Query psy5744
Match_columns 157
No_of_seqs 101 out of 233
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 16:54:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5744.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5744hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2593|consensus 100.0 4.6E-43 9.9E-48 297.7 11.7 148 9-156 7-157 (436)
2 TIGR00373 conserved hypothetic 100.0 5.3E-40 1.1E-44 250.8 15.5 132 19-157 2-133 (158)
3 smart00531 TFIIE Transcription 100.0 1.5E-39 3.2E-44 245.5 12.4 127 31-157 1-128 (147)
4 PRK06266 transcription initiat 100.0 2.4E-36 5.1E-41 234.6 16.0 134 15-157 8-141 (178)
5 COG1675 TFA1 Transcription ini 100.0 2.7E-31 5.8E-36 205.1 15.0 134 14-157 4-137 (176)
6 PF02002 TFIIE_alpha: TFIIE al 100.0 1.3E-30 2.7E-35 186.2 6.3 105 19-126 1-105 (105)
7 COG3355 Predicted transcriptio 98.5 3E-06 6.5E-11 62.5 11.3 101 21-125 15-119 (126)
8 PF04703 FaeA: FaeA-like prote 98.1 1.3E-05 2.8E-10 52.2 5.7 56 36-98 5-61 (62)
9 smart00550 Zalpha Z-DNA-bindin 97.8 6.2E-05 1.3E-09 49.6 5.4 45 34-78 9-55 (68)
10 KOG2587|consensus 97.8 0.00012 2.6E-09 64.8 8.3 86 19-109 7-93 (551)
11 PF08221 HTH_9: RNA polymerase 97.8 8.2E-05 1.8E-09 48.3 5.4 60 19-78 1-60 (62)
12 PHA02943 hypothetical protein; 97.7 0.00055 1.2E-08 52.1 9.9 83 35-133 15-97 (165)
13 PF13412 HTH_24: Winged helix- 97.6 0.0002 4.3E-09 43.5 5.2 44 33-76 5-48 (48)
14 PF01978 TrmB: Sugar-specific 97.4 0.00033 7.1E-09 45.6 4.5 46 33-78 10-55 (68)
15 PF12840 HTH_20: Helix-turn-he 97.4 0.00092 2E-08 42.7 6.5 56 23-78 2-57 (61)
16 PRK10141 DNA-binding transcrip 97.4 0.0051 1.1E-07 44.8 10.9 68 23-99 8-75 (117)
17 COG2345 Predicted transcriptio 97.3 0.00093 2E-08 53.7 6.5 60 35-98 15-74 (218)
18 cd00090 HTH_ARSR Arsenical Res 97.2 0.0046 1E-07 39.2 8.8 66 32-107 8-74 (78)
19 smart00418 HTH_ARSR helix_turn 97.1 0.0042 9.1E-08 38.4 7.6 62 36-107 2-63 (66)
20 PF13601 HTH_34: Winged helix 97.0 0.0089 1.9E-07 40.5 8.6 74 35-114 4-77 (80)
21 TIGR02702 SufR_cyano iron-sulf 97.0 0.0027 5.9E-08 49.9 6.6 44 35-78 5-48 (203)
22 PF08220 HTH_DeoR: DeoR-like h 96.9 0.0031 6.7E-08 40.0 5.2 44 35-78 4-47 (57)
23 PF09339 HTH_IclR: IclR helix- 96.9 0.0025 5.5E-08 39.4 4.7 45 33-77 5-50 (52)
24 PF02082 Rrf2: Transcriptional 96.9 0.0032 6.8E-08 42.7 5.5 45 34-78 11-58 (83)
25 smart00420 HTH_DEOR helix_turn 96.9 0.0048 1E-07 37.1 5.8 44 35-78 4-47 (53)
26 smart00347 HTH_MARR helix_turn 96.9 0.023 5E-07 38.3 9.8 61 33-99 12-72 (101)
27 PF01022 HTH_5: Bacterial regu 96.8 0.0033 7.1E-08 38.1 4.8 43 34-77 5-47 (47)
28 KOG2587|consensus 96.7 0.032 6.9E-07 49.8 11.5 103 22-124 388-490 (551)
29 smart00346 HTH_ICLR helix_turn 96.7 0.0065 1.4E-07 41.0 5.8 45 33-77 7-52 (91)
30 PF01047 MarR: MarR family; I 96.5 0.0073 1.6E-07 37.8 5.1 47 33-79 5-51 (59)
31 PRK11014 transcriptional repre 96.5 0.0029 6.3E-08 47.0 3.7 36 44-79 24-59 (141)
32 PF12802 MarR_2: MarR family; 96.5 0.0087 1.9E-07 37.6 5.5 48 31-78 5-54 (62)
33 smart00345 HTH_GNTR helix_turn 96.5 0.0055 1.2E-07 37.8 4.1 36 43-78 17-53 (60)
34 PHA00738 putative HTH transcri 96.3 0.018 4E-07 41.4 6.7 60 34-102 15-74 (108)
35 TIGR02337 HpaR homoprotocatech 96.3 0.15 3.2E-06 36.3 11.4 83 32-120 29-113 (118)
36 PF00325 Crp: Bacterial regula 96.2 0.0095 2.1E-07 33.8 3.7 30 46-75 3-32 (32)
37 smart00344 HTH_ASNC helix_turn 96.2 0.051 1.1E-06 37.9 8.3 46 33-78 5-50 (108)
38 COG1959 Predicted transcriptio 96.2 0.012 2.7E-07 44.4 5.4 36 45-80 25-60 (150)
39 TIGR01610 phage_O_Nterm phage 96.1 0.034 7.3E-07 38.7 7.1 36 43-78 45-80 (95)
40 PRK11512 DNA-binding transcrip 96.1 0.047 1E-06 40.3 8.2 46 33-78 42-87 (144)
41 TIGR02010 IscR iron-sulfur clu 96.1 0.02 4.3E-07 42.2 6.0 45 34-78 11-58 (135)
42 PF13463 HTH_27: Winged helix 96.1 0.038 8.3E-07 35.2 6.7 47 32-78 4-51 (68)
43 PRK11920 rirA iron-responsive 96.0 0.017 3.7E-07 43.7 5.3 37 43-79 22-58 (153)
44 PF00392 GntR: Bacterial regul 96.0 0.04 8.6E-07 35.3 6.4 35 44-78 22-57 (64)
45 PF05584 Sulfolobus_pRN: Sulfo 96.0 0.069 1.5E-06 35.7 7.5 59 36-100 10-68 (72)
46 cd00092 HTH_CRP helix_turn_hel 96.0 0.017 3.7E-07 36.6 4.6 37 42-78 22-58 (67)
47 PRK06474 hypothetical protein; 96.0 0.041 8.8E-07 42.7 7.5 73 25-101 5-79 (178)
48 PF01325 Fe_dep_repress: Iron 95.9 0.027 5.8E-07 36.2 5.4 37 42-78 19-55 (60)
49 PRK03837 transcriptional regul 95.9 0.036 7.8E-07 44.0 7.3 53 15-78 17-70 (241)
50 cd07377 WHTH_GntR Winged helix 95.9 0.028 6E-07 35.2 5.4 33 46-78 26-58 (66)
51 smart00419 HTH_CRP helix_turn_ 95.9 0.019 4.1E-07 34.0 4.4 34 45-78 8-41 (48)
52 PRK11414 colanic acid/biofilm 95.8 0.035 7.7E-07 43.7 6.8 36 43-78 32-67 (221)
53 TIGR00738 rrf2_super rrf2 fami 95.8 0.028 6E-07 40.7 5.7 45 34-78 11-58 (132)
54 PF09012 FeoC: FeoC like trans 95.6 0.028 6.1E-07 36.7 4.7 43 36-78 5-47 (69)
55 PHA02701 ORF020 dsRNA-binding 95.6 0.027 5.8E-07 44.1 5.2 48 31-78 4-52 (183)
56 cd07153 Fur_like Ferric uptake 95.6 0.13 2.9E-06 36.2 8.5 78 34-143 4-87 (116)
57 TIGR02944 suf_reg_Xantho FeS a 95.6 0.039 8.3E-07 40.1 5.7 46 33-78 11-58 (130)
58 PF08279 HTH_11: HTH domain; 95.5 0.034 7.3E-07 34.3 4.5 39 35-73 4-43 (55)
59 PRK10870 transcriptional repre 95.5 0.17 3.6E-06 39.0 9.2 71 8-78 20-104 (176)
60 COG1522 Lrp Transcriptional re 95.4 0.049 1.1E-06 40.2 5.9 70 31-101 8-78 (154)
61 COG1378 Predicted transcriptio 95.4 0.27 5.9E-06 40.1 10.6 83 33-124 18-100 (247)
62 TIGR03338 phnR_burk phosphonat 95.3 0.058 1.3E-06 42.0 6.2 36 43-78 32-67 (212)
63 TIGR01884 cas_HTH CRISPR locus 95.3 0.05 1.1E-06 42.7 5.9 50 29-78 141-190 (203)
64 PRK11169 leucine-responsive tr 95.3 0.049 1.1E-06 41.4 5.5 46 33-78 16-61 (164)
65 TIGR01889 Staph_reg_Sar staphy 95.2 0.09 1.9E-06 37.2 6.5 63 16-78 9-76 (109)
66 PRK00398 rpoP DNA-directed RNA 95.2 0.01 2.2E-07 36.0 1.4 24 128-156 2-25 (46)
67 TIGR02787 codY_Gpos GTP-sensin 95.2 0.038 8.3E-07 45.1 5.0 62 18-79 167-232 (251)
68 PF03428 RP-C: Replication pro 95.2 0.15 3.2E-06 39.8 8.0 86 14-103 25-133 (177)
69 PF13730 HTH_36: Helix-turn-he 95.2 0.035 7.7E-07 34.2 3.8 31 45-75 25-55 (55)
70 COG2512 Predicted membrane-ass 95.2 0.046 9.9E-07 45.0 5.4 48 31-78 195-243 (258)
71 PRK10857 DNA-binding transcrip 95.1 0.062 1.3E-06 41.2 5.7 35 44-78 24-58 (164)
72 PRK14999 histidine utilization 95.1 0.1 2.2E-06 41.8 7.2 35 45-79 35-70 (241)
73 PHA03103 double-strand RNA-bin 95.1 0.039 8.5E-07 43.2 4.5 43 36-78 18-60 (183)
74 PF13545 HTH_Crp_2: Crp-like h 95.0 0.058 1.3E-06 35.2 4.6 34 45-78 28-61 (76)
75 PRK11179 DNA-binding transcrip 95.0 0.06 1.3E-06 40.4 5.2 47 32-78 10-56 (153)
76 TIGR02325 C_P_lyase_phnF phosp 94.9 0.037 8.1E-07 43.8 4.2 34 46-79 33-66 (238)
77 PRK04984 fatty acid metabolism 94.9 0.096 2.1E-06 41.6 6.6 36 43-78 28-64 (239)
78 PRK09464 pdhR transcriptional 94.9 0.098 2.1E-06 42.0 6.6 36 43-78 31-67 (254)
79 TIGR02812 fadR_gamma fatty aci 94.9 0.1 2.2E-06 41.4 6.5 36 43-78 27-63 (235)
80 PRK11534 DNA-binding transcrip 94.8 0.11 2.4E-06 40.9 6.6 36 43-78 28-63 (224)
81 PRK10906 DNA-binding transcrip 94.8 0.061 1.3E-06 43.8 5.2 47 32-78 6-52 (252)
82 PRK10225 DNA-binding transcrip 94.7 0.12 2.6E-06 41.6 6.7 37 43-79 30-67 (257)
83 PF08784 RPA_C: Replication pr 94.7 0.058 1.3E-06 37.7 4.3 43 34-76 50-96 (102)
84 TIGR02404 trehalos_R_Bsub treh 94.7 0.046 1E-06 43.4 4.2 33 47-79 26-58 (233)
85 PRK13509 transcriptional repre 94.7 0.063 1.4E-06 43.6 5.0 47 32-78 6-52 (251)
86 TIGR02018 his_ut_repres histid 94.7 0.05 1.1E-06 43.1 4.3 33 47-79 27-59 (230)
87 PRK11402 DNA-binding transcrip 94.6 0.05 1.1E-06 43.4 4.3 35 45-79 33-67 (241)
88 COG1846 MarR Transcriptional r 94.6 0.1 2.2E-06 36.2 5.3 50 29-78 20-69 (126)
89 PF09824 ArsR: ArsR transcript 94.6 0.05 1.1E-06 41.6 3.8 95 24-123 10-119 (160)
90 PRK11050 manganese transport r 94.5 0.12 2.6E-06 39.0 5.8 44 35-78 41-84 (152)
91 PF02295 z-alpha: Adenosine de 94.5 0.032 6.8E-07 36.6 2.3 44 35-78 8-53 (66)
92 PF04423 Rad50_zn_hook: Rad50 94.4 0.06 1.3E-06 33.6 3.4 38 111-149 3-40 (54)
93 PF01475 FUR: Ferric uptake re 94.4 0.34 7.4E-06 34.6 7.9 79 34-144 11-95 (120)
