALLTSV-----RQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRK 156 (166)
T ss_pred HHHHHHHHHHH-----HccccHHHHHHHhCCcHHHHHHHHHHHHhccchhh
Confidence 45567777654 35999999999999999999999999999998754
No 371
>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=62.73 E-value=3.4 Score=27.55 Aligned_cols=25 Identities=12% Similarity=0.307 Sum_probs=18.7
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
+.|.+..+|++.|+++..+|.+++.
T Consensus 20 e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 20 EEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3477999999999999999988764
No 372
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.29 E-value=16 Score=31.87 Aligned_cols=49 Identities=16% Similarity=0.225 Sum_probs=44.0
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+++.++.|+++|+.+ .|.+..|+.+.+.++....|=-|..|..++.|=+
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 456888999999874 4999999999999999999999999999998865
No 373
>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=62.26 E-value=29 Score=25.46 Aligned_cols=52 Identities=13% Similarity=0.152 Sum_probs=40.7
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc--CCC------HHHHHHHHHHHhhCCeEEee
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL--NLP------MDKLMEALESLNENSLVYSI 254 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l--~~~------~~~v~~al~~L~~eG~IYsi 254 (265)
.....+|++.|... ....|.+...|.+-+ +++ ..-++.+|..|++.|.|..+
T Consensus 5 P~y~~MI~eAI~~l---~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~ 64 (88)
T cd00073 5 PPYSEMVTEAIKAL---KERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQV 64 (88)
T ss_pred CCHHHHHHHHHHHc---CCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEee
Confidence 35788999999876 456899999999877 333 23378899999999998763
No 374
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=62.20 E-value=18 Score=31.20 Aligned_cols=43 Identities=21% Similarity=0.220 Sum_probs=36.9
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..|++-+.+|+.++.. |.+..+|++.|++++..|+.-+..+..
T Consensus 154 ~~Lt~rE~~Vl~l~~~--------G~s~~eIA~~L~iS~~TVk~~~~~i~~ 196 (216)
T PRK10100 154 ALLTHREKEILNKLRI--------GASNNEIARSLFISENTVKTHLYNLFK 196 (216)
T ss_pred CCCCHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3488889999999853 899999999999999999998887754
No 375
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=61.66 E-value=22 Score=22.86 Aligned_cols=37 Identities=14% Similarity=0.337 Sum_probs=30.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.++..|++.+++ ..++.+|++.++++.+.|+.+++..
T Consensus 15 ~~~~~i~~~~~~--------~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 15 RLEQYILKLLRE--------SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHHhh--------cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 577788888764 2699999999999999999988753
No 376
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=61.06 E-value=27 Score=31.80 Aligned_cols=66 Identities=17% Similarity=0.164 Sum_probs=55.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA 265 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~ 265 (265)
.++...=+||..|.... ..-+=|+.+.|.+..+++++++...|..|..-+.|-- +..+-|+.|..|
T Consensus 10 ~l~~~D~rlLraiE~~m--R~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l~lv~r~~~~y~Gy~lT~~G 77 (304)
T COG0478 10 KLSKEDFRLLRAIEGGM--RSHEWVPLELIKKRARMDEEELLYRLKRLDKLKLVSRRTISYEGYQLTFSG 77 (304)
T ss_pred hcCHHHHHHHHHHHhcc--cccccccHHHHHHHcCCCHHHHHHHHHHHHhcCceeccCCcceeEEEEecc
Confidence 35666777888876543 3346899999999999999999999999999999866 788999999876
No 377
>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=60.95 E-value=8.9 Score=27.18 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=31.0
Q ss_pred CCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeecc
Q 024592 219 NNGVHRNVISQQL---NLPMDKLMEALESLNENSLVYS-IDEF--HYKSAV 263 (265)
Q Consensus 219 ~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t~ 263 (265)
..-++...+++-+ ++++..+|.+|..|..+|.+-+ -+.. .|..|.
T Consensus 18 g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~ 68 (70)
T PF07848_consen 18 GGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTE 68 (70)
T ss_dssp TS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-H
T ss_pred CCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeecCccceEeeCC
Confidence 3457788877665 7999999999999999999988 3321 455553
No 378
>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=60.94 E-value=14 Score=31.47 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=29.7
Q ss_pred CcCHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEe
Q 024592 221 GVHRNVISQQL--NLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 221 Gv~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYs 253 (265)
.-++++|++.+ .++.++|.++|+.|.+.|+|-.
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 4899999999999999999865
No 379
>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=60.51 E-value=26 Score=24.49 Aligned_cols=50 Identities=8% Similarity=0.298 Sum_probs=37.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID 255 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD 255 (265)
.++=.++.+++.+. .-+++..|.++|++.-..-...++.|..+|.|=..+
T Consensus 5 D~ly~~a~~~V~~~------~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 5 DPLYEEAVEFVIEE------GKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp STTHHHHHHHHHHC------TCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---
T ss_pred cHHHHHHHHHHHHc------CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCC
Confidence 35666777777653 368999999999999999999999999999885533
No 380
>PRK09483 response regulator; Provisional
Probab=60.50 E-value=21 Score=29.34 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=35.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..|++-..+||.++. .|.+..+|+++|++++..|+.-+..+..
T Consensus 147 ~~Lt~rE~~vl~~~~--------~G~~~~~Ia~~l~is~~TV~~~~~~i~~ 189 (217)
T PRK09483 147 ASLSERELQIMLMIT--------KGQKVNEISEQLNLSPKTVNSYRYRMFS 189 (217)
T ss_pred cccCHHHHHHHHHHH--------CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 358888899998874 3889999999999999999887776654
No 381
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=60.47 E-value=31 Score=21.23 Aligned_cols=41 Identities=12% Similarity=0.109 Sum_probs=31.1
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
+++.++.++..+- ..|.+..+|++.++++...|...+....
T Consensus 11 l~~~~~~~~~~~~-------~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRF-------GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHH-------hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556666665542 1478999999999999999988877643
No 382
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=60.25 E-value=17 Score=30.39 Aligned_cols=40 Identities=13% Similarity=0.159 Sum_probs=31.2
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
+.+-+.+++++..- .|++..||++.|++++..|+..+...
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 44555666666443 49999999999999999999888765
No 383
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=60.14 E-value=24 Score=35.28 Aligned_cols=51 Identities=10% Similarity=0.020 Sum_probs=41.2
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCce
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHY 259 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hy 259 (265)
+.++|++.++. ....+.|+++.+++++..+++.|..|..+|.++.++++.|
T Consensus 476 ~~~~i~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~~~ 526 (581)
T TIGR00475 476 IWQKIKGTFGT-------KGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVKDRL 526 (581)
T ss_pred HHHHHHHHHhc-------CCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeCCeE
Confidence 45667777763 2468899999999999999999999999999999555554
No 384
>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=60.03 E-value=20 Score=27.42 Aligned_cols=42 Identities=14% Similarity=0.165 Sum_probs=31.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
.+++.++.|+...- -.|.+..+|++.++++++.|+..+....
T Consensus 110 ~L~~~~~~ii~~~~-------~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPEREREVLVLRY-------LEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHHHHhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46667777765432 1388999999999999999998887653
No 385
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=59.52 E-value=13 Score=32.00 Aligned_cols=31 Identities=26% Similarity=0.435 Sum_probs=29.1
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++.++|++.++++.+.+-.+|..|.++|.|-
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 6789999999999999999999999999984
No 386
>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=59.47 E-value=86 Score=24.74 Aligned_cols=78 Identities=12% Similarity=0.141 Sum_probs=46.0
Q ss_pred eEEEEEEEEEEeeeCCCeEEEEEEcC--C---C-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCC-----ccEE
Q 024592 68 NTITVVGIVCDMQDKEPQFIFLIDDG--T---G-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQD-----KRSL 136 (265)
Q Consensus 68 ~~V~iVG~V~~v~~~~t~~~y~LdDg--T---G-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~-----~~~i 136 (265)
.+|+|+|.|.+...... .++|+.. . . .-.+..+.+.--++-....++.|.+|-|+|-++.-.. ...+
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 78999999998875544 4455552 1 1 1234445443322234578999999999999987652 2357
Q ss_pred EEEEeeeCCCh
Q 024592 137 NAYSLRPIIDF 147 (265)
Q Consensus 137 ~~~~i~~v~d~ 147 (265)
.|-.|.++-..