94 PRK03573 transcriptional regul 94.4 0.44 9.5E-06 34.9 8.6 46 33-78 33-79 (144)
95 TIGR02098 MJ0042_CXXC MJ0042 f 94.4 0.031 6.7E-07 32.2 1.9 29 129-157 2-30 (38)
96 PRK09990 DNA-binding transcrip 94.4 0.15 3.3E-06 40.8 6.5 37 43-79 28-65 (251)
97 PRK10079 phosphonate metabolis 94.4 0.062 1.4E-06 42.9 4.2 34 46-79 36-69 (241)
98 PF08271 TF_Zn_Ribbon: TFIIB z 94.3 0.015 3.2E-07 34.8 0.4 23 130-156 1-23 (43)
99 PF13404 HTH_AsnC-type: AsnC-t 94.3 0.13 2.8E-06 30.7 4.5 37 34-70 6-42 (42)
100 PRK11523 DNA-binding transcrip 94.3 0.17 3.6E-06 40.7 6.6 36 43-78 29-65 (253)
101 COG5625 Predicted transcriptio 94.2 0.4 8.7E-06 34.2 7.5 105 16-126 6-112 (113)
102 PRK10421 DNA-binding transcrip 94.1 0.18 4E-06 40.5 6.6 36 43-78 23-59 (253)
103 PRK09764 DNA-binding transcrip 94.1 0.075 1.6E-06 42.5 4.3 35 45-79 28-63 (240)
104 COG1321 TroR Mn-dependent tran 94.1 0.13 2.9E-06 39.1 5.3 41 39-79 18-58 (154)
105 PRK09834 DNA-binding transcrip 94.0 0.17 3.6E-06 41.2 6.0 46 33-78 13-59 (263)
106 PRK13777 transcriptional regul 93.9 0.25 5.4E-06 38.7 6.8 46 33-78 47-92 (185)
107 PRK10434 srlR DNA-bindng trans 93.9 0.13 2.8E-06 41.9 5.3 49 31-79 5-53 (256)
108 PF08280 HTH_Mga: M protein tr 93.9 0.13 2.9E-06 32.6 4.3 39 33-71 7-45 (59)
109 PRK03902 manganese transport t 93.9 0.17 3.7E-06 37.3 5.5 37 42-78 19-55 (142)
110 PF04182 B-block_TFIIIC: B-blo 93.9 0.62 1.3E-05 30.9 7.7 49 32-80 3-53 (75)
111 PRK15090 DNA-binding transcrip 93.8 0.16 3.5E-06 41.0 5.7 45 34-78 17-61 (257)
112 PF10007 DUF2250: Uncharacteri 93.6 0.27 5.8E-06 34.4 5.7 49 31-79 7-55 (92)
113 PRK10411 DNA-binding transcrip 93.6 0.17 3.7E-06 40.9 5.5 45 33-77 6-50 (240)
114 PRK09802 DNA-binding transcrip 93.6 0.17 3.7E-06 41.6 5.5 47 32-78 18-64 (269)
115 COG1414 IclR Transcriptional r 93.6 0.17 3.7E-06 41.0 5.4 46 33-78 6-52 (246)
116 TIGR00122 birA_repr_reg BirA b 93.5 0.23 5E-06 32.1 5.0 43 35-78 4-46 (69)
117 COG1802 GntR Transcriptional r 93.4 0.28 6.2E-06 38.8 6.4 36 43-78 37-72 (230)
118 PF00096 zf-C2H2: Zinc finger, 93.4 0.04 8.6E-07 28.0 1.0 16 130-145 1-16 (23)
119 PRK09954 putative kinase; Prov 93.4 0.15 3.2E-06 43.1 5.0 44 34-77 6-49 (362)
120 TIGR03697 NtcA_cyano global ni 93.4 0.13 2.7E-06 39.0 4.2 34 45-78 143-176 (193)
121 COG1777 Predicted transcriptio 93.4 0.11 2.5E-06 41.5 3.9 43 35-78 19-61 (217)
122 COG2188 PhnF Transcriptional r 93.2 0.14 3.1E-06 41.0 4.5 35 45-79 31-65 (236)
123 PRK04424 fatty acid biosynthes 93.2 0.12 2.5E-06 40.3 3.8 47 32-78 8-54 (185)
124 PF03962 Mnd1: Mnd1 family; I 93.1 0.65 1.4E-05 36.4 7.9 74 37-119 2-80 (188)
125 COG0735 Fur Fe2+/Zn2+ uptake r 93.1 0.91 2E-05 34.0 8.4 49 30-78 20-74 (145)
126 PF01726 LexA_DNA_bind: LexA D 92.9 0.3 6.5E-06 31.8 4.8 38 41-78 20-59 (65)
127 PF13814 Replic_Relax: Replica 92.9 0.31 6.7E-06 37.2 5.8 62 38-101 2-66 (191)
128 PRK10402 DNA-binding transcrip 92.8 0.43 9.3E-06 37.6 6.6 33 46-78 170-202 (226)
129 COG1349 GlpR Transcriptional r 92.8 0.23 5E-06 40.4 5.2 48 32-79 6-53 (253)
130 COG4190 Predicted transcriptio 92.7 1.1 2.4E-05 33.6 8.1 49 30-78 63-111 (144)
131 PF13894 zf-C2H2_4: C2H2-type 92.7 0.066 1.4E-06 26.8 1.2 17 130-146 1-17 (24)
132 COG1654 BirA Biotin operon rep 92.6 0.31 6.8E-06 33.1 4.8 35 42-76 16-50 (79)
133 PRK11753 DNA-binding transcrip 92.5 0.19 4.2E-06 38.5 4.2 34 45-78 168-201 (211)
134 COG1725 Predicted transcriptio 92.5 0.19 4.2E-06 37.1 3.9 37 44-80 34-70 (125)
135 PF04492 Phage_rep_O: Bacterio 92.5 0.61 1.3E-05 33.0 6.3 62 17-78 18-87 (100)
136 PF09202 Rio2_N: Rio2, N-termi 92.5 0.23 4.9E-06 34.0 4.0 47 32-78 7-57 (82)
137 PRK09462 fur ferric uptake reg 92.4 1.6 3.5E-05 32.4 8.9 78 33-142 19-103 (148)
138 PRK09391 fixK transcriptional 92.3 0.47 1E-05 37.5 6.2 33 46-78 180-212 (230)
139 PF14947 HTH_45: Winged helix- 92.3 0.32 6.9E-06 32.4 4.5 42 35-76 7-50 (77)
140 PF13465 zf-H2C2_2: Zinc-finge 92.3 0.12 2.7E-06 27.4 1.9 17 124-140 9-25 (26)
141 PRK11886 bifunctional biotin-- 92.2 0.33 7.1E-06 40.6 5.4 43 34-76 7-49 (319)
142 PRK11569 transcriptional repre 92.2 0.39 8.4E-06 39.3 5.7 44 34-77 31-75 (274)
143 PF01638 HxlR: HxlR-like helix 92.2 0.93 2E-05 30.9 6.8 45 33-78 7-52 (90)
144 PHA02768 hypothetical protein; 92.2 0.057 1.2E-06 34.3 0.6 20 128-147 4-23 (55)
145 PF13717 zinc_ribbon_4: zinc-r 92.1 0.12 2.7E-06 29.8 1.9 28 129-157 2-30 (36)
146 TIGR02431 pcaR_pcaU beta-ketoa 92.1 0.4 8.7E-06 38.5 5.6 44 33-76 11-55 (248)
147 PRK13918 CRP/FNR family transc 91.9 0.23 4.9E-06 38.0 3.8 34 45-78 149-182 (202)
148 TIGR03337 phnR transcriptional 91.8 0.26 5.6E-06 38.8 4.2 34 46-79 26-59 (231)
149 PRK13824 replication initiatio 91.8 1.1 2.4E-05 39.2 8.4 104 15-122 38-184 (404)
150 PF13719 zinc_ribbon_5: zinc-r 91.6 0.12 2.6E-06 29.9 1.5 27 130-157 3-30 (37)
151 PF08274 PhnA_Zn_Ribbon: PhnA 91.4 0.075 1.6E-06 29.6 0.5 20 131-156 4-23 (30)
152 COG2186 FadR Transcriptional r 91.4 0.25 5.5E-06 39.8 3.8 33 47-79 36-68 (241)
153 PF08461 HTH_12: Ribonuclease 91.4 0.51 1.1E-05 30.8 4.6 44 35-78 2-51 (66)
154 PRK14165 winged helix-turn-hel 91.2 0.5 1.1E-05 38.0 5.2 36 43-78 19-54 (217)
155 COG0640 ArsR Predicted transcr 91.1 2.9 6.4E-05 27.2 11.3 75 18-101 12-86 (110)
156 COG4189 Predicted transcriptio 91.0 0.86 1.9E-05 37.5 6.4 49 33-81 25-73 (308)
157 PRK10163 DNA-binding transcrip 90.8 0.67 1.5E-05 37.9 5.8 44 34-77 28-72 (271)
158 PRK11161 fumarate/nitrate redu 90.7 0.37 8.1E-06 37.8 4.1 34 45-78 184-217 (235)
159 TIGR00498 lexA SOS regulatory 90.7 0.34 7.4E-06 37.6 3.8 45 34-78 9-59 (199)
160 COG2901 Fis Factor for inversi 90.4 0.78 1.7E-05 32.0 4.8 68 4-74 13-97 (98)
161 smart00529 HTH_DTXR Helix-turn 90.4 0.43 9.4E-06 32.4 3.7 30 49-78 3-32 (96)
162 PRK10430 DNA-binding transcrip 90.4 1.2 2.6E-05 35.0 6.7 50 44-97 177-226 (239)
163 COG1510 Predicted transcriptio 90.3 1.3 2.9E-05 34.5 6.6 67 12-78 6-74 (177)
164 PRK10046 dpiA two-component re 90.2 1.1 2.5E-05 34.9 6.4 52 36-90 167-220 (225)
165 PF13912 zf-C2H2_6: C2H2-type 90.1 0.16 3.4E-06 26.8 1.0 17 130-146 2-18 (27)
166 COG4901 Ribosomal protein S25 89.9 0.56 1.2E-05 33.5 3.9 44 36-79 50-93 (107)
167 PF11994 DUF3489: Protein of u 89.7 0.99 2.1E-05 30.2 4.8 47 32-78 11-59 (72)
168 PF14394 DUF4423: Domain of un 89.5 8 0.00017 29.7 11.2 98 25-123 17-154 (171)
169 PF04539 Sigma70_r3: Sigma-70 89.2 0.44 9.5E-06 31.3 2.8 29 44-72 19-47 (78)
170 COG2390 DeoR Transcriptional r 88.7 0.72 1.6E-05 39.2 4.5 37 43-79 24-60 (321)
171 PRK05638 threonine synthase; V 88.6 1.5 3.2E-05 38.5 6.5 60 33-101 373-434 (442)
172 smart00834 CxxC_CXXC_SSSS Puta 88.4 0.3 6.5E-06 28.2 1.5 18 129-146 5-22 (41)
173 COG4738 Predicted transcriptio 88.4 8 0.00017 28.2 10.3 105 3-113 2-108 (124)
174 COG3388 Predicted transcriptio 88.4 1.5 3.2E-05 30.9 5.1 78 32-121 15-93 (101)
175 PRK09334 30S ribosomal protein 88.3 1 2.3E-05 31.1 4.3 37 42-78 38-74 (86)
176 PRK04172 pheS phenylalanyl-tRN 88.2 1.5 3.2E-05 39.1 6.3 47 33-79 8-54 (489)
177 PF03444 HrcA_DNA-bdg: Winged 88.2 1.5 3.2E-05 29.8 4.9 35 43-77 21-55 (78)
178 PF13384 HTH_23: Homeodomain-l 88.1 0.9 2E-05 27.1 3.5 31 45-75 17-47 (50)
179 TIGR03433 padR_acidobact trans 87.7 7.3 0.00016 27.0 9.4 80 34-118 7-96 (100)
180 PRK12423 LexA repressor; Provi 87.6 1.5 3.3E-05 34.3 5.4 33 46-78 26-59 (202)
181 COG3888 Predicted transcriptio 87.4 1.9 4.1E-05 36.0 6.0 44 36-79 9-54 (321)
182 PF06971 Put_DNA-bind_N: Putat 87.2 1 2.2E-05 28.0 3.4 32 35-66 16-49 (50)
183 COG1733 Predicted transcriptio 87.1 3.7 8E-05 29.8 6.9 48 30-78 22-70 (120)
184 PRK15418 transcriptional regul 86.9 1.5 3.2E-05 37.0 5.4 46 20-78 17-62 (318)
185 smart00659 RPOLCX RNA polymera 86.7 0.53 1.1E-05 28.4 1.9 22 129-156 2-23 (44)
186 TIGR02698 CopY_TcrY copper tra 86.7 2.3 5E-05 31.2 5.7 46 33-78 6-55 (130)
187 PRK04214 rbn ribonuclease BN/u 86.4 1.7 3.7E-05 37.8 5.6 34 43-76 308-341 (412)
188 PF07754 DUF1610: Domain of un 86.4 0.47 1E-05 25.1 1.3 12 126-137 13-24 (24)
189 COG4860 Uncharacterized protei 86.4 8.1 0.00017 29.4 8.4 97 24-126 17-129 (170)
190 COG1497 Predicted transcriptio 86.4 1.9 4.1E-05 35.4 5.4 46 35-80 15-60 (260)
191 COG1594 RPB9 DNA-directed RNA 86.4 0.29 6.3E-06 35.4 0.7 25 117-141 88-112 (113)
192 COG5124 Protein predicted to b 86.3 2.8 6.1E-05 32.9 6.1 44 49-100 32-75 (209)
193 PF12324 HTH_15: Helix-turn-he 86.0 1.7 3.6E-05 29.5 4.2 37 34-70 27-63 (77)
194 COG1996 RPC10 DNA-directed RNA 85.7 0.41 8.9E-06 29.7 1.0 20 126-145 3-22 (49)
195 PHA02591 hypothetical protein; 85.4 2 4.4E-05 29.2 4.3 41 26-67 39-81 (83)
196 PF02796 HTH_7: Helix-turn-hel 85.1 2.2 4.7E-05 25.4 4.0 30 37-67 14-43 (45)
197 TIGR01714 phage_rep_org_N phag 85.0 1.4 3.1E-05 32.1 3.8 55 20-78 30-84 (119)
198 PHA00626 hypothetical protein 84.9 0.53 1.2E-05 30.0 1.3 16 127-142 21-36 (59)
199 PF05605 zf-Di19: Drought indu 84.8 0.64 1.4E-05 28.8 1.6 9 129-137 2-10 (54)
200 PF06163 DUF977: Bacterial pro 84.8 2.5 5.3E-05 31.3 4.9 43 36-78 17-59 (127)
201 PF12171 zf-C2H2_jaz: Zinc-fin 84.7 0.58 1.3E-05 24.8 1.2 17 130-146 2-18 (27)
202 KOG2907|consensus 84.4 0.5 1.1E-05 34.3 1.1 27 115-141 88-114 (116)
203 COG2865 Predicted transcriptio 84.4 1.6 3.4E-05 39.0 4.4 59 33-100 404-462 (467)
204 COG1592 Rubrerythrin [Energy p 84.2 2.2 4.8E-05 32.9 4.7 37 106-146 114-150 (166)
205 COG5340 Predicted transcriptio 84.1 0.81 1.8E-05 37.3 2.3 35 43-77 28-62 (269)
206 TIGR02605 CxxC_CxxC_SSSS putat 84.1 0.76 1.6E-05 28.1 1.7 15 129-143 5-19 (52)
207 smart00440 ZnF_C2C2 C2C2 Zinc 84.1 0.33 7.1E-06 28.6 0.0 21 120-140 19-39 (40)
208 PLN02853 Probable phenylalanyl 83.9 3.5 7.6E-05 37.0 6.4 49 33-81 5-54 (492)
209 PF12760 Zn_Tnp_IS1595: Transp 83.8 0.95 2.1E-05 27.2 2.1 28 125-156 14-41 (46)
210 TIGR02844 spore_III_D sporulat 83.8 1.6 3.4E-05 29.7 3.3 36 31-67 6-41 (80)
211 PF03551 PadR: Transcriptional 83.8 7.2 0.00016 25.3 6.5 40 56-99 28-67 (75)
212 PHA00616 hypothetical protein 83.7 0.27 5.9E-06 29.8 -0.4 13 130-142 2-14 (44)
213 PRK09392 ftrB transcriptional 83.2 7.3 0.00016 30.4 7.5 30 46-75 174-203 (236)
214 cd06170 LuxR_C_like C-terminal 83.1 4.1 8.8E-05 24.1 4.8 28 44-71 14-41 (57)
215 TIGR02716 C20_methyl_CrtF C-20 83.1 2.5 5.4E-05 34.9 4.9 44 34-78 13-56 (306)
216 PF05043 Mga: Mga helix-turn-h 83.0 2.2 4.8E-05 28.5 3.9 41 31-71 16-56 (87)
217 COG4049 Uncharacterized protei 83.0 0.36 7.7E-06 30.9 -0.1 19 123-141 11-29 (65)
218 PF08222 HTH_CodY: CodY helix- 82.5 2.6 5.7E-05 27.1 3.7 35 44-78 3-37 (61)
219 PF01780 Ribosomal_L37ae: Ribo 82.5 1.6 3.5E-05 30.4 3.0 26 109-139 20-45 (90)
220 PF03965 Penicillinase_R: Peni 82.5 3.3 7.1E-05 29.4 4.8 46 33-78 5-54 (115)
221 cd08324 CARD_NOD1_CARD4 Caspas 82.4 3.6 7.8E-05 28.4 4.6 39 35-73 19-59 (85)
222 KOG3623|consensus 82.4 0.88 1.9E-05 42.7 2.1 35 102-141 287-321 (1007)
223 PTZ00326 phenylalanyl-tRNA syn 82.1 4.6 9.9E-05 36.4 6.4 49 33-81 8-57 (494)
224 PF13913 zf-C2HC_2: zinc-finge 81.9 0.84 1.8E-05 24.1 1.1 15 130-144 3-17 (25)
225 PRK00215 LexA repressor; Valid 81.6 4.1 8.8E-05 31.6 5.4 34 45-78 23-57 (205)
226 TIGR03879 near_KaiC_dom probab 81.6 2.3 4.9E-05 28.5 3.4 33 43-75 30-62 (73)
227 COG4565 CitB Response regulato 81.6 6.9 0.00015 31.6 6.7 43 36-78 163-206 (224)
228 PRK13239 alkylmercury lyase; P 81.4 3 6.5E-05 33.3 4.6 38 33-70 24-61 (206)
229 PF13518 HTH_28: Helix-turn-he 81.4 4.9 0.00011 23.8 4.7 41 36-78 5-45 (52)
230 cd00350 rubredoxin_like Rubred 81.2 1.1 2.4E-05 25.1 1.5 14 130-143 2-15 (33)
231 PF05732 RepL: Firmicute plasm 81.2 4.1 9E-05 31.2 5.2 49 30-78 54-108 (165)
232 PF10668 Phage_terminase: Phag 81.1 2.5 5.4E-05 27.3 3.3 23 43-65 20-42 (60)
233 PRK03824 hypA hydrogenase nick 81.0 0.79 1.7E-05 34.0 1.1 17 127-143 68-84 (135)
234 PRK15481 transcriptional regul 80.9 2.3 5.1E-05 36.5 4.2 36 44-79 27-63 (431)
235 COG5647 Cullin, a subunit of E 80.5 6.4 0.00014 37.0 6.9 73 5-78 547-655 (773)
236 PF07848 PaaX: PaaX-like prote 80.3 1.7 3.7E-05 28.7 2.4 35 44-78 19-56 (70)
237 PF01927 Mut7-C: Mut7-C RNAse 80.1 1.1 2.3E-05 33.6 1.5 14 126-139 121-134 (147)
238 PF03297 Ribosomal_S25: S25 ri 79.8 4 8.6E-05 29.2 4.3 37 42-78 56-92 (105)
239 PF05158 RNA_pol_Rpc34: RNA po 79.8 4.6 0.0001 34.3 5.5 86 30-116 83-184 (327)
240 TIGR02937 sigma70-ECF RNA poly 79.7 7.6 0.00016 27.1 5.9 53 16-70 99-151 (158)
241 PF09723 Zn-ribbon_8: Zinc rib 79.7 1.4 3E-05 26.0 1.7 26 129-156 5-30 (42)
242 TIGR00280 L37a ribosomal prote 79.7 2.2 4.7E-05 29.8 2.9 25 109-138 20-44 (91)
243 PF10071 DUF2310: Zn-ribbon-co 79.6 1.7 3.7E-05 35.9 2.7 46 110-157 184-246 (258)
244 smart00421 HTH_LUXR helix_turn 79.1 5.4 0.00012 23.4 4.3 36 34-71 9-44 (58)
245 PF08100 Dimerisation: Dimeris 78.9 2.2 4.9E-05 26.4 2.5 35 35-69 10-50 (51)
246 COG3398 Uncharacterized protei 78.8 6.3 0.00014 32.0 5.6 56 35-99 178-233 (240)
247 PTZ00034 40S ribosomal protein 78.5 3.8 8.3E-05 30.2 4.0 46 55-110 36-81 (124)
248 PRK00135 scpB segregation and 78.5 14 0.0003 29.0 7.4 46 33-81 92-137 (188)
249 PF03501 S10_plectin: Plectin/ 78.5 3.4 7.3E-05 29.1 3.5 39 55-102 33-71 (95)
250 PF09681 Phage_rep_org_N: N-te 78.0 4.7 0.0001 29.4 4.4 34 44-77 52-85 (121)
251 KOG3433|consensus 78.0 2.3 5E-05 33.5 2.9 61 49-118 31-91 (203)
252 PRK00464 nrdR transcriptional 77.9 0.89 1.9E-05 34.7 0.6 21 128-148 27-47 (154)
253 PF04545 Sigma70_r4: Sigma-70, 77.8 6.3 0.00014 23.5 4.3 26 43-68 18-43 (50)
254 PRK10681 DNA-binding transcrip 77.6 4.8 0.0001 32.6 4.8 43 31-73 7-49 (252)
255 PRK03976 rpl37ae 50S ribosomal 77.5 2.7 5.9E-05 29.3 2.9 25 109-138 21-45 (90)
256 PF12874 zf-met: Zinc-finger o 77.4 1.3 2.9E-05 22.6 1.0 17 130-146 1-17 (25)
257 PTZ00255 60S ribosomal protein 77.4 2.5 5.5E-05 29.4 2.6 24 110-138 22-45 (90)
258 PF04438 zf-HIT: HIT zinc fing 77.3 1.3 2.8E-05 24.5 1.0 17 127-143 11-27 (30)
259 TIGR02147 Fsuc_second hypothet 77.1 41 0.00088 27.9 11.5 91 33-124 124-253 (271)
260 PF12793 SgrR_N: Sugar transpo 77.0 15 0.00033 26.4 6.8 54 45-102 19-72 (115)
261 cd08785 CARD_CARD9-like Caspas 76.8 7 0.00015 26.9 4.7 38 36-73 21-63 (86)
262 cd06171 Sigma70_r4 Sigma70, re 76.8 11 0.00025 21.4 6.0 40 30-70 12-51 (55)
263 PF01096 TFIIS_C: Transcriptio 76.3 0.98 2.1E-05 26.4 0.3 19 122-140 21-39 (39)
264 PF08792 A2L_zn_ribbon: A2L zi 76.3 1.7 3.8E-05 24.6 1.3 16 125-140 17-32 (33)
265 PF11972 HTH_13: HTH DNA bindi 76.3 7.6 0.00016 24.5 4.3 35 36-70 4-38 (54)
266 PF00301 Rubredoxin: Rubredoxi 75.4 2.5 5.3E-05 25.9 1.9 16 130-145 2-17 (47)
267 COG1656 Uncharacterized conser 75.2 1.5 3.2E-05 33.9 1.2 16 124-139 125-140 (165)
268 PF04157 EAP30: EAP30/Vps36 fa 75.2 4 8.6E-05 32.5 3.6 44 33-76 176-221 (223)
269 PF09397 Ftsk_gamma: Ftsk gamm 75.1 11 0.00023 24.6 5.0 44 35-78 10-53 (65)
270 smart00355 ZnF_C2H2 zinc finge 74.9 1.5 3.2E-05 21.7 0.8 16 130-145 1-16 (26)
271 smart00437 TOP1Ac Bacterial DN 74.9 4 8.7E-05 33.4 3.7 31 49-79 20-50 (259)
272 COG0478 RIO-like serine/threon 74.9 10 0.00023 31.9 6.1 95 30-132 12-110 (304)
273 PRK05472 redox-sensing transcr 74.5 5.7 0.00012 31.2 4.3 45 31-75 16-62 (213)
274 COG2524 Predicted transcriptio 74.5 6.3 0.00014 32.9 4.6 36 43-78 23-58 (294)
275 PF10609 ParA: ParA/MinD ATPas 74.4 1.6 3.6E-05 29.8 1.1 31 110-140 45-76 (81)
276 PF07900 DUF1670: Protein of u 74.4 4.6 9.9E-05 32.6 3.8 38 43-80 103-141 (220)
277 PF09538 FYDLN_acid: Protein o 73.9 1.3 2.8E-05 31.8 0.5 16 128-143 8-23 (108)
278 PF14353 CpXC: CpXC protein 73.7 3.3 7.2E-05 29.9 2.6 33 117-150 27-59 (128)
279 cd00729 rubredoxin_SM Rubredox 73.6 2.2 4.8E-05 24.1 1.3 17 129-145 2-18 (34)
280 TIGR00331 hrcA heat shock gene 73.3 6.6 0.00014 33.4 4.7 42 37-78 12-56 (337)
281 PF08281 Sigma70_r4_2: Sigma-7 73.3 6.6 0.00014 23.6 3.6 26 43-68 24-49 (54)
282 PF08328 ASL_C: Adenylosuccina 73.3 6.7 0.00014 28.6 4.0 47 9-55 47-93 (115)
283 PLN02839 nudix hydrolase 73.2 2.7 5.9E-05 36.4 2.3 33 17-49 321-355 (372)
284 PF08209 Sgf11: Sgf11 (transcr 73.1 2.7 5.9E-05 23.9 1.6 15 127-141 2-16 (33)
285 COG1327 Predicted transcriptio 73.0 1.3 2.9E-05 33.8 0.4 18 131-148 30-47 (156)
286 PF00196 GerE: Bacterial regul 72.6 8.3 0.00018 23.7 4.0 37 33-71 8-44 (58)
287 cd00569 HTH_Hin_like Helix-tur 72.2 8.6 0.00019 19.6 3.6 20 46-65 22-41 (42)
288 PRK09333 30S ribosomal protein 71.6 9.7 0.00021 29.0 4.8 46 33-78 55-114 (150)