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 387
>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=59.37 E-value=11 Score=35.22 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=29.3
Q ss_pred CCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCe
Q 024592 218 NNNGVHRNVISQQL---NLPMDKLMEALESLNENSL 250 (265)
Q Consensus 218 ~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~ 250 (265)
.-..+.++|+++++ ||..|.||..++.|++.|.
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 34578899999988 8999999999999999995
No 388
>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=59.37 E-value=21 Score=26.18 Aligned_cols=38 Identities=5% Similarity=0.073 Sum_probs=32.4
Q ss_pred CHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 223 HRNVISQQLN--LPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 223 ~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
-++.+++.+. -+.+|-...-+.|++.|.|+. .|+.+|+
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 4677888774 577788899999999999999 9999986
No 389
>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=58.87 E-value=17 Score=25.01 Aligned_cols=35 Identities=9% Similarity=0.234 Sum_probs=28.1
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHH
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLME 240 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~ 240 (265)
+-.+.-++++++. .-.+...+||.+|++++.+|+.
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 4566677887763 3479999999999999999985
No 390
>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=58.32 E-value=16 Score=28.16 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=34.1
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF 257 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~ 257 (265)
..=|+...|+++|++..+=-|.+|++|.+.|.|-.+.-+
T Consensus 57 ~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~ 95 (105)
T PF03297_consen 57 MKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKH 95 (105)
T ss_dssp SSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECC
T ss_pred CcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEecc
Confidence 357899999999999999999999999999999774433
No 391
>PLN02532 asparagine-tRNA synthetase
Probab=58.29 E-value=45 Score=33.74 Aligned_cols=64 Identities=16% Similarity=0.058 Sum_probs=43.5
Q ss_pred eeeCCCeEEEEEEcCCCe--EEEEEecccccccccccccCCCCEEEEEEEeeeeC-----CccEEEEEEeeeCC
Q 024592 79 MQDKEPQFIFLIDDGTGR--IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ-----DKRSLNAYSLRPII 145 (265)
Q Consensus 79 v~~~~t~~~y~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~-----~~~~i~~~~i~~v~ 145 (265)
++.......+.|.||||. |.|..-..... ....+..+.-|.|.|.|+.-+ +...|.+..|..+.
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 APPPPSVAYLLISDGSCVASLQVVVDSALAP---LTQLMATGTCILAEGVLKLPLPAQGKHVIELEVEKILHIG 199 (633)
T ss_pred cccCCCcEEEEEECCCCccceEEEEeCCccc---HhhcCCCceEEEEEEEEEecCCCCCCCcEEEEeeEEEEEe
Confidence 344556677799999998 99976433211 125688999999999998752 23466666665544
No 392
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=57.18 E-value=31 Score=30.18 Aligned_cols=51 Identities=14% Similarity=0.252 Sum_probs=37.4
Q ss_pred hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
+-.+|.+.|.+..- ....=+ +-.+++++|+.+..-||+||..|...|.|-.
T Consensus 15 v~~~i~~~I~~g~~-~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~ 66 (241)
T COG2186 15 VAEQIGALIVSGEL-PPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI 66 (241)
T ss_pred HHHHHHHHHHcCCC-CCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee
Confidence 44445555655321 212223 5799999999999999999999999999875
No 393
>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=56.84 E-value=18 Score=29.59 Aligned_cols=39 Identities=10% Similarity=0.127 Sum_probs=30.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+.. -+|++..||++.|++++..|+..|.
T Consensus 134 ~Lp~~~r~v~~l~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 134 QVDPRQAEVVELRF-------FAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred cCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 36667777775543 2599999999999999999887664
No 394
>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=56.79 E-value=29 Score=25.14 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=31.6
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
...|.+-+|..|.. ..-|++.+++..++.+.++|+.+|..+-+
T Consensus 22 ~~~L~r~LLr~LA~------G~PVt~~~LA~a~g~~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 22 FAWLLRPLLRLLAK------GQPVTVEQLAAALGWPVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHHHHHHHHTT------TS-B-HHHHHHHHT--HHHHHHHHHH-TT
T ss_pred cHHHHHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHhCCC
Confidence 34678888888875 34799999999999999999999998764
No 395
>PRK00118 putative DNA-binding protein; Validated
Probab=56.77 E-value=29 Score=26.61 Aligned_cols=40 Identities=5% Similarity=0.119 Sum_probs=31.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.+++-++.|+..... .|.++.+|++.+++++..|...+..
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 466778888755432 4899999999999999998877653
No 396
>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=56.57 E-value=26 Score=28.07 Aligned_cols=42 Identities=7% Similarity=-0.095 Sum_probs=32.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
..|++.++.|+...- -+|.+..+|++.|++++..|+..+...
T Consensus 121 ~~L~~~~r~vl~l~~-------~~g~s~~eIA~~l~is~~tv~~~l~ra 162 (170)
T TIGR02952 121 KILTPKQQHVIALRF-------GQNLPIAEVARILGKTEGAVKILQFRA 162 (170)
T ss_pred HhCCHHHHHHHHHHH-------hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356777777776632 248999999999999999999877654
No 397
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=56.22 E-value=30 Score=28.03 Aligned_cols=39 Identities=13% Similarity=0.068 Sum_probs=30.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.-|++-++.||... . .|++.++|++.|+++...|.....
T Consensus 5 ~~Lt~rqreVL~lr-~-------~GlTq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 5 SFLTERQIEVLRLR-E-------RGLTQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred cCCCHHHHHHHHHH-H-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35788999999884 2 489999999999999877655443
No 398
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=55.63 E-value=13 Score=31.51 Aligned_cols=30 Identities=23% Similarity=0.405 Sum_probs=27.2
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNEN 248 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~e 248 (265)
+.|+++.+|++.++.+..+|+++|+.|..+
T Consensus 18 ~pgls~~~La~~l~~~~~~v~~~l~~L~~~ 47 (188)
T PRK00135 18 EEGLSLEQLAEILELEPTEVQQLLEELQEK 47 (188)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 458999999999999999999999999764
No 399
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=55.54 E-value=19 Score=28.78 Aligned_cols=39 Identities=13% Similarity=-0.112 Sum_probs=28.5
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.. -+|++.+||++.|++++..|+..|.
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 45556666664432 2599999999999999999966553
No 400
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.01 E-value=21 Score=28.69 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=31.3
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
..|++.++.|+....- .|++..+|++.|++++..|+..+..
T Consensus 124 ~~L~~~~r~i~~l~~~-------~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 124 DALPVKQREVFLLRYV-------EGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred HhCCHHHHHHhhHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3466677777665432 4899999999999999999887654
No 401
>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=54.99 E-value=27 Score=25.35 Aligned_cols=37 Identities=11% Similarity=0.057 Sum_probs=28.9
Q ss_pred HHHHHHhcC-CCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 224 RNVISQQLN-LPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 224 ~~~I~~~l~-~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
|+.+++... .+.++-....+.|++.|.|.. .|+.+|+
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 344554432 677788889999999999999 8888887
No 402
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=54.97 E-value=13 Score=27.66 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=22.4
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
-.|++.++|++.|++++++|.++|+
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3599999999999999999998875
No 403
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=54.97 E-value=21 Score=28.41 Aligned_cols=40 Identities=0% Similarity=-0.113 Sum_probs=29.6
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..|++-++.|+.+.. -+|++.+||++.|++++..|+..+.