289 PF14502 HTH_41: Helix-turn-he 71.2 10 0.00022 23.4 3.9 33 46-78 7-39 (48)
290 PF05331 DUF742: Protein of un 71.1 10 0.00022 27.5 4.6 49 29-79 41-89 (114)
291 PF01399 PCI: PCI domain; Int 70.9 11 0.00024 25.2 4.7 37 42-78 57-93 (105)
292 PRK00082 hrcA heat-inducible t 70.6 8.2 0.00018 32.9 4.7 37 42-78 22-60 (339)
293 KOG2462|consensus 70.4 2.3 5.1E-05 35.4 1.3 29 114-142 228-256 (279)
294 PF13551 HTH_29: Winged helix- 70.0 9.5 0.00021 26.0 4.2 35 43-77 10-44 (112)
295 PF05191 ADK_lid: Adenylate ki 69.8 2.1 4.5E-05 24.7 0.6 13 130-142 2-14 (36)
296 TIGR02392 rpoH_proteo alternat 69.4 16 0.00035 29.6 6.1 28 44-71 235-266 (270)
297 PRK15431 ferrous iron transpor 69.2 18 0.00038 24.6 5.1 43 36-78 7-49 (78)
298 PF13443 HTH_26: Cro/C1-type H 68.9 6.6 0.00014 24.3 2.9 29 39-67 4-32 (63)
299 TIGR00100 hypA hydrogenase nic 68.9 2.1 4.5E-05 30.9 0.6 22 122-143 63-84 (115)
300 PF09079 Cdc6_C: CDC6, C termi 68.7 31 0.00067 22.8 7.0 33 49-81 26-61 (85)
301 PF09855 DUF2082: Nucleic-acid 68.7 2.1 4.5E-05 27.9 0.5 9 130-138 1-9 (64)
302 PF00619 CARD: Caspase recruit 68.5 16 0.00035 23.9 5.0 41 33-73 18-60 (85)
303 PRK10220 hypothetical protein; 68.5 3.1 6.8E-05 30.0 1.5 19 126-144 17-35 (111)
304 TIGR03830 CxxCG_CxxCG_HTH puta 68.5 19 0.00041 25.4 5.6 52 15-66 48-99 (127)
305 cd08332 CARD_CASP2 Caspase act 68.4 14 0.0003 25.4 4.7 38 35-72 24-63 (90)
306 COG2331 Uncharacterized protei 68.2 2.7 5.9E-05 28.5 1.0 27 128-156 11-37 (82)
307 KOG0402|consensus 68.2 3.7 8.1E-05 28.3 1.7 31 110-145 22-52 (92)
308 cd00186 TOP1Ac DNA Topoisomera 67.7 6.5 0.00014 33.9 3.5 31 49-79 94-124 (381)
309 COG1997 RPL43A Ribosomal prote 67.6 6.1 0.00013 27.4 2.7 12 127-138 33-44 (89)
310 PF06806 DUF1233: Putative exc 67.5 4.5 9.8E-05 27.0 2.0 28 39-66 3-30 (72)
311 PF10771 DUF2582: Protein of u 66.8 17 0.00037 23.7 4.6 45 34-78 11-55 (65)
312 PRK00432 30S ribosomal protein 66.4 3.1 6.7E-05 25.7 1.0 8 131-138 22-29 (50)
313 PF03374 ANT: Phage antirepres 66.3 14 0.0003 25.8 4.5 42 33-77 11-53 (111)
314 PF02318 FYVE_2: FYVE-type zin 66.2 7.6 0.00017 27.9 3.1 37 108-144 27-69 (118)
315 PF00888 Cullin: Cullin family 66.1 5.2 0.00011 35.6 2.7 68 11-78 468-567 (588)
316 PF14787 zf-CCHC_5: GAG-polypr 65.9 2.9 6.3E-05 24.2 0.7 10 131-140 4-13 (36)
317 TIGR00244 transcriptional regu 65.7 2.3 5E-05 32.3 0.3 18 131-148 30-47 (147)
318 COG0664 Crp cAMP-binding prote 65.5 15 0.00033 27.3 4.9 35 45-79 171-205 (214)
319 PRK10360 DNA-binding transcrip 65.2 33 0.00072 25.0 6.6 37 33-71 142-178 (196)
320 cd08330 CARD_ASC_NALP1 Caspase 65.1 19 0.00042 24.2 4.8 38 34-71 18-57 (82)
321 PF07638 Sigma70_ECF: ECF sigm 64.9 32 0.00068 26.2 6.6 58 12-70 118-176 (185)
322 cd00730 rubredoxin Rubredoxin; 64.9 4.4 9.5E-05 25.1 1.4 13 130-142 2-14 (50)
323 PF03604 DNA_RNApol_7kD: DNA d 64.8 5.9 0.00013 22.2 1.8 11 130-140 1-11 (32)
324 PF01131 Topoisom_bac: DNA top 64.8 6.5 0.00014 34.1 3.0 30 49-78 125-155 (403)
325 PF04079 DUF387: Putative tran 64.6 13 0.00029 28.2 4.4 36 36-72 2-39 (159)
326 smart00753 PAM PCI/PINT associ 64.5 30 0.00064 22.7 5.7 37 42-78 21-57 (88)
327 smart00088 PINT motif in prote 64.5 30 0.00064 22.7 5.7 37 42-78 21-57 (88)
328 PF07503 zf-HYPF: HypF finger; 64.2 2.9 6.2E-05 24.0 0.5 16 128-143 20-35 (35)
329 PF03965 Penicillinase_R: Peni 64.1 21 0.00046 25.1 5.1 40 15-54 70-109 (115)
330 cd08327 CARD_RAIDD Caspase act 64.0 20 0.00043 25.0 4.8 64 35-121 25-90 (94)
331 TIGR02698 CopY_TcrY copper tra 63.9 19 0.00042 26.2 5.0 40 15-54 71-110 (130)
332 PF09756 DDRGK: DDRGK domain; 63.5 9.4 0.0002 30.0 3.4 43 36-78 104-146 (188)
333 PF06827 zf-FPG_IleRS: Zinc fi 63.4 1.7 3.6E-05 23.6 -0.6 10 131-140 3-12 (30)
334 PF01381 HTH_3: Helix-turn-hel 63.3 11 0.00025 22.5 3.1 26 43-68 7-32 (55)
335 PF07120 DUF1376: Protein of u 62.9 19 0.00042 24.4 4.5 41 34-74 26-69 (88)
336 PRK14136 recX recombination re 62.7 20 0.00044 30.4 5.4 60 18-77 180-243 (309)
337 PRK10736 hypothetical protein; 62.7 16 0.00034 31.8 4.9 43 35-78 312-354 (374)
338 PRK07758 hypothetical protein; 62.7 12 0.00026 26.3 3.4 30 45-74 63-92 (95)
339 PF13542 HTH_Tnp_ISL3: Helix-t 62.6 20 0.00043 21.3 4.1 31 36-68 20-50 (52)
340 PF04760 IF2_N: Translation in 62.6 9.5 0.00021 23.3 2.7 23 46-68 4-26 (54)
341 cd01671 CARD Caspase activatio 62.5 22 0.00048 23.0 4.7 42 32-73 14-57 (80)
342 PRK00135 scpB segregation and 62.5 15 0.00033 28.8 4.4 38 35-72 7-47 (188)
343 TIGR01384 TFS_arch transcripti 62.5 2.3 5.1E-05 29.6 -0.1 20 122-141 83-102 (104)
344 PF03966 Trm112p: Trm112p-like 62.1 4.1 8.8E-05 26.4 1.0 21 122-142 46-66 (68)
345 TIGR02985 Sig70_bacteroi1 RNA 62.1 43 0.00092 23.9 6.6 39 31-70 116-154 (161)
346 PHA02998 RNA polymerase subuni 62.1 2.6 5.7E-05 33.0 0.1 24 118-141 160-183 (195)
347 PF10571 UPF0547: Uncharacteri 62.0 4 8.6E-05 21.8 0.7 11 130-140 15-25 (26)
348 TIGR03070 couple_hipB transcri 61.8 15 0.00032 21.7 3.5 27 41-67 11-37 (58)
349 PF12728 HTH_17: Helix-turn-he 61.7 12 0.00026 22.2 3.0 48 45-107 1-48 (51)
350 PF10078 DUF2316: Uncharacteri 61.6 9.6 0.00021 26.5 2.8 25 43-67 21-45 (89)
351 smart00843 Ftsk_gamma This dom 61.6 22 0.00047 23.1 4.3 44 35-78 9-52 (63)
352 PF02787 CPSase_L_D3: Carbamoy 61.2 22 0.00047 25.9 4.8 38 43-83 70-107 (123)
353 TIGR00686 phnA alkylphosphonat 61.1 4.4 9.6E-05 29.2 1.1 18 126-143 16-33 (109)
354 PF08679 DsrD: Dissimilatory s 60.6 17 0.00036 24.0 3.6 44 35-78 5-53 (67)
355 PF06170 DUF983: Protein of un 60.5 3.3 7.3E-05 28.5 0.3 16 131-146 10-25 (86)
356 COG5595 Zn-ribbon-containing, 60.4 8 0.00017 31.0 2.5 24 131-156 220-243 (256)
357 PF13936 HTH_38: Helix-turn-he 60.2 21 0.00046 20.9 3.9 33 34-67 10-42 (44)
358 TIGR00635 ruvB Holliday juncti 60.2 28 0.0006 28.3 5.8 60 17-76 222-287 (305)
359 COG2996 Predicted RNA-bindinin 59.8 25 0.00053 29.5 5.3 48 30-77 224-278 (287)
360 PF04963 Sigma54_CBD: Sigma-54 59.8 38 0.00081 26.3 6.2 55 17-71 18-78 (194)
361 TIGR01321 TrpR trp operon repr 59.7 36 0.00078 23.9 5.5 34 36-70 47-80 (94)
362 cd08326 CARD_CASP9 Caspase act 59.3 26 0.00056 23.8 4.6 39 35-73 20-60 (84)
363 TIGR00721 tfx DNA-binding prot 59.3 19 0.00041 26.9 4.2 39 28-68 6-44 (137)
364 TIGR01764 excise DNA binding d 59.1 15 0.00033 20.9 3.1 30 45-78 1-30 (49)
365 PF04967 HTH_10: HTH DNA bindi 59.1 41 0.00089 20.9 5.5 41 16-67 5-45 (53)
366 PF07282 OrfB_Zn_ribbon: Putat 58.5 7.1 0.00015 25.0 1.7 21 125-145 42-62 (69)
367 PRK11924 RNA polymerase sigma 58.5 31 0.00067 25.1 5.4 25 44-68 140-164 (179)
368 PRK11639 zinc uptake transcrip 58.4 30 0.00065 26.3 5.4 46 33-78 28-79 (169)
369 TIGR02607 antidote_HigA addict 57.9 19 0.00042 23.0 3.7 29 39-67 12-40 (78)
370 PRK07571 bidirectional hydroge 57.9 85 0.0018 24.2 8.2 55 13-68 16-77 (169)
371 PRK08295 RNA polymerase factor 57.8 38 0.00082 25.7 5.9 28 43-70 168-195 (208)
372 COG3677 Transposase and inacti 57.6 4.1 9E-05 30.0 0.4 18 127-144 51-68 (129)
373 PF01155 HypA: Hydrogenase exp 57.6 4.4 9.5E-05 29.0 0.6 25 121-145 62-86 (113)
374 COG3695 Predicted methylated D 57.5 14 0.00031 26.3 3.1 47 35-81 13-61 (103)
375 PRK09775 putative DNA-binding 57.4 22 0.00048 31.5 5.0 41 37-79 5-45 (442)
376 PF13744 HTH_37: Helix-turn-he 57.2 25 0.00055 23.2 4.3 29 39-67 25-53 (80)
377 PF13878 zf-C2H2_3: zinc-finge 57.2 5.2 0.00011 23.5 0.8 17 130-146 14-30 (41)
378 TIGR00373 conserved hypothetic 57.1 4.2 9.2E-05 30.9 0.4 19 129-147 128-146 (158)
379 COG2888 Predicted Zn-ribbon RN 57.1 5.3 0.00011 25.8 0.8 11 127-137 48-58 (61)
380 PRK07408 RNA polymerase sigma 56.9 50 0.0011 26.6 6.7 33 43-75 127-159 (256)
381 smart00114 CARD Caspase recrui 56.8 23 0.0005 23.7 4.0 39 35-73 24-64 (88)
382 TIGR01057 topA_arch DNA topois 56.7 12 0.00027 34.3 3.5 30 49-78 282-311 (618)
383 PF10058 DUF2296: Predicted in 56.7 7.2 0.00016 24.5 1.4 14 124-137 39-52 (54)
384 PRK09863 putative frv operon r 56.4 19 0.00042 32.5 4.6 38 33-71 6-43 (584)
385 PF14447 Prok-RING_4: Prokaryo 56.3 5.1 0.00011 25.4 0.6 13 131-143 41-53 (55)
386 smart00661 RPOL9 RNA polymeras 56.2 8.8 0.00019 23.0 1.7 15 127-141 18-32 (52)