T Consensus 105 ~~Lp~~~r~v~~l~~-------~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 105 QKLPARQREAFLLRY-------WEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HhCCHHHHHHHHHHH-------HhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 345666666665532 2599999999999999999886554
No 404
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=54.52 E-value=17 Score=31.01 Aligned_cols=33 Identities=15% Similarity=0.293 Sum_probs=30.2
Q ss_pred CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
-++.++|++.+|++...|..+|..|..+|.|--
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAV 216 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 367899999999999999999999999999864
No 405
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=54.40 E-value=25 Score=32.44 Aligned_cols=41 Identities=17% Similarity=0.248 Sum_probs=36.8
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
+|++-.||+++|+++...|..-|++..++|.|=- |++....
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 5999999999999999999999999999999988 8854433
No 406
>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=54.00 E-value=18 Score=23.87 Aligned_cols=33 Identities=15% Similarity=0.264 Sum_probs=23.3
Q ss_pred HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
+|+-+++. ..+-|+-.+|++.+++++.+||+-|
T Consensus 17 ~L~~l~~~----G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 17 YLEQLKEE----GVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHT----T-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHc----CCeeECHHHHHHHHCCCHHHhcccC
Confidence 44555542 3567899999999999999999876
No 407
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=53.58 E-value=48 Score=21.77 Aligned_cols=41 Identities=12% Similarity=0.272 Sum_probs=33.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
.++.-+..|+..+.+ |.+..+|+..+++++..|+.-+..+.
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 466777788888753 78999999999999999988776653
No 408
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=53.49 E-value=26 Score=28.29 Aligned_cols=41 Identities=2% Similarity=-0.029 Sum_probs=31.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.|++.++.|+.+.. -+|.+..||++.|++++..|+..|...
T Consensus 112 ~L~~~~r~v~~l~~-------~~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 112 LLSADQREAIILIG-------ASGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45666666665532 259999999999999999998877653
No 409
>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=53.30 E-value=33 Score=26.16 Aligned_cols=39 Identities=8% Similarity=0.242 Sum_probs=28.0
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
|+..|+.+++..-. +..|..|||..++++...|.+.+..
T Consensus 18 LT~kQ~~~l~lyy~-------eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 18 LTEKQREILELYYE-------EDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp S-HHHHHHHHHHCT-------S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHc-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 68899999998753 4789999999999998887776654
No 410
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.98 E-value=27 Score=27.57 Aligned_cols=40 Identities=5% Similarity=-0.111 Sum_probs=30.5
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+...- -+|.+..||++.+++++..|+..+..
T Consensus 106 ~L~~~~r~ii~l~~-------~~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERF-------FVGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHH-------hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46666777665432 24899999999999999999887754
No 411
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=52.77 E-value=34 Score=32.27 Aligned_cols=46 Identities=15% Similarity=0.302 Sum_probs=38.8
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
..|+....+.++++.+.+++...|+.|.+.|.|. .|+++++.|..|
T Consensus 336 ~~Gld~~~f~~~~g~~~~~~~~~l~~l~~~gll~-~~~~~~~LT~~G 381 (394)
T PRK08898 336 TDGVPAHLFQERTGLPLAAIEPQLAAAEQRGLLE-RDHTRIRPTPLG 381 (394)
T ss_pred hCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EECCEEEEChhH
Confidence 3589999999998888888889999999999866 677789988764
No 412
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=52.69 E-value=25 Score=28.42 Aligned_cols=60 Identities=17% Similarity=0.174 Sum_probs=42.8
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeEEe-ecC-------CceeeccC
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL---NLPMDKLMEALESLNENSLVYS-IDE-------FHYKSAVN 264 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~IYs-iDd-------~hyk~t~~ 264 (265)
.+.-.||.+|... .-.|..+.+.++.+ .+++..|--+|..|..+|.|-+ -++ -.|..|..
T Consensus 24 ~l~~~IL~~L~~~----p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~ 94 (138)
T TIGR02719 24 FLVPFLLLCLKDW----NLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDA 94 (138)
T ss_pred HHHHHHHHHHccC----CCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHH
Confidence 4667789999763 23677665555554 3788889999999999999987 443 23666653
No 413
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=52.34 E-value=22 Score=29.28 Aligned_cols=41 Identities=2% Similarity=0.053 Sum_probs=31.1
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
..|++.++.|+.+.-- +|++.++|++.|++|...|+..|..
T Consensus 130 ~~L~~~~r~v~~l~~~-------~g~s~~eIA~~lgis~~tV~~~l~r 170 (184)
T PRK12539 130 ARLPEKMRLAIQAVKL-------EGLSVAEAATRSGMSESAVKVSVHR 170 (184)
T ss_pred HhCCHHHHHHHHHHHH-------cCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 3466777777754321 4999999999999999999877643
No 414
>PRK05660 HemN family oxidoreductase; Provisional
Probab=52.23 E-value=29 Score=32.52 Aligned_cols=46 Identities=11% Similarity=0.095 Sum_probs=39.2
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
..|++..++.++++.+..+....|+.|.++|.+. .|+++++.|..|
T Consensus 319 ~~G~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~-~~~~~~~lt~~G 364 (378)
T PRK05660 319 LEAAPRADFEAYTGLPESVIRPQLDEALAQGYLT-ETADHWQITEHG 364 (378)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EeCCEEEECcch
Confidence 3699999999999987777889999999999755 677899988754
No 415
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=52.01 E-value=35 Score=27.27 Aligned_cols=42 Identities=12% Similarity=0.209 Sum_probs=34.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.++..+.+||.++.+ |.+..+|++.+++++..|+..+..|..
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 477888999998743 678999999999999998887776654
No 416
>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=51.77 E-value=19 Score=25.28 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=20.8
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
-+.++|++.|+++.++|++++....
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 4889999999999999999998643
No 417
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=51.77 E-value=22 Score=29.15 Aligned_cols=40 Identities=13% Similarity=0.218 Sum_probs=30.4
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..|++-++.|+.+.. -+|++.+||++.|++++..|+..|.
T Consensus 126 ~~Lp~~~R~v~~L~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 126 DTLRPRVKQAFLMAT-------LDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 346677777775533 2499999999999999999877654
No 418
>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=51.60 E-value=33 Score=26.90 Aligned_cols=41 Identities=10% Similarity=0.111 Sum_probs=30.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.|++.++.|+.+.- -+|.+..+|++.+++++..|+..+...
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 35556666665421 248999999999999999998877653
No 419
>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=51.56 E-value=16 Score=30.18 Aligned_cols=28 Identities=32% Similarity=0.404 Sum_probs=22.7
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.+.+++++|++.++ ++++|+++|++|.+
T Consensus 11 ~~pvs~~~La~~l~-~~~~v~~~l~~L~~ 38 (159)
T PF04079_consen 11 GEPVSIEELAEILG-SEDEVEEALEELQE 38 (159)
T ss_dssp SS-B-HHHHHHHCT--HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhC-CHHHHHHHHHHHHH
Confidence 34699999999999 99999999999975
No 420
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=51.34 E-value=26 Score=28.18 Aligned_cols=39 Identities=8% Similarity=0.106 Sum_probs=29.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+..- .|++..+|++.|++++..|+..+.