387 PLN03238 probable histone acet 56.1 29 0.00063 29.2 5.2 42 34-78 211-253 (290)
388 COG4367 Uncharacterized protei 55.9 15 0.00033 25.6 3.0 24 44-67 22-45 (97)
389 TIGR02859 spore_sigH RNA polym 55.7 52 0.0011 24.7 6.4 28 43-70 163-190 (198)
390 PRK12380 hydrogenase nickel in 55.7 7 0.00015 28.0 1.4 17 126-142 67-83 (113)
391 PRK06759 RNA polymerase factor 55.6 37 0.00081 24.3 5.3 25 44-68 121-145 (154)
392 PF09669 Phage_pRha: Phage reg 55.6 43 0.00093 22.8 5.3 57 46-103 2-64 (93)
393 KOG2165|consensus 55.6 22 0.00047 33.5 4.8 47 33-79 604-650 (765)
394 KOG1088|consensus 55.6 16 0.00034 26.8 3.1 76 55-143 35-112 (124)
395 TIGR03831 YgiT_finger YgiT-typ 55.5 6.1 0.00013 22.9 0.9 17 125-141 28-44 (46)
396 TIGR03829 YokU_near_AblA uncha 55.3 6.8 0.00015 27.3 1.2 22 125-146 31-52 (89)
397 PRK09935 transcriptional regul 54.5 29 0.00062 25.5 4.7 37 33-71 154-190 (210)
398 KOG0978|consensus 54.2 8.3 0.00018 36.1 1.9 40 100-147 651-696 (698)
399 TIGR02393 RpoD_Cterm RNA polym 54.2 54 0.0012 25.9 6.4 26 43-68 101-126 (238)
400 PF07106 TBPIP: Tat binding pr 53.9 72 0.0016 24.0 6.8 45 34-78 4-51 (169)
401 PRK07122 RNA polymerase sigma 53.9 66 0.0014 26.1 7.0 33 44-76 142-174 (264)
402 COG2824 PhnA Uncharacterized Z 53.6 6.9 0.00015 28.2 1.0 19 126-144 17-35 (112)
403 PRK00411 cdc6 cell division co 53.6 65 0.0014 27.1 7.2 72 34-111 299-385 (394)
404 TIGR02850 spore_sigG RNA polym 53.3 51 0.0011 26.4 6.2 28 43-70 134-161 (254)
405 cd00093 HTH_XRE Helix-turn-hel 52.8 28 0.00061 19.3 3.6 25 43-67 10-34 (58)
406 TIGR01206 lysW lysine biosynth 52.7 6.1 0.00013 24.9 0.6 16 129-144 2-17 (54)
407 TIGR02948 SigW_bacill RNA poly 52.6 61 0.0013 24.0 6.2 50 19-70 128-177 (187)
408 PRK00118 putative DNA-binding 52.6 27 0.00058 24.8 3.9 28 42-69 30-57 (104)
409 smart00530 HTH_XRE Helix-turn- 52.5 25 0.00055 19.4 3.3 24 43-66 8-31 (56)
410 COG3944 Capsular polysaccharid 52.5 32 0.00069 27.8 4.7 55 5-59 161-215 (226)
411 TIGR02395 rpoN_sigma RNA polym 52.0 30 0.00064 30.5 4.9 57 15-71 77-139 (429)
412 PF08882 Acetone_carb_G: Aceto 52.0 8 0.00017 28.0 1.1 11 129-139 74-84 (112)
413 COG3413 Predicted DNA binding 51.8 45 0.00096 26.1 5.5 46 15-71 159-208 (215)
414 PRK09641 RNA polymerase sigma 51.8 51 0.0011 24.4 5.7 27 43-69 150-176 (187)
415 PRK14890 putative Zn-ribbon RN 51.7 7.4 0.00016 25.0 0.8 11 127-137 46-56 (59)
416 COG1191 FliA DNA-directed RNA 51.7 30 0.00064 28.4 4.6 44 36-79 115-160 (247)
417 PRK05776 DNA topoisomerase I; 51.7 15 0.00033 34.2 3.2 30 50-79 286-315 (670)
418 PRK04217 hypothetical protein; 51.7 28 0.0006 25.0 3.9 27 43-69 56-82 (110)
419 COG1885 Uncharacterized protei 51.6 12 0.00027 26.8 2.0 44 98-141 16-61 (115)
420 PRK06835 DNA replication prote 51.4 28 0.0006 29.5 4.5 39 100-138 64-107 (329)
421 PRK09639 RNA polymerase sigma 51.3 60 0.0013 23.6 5.9 26 44-69 126-151 (166)
422 PF09106 SelB-wing_2: Elongati 51.3 16 0.00036 22.7 2.4 35 44-78 16-53 (59)
423 COG1571 Predicted DNA-binding 51.1 6.9 0.00015 34.5 0.8 23 122-145 361-383 (421)
424 smart00351 PAX Paired Box doma 50.8 30 0.00066 24.9 4.1 35 44-78 32-66 (125)
425 TIGR02983 SigE-fam_strep RNA p 50.7 24 0.00051 25.7 3.6 28 43-70 124-151 (162)
426 PF07975 C1_4: TFIIH C1-like d 50.7 7.5 0.00016 24.2 0.7 15 127-141 19-33 (51)
427 TIGR02989 Sig-70_gvs1 RNA poly 50.3 83 0.0018 22.5 6.5 27 44-70 126-152 (159)
428 PF13986 DUF4224: Domain of un 50.3 25 0.00053 21.3 3.0 32 45-78 2-33 (47)
429 COG2238 RPS19A Ribosomal prote 50.3 35 0.00077 25.8 4.4 33 56-88 92-125 (147)
430 PF13240 zinc_ribbon_2: zinc-r 50.1 7.4 0.00016 20.0 0.6 11 131-141 1-11 (23)
431 PRK05654 acetyl-CoA carboxylas 50.1 8.7 0.00019 32.2 1.3 25 129-153 46-73 (292)
432 PF09940 DUF2172: Domain of un 49.8 21 0.00045 31.2 3.5 43 34-76 343-386 (386)
433 PRK05932 RNA polymerase factor 49.7 31 0.00067 30.7 4.7 58 14-71 101-164 (455)
434 PRK05988 formate dehydrogenase 49.7 97 0.0021 23.4 6.9 57 11-69 2-65 (156)
435 cd08329 CARD_BIRC2_BIRC3 Caspa 49.5 41 0.00088 23.3 4.4 39 35-73 27-67 (94)
436 PHA00542 putative Cro-like pro 49.4 47 0.001 22.1 4.6 25 43-67 29-53 (82)
437 PF01710 HTH_Tnp_IS630: Transp 49.2 37 0.00081 24.2 4.3 36 39-77 65-100 (119)
438 TIGR02277 PaaX_trns_reg phenyl 49.2 22 0.00048 29.4 3.5 37 43-79 15-54 (280)
439 COG5602 SIN3 Histone deacetyla 49.1 40 0.00086 32.8 5.5 52 17-68 605-657 (1163)
440 PF01418 HTH_6: Helix-turn-hel 49.0 34 0.00074 22.4 3.8 44 31-74 16-63 (77)
441 smart00734 ZnF_Rad18 Rad18-lik 48.8 8.2 0.00018 20.5 0.6 19 131-149 3-21 (26)
442 KOG3233|consensus 48.7 20 0.00044 30.0 3.1 85 34-119 87-187 (297)
443 PF02042 RWP-RK: RWP-RK domain 48.4 37 0.0008 21.2 3.6 32 38-69 8-39 (52)
444 KOG1994|consensus 48.3 15 0.00033 30.0 2.3 18 129-146 239-256 (268)
445 PRK12522 RNA polymerase sigma 48.2 27 0.00058 25.9 3.6 26 43-68 133-158 (173)
446 PF06397 Desulfoferrod_N: Desu 48.2 7.4 0.00016 22.5 0.4 19 126-144 3-21 (36)
447 PRK09210 RNA polymerase sigma 48.2 64 0.0014 27.6 6.3 26 43-68 230-255 (367)
448 COG4530 Uncharacterized protei 48.1 6.8 0.00015 28.5 0.3 9 131-139 28-36 (129)
449 PF01853 MOZ_SAS: MOZ/SAS fami 47.7 27 0.00059 27.5 3.6 42 34-78 136-180 (188)
450 PRK00564 hypA hydrogenase nick 47.7 7.6 0.00016 28.0 0.5 22 121-142 63-84 (117)
451 COG1386 scpB Chromosome segreg 47.4 40 0.00087 26.3 4.5 37 36-72 12-51 (184)
452 PF07647 SAM_2: SAM domain (St 47.3 33 0.00072 21.3 3.4 26 44-70 37-63 (66)
453 PRK07561 DNA topoisomerase I s 47.2 22 0.00049 34.0 3.7 29 50-78 279-307 (859)
454 KOG3993|consensus 47.1 8.6 0.00019 34.1 0.8 14 127-140 293-306 (500)
455 TIGR00515 accD acetyl-CoA carb 47.0 9.4 0.0002 31.9 1.0 25 129-153 45-72 (285)
456 COG4391 Uncharacterized protei 47.0 11 0.00024 24.4 1.1 16 126-141 45-60 (62)
457 PF07535 zf-DBF: DBF zinc fing 46.9 11 0.00024 23.2 1.1 18 127-145 4-21 (49)
458 PF04218 CENP-B_N: CENP-B N-te 46.8 32 0.00069 21.1 3.2 32 34-67 13-44 (53)
459 PF06870 RNA_pol_I_A49: A49-li 46.7 41 0.00088 28.8 4.9 52 19-70 273-344 (385)
460 cd04762 HTH_MerR-trunc Helix-T 46.5 31 0.00066 19.4 3.0 27 47-77 2-28 (49)
461 COG1813 Predicted transcriptio 46.5 20 0.00044 27.7 2.7 30 35-65 83-112 (165)
462 COG2771 CsgD DNA-binding HTH d 46.4 49 0.0011 19.9 4.1 34 35-70 11-44 (65)
463 PRK12537 RNA polymerase sigma 46.4 77 0.0017 23.6 5.9 48 20-69 126-173 (182)
464 PRK12373 NADH dehydrogenase su 46.4 1.2E+02 0.0025 26.8 7.6 64 7-70 9-80 (400)
465 COG3682 Predicted transcriptio 46.3 39 0.00085 24.8 4.0 45 34-78 9-57 (123)
466 COG2093 DNA-directed RNA polym 46.2 10 0.00022 24.8 0.8 20 123-142 12-32 (64)
467 TIGR01056 topB DNA topoisomera 46.2 24 0.00053 32.8 3.6 31 49-79 291-322 (660)
468 PRK01381 Trp operon repressor; 46.0 61 0.0013 22.9 4.9 35 36-71 47-81 (99)
469 PF13613 HTH_Tnp_4: Helix-turn 46.0 39 0.00086 20.5 3.5 28 43-70 17-44 (53)
470 PF04433 SWIRM: SWIRM domain; 45.9 53 0.0012 21.9 4.5 36 42-77 50-86 (86)
471 PF08273 Prim_Zn_Ribbon: Zinc- 45.6 8.9 0.00019 22.6 0.5 20 132-155 6-29 (40)
472 TIGR03209 P21_Cbot clostridium 45.6 14 0.00031 26.4 1.7 22 43-64 121-142 (142)
473 COG1379 PHP family phosphoeste 45.6 6.8 0.00015 33.7 -0.0 22 131-156 248-269 (403)
474 PRK00441 argR arginine repress 45.5 45 0.00098 25.0 4.4 43 33-78 6-53 (149)
475 PRK12496 hypothetical protein; 45.5 11 0.00024 28.8 1.1 14 129-142 127-140 (164)
476 PRK11511 DNA-binding transcrip 45.4 45 0.00097 23.9 4.3 36 36-71 14-51 (127)
477 TIGR01636 phage_rinA phage tra 45.4 1E+02 0.0022 22.4 6.3 50 17-67 72-122 (134)
478 PF08671 SinI: Anti-repressor 45.4 29 0.00064 19.2 2.5 18 51-68 11-28 (30)
479 PF07295 DUF1451: Protein of u 45.1 43 0.00094 25.2 4.3 91 40-149 27-132 (146)
480 PRK07726 DNA topoisomerase III 45.0 24 0.00051 32.8 3.4 31 49-79 288-319 (658)
481 COG4742 Predicted transcriptio 45.0 42 0.00092 27.8 4.5 50 28-78 10-59 (260)
482 PRK03975 tfx putative transcri 44.8 48 0.001 24.8 4.4 38 29-68 7-44 (141)
483 PRK09642 RNA polymerase sigma 44.7 33 0.00071 24.9 3.6 26 43-68 120-145 (160)
484 PRK07219 DNA topoisomerase I; 44.7 24 0.00051 33.7 3.4 31 49-79 291-321 (822)
485 PHA01976 helix-turn-helix prot 44.3 41 0.00089 20.8 3.5 25 43-67 13-37 (67)
486 TIGR00637 ModE_repress ModE mo 44.2 41 0.00088 23.4 3.8 43 28-72 1-43 (99)
487 COG4465 CodY Pleiotropic trans 44.2 36 0.00079 27.7 3.9 60 19-78 174-237 (261)
488 PRK06596 RNA polymerase factor 44.2 69 0.0015 26.3 5.8 24 44-67 247-270 (284)
489 PRK10403 transcriptional regul 44.0 52 0.0011 24.0 4.6 36 34-71 159-194 (215)
490 cd08810 CARD_BCL10 Caspase act 43.9 65 0.0014 22.0 4.6 35 36-70 21-57 (84)
491 TIGR02999 Sig-70_X6 RNA polyme 43.8 35 0.00076 25.3 3.7 26 43-68 148-173 (183)
492 PHA02325 hypothetical protein 43.8 10 0.00022 24.9 0.6 10 131-140 5-14 (72)
493 COG0550 TopA Topoisomerase IA 43.7 28 0.0006 32.0 3.5 30 49-78 267-297 (570)
494 PRK05911 RNA polymerase sigma 43.6 1.2E+02 0.0025 24.5 6.9 26 44-69 125-150 (257)
495 TIGR02719 repress_PhaQ poly-be 43.6 1.4E+02 0.0029 22.3 10.3 63 34-101 27-95 (138)
496 PRK05602 RNA polymerase sigma 43.6 39 0.00086 25.3 3.9 28 43-70 142-169 (186)
497 PF00165 HTH_AraC: Bacterial r 43.6 41 0.00089 19.1 3.2 26 44-69 7-32 (42)
498 PF10013 DUF2256: Uncharacteri 43.4 11 0.00024 22.6 0.6 14 128-141 7-20 (42)
499 smart00451 ZnF_U1 U1-like zinc 43.3 15 0.00033 19.9 1.2 16 129-144 3-18 (35)
500 cd08323 CARD_APAF1 Caspase act 43.0 69 0.0015 21.8 4.7 36 35-70 18-55 (86)
No 1
>KOG2593|consensus
Probab=100.00 E-value=4.6e-43 Score=297.73 Aligned_cols=148 Identities=45% Similarity=0.779 Sum_probs=143.3
Q ss_pred ccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCc
Q psy5744 9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGK 88 (157)
Q Consensus 9 ~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk 88 (157)
.+.++|..+++|+++|||.||+.+|++|+|+|+|++|++|||||++|+|+.|++|++|.+|++|+||+.++|.|..+||+
T Consensus 7 ~~~~~~~~~~~l~k~vvr~fy~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr 86 (436)
T KOG2593|consen 7 VVYDIPTALNDLLKKVVRGFYGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGR 86 (436)
T ss_pred EeecCcHHHHHHHHHHHHhcccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999989998
Q ss_pred eeE-EEEEEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCC--CCcccC
Q psy5744 89 AQK-VNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLW--CACPCK 156 (157)
Q Consensus 89 ~~~-~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~--~~F~C~ 156 (157)
+.. ++||||||.+++||||||||+|+++|+.++++.++..+|+||.|+++||.|||++|+|+ +.|+|-
T Consensus 87 ~~~~~~YyyInY~~~idvVKyKlh~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~ 157 (436)
T KOG2593|consen 87 AVDKHTYYYINYAQVIDVVKYKLHQMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCE 157 (436)
T ss_pred ceeeeEEEEeehHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEe
Confidence 874 79999999999999999999999999999999999999999999999999999999996 799995
No 2
>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=100.00 E-value=5.3e-40 Score=250.78 Aligned_cols=132 Identities=20% Similarity=0.208 Sum_probs=124.0
Q ss_pred HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744 19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN 98 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~ 98 (157)
.||+.+++.|||++++.|+|+|++++++||||||+.||++.|+||++|++|+++|||+++++. + ++ ++|..|||+||
T Consensus 2 ~~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r-~-~~-~gw~~Y~w~i~ 78 (158)
T TIGR00373 2 ELLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRK-D-DE-TGWYEYTWRIN 78 (158)
T ss_pred hHHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeee-e-cC-CCcEEEEEEeC
Confidence 478999999999999999999999999999999999999999999999999999999977543 3 23 46899999999
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744 99 YQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR 157 (157)
Q Consensus 99 y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~ 157 (157)
|+.++++|+||++++.++|++++++++++.+|+||+|+.+|||+||++ .+|.||+
T Consensus 79 ~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~----~~F~Cp~ 133 (158)
T TIGR00373 79 YEKALDVLKRKLEETAKKLREKLEFETNNMFFICPNMCVRFTFNEAME----LNFTCPR 133 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEECCCCCcEeeHHHHHH----cCCcCCC
Confidence 999999999999999999999999999999999999999999999998 7999995
No 3
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=100.00 E-value=1.5e-39 Score=245.52 Aligned_cols=127 Identities=38% Similarity=0.640 Sum_probs=117.5
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHH
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKL 110 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl 110 (157)
.+|++|||+|+++++++|||||+.|||+.|+||++|++|++||++....+.+..+++++|.++||||||+.++++|+||+
T Consensus 1 ~e~~~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~ 80 (147)
T smart00531 1 GEAFLVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKL 80 (147)
T ss_pred CcEEeehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999877766665566567999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCC-CcccCC
Q psy5744 111 DVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWC-ACPCKR 157 (157)
Q Consensus 111 ~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~-~F~C~~ 157 (157)
++|+++|+++++.+.++.+|+||+||.+|+++||+.+.|++ .|.||.
T Consensus 81 ~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~ 128 (147)
T smart00531 81 DKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPR 128 (147)
T ss_pred HHHHHHHHHHHhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCC
Confidence 99999999999999999999999999999999999998764 599984
No 4
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=100.00 E-value=2.4e-36 Score=234.60 Aligned_cols=134 Identities=13% Similarity=0.190 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEE
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY 94 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~y 94 (157)
+.++.|++.+++ .++.++.|||+|.++|++||+|||+.||++.+.||++|++|+++|||.+++.++. +++|+.+|
T Consensus 8 ~~v~~~l~~~~~--~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~---~~Gr~~y~ 82 (178)
T PRK06266 8 PLVQKVLFEIME--GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDE---ETNWYTYT 82 (178)
T ss_pred HHHHHHHHHHhc--CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeecc---CCCcEEEE
Confidence 345667777776 3777999999999999999999999999999999999999999999998754432 35699999
Q ss_pred EEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744 95 YFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR 157 (157)
Q Consensus 95 w~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~ 157 (157)
|++|++.++++|+||++++.++|+++++.+.++++|+||+|+++|||+||+. .+|.||+
T Consensus 83 w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~----~~F~Cp~ 141 (178)
T PRK06266 83 WKPELEKLPEIIKKKKMEELKKLKEQLEEEENNMFFFCPNCHIRFTFDEAME----YGFRCPQ 141 (178)
T ss_pred EEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCEEECCCCCcEEeHHHHhh----cCCcCCC
Confidence 9999999999999999999999999999999999999999999999999997 7999995
No 5
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=99.97 E-value=2.7e-31 Score=205.07 Aligned_cols=134 Identities=20% Similarity=0.395 Sum_probs=124.8
Q ss_pred hHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEE
Q psy5744 14 PTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVN 93 (157)
Q Consensus 14 p~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~ 93 (157)
.+.+..++..|++ |++++.|+|+|+.+|.++||+||..+|+.+++||++|+.|+++|+|++++..+. + +.|.+|
T Consensus 4 ~~~~~~~~~~i~~---g~~~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~-~--~~~~~y 77 (176)
T COG1675 4 DPVLQELLKSIVR---GDEAVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE-E--SGWEEY 77 (176)
T ss_pred cHHHHHHHHHHcc---CchhhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc-C--CCcEEE
Confidence 3567888888888 999999999999989999999999999999999999999999999999866543 2 359999
Q ss_pred EEEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744 94 YYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR 157 (157)
Q Consensus 94 yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~ 157 (157)
||++||+.+.++|+++++++.++|+..++.++++.+|+||.|+.+||++||.. .+|.||.