T Consensus 128 ~L~~~~r~vl~l~~~-------~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREI-------EGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 466677777765432 489999999999999999876654
No 421
>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=51.13 E-value=13 Score=29.09 Aligned_cols=37 Identities=5% Similarity=0.051 Sum_probs=27.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLME 240 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~ 240 (265)
..|++-++.|+.+-. -+|++.+||++.|++++..|++
T Consensus 106 ~~Lp~~~r~v~~l~~-------~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 106 SILPNKQKKIIYMKF-------FEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHhhcC
Confidence 346666777765532 2599999999999999998863
No 422
>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=50.99 E-value=35 Score=24.78 Aligned_cols=38 Identities=8% Similarity=0.073 Sum_probs=29.9
Q ss_pred CHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 223 HRNVISQQLN--LPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 223 ~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
-|+.+++.+. -+..+--...+.|.++|.|.. .++.+|+
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 3456666654 677788889999999999999 8877775
No 423
>PRK13239 alkylmercury lyase; Provisional
Probab=50.83 E-value=31 Score=29.82 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=34.4
Q ss_pred ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
..+..-||..|.. ..-+++.+|++.++.++++|+++|+.|-
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 2468999999999999999999999985
No 424
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=50.79 E-value=26 Score=28.51 Aligned_cols=41 Identities=15% Similarity=0.255 Sum_probs=31.1
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
..|++-++.|+.+..- +|++..||++.|++++..|+..|..
T Consensus 118 ~~Lp~~~r~v~~L~~~-------~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 118 GKLSSKARAAFLYNRL-------DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred HhCCHHHHHHHHHHHH-------cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3466677777765432 4899999999999999998876643
No 425
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=50.61 E-value=26 Score=29.30 Aligned_cols=41 Identities=5% Similarity=0.046 Sum_probs=30.8
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
..|++.++.|+.+.. -+|.+.++|++.|++++..|+..|..
T Consensus 112 ~~Lp~~~r~v~~L~~-------~~g~s~~EIA~~LgiS~~tVk~~l~R 152 (188)
T PRK12546 112 AQLPDEQREALILVG-------ASGFSYEEAAEMCGVAVGTVKSRANR 152 (188)
T ss_pred HhCCHHHhHHhhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 346667777765533 25999999999999999998876653
No 426
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=50.52 E-value=8.6 Score=27.08 Aligned_cols=33 Identities=27% Similarity=0.366 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHhhCCeEEe-ecC-------CceeeccC
Q 024592 232 NLPMDKLMEALESLNENSLVYS-IDE-------FHYKSAVN 264 (265)
Q Consensus 232 ~~~~~~v~~al~~L~~eG~IYs-iDd-------~hyk~t~~ 264 (265)
.++...|-.+|..|.++|.|-+ ..+ ..|+.|..
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~ 68 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEK 68 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHH
Confidence 3889999999999999999999 443 24666643
No 427
>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=50.46 E-value=15 Score=31.18 Aligned_cols=52 Identities=15% Similarity=0.287 Sum_probs=35.4
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCc
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH 258 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~h 258 (265)
=....|+++|.+. ..+..+++++|.+..++..++|-.+|+.| |.|....+.|
T Consensus 133 YW~~~i~~~L~~~---~~~~~isi~~is~~Tgi~~~DIi~tL~~l---~~l~~~~~~~ 184 (188)
T PF01853_consen 133 YWRRVILEYLLEF---KGKKSISIKDISQETGIRPEDIISTLQQL---GMLKYYKGQH 184 (188)
T ss_dssp HHHHHHHHHHHHT---SSE--EEHHHHHHHH-BTHHHHHHHHHHT---T-EEEETTEE
T ss_pred HHHHHHHHHHHhc---CCCCeEEHHHHHHHHCCCHHHHHHHHHHC---CCEEEECCcE
Confidence 3778899999875 22348999999999999999888777765 4444433333
No 428
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=50.21 E-value=40 Score=27.14 Aligned_cols=42 Identities=19% Similarity=0.180 Sum_probs=35.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.+++....|+.++-+ |++.++|++++++++..|+..+..|..
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 477788889988853 789999999999999999988877754
No 429
>KOG3818 consensus DNA polymerase epsilon, subunit B [Replication, recombination and repair]
Probab=50.17 E-value=37 Score=32.74 Aligned_cols=73 Identities=15% Similarity=0.316 Sum_probs=53.4
Q ss_pred CeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592 64 GADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143 (265)
Q Consensus 64 g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~ 143 (265)
++.+..+.+.|.+....+ =.|-|+|-||+++.-.-. .. ....-+-+|++|-|.|.... +...++....-|
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 TRALQSFLVLGLLTQLKE----GKFHLEDPSGSVQLDLSQ-AK---FHHGLFCEGCFVLVEGTFES--GVFHVNELGFPP 242 (525)
T ss_pred cccccceeeeehhhhccC----CcEEEeCCCCcEEEeecc-cc---cccceeccceEEEEeeeeec--ceEEEeeccCCC
Confidence 556678888888876655 467899999987654332 11 12345789999999999765 778888888877
Q ss_pred CCC
Q 024592 144 IID 146 (265)
Q Consensus 144 v~d 146 (265)
++.
T Consensus 243 ~E~ 245 (525)
T KOG3818|consen 243 VER 245 (525)
T ss_pred CCc
Confidence 764
No 430
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=49.92 E-value=23 Score=32.28 Aligned_cols=54 Identities=13% Similarity=0.109 Sum_probs=42.7
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH-HHhhCCeEEe
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE-SLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~-~L~~eG~IYs 253 (265)
.++...+...|..+...- ....+.++.|+..++.+...+.+.++ +|++.|.|..
T Consensus 255 ~~l~~~~~~~l~~~~~~~---~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~ 309 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKF---GGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQR 309 (328)
T ss_pred CCCCHHHHHHHHHHHHHc---CCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCccc
Confidence 457778888887443321 12358999999999999999999999 9999999954
No 431
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=49.82 E-value=26 Score=28.96 Aligned_cols=39 Identities=13% Similarity=-0.009 Sum_probs=28.8
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.. -+|.+.+||++.|++++..|+..|.
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 35555666664432 2589999999999999999887754
No 432
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=49.75 E-value=34 Score=29.82 Aligned_cols=51 Identities=18% Similarity=0.227 Sum_probs=43.4
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
..|+.-|..||++-... .-+++..|...|+-......++|++|+.||+..-
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 45777899999987653 2489999999999999999999999999999763
No 433
>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=49.51 E-value=35 Score=30.72 Aligned_cols=55 Identities=9% Similarity=0.117 Sum_probs=43.9
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV 263 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~ 263 (265)
.++..|++.|.+ ...+.++|+++++.++.-++..|+.|..-|.+=. +++.|+.|.
T Consensus 10 a~~Lglfd~L~~-------gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~-~~~~y~~t~ 64 (306)
T TIGR02716 10 AIELDLFSHMAE-------GPKDLATLAADTGSVPPRLEMLLETLRQMRVINL-EDGKWSLTE 64 (306)
T ss_pred HHHcCcHHHHhc-------CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEe-cCCcEecch
Confidence 355667888854 2569999999999999999999999999999844 456787653
No 434
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=49.38 E-value=30 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.273 Sum_probs=29.5
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..|++.++.|+.+.. -+|.+.++|++.+++++..|+..|.
T Consensus 134 ~~L~~~~r~vl~l~~-------~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 134 KALSPEERRVIEVLY-------YQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345666666665432 2589999999999999999986554
No 435
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=48.88 E-value=28 Score=28.17 Aligned_cols=39 Identities=18% Similarity=0.147 Sum_probs=28.8
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
..|++-++.|+.+.. -+|.+..||++.|++++..|+..+
T Consensus 117 ~~L~~~~r~vl~L~~-------~~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 117 AQLSPEHRAVLVRSY-------YRGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 346666777765532 249999999999999999985543
No 436
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=48.51 E-value=27 Score=27.12 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=30.8
Q ss_pred CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592 219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I 251 (265)
+.-+++++|+..|.-++..++..|..|.++|-|
T Consensus 17 ~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi 49 (115)
T PF12793_consen 17 PVEVTLDELAELLFCSRRNARTLLKKMQEEGWI 49 (115)
T ss_pred CcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence 457899999999999999999999999999987
No 437
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=48.45 E-value=27 Score=33.18 Aligned_cols=56 Identities=16% Similarity=0.335 Sum_probs=43.1
Q ss_pred CChhHHHHHHH-hcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592 199 GKSIDQMVLDF-LRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE 256 (265)
Q Consensus 199 l~~~~~~Vl~~-i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd 256 (265)
+++++.+|.+. ||-.+ .=..-+|..+++..+++|.+++.+-|.+|+..|+||. ||-
T Consensus 332 ~~dL~~RIiEHNiRiiA--~yYSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidr 389 (439)
T KOG1498|consen 332 WSDLKLRIIEHNIRIIA--KYYSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDR 389 (439)
T ss_pred HHHHHHHHHHHHHHHHH--HHHhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecC
Confidence 56677777653 22111 1134689999999999999999999999999999998 874
No 438
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=48.35 E-value=29 Score=28.85 Aligned_cols=38 Identities=3% Similarity=0.018 Sum_probs=28.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
.|++-++.|+.+.. -+|++..||++.|++++..|+.-|
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 45566666665432 259999999999999999887654
No 439
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=48.28 E-value=30 Score=28.25 Aligned_cols=41 Identities=17% Similarity=0.154 Sum_probs=29.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.|++.++.|+...- -+|.+.++|++.|++++..|+..|...