T Consensus 78 ~w~~~~~~v~~~l~~~~~~~le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~----~~F~Cp~ 137 (176)
T COG1675 78 TWYINYEKVLEVLKGKKRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAME----LGFTCPK 137 (176)
T ss_pred EEEechHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeCCCCCCcccHHHHHH----hCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999 7899995
No 6
>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=99.96 E-value=1.3e-30 Score=186.17 Aligned_cols=105 Identities=26% Similarity=0.504 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744 19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN 98 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~ 98 (157)
+||+.|+|+|||++|++|||+|+++++++|||||+.+|+++|+||++|++|+++|||+++++.+ ++++|+.+|||||
T Consensus 1 ~L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d---~~~~~~~~yw~i~ 77 (105)
T PF02002_consen 1 ELLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKD---DERGWTRYYWYID 77 (105)
T ss_dssp -----HHHTTS-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE-----------EEEEE-T
T ss_pred ChHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEc---CCCcEEEEEEEEc
Confidence 4899999999999999999999999999999999999999999999999999999999986654 2367999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy5744 99 YQTFVNIVKYKLDVMRKRMEMEERDATS 126 (157)
Q Consensus 99 y~~~~~vik~rl~~m~~~L~~~~~~~~~ 126 (157)
|+.++++|+||+++|.++|++++++++|
T Consensus 78 ~~~~~~~ik~r~~~~~~~l~~~l~~e~n 105 (105)
T PF02002_consen 78 YDQIIDVIKYRIYKMREKLKKRLEFEEN 105 (105)
T ss_dssp HHHH------------------SSS--S
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999988754
No 7
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=98.50 E-value=3e-06 Score=62.52 Aligned_cols=101 Identities=16% Similarity=0.186 Sum_probs=81.1
Q ss_pred HHHHHHHcCCC--chHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEE-EEE
Q psy5744 21 SRLVVRGFYSI--EDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVN-YYF 96 (157)
Q Consensus 21 v~~v~R~Fy~~--e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~-yw~ 96 (157)
+..+.+-+||= -.+-++-+|+ .++.++-||||+.|+.+...+.+.|++|.+.|||..++..- +.| .+.| |--
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~--~~G--gy~yiY~~ 90 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL--KGG--GYYYLYKP 90 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc--CCC--ceeEEEec
Confidence 45667777873 3577888888 69999999999999999999999999999999999874432 233 4455 447
Q ss_pred ecchhHHHHHHHHHHHHHHHHHHHHhhcC
Q psy5744 97 INYQTFVNIVKYKLDVMRKRMEMEERDAT 125 (157)
Q Consensus 97 I~y~~~~~vik~rl~~m~~~L~~~~~~~~ 125 (157)
++++.+.+.++..+..--+++++-++...
T Consensus 91 i~~ee~k~~i~~~l~~w~~~~~~~i~~~~ 119 (126)
T COG3355 91 IDPEEIKKKILKDLDEWYDKMKQLIEEFE 119 (126)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999888888887766543
No 8
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=98.06 E-value=1.3e-05 Score=52.23 Aligned_cols=56 Identities=16% Similarity=0.314 Sum_probs=43.1
Q ss_pred HHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744 36 IIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN 98 (157)
Q Consensus 36 IlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~ 98 (157)
|+++|-. ++.++-.|||+.+|++..++|.+|..|+++|.|... . -|++.. +||.++
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~---~---~~rG~~-~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS---P---VRRGKS-TYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE---S----SSSSS--EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---c---CCCCcc-eeeeec
Confidence 6778777 889999999999999999999999999999999743 1 122222 489987
No 9
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.79 E-value=6.2e-05 Score=49.60 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-.|+.+|-+++. ++-.|||+.+|++.+.|+++|+.|.++|+|...
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 468888888876 999999999999999999999999999999754
No 10
>KOG2587|consensus
Probab=97.77 E-value=0.00012 Score=64.78 Aligned_cols=86 Identities=14% Similarity=0.231 Sum_probs=73.4
Q ss_pred HHHHHHHHHcCCCchHHHHHHHHhCCCcC-HHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744 19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMK-EDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI 97 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~-dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I 97 (157)
+|-..++-.|+|+-.-.|+.+|+++|.++ +.-++...||+.+.||++|..|-++++|+|..- +.++| ..++|+-
T Consensus 7 elc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~--~~~~g---~vt~Y~~ 81 (551)
T KOG2587|consen 7 ELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVH--TRNSG---KVTTYEA 81 (551)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEe--cCCCC---ceEEEEe
Confidence 36777888999999889999999999988 999999999999999999999999999999833 33444 5666777
Q ss_pred cchhHHHHHHHH
Q psy5744 98 NYQTFVNIVKYK 109 (157)
Q Consensus 98 ~y~~~~~vik~r 109 (157)
.++.+..+++|=
T Consensus 82 ~~~ei~hilry~ 93 (551)
T KOG2587|consen 82 QCSEILHILRYP 93 (551)
T ss_pred hhhHHHHHHhcc
Confidence 778888888875
No 11
>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=97.75 E-value=8.2e-05 Score=48.30 Aligned_cols=60 Identities=12% Similarity=0.196 Sum_probs=53.3
Q ss_pred HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+|...++...||+-.-.|.+.|+++|..|=.+|+..+++++++||+.|..|-+.++|.+.
T Consensus 1 ~L~~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 1 ELCTLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeee
Confidence 366778889999999999999999999999999999999999999999999999999986
No 12
>PHA02943 hypothetical protein; Provisional
Probab=97.70 E-value=0.00055 Score=52.11 Aligned_cols=83 Identities=16% Similarity=0.304 Sum_probs=62.6
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHH
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR 114 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~ 114 (157)
-|+..| ..|+.|-.+||+.||++-.+++=+|..|+.+|.|... +- ...+||+++.+...+. +..+.
T Consensus 15 eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV---~~------G~~tyw~l~~day~~~----v~~~~ 80 (165)
T PHA02943 15 KTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKV---EI------GRAAIWCLDEDAYTNL----VFEIK 80 (165)
T ss_pred HHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEE---ee------cceEEEEEChHHHHHH----HHHHH
Confidence 466666 7899999999999999999999999999999999874 22 2368999998766666 55555
Q ss_pred HHHHHHHhhcCCCCeeecC
Q psy5744 115 KRMEMEERDATSRSSFKCP 133 (157)
Q Consensus 115 ~~L~~~~~~~~~~~~Y~Cp 133 (157)
+.|..-++. ++--|+-|
T Consensus 81 Relwrlv~s--~~~kfi~p 97 (165)
T PHA02943 81 RELWRLVCN--SRLKFITP 97 (165)
T ss_pred HHHHHHHHh--ccccccCh
Confidence 555554443 34455554
No 13
>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=97.60 E-value=0.0002 Score=43.54 Aligned_cols=44 Identities=20% Similarity=0.428 Sum_probs=38.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
..-|+.+|..++.+|-.+||+.+|++...+++++..|.++|+|+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 45688999999999999999999999999999999999999985
No 14
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=97.39 E-value=0.00033 Score=45.63 Aligned_cols=46 Identities=15% Similarity=0.305 Sum_probs=41.5
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..-|.-+|+.++.++-+|||+.+|++...|+++|..|.+.|||...
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3556677778999999999999999999999999999999999865
No 15
>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=97.38 E-value=0.00092 Score=42.70 Aligned_cols=56 Identities=14% Similarity=0.244 Sum_probs=49.5
Q ss_pred HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+.+++-++--.-|++.|..++.++=.+||+.+|+++..+..-|..|.+.|||..+
T Consensus 2 ~i~~aL~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 2 EIFKALSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHhCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 35677777777889999967899999999999999999999999999999999976
No 16
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=97.36 E-value=0.0051 Score=44.83 Aligned_cols=68 Identities=15% Similarity=0.178 Sum_probs=56.6
Q ss_pred HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744 23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY 99 (157)
Q Consensus 23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y 99 (157)
.+.+++-++--.-|++.|..++.++=-|||+.+|+++..|-+.|..|++.|||..++ +| ...||++|.
T Consensus 8 ~~fkaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r------~G---r~~~Y~l~~ 75 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRK------QG---KWVHYRLSP 75 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEE------Ec---CEEEEEECc
Confidence 566677777778899998877889999999999999999999999999999999762 12 246788885
No 17
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=97.25 E-value=0.00093 Score=53.68 Aligned_cols=60 Identities=15% Similarity=0.375 Sum_probs=48.6
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN 98 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~ 98 (157)
.|+-.|.+++.+|-+|||+.||++..-+|+-|..|..+|+|..+.. +.|+++....|++-
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~----~~g~GRP~~~y~Lt 74 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQ----QGGRGRPAKLYRLT 74 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeec----cCCCCCCceeeeec
Confidence 4566666799999999999999999999999999999999998822 23345666666664
No 18
>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=97.25 E-value=0.0046 Score=39.22 Aligned_cols=66 Identities=15% Similarity=0.424 Sum_probs=50.1
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc-hhHHHHHH
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY-QTFVNIVK 107 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y-~~~~~vik 107 (157)
....|++.+..++ ++-.+||+.+|++...++++|..|.+.|++.... . + ...+|.++. +.+.+.++
T Consensus 8 ~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~---~---~---~~~~~~~~~g~~~~~~~~ 74 (78)
T cd00090 8 TRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR---E---G---RRVYYSLTDAERLLALLE 74 (78)
T ss_pred HHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE---e---c---cEEEEEeCCchHHHHHHH
Confidence 3467888888777 9999999999999999999999999999998641 1 1 245666664 44544443
No 19
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.15 E-value=0.0042 Score=38.37 Aligned_cols=62 Identities=16% Similarity=0.419 Sum_probs=47.0
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK 107 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik 107 (157)
|+..|. ++.++-.+|++.+|++...++++|..|.++|++.... +|+ ..+|+++.+...+++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~------~~~---~~~~~~~~~~~~~~~~ 63 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR------EGK---RVYYSLTDEKVADLLE 63 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee------cCC---EEEEEEchHHHHHHHH
Confidence 455555 7778999999999999999999999999999998441 111 3557777665555544
No 20
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=97.01 E-value=0.0089 Score=40.52 Aligned_cols=74 Identities=14% Similarity=0.186 Sum_probs=52.8
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHH
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR 114 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~ 114 (157)
-||-.|...+.++=.+|.+.+|++.-.+.+.|.+|+++|+|+.+.. . .| ...++||.|-- .=..+++..+..++
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~--~--~~-~~p~t~~~lT~-~Gr~~~~~~~~~L~ 77 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKE--F--EG-RRPRTWYSLTD-KGREAFERYVAALR 77 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-----SS-S--EEEEEE-H-HHHHHHHHHHHHHH
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEe--c--cC-CCCeEEEEECH-HHHHHHHHHHHHHH
Confidence 4777788788999999999999999999999999999999998732 2 22 35688999884 34455555444444
No 21
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=96.97 E-value=0.0027 Score=49.89 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=40.5
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-||..|..++.++-.+||+.+|+++.-|++.|..|.++|||...
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 47778888888999999999999999999999999999999865
No 22
>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=96.89 E-value=0.0031 Score=40.00 Aligned_cols=44 Identities=14% Similarity=0.309 Sum_probs=40.9
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-|++.|-.++.++-+|||+.+|++...+|+=|..|.+.|++...
T Consensus 4 ~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 47888888999999999999999999999999999999998865
No 23
>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=96.88 E-value=0.0025 Score=39.40 Aligned_cols=45 Identities=13% Similarity=0.241 Sum_probs=39.8
Q ss_pred hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.+-||++|..+ +.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 46799999975 5589999999999999999999999999999975
No 24
>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=96.88 E-value=0.0032 Score=42.65 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=36.0
Q ss_pred HHHHHHHHhCC---CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNP---CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~---~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-+|-.|..++ .++=++||+.+|+++..+++++..|.+.|||...
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 44555555432 3999999999999999999999999999999875
No 25
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.87 E-value=0.0048 Score=37.07 Aligned_cols=44 Identities=16% Similarity=0.380 Sum_probs=40.0
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|++.|.+++.++-.+||+.+|++...+++.|..|.+.|+|...
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 47788888888999999999999999999999999999999754
No 26
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.86 E-value=0.023 Score=38.33 Aligned_cols=61 Identities=8% Similarity=0.153 Sum_probs=48.7
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY 99 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y 99 (157)
...||..|..++.++-.+||+.++++...+.+++..|.+.|+|.... .+ +.....++.+.-
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~---~~---~~~r~~~~~lT~ 72 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP---SP---EDRRSVLVSLTE 72 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC---CC---CCCCeEEEEECH
Confidence 56788888878889999999999999999999999999999998651 11 123345677764
No 27
>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=96.83 E-value=0.0033 Score=38.14 Aligned_cols=43 Identities=12% Similarity=0.294 Sum_probs=37.2
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
+-|+.+|. ++..+=.|||+.+|+++..|.+.|..|.+.|+|.+
T Consensus 5 ~~Il~~L~-~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 5 LRILKLLS-EGPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHT-TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHH-hCCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 45677766 48899999999999999999999999999999975
No 28
>KOG2587|consensus
Probab=96.67 E-value=0.032 Score=49.80 Aligned_cols=103 Identities=10% Similarity=0.105 Sum_probs=83.3
Q ss_pred HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744 22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~ 101 (157)
..|++.=||+.++=++-.|..++.+.++.++..--|+.|+.|..|++|-++|.|.-.....+..-+-+++-+.|+.|...