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 35555555554321 258999999999999999999887653
No 440
>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=48.14 E-value=1.4e+02 Score=23.86 Aligned_cols=63 Identities=16% Similarity=0.261 Sum_probs=39.1
Q ss_pred EEEEEEEEEEeeeC----CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccE
Q 024592 69 TITVVGIVCDMQDK----EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRS 135 (265)
Q Consensus 69 ~V~iVG~V~~v~~~----~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~ 135 (265)
+|.-+|.|+.+-.. +..-.|.|.=.+| +|.+..-.+-. ...+.+++|+.|.++|.. .|+.+..
T Consensus 38 qv~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla---prip~l~~GD~V~f~GeY-e~n~kgg 105 (131)
T PF11948_consen 38 QVSGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA---PRIPWLQKGDQVEFYGEY-EWNPKGG 105 (131)
T ss_pred eEeccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc---ccCcCcCCCCEEEEEEEE-EECCCCC
Confidence 34448999888532 3334444444556 36666444432 356779999999999998 4555543
No 441
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=48.06 E-value=29 Score=28.52 Aligned_cols=25 Identities=12% Similarity=0.137 Sum_probs=22.1
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
+|++.+||++.|++++..|+..|..
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5999999999999999999887654
No 442
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=47.50 E-value=35 Score=28.17 Aligned_cols=38 Identities=13% Similarity=0.156 Sum_probs=28.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
.|++.++.|+.+.- -.|++.++|++.|++++..|+..+
T Consensus 106 ~L~~~~r~i~~l~~-------~~g~~~~EIA~~lgis~~tV~~~l 143 (181)
T PRK09637 106 ALPEKYAEALRLTE-------LEGLSQKEIAEKLGLSLSGAKSRV 143 (181)
T ss_pred hCCHHHHHHHHHHH-------hcCCCHHHHHHHhCCCHHHHHHHH
Confidence 45566666664432 259999999999999998886654
No 443
>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=47.21 E-value=34 Score=27.07 Aligned_cols=40 Identities=18% Similarity=0.264 Sum_probs=30.7
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+.+.. -+|.+..+|++.++++...|+..+..
T Consensus 111 ~L~~~~r~v~~l~~-------~~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRY-------QRGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHH-------hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46666677766532 24999999999999999999887654
No 444
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=47.21 E-value=43 Score=29.30 Aligned_cols=41 Identities=10% Similarity=0.145 Sum_probs=35.6
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
.|++-+.+||..+. +|.+..||++.|++++..|+..+..+.
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 57889999999985 389999999999999999998887654
No 445
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=47.16 E-value=32 Score=28.22 Aligned_cols=39 Identities=8% Similarity=0.010 Sum_probs=28.7
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.. -+|.+.++|++.|++++..|+..+.
T Consensus 127 ~L~~~~r~v~~l~~-------~~g~s~~EIA~~l~is~~tv~~~l~ 165 (179)
T PRK09415 127 SLPIKYREVIYLFY-------YEELSIKEIAEVTGVNENTVKTRLK 165 (179)
T ss_pred hCCHHHhhHhHhHH-------hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45556666654432 2599999999999999999887664
No 446
>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=47.02 E-value=1.2e+02 Score=22.79 Aligned_cols=79 Identities=13% Similarity=0.197 Sum_probs=45.4
Q ss_pred eEEeEEEEEEEEEEe-eeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeC-CccEEEEEEe
Q 024592 65 ADVNTITVVGIVCDM-QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQ-DKRSLNAYSL 141 (265)
Q Consensus 65 ~~v~~V~iVG~V~~v-~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~-~~~~i~~~~i 141 (265)
.|+-+|.=+-.+... .....+..+.|.||.-.+.|..-. ...+.-....++.|++||+.== ++..+ +++.|.+..+
T Consensus 18 ~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLat-qln~lv~~g~l~~~siirl~~y~~n~v~~~k~iiiil~l 96 (101)
T PF04057_consen 18 NPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLAT-QLNHLVESGELQKGSIIRLKQYTCNTVKNGKKIIIILDL 96 (101)
T ss_dssp -TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESG-GGHHHHHTTSSSTT-EEEEEEEEEEESTTSSEEEEEEEE
T ss_pred CcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHH-HhHHHHhcCCcccCCEEEEeEEEEeeccCCCEEEEEEee
Confidence 344444444443332 224578999999999998884432 2221123457899999999854 34456 6777777766
Q ss_pred eeC
Q 024592 142 RPI 144 (265)
Q Consensus 142 ~~v 144 (265)
..+
T Consensus 97 eVv 99 (101)
T PF04057_consen 97 EVV 99 (101)
T ss_dssp EEE
T ss_pred EEE
Confidence 554
No 447
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.02 E-value=41 Score=29.46 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=39.2
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
..++.|+..|+++ .+.+.-+|++.++++...|+=.+..|.+-|.|=
T Consensus 174 ~~~k~I~~eiq~~------~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~ 219 (240)
T COG3398 174 ETSKAIIYEIQEN------KCNTNLLIAYELNLSVATVAYHLKKLEELGIIP 219 (240)
T ss_pred hhHHHHHHHHhcC------CcchHHHHHHHcCccHHHHHHHHHHHHHcCCCc
Confidence 4667788888764 478999999999999999999999999988653
No 448
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=46.98 E-value=37 Score=27.46 Aligned_cols=46 Identities=22% Similarity=0.312 Sum_probs=36.7
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeE
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL---NLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~I 251 (265)
........+.+|.. ...+..+|.++| +++++.|.++|+.|.++|.|
T Consensus 10 ~~~a~~~al~~L~~-------r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~l 58 (157)
T PRK00117 10 YASARARALRLLAR-------REHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLL 58 (157)
T ss_pred HHHHHHHHHHHHcc-------chhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCC
Confidence 44566677777754 256888999888 59999999999999998876
No 449
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=46.75 E-value=35 Score=28.92 Aligned_cols=40 Identities=8% Similarity=0.070 Sum_probs=29.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++-++.|+.+.. -+|.+.++|++.|++++..|+..|..
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 45555556554432 25999999999999999998877653
No 450
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=46.73 E-value=34 Score=28.31 Aligned_cols=39 Identities=8% Similarity=0.036 Sum_probs=29.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+-. -+|++..||++.|++++..|+..|.
T Consensus 130 ~Lp~~~r~v~~L~~-------~~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 130 DLTTDQREALLLTQ-------LLGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred hCCHHHhHHhhhHH-------HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666665432 2589999999999999999887654
No 451
>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=46.46 E-value=45 Score=29.60 Aligned_cols=44 Identities=5% Similarity=0.174 Sum_probs=32.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHH----HHHHHHh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLM----EALESLN 246 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~----~al~~L~ 246 (265)
.|++-++.|+...-- . ++|++..+|++.|+++...|+ +||..|-
T Consensus 218 ~L~~rer~vl~l~y~----~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 218 SLDARSRRIIEARWL----D-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred cCCHHHHHHHHHHhc----C-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 466667777765431 1 459999999999999999999 5666553
No 452
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=46.36 E-value=31 Score=28.38 Aligned_cols=39 Identities=13% Similarity=0.161 Sum_probs=29.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+-. -+|.+..+|++.|++++..|+..+.
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 45666777765422 2589999999999999999887654
No 453
>PRK10651 transcriptional regulator NarL; Provisional
Probab=46.29 E-value=48 Score=26.80 Aligned_cols=43 Identities=9% Similarity=0.290 Sum_probs=36.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhC
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNEN 248 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~e 248 (265)
.|+.-+.+||+++. .|.+..+|++.+++++..|+..+..|...
T Consensus 155 ~Lt~rE~~vl~~l~--------~g~~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 155 QLTPRERDILKLIA--------QGLPNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred cCCHHHHHHHHHHH--------cCCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 47888889999875 37899999999999999999888887653
No 454
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=46.27 E-value=43 Score=26.50 Aligned_cols=56 Identities=14% Similarity=0.151 Sum_probs=45.9
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEFHYK 260 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~hyk 260 (265)
++++...||++|=..+ -.++++|...+. .+...|+..|..|..-|.|=+ -|..+|.
T Consensus 4 Is~aE~eVM~ilW~~~------~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~ 64 (123)
T COG3682 4 ISAAEWEVMEILWSRG------PATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFR 64 (123)
T ss_pred ccHHHHHHHHHHHHcC------CccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcCCeee
Confidence 5678889999996532 358899988873 889999999999999999888 7777664
No 455
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.10 E-value=36 Score=27.88 Aligned_cols=41 Identities=12% Similarity=0.126 Sum_probs=30.8
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
..|++.++.|+...-- +|.+.++|++.|+++...|+..+..
T Consensus 130 ~~L~~~~r~v~~l~~~-------~g~s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 130 ETLPPRQRDVVQSISV-------EGASIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred HhCCHHHHHHHHHHHH-------cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3466666666655422 4999999999999999998887653
No 456
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=38 Score=28.22 Aligned_cols=40 Identities=5% Similarity=0.076 Sum_probs=29.7
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+.+.. -+|.+.++|++.|++++..|+..|..
T Consensus 136 ~L~~~~r~i~~L~~-------~~g~s~~eIA~~lgis~~tV~~~l~R 175 (196)
T PRK12524 136 ALPERQRQAVVLRH-------IEGLSNPEIAEVMEIGVEAVESLTAR 175 (196)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45666666665432 24899999999999999998876653
No 457
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=45.99 E-value=35 Score=27.26 Aligned_cols=39 Identities=13% Similarity=0.182 Sum_probs=29.5
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.-- +|.+.+||++.+++++..|+..+.
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 466677777755322 489999999999999999877643
No 458
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=45.98 E-value=33 Score=34.49 Aligned_cols=39 Identities=8% Similarity=0.077 Sum_probs=34.5
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYK 260 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk 260 (265)
..+.++++.+++++..+++.|..|+.+|.|..++++.|-
T Consensus 507 ~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~~~~ 545 (614)
T PRK10512 507 WWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYY 545 (614)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEE
Confidence 467899999999999999999999999999996666664
No 459
>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=45.76 E-value=37 Score=24.70 Aligned_cols=35 Identities=0% Similarity=-0.007 Sum_probs=27.7
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
=+..|+++|++ + -+++.+|++.++++...|+.+|.
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 35568888876 3 35899999999999999988773
No 460
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=45.61 E-value=51 Score=28.17 Aligned_cols=51 Identities=16% Similarity=0.171 Sum_probs=37.3
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHH----HHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDK----LMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~----v~~al~~L~~ 247 (265)
..|++.|.+||..=-..+--.-...++..+|++.||++.+. +|.|...|+.
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 36899999998864443433456899999999999988776 5555566654
No 461
>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=45.57 E-value=42 Score=26.74 Aligned_cols=41 Identities=7% Similarity=0.114 Sum_probs=30.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL 245 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L 245 (265)
.|++.++.|+.+.- -+|++.++|++.+++++..|+..+...
T Consensus 110 ~L~~~~r~i~~l~~-------~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 110 RLPARQRAVVVLRY-------YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred hCCHHHHHHhhhHH-------HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35555666654422 249999999999999999998877543
No 462
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=45.56 E-value=34 Score=28.77 Aligned_cols=39 Identities=13% Similarity=-0.061 Sum_probs=28.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.. -+|.+..||++.|++++..|+..|.
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 35555666665432 2599999999999999999885543
No 463
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=45.42 E-value=31 Score=28.67 Aligned_cols=40 Identities=10% Similarity=0.189 Sum_probs=29.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|+.-++.|+.+.. -+|.+.++|++.|+++...|+..|..
T Consensus 141 ~Lp~~~r~v~~l~~-------~eg~s~~EIA~~lgis~~tVk~rl~r 180 (194)
T PRK12531 141 RLPKAQRDVLQAVY-------LEELPHQQVAEMFDIPLGTVKSRLRL 180 (194)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 35555666665432 25899999999999999998877653
No 464
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.25 E-value=33 Score=25.39 Aligned_cols=30 Identities=20% Similarity=0.313 Sum_probs=27.6
Q ss_pred CCcC-HHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592 220 NGVH-RNVISQQLNLPMDKLMEALESLNENS 249 (265)
Q Consensus 220 ~Gv~-~~~I~~~l~~~~~~v~~al~~L~~eG 249 (265)
+|.+ +.+|++.++++...|...+....++|
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 465
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=45.24 E-value=38 Score=26.98 Aligned_cols=39 Identities=10% Similarity=0.107 Sum_probs=29.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+.. -+|++.++|++.|++++..|+..|.
T Consensus 105 ~L~~~~r~v~~l~~-------~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 105 ELPPACRDSFLLRK-------LEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 46666777776542 2589999999999999998876543
No 466
>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=45.11 E-value=36 Score=27.68 Aligned_cols=39 Identities=13% Similarity=0.188 Sum_probs=29.3
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
..|++.++.|+.+.. -.|.+.++|++.|++++..|+..|
T Consensus 99 ~~L~~~~r~v~~l~~-------~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 99 KELPDEYREAIRLTE-------LEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 346667777766532 248999999999999999887665
No 467
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity 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 RPA 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.
Probab=45.00 E-value=82 Score=22.55 Aligned_cols=41 Identities=12% Similarity=0.152 Sum_probs=30.6
Q ss_pred CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE
Q 024592 83 EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG 125 (265)
Q Consensus 83 ~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G 125 (265)
...+.+.|-|..| .|.|..+.+... .-.+.|++|....+..
T Consensus 18 ~~~~~miL~De~G~~I~a~i~~~~~~--~f~~~L~eg~vy~is~ 59 (86)
T cd04480 18 GESLEMVLVDEKGNRIHATIPKRLAA--KFRPLLKEGKWYTISN 59 (86)
T ss_pred CcEEEEEEEcCCCCEEEEEECHHHHH--hhhhhceeCCEEEEee
Confidence 3567888999999 799999976432 3356788898776653
No 468
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=44.98 E-value=34 Score=29.21 Aligned_cols=31 Identities=16% Similarity=0.315 Sum_probs=27.3
Q ss_pred cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 222 VHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
++.++|+..++++.+.|..+|..|.++|.++
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~~~gl~~ 204 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALASHGVHV 204 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHhCCeEe
Confidence 3458999999999999999999999999543
No 469
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=44.64 E-value=37 Score=27.09 Aligned_cols=40 Identities=10% Similarity=0.160 Sum_probs=30.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+.+.- -+|++.+||++.++++...|+.-|..
T Consensus 113 ~L~~~~r~v~~L~~-------~~g~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 113 GLPPLVKRAFLLAQ-------VDGLGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred HCCHHHHHHHHHHH-------HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45666777665432 14999999999999999998877654
No 470
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=44.53 E-value=26 Score=31.52 Aligned_cols=64 Identities=20% Similarity=0.132 Sum_probs=46.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeec
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSA 262 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t 262 (265)
.|++.|+.||..|=+.=+ ..+.-+-=+|||..++..+-.||..++.|-.-|++-+ =----|++|
T Consensus 3 ~LT~~QkeIL~aLi~LY~-~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT 68 (294)
T COG2524 3 ELTSSQKEILQALINLYR-RKKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPT 68 (294)
T ss_pred cccHHHHHHHHHHHHHHH-hcCCCcchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCCcccc
Confidence 477889888876532211 1233566699999999999999999999999999876 233345554
No 471
>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=44.46 E-value=71 Score=22.49 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=32.4
Q ss_pred EEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE
Q 024592 71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG 125 (265)
Q Consensus 71 ~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G 125 (265)
.+-|.|++++...-++.+.+++=+|-|... +-. ....+++|+-|.|.=
T Consensus 7 ~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~----~~~---~~~~~~~Gq~v~~~V 54 (74)
T cd05694 7 VLSGCVSSVEDHGYILDIGIPGTTGFLPKK----DAG---NFSKLKVGQLLLCVV 54 (74)
T ss_pred EEEEEEEEEeCCEEEEEeCCCCcEEEEEHH----HCC---cccccCCCCEEEEEE
Confidence 378999999988888887666645655422 111 115689999887764
No 472
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=44.41 E-value=40 Score=27.59 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=29.2
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEAL 242 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al 242 (265)
..|++.++.|+.+.. -+|.+.+||++.|++++..|+..+
T Consensus 116 ~~Lp~~~r~i~~l~~-------~e~~s~~EIA~~lgis~~tV~~~l 154 (179)
T PRK12543 116 HKLPYKLRQVIILRY-------LHDYSQEEIAQLLQIPIGTVKSRI 154 (179)
T ss_pred HhCCHHHHHHHHHHH-------HccCCHHHHHHHHCCCHHHHHHHH
Confidence 356677777775532 248999999999999999876654
No 473
>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=44.19 E-value=54 Score=29.03 Aligned_cols=43 Identities=14% Similarity=0.214 Sum_probs=36.1
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
..|++-+.+|+..+. +|.+..+|++.|++++..|+.-+..+..
T Consensus 189 ~~LT~RE~evl~l~a--------~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 189 GLITAREAEILAWVR--------DGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred cCCCHHHHHHHHHHH--------CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457888889998863 3899999999999999999988877653
No 474
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=44.14 E-value=54 Score=26.54 Aligned_cols=42 Identities=14% Similarity=0.179 Sum_probs=35.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE 247 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~ 247 (265)
.++....+||.++.+ |.+.++|++.+++++..|+.-+..|..
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 477788889999864 678999999999999999988877754
No 475
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=44.09 E-value=38 Score=27.52 Aligned_cols=40 Identities=8% Similarity=0.130 Sum_probs=29.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++-++.|+.+.. -+|.+..||++.|++++..|+..+..
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 45556666654322 25999999999999999998876644
No 476
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=44.06 E-value=39 Score=24.43 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=35.6
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHHHHHHHHHHhhCCeE
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDKLMEALESLNENSLV 251 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~v~~al~~L~~eG~I 251 (265)
.++..|+...+.+ ...-+++.+..+.++ .+...+..+.++|...|.|
T Consensus 37 ~iRn~il~~w~~n----~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~I 84 (86)
T PF04433_consen 37 KIRNTILAEWRKN----PNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLI 84 (86)
T ss_dssp HHHHHHHHHHHHH----TTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHC----CCCcccHHHHHHHccccCHHHHHHHHHHHHHcCcc
Confidence 4677777775443 245689999999998 8999999999999999986
No 477
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=43.90 E-value=41 Score=27.74 Aligned_cols=24 Identities=13% Similarity=0.285 Sum_probs=21.0
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
+|.+.++|++.|++++..|+..+.
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~ 176 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 599999999999999998887654
No 478
>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=43.87 E-value=62 Score=22.48 Aligned_cols=47 Identities=9% Similarity=0.280 Sum_probs=37.5
Q ss_pred hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592 201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS 253 (265)
Q Consensus 201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs 253 (265)
++=.++.+++.+. .-.++..|.++|++.-+.-...++.|.++|.|=.
T Consensus 5 ~ly~~a~~~V~~~------~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 5 ELYDEAVELVIET------QKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred HHHHHHHHHHHHh------CCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 4556677777653 3569999999998888888999999999998744
No 479
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.75 E-value=39 Score=27.95 Aligned_cols=40 Identities=15% Similarity=0.153 Sum_probs=30.1
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..|++-++.|+.+.. -+|.+..||++.|+++...|+..+.
T Consensus 130 ~~L~~~~r~i~~l~~-------~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 130 NDLEKLDREIFIRRY-------LLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HhCCHHHHHHHHHHH-------HccCCHHHHHHHHCCCHHHHHHHHH
Confidence 346666777765432 1489999999999999999887765
No 480
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=43.65 E-value=36 Score=27.60 Aligned_cols=24 Identities=21% Similarity=0.322 Sum_probs=21.3
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
+|.+.++|++.|++++..|+..|.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 599999999999999999887764
No 481
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=43.62 E-value=37 Score=28.13 Aligned_cols=39 Identities=15% Similarity=0.291 Sum_probs=28.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++.++.|+.+.. -+|++.++|++.|++++..|+..+.
T Consensus 111 ~Lp~~~R~v~~L~~-------~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 111 DLPEEQRAALHLVA-------IEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 45566666664432 2599999999999999999887753
No 482
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=43.56 E-value=36 Score=28.22 Aligned_cols=24 Identities=17% Similarity=0.155 Sum_probs=20.7
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
+|++..||++.|++++..|+..|.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 599999999999999999866543
No 483
>PRK05853 hypothetical protein; Validated
Probab=43.55 E-value=15 Score=30.50 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=26.7
Q ss_pred CCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592 93 GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129 (265)
Q Consensus 93 gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~ 129 (265)
.|--|.|..|..... .-...+..|+.|-|.|+|+.
T Consensus 41 ~T~wi~V~~wg~lAe--~v~~~L~KG~~V~V~GrL~~ 75 (161)
T PRK05853 41 NSLFITVNCWGRLVT--GVGAALGKGAPVIVVGHVYT 75 (161)
T ss_pred CccEEEEEEEhHHHH--HHHHHcCCCCEEEEEEEEEc
Confidence 466799999976432 12456899999999999986
No 484
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=43.54 E-value=17 Score=35.70 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=40.0
Q ss_pred CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592 199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252 (265)
Q Consensus 199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY 252 (265)
.+.+|-.||-.+.+ ...+++++|++.+++++++++.+|..|+..|.+.
T Consensus 518 ~s~~q~~iLl~Fn~------~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~ 565 (588)
T PF00888_consen 518 VSTLQAAILLLFND------NDSLTVEEISEKTGISEEELKRALKSLVKSKILI 565 (588)
T ss_dssp EEHHHHHHHHGGGS------SSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCS
T ss_pred eeHHHHHHHHHHcc------CCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcce
Confidence 45789999999876 3579999999999999999999999999999886
No 485
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=43.13 E-value=40 Score=21.46 Aligned_cols=23 Identities=39% Similarity=0.524 Sum_probs=15.4
Q ss_pred HHHHHhcCCCHHH-HHHHHHHHhh
Q 024592 225 NVISQQLNLPMDK-LMEALESLNE 247 (265)
Q Consensus 225 ~~I~~~l~~~~~~-v~~al~~L~~ 247 (265)
+++++..+++.++ |++||+.|..
T Consensus 18 ~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 18 KELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3455555666666 7788888765
No 486
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=43.07 E-value=35 Score=29.31 Aligned_cols=40 Identities=15% Similarity=0.124 Sum_probs=29.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++-++.|+.+.. -+|++..||++.|++++..|+..|..
T Consensus 134 ~Lp~~~R~v~~L~y-------~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 134 KLPVEYREVLVLRE-------LEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred cCCHHHHhHhhhHH-------hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34555565654432 25999999999999999998877653
No 487
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.07 E-value=35 Score=27.77 Aligned_cols=25 Identities=12% Similarity=0.397 Sum_probs=22.2
Q ss_pred CCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 220 NGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 220 ~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
+|.+.++|++.|++++..|+..|..
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~R 168 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRR 168 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHH
Confidence 5899999999999999999887654
No 488
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=42.99 E-value=49 Score=23.56 Aligned_cols=31 Identities=10% Similarity=0.303 Sum_probs=24.4
Q ss_pred CCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCe
Q 024592 220 NGVHRNVISQQL-----NLPMDKLMEALESLNENSL 250 (265)
Q Consensus 220 ~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~ 250 (265)
.|-+++++.++| +.+..+|..+=+.|+.+|.
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~~EI~~~Eq~Li~eG~ 46 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSASEISAAEQELIQEGM 46 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCC
Confidence 366788887766 4888888888888888884
No 489
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=42.99 E-value=51 Score=26.27 Aligned_cols=39 Identities=18% Similarity=0.163 Sum_probs=29.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++-++.|+.+.- .|.+..+|++.|++++..|+..+..
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 45556666665432 4899999999999999998877653
No 490
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=42.82 E-value=38 Score=27.02 Aligned_cols=40 Identities=18% Similarity=0.086 Sum_probs=30.0
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+.+-. -+|.+.++|++.|++++..|+..+..
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 45666666665422 25899999999999999999887654
No 491
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=42.81 E-value=38 Score=27.38 Aligned_cols=39 Identities=8% Similarity=0.137 Sum_probs=29.9
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+..- +|.+.+||++.|++++..|+.-|.
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 466677777755322 489999999999999998877654
No 492
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=42.81 E-value=41 Score=27.95 Aligned_cols=39 Identities=8% Similarity=-0.028 Sum_probs=29.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+.. -+|++.+||++.++++...|+..|.
T Consensus 134 ~Lp~~~r~i~~l~~-------~~g~s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 134 RLPVEQRAALVAVD-------MQGYSVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46666777774432 2489999999999999999887763
No 493
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=42.75 E-value=39 Score=27.97 Aligned_cols=39 Identities=5% Similarity=0.009 Sum_probs=28.4
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
.|++-++.|+.+.. -+|.+..||++.|++++..|+..|.
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 35555666654432 2599999999999999998877653
No 494
>PLN03239 histone acetyltransferase; Provisional
Probab=42.67 E-value=43 Score=31.30 Aligned_cols=43 Identities=19% Similarity=0.316 Sum_probs=34.4
Q ss_pred hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592 202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN 246 (265)
Q Consensus 202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~ 246 (265)
....|+++|.+.. ..+.-+++++|++..++..++|-.+|+.|-
T Consensus 267 W~~~il~~L~~~~--~~~~~~si~dis~~Tgi~~~DIi~tL~~l~ 309 (351)
T PLN03239 267 WGSTIVDFLLNHS--GNDSSLSIMDIAKKTSIMAEDIVFALNQLG 309 (351)
T ss_pred HHHHHHHHHHhcc--CCCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 6788999987642 223579999999999999999988888774
No 495
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=42.63 E-value=1e+02 Score=26.16 Aligned_cols=61 Identities=18% Similarity=0.223 Sum_probs=40.4
Q ss_pred EeEEEEEEEEEEeeeCCCeEEEEEEc----C----------CCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCC
Q 024592 67 VNTITVVGIVCDMQDKEPQFIFLIDD----G----------TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQD 132 (265)
Q Consensus 67 v~~V~iVG~V~~v~~~~t~~~y~LdD----g----------TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~ 132 (265)
.+.|++=|+|+++....+...++|-- . +|++-|.+ +. --++..++ |.+|.|+|+|...+.
T Consensus 53 gq~aR~GGkVvnv~n~~~rTrlEi~slPldS~arP~l~~~~qGRfiAy~--~G---FlDPv~~~-gr~vTv~G~i~g~E~ 126 (191)
T COG3065 53 GQQARFGGKVVNVINQKGRTRLEIASLPLDSGARPDLEAESQGRFIAYV--NG---FLDPVNFR-GRLVTVVGTIAGTED 126 (191)
T ss_pred cceeeeCcEEEEEecCCCcEEEEEEeeccCcccCCCcCCCCCceEEEEc--cc---ccChhhhc-CcEEEEEeeeccccC
Confidence 37889999999999888877777642 1 12222211 10 11345667 999999999998764
Q ss_pred c
Q 024592 133 K 133 (265)
Q Consensus 133 ~ 133 (265)
.
T Consensus 127 G 127 (191)
T COG3065 127 G 127 (191)
T ss_pred C
Confidence 3
No 496
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=42.40 E-value=75 Score=23.23 Aligned_cols=30 Identities=10% Similarity=0.074 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592 236 DKLMEALESLNENSLVYSIDEFHYKSAVNA 265 (265)
Q Consensus 236 ~~v~~al~~L~~eG~IYsiDd~hyk~t~~~ 265 (265)
..|+=++.+|...|.|-..+--+|+.|..|
T Consensus 55 ~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G 84 (92)
T PF14338_consen 55 NRIRWARSYLKKAGLIERPKRGIWRITEKG 84 (92)
T ss_pred HhHHHHHHHHHHCCCccCCCCCceEECHhH
Confidence 446678889999999966777799988754
No 497
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=42.37 E-value=39 Score=28.08 Aligned_cols=40 Identities=10% Similarity=0.257 Sum_probs=29.9
Q ss_pred CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592 197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE 243 (265)
Q Consensus 197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~ 243 (265)
..|++-++.|+.+-. -+|.+.+||++.|++++..|+..+.
T Consensus 141 ~~L~~~~r~vl~l~~-------~~~~s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 141 DALTDTQRESVTLAY-------YGGLTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred HhCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCChHhHHHHHH
Confidence 346667777765422 2489999999999999999887664
No 498
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.36 E-value=51 Score=27.77 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=29.3
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+.+.- -+|.+.++|++.|++++..|+..|..
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 45566666654322 25999999999999999998877543
No 499
>PRK14136 recX recombination regulator RecX; Provisional
Probab=42.27 E-value=30 Score=31.69 Aligned_cols=47 Identities=19% Similarity=0.327 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeE
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL---NLPMDKLMEALESLNENSLV 251 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~I 251 (265)
....+....|.+|..- --+..||.++| +++++.|..+|++|.++|.|
T Consensus 160 ~~~~lk~kAL~lLSrR-------eRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYL 209 (309)
T PRK14136 160 PARSLKGRALGYLSRR-------EYSRAELARKLAPYADESDSVEPLLDALEREGWL 209 (309)
T ss_pred cHHHHHHHHHHHhhcc-------cccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCc
Confidence 3456778888888652 34789999988 59999999999999998875
No 500
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=42.25 E-value=38 Score=27.79 Aligned_cols=40 Identities=8% Similarity=0.113 Sum_probs=29.2
Q ss_pred CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244 (265)
Q Consensus 198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~ 244 (265)
.|++.++.|+...- -+|.+.++|++.|++++..|+..|..
T Consensus 137 ~L~~~~r~i~~l~~-------~~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 137 ELEPPRSELIRTAF-------FEGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred hCCHHHHHHHHHHH-------HcCCCHHHHHHHhCCChhHHHHHHHH
Confidence 34555555554322 25999999999999999999887754
Done!