T Consensus 388 E~vI~~rfG~rAiRl~R~l~~k~~veekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~psrtF~L~~v~~~~ 467 (551)
T KOG2587|consen 388 ESVIQERFGSRAIRLFRLLLQKKHVEEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAPSRTFYLYTVNILR 467 (551)
T ss_pred HHHHHHHhhHHHHHHHHHHHhcccchHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCCcceEEEEEeccHH
Confidence 45667778889999999998888999999999999999999999999999999986543333212345677899999888
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy5744 102 FVNIVKYKLDVMRKRMEMEERDA 124 (157)
Q Consensus 102 ~~~vik~rl~~m~~~L~~~~~~~ 124 (157)
...-+.-.+++...+|=.+++.+
T Consensus 468 a~~~lld~ly~~iaNL~~R~~~e 490 (551)
T KOG2587|consen 468 AYRMLLDELYKSIANLIERLRHE 490 (551)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 88888888888777776666554
No 29
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.66 E-value=0.0065 Score=41.04 Aligned_cols=45 Identities=11% Similarity=0.196 Sum_probs=41.2
Q ss_pred hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.+.|++.|..+ +.++-.|||+.+|++...++++|..|.+.|+|..
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 46789998876 7899999999999999999999999999999975
No 30
>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=96.55 E-value=0.0073 Score=37.76 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=41.7
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
...+|..|-.++.++-.+||+.++++..-+-+++..|.+.|+|....
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 46678888888889999999999999999999999999999999873
No 31
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=96.54 E-value=0.0029 Score=46.98 Aligned_cols=36 Identities=11% Similarity=0.134 Sum_probs=33.6
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
..++.++||+.+|++..-||++|..|..+|||...+
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence 468999999999999999999999999999999873
No 32
>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=96.54 E-value=0.0087 Score=37.60 Aligned_cols=48 Identities=13% Similarity=0.313 Sum_probs=41.9
Q ss_pred CchHHHHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 31 IEDSLIIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+.-||-+|..++. ++-.|||+.+++++.-+.+++..|.+.|+|..+
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 345678888888766 999999999999999999999999999999876
No 33
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.46 E-value=0.0055 Score=37.81 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=32.4
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++.+ +..+||+.+|++...||+++..|.++|+|...
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4456 89999999999999999999999999999754
No 34
>PHA00738 putative HTH transcription regulator
Probab=96.35 E-value=0.018 Score=41.39 Aligned_cols=60 Identities=15% Similarity=0.192 Sum_probs=48.9
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF 102 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~ 102 (157)
.-||+.|..++.++=-||++.++|.+.-|-+-|..|++.|||..+ + . | ...||+|+.+.-
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr--K-~---G---r~vyY~Ln~~~~ 74 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELY--K-E---G---RTLYAKIRENSK 74 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE--E-E---C---CEEEEEECCCcc
Confidence 568888887777889999999999999999999999999999976 1 1 2 245778876543
No 35
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=96.31 E-value=0.15 Score=36.27 Aligned_cols=83 Identities=14% Similarity=0.184 Sum_probs=57.4
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc--hhHHHHHHHH
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY--QTFVNIVKYK 109 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y--~~~~~vik~r 109 (157)
....||..|..++.++-.+||+.+|++...+-+++..|.++|+|..... ..| ....++++.- ..+...+...
T Consensus 29 ~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~---~~D---~R~~~v~LT~~G~~~~~~~~~~ 102 (118)
T TIGR02337 29 QQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKA---SND---QRRVYISLTPKGQALYASLSPQ 102 (118)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccC---CCC---CCeeEEEECHhHHHHHHHhhHH
Confidence 3567888888888999999999999999999999999999999997521 123 2345566664 2333444444
Q ss_pred HHHHHHHHHHH
Q psy5744 110 LDVMRKRMEME 120 (157)
Q Consensus 110 l~~m~~~L~~~ 120 (157)
.......+.+.
T Consensus 103 ~~~~~~~~~~~ 113 (118)
T TIGR02337 103 IEEIYAAIEER 113 (118)
T ss_pred HHHHHHHHHHH
Confidence 44444444333
No 36
>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=96.20 E-value=0.0095 Score=33.76 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=26.0
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
++-+|||..+|.....|-++|.+|+++|++
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 677899999999999999999999999986
No 37
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.19 E-value=0.051 Score=37.93 Aligned_cols=46 Identities=13% Similarity=0.325 Sum_probs=42.0
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..-|+.+|.+++.++-.+||+.+|++...+++.+..|.+.|+|...
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 4568888888899999999999999999999999999999999843
No 38
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.19 E-value=0.012 Score=44.42 Aligned_cols=36 Identities=14% Similarity=0.197 Sum_probs=33.9
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR 80 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~ 80 (157)
.++=++||+..|+++..++|++..|.+.|||++++.
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence 688999999999999999999999999999999843
No 39
>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=96.14 E-value=0.034 Score=38.75 Aligned_cols=36 Identities=22% Similarity=0.291 Sum_probs=33.9
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...++..+||+.+|++...|.++|..|++.|+|...
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 568999999999999999999999999999999865
No 40
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.12 E-value=0.047 Score=40.31 Aligned_cols=46 Identities=9% Similarity=0.149 Sum_probs=41.1
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+..||-.|..++.++-.+||+.+++++..+-+++..|++.|+|...
T Consensus 42 q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 42 QFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4567767766788999999999999999999999999999999965
No 41
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=96.08 E-value=0.02 Score=42.20 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=37.4
Q ss_pred HHHHHHHHh---CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVR---NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~---~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-+|-.|.. ++.++-++||+.++++.+.++++|..|.+.|||.+.
T Consensus 11 l~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 444545553 246999999999999999999999999999999864
No 42
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=96.08 E-value=0.038 Score=35.18 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=38.1
Q ss_pred chHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+..||..|. .++.++-.+||+.++++...+.+++.+|.+.|+|...
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 3567788877 6788999999999999999999999999999999654
No 43
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=95.98 E-value=0.017 Score=43.69 Aligned_cols=37 Identities=11% Similarity=0.097 Sum_probs=33.9
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+.++=.+||+..|++.+.|+||+..|.+.|||.+.+
T Consensus 22 ~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 22 GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 3458899999999999999999999999999999873
No 44
>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=95.98 E-value=0.04 Score=35.27 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=30.9
Q ss_pred CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+ ++.+||+.+|++...+|++|..|.++|+|...
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 467 99999999999999999999999999999865
No 45
>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=95.97 E-value=0.069 Score=35.75 Aligned_cols=59 Identities=24% Similarity=0.441 Sum_probs=44.9
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ 100 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~ 100 (157)
|+..|. +++.|=|+|-+.+|++.+.+-..|..|++.|+|...-+. -+|+.... |++-|+
T Consensus 10 IL~~ls-~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~---~~gkk~R~--YclK~~ 68 (72)
T PF05584_consen 10 ILIILS-KRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK---FGGKKYRE--YCLKYK 68 (72)
T ss_pred HHHHHH-hccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE---ecCeEEEE--EEecch
Confidence 444555 449999999999999999999999999999999976333 24433333 777664
No 46
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.97 E-value=0.017 Score=36.64 Aligned_cols=37 Identities=16% Similarity=0.364 Sum_probs=34.2
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+..++-.|||+.+|++...+.++|..|.++|+|...
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 3567999999999999999999999999999999865
No 47
>PRK06474 hypothetical protein; Provisional
Probab=95.96 E-value=0.041 Score=42.69 Aligned_cols=73 Identities=16% Similarity=0.246 Sum_probs=54.9
Q ss_pred HHHcCCCchHHHHHHHHhCCC-cCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744 25 VRGFYSIEDSLIIDMLVRNPC-MKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 25 ~R~Fy~~e~ivIlD~L~~~~~-i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~ 101 (157)
+.++-.+.-..|++.|..++. ++-.+|+..+ +++...|-+.|..|.+.|||........ ++....||.++...
T Consensus 5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~----~~~~ek~y~~~~~~ 79 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKV----RSVSEKYYAINEED 79 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccc----cCceeEEEEeccce
Confidence 344445556789999987665 9999999999 7999999999999999999997632211 23445677777643
No 48
>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=95.95 E-value=0.027 Score=36.15 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=34.0
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+.++--|||+.||+++--+-..+.+|.++|||.+.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 4688999999999999999999999999999999976
No 49
>PRK03837 transcriptional regulator NanR; Provisional
Probab=95.95 E-value=0.036 Score=43.98 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.....|...+..+.|.+ ...+ ++.+||+.+|++..-||.+|..|..+|||..+
T Consensus 17 ~v~~~l~~~I~~g~l~p-----------G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 17 EVEERLEQMIRSGEFGP-----------GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred HHHHHHHHHHHhCCCCC-----------CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34455555555555554 4467 89999999999999999999999999999986
No 50
>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=95.94 E-value=0.028 Score=35.24 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=30.1
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+..+||..+|++...|++.+.+|.+.|+|...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 359999999999999999999999999998743
No 51
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.94 E-value=0.019 Score=34.00 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=31.4
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++-.|||+.+|++...++++|..|.++|++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4788999999999999999999999999999753
No 52
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=95.84 E-value=0.035 Score=43.68 Aligned_cols=36 Identities=11% Similarity=0.152 Sum_probs=33.4
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+++++||+.+|++..-||.+|..|..+|||...
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec
Confidence 457889999999999999999999999999999865
No 53
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=95.80 E-value=0.028 Score=40.73 Aligned_cols=45 Identities=18% Similarity=0.173 Sum_probs=37.5
Q ss_pred HHHHHHHHhC---CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRN---PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~---~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-+|-.|.++ +.++-++||+.+|++...|++++..|.+.|+|.+.
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 4455555532 37999999999999999999999999999999864
No 54
>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=95.65 E-value=0.028 Score=36.72 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=37.2
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|.++|-.++.++-.|||..+++++..|+..|..|...|-|...
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 6677778999999999999999999999999999999999976
No 55
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=95.64 E-value=0.027 Score=44.11 Aligned_cols=48 Identities=15% Similarity=0.154 Sum_probs=42.9
Q ss_pred CchHHHHHHHHhCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 31 IEDSLIIDMLVRNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 31 ~e~ivIlD~L~~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-.-.|+|+|-++| .++--+||.+|||+..+|++.|++|.+.+.|...
T Consensus 4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 33568999999887 6999999999999999999999999999999653
No 56
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=95.60 E-value=0.13 Score=36.25 Aligned_cols=78 Identities=18% Similarity=0.316 Sum_probs=58.2
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK 107 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik 107 (157)
..|+++|.. ++.+|-+||.+.+ +++...|=++|..|.+.|+|... +. ++| .++|..+-
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~---~~-~~~----~~~y~~~~-------- 67 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI---EL-GDG----KARYELNT-------- 67 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE---Ee-CCC----ceEEEeCC--------
Confidence 468899886 4679999999999 69999999999999999999965 22 232 12332331
Q ss_pred HHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744 108 YKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE 143 (157)
Q Consensus 108 ~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld 143 (157)
......++|-.||+.+.+..
T Consensus 68 ----------------~~~h~H~~C~~Cg~i~~~~~ 87 (116)
T cd07153 68 ----------------DEHHHHLICTKCGKVIDFED 87 (116)
T ss_pred ----------------CCCCCceEeCCCCCEEEecC
Confidence 02345799999999998744
No 57
>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=95.57 E-value=0.039 Score=40.14 Aligned_cols=46 Identities=15% Similarity=0.268 Sum_probs=39.2
Q ss_pred hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++-+|..|..+ +.++-.+||..+|+++..|+++|..|.+.|+|...
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 45566666643 56999999999999999999999999999999764
No 58
>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=95.51 E-value=0.034 Score=34.32 Aligned_cols=39 Identities=21% Similarity=0.375 Sum_probs=33.7
Q ss_pred HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744 35 LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDK 73 (157)
Q Consensus 35 vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~ 73 (157)
-|+.+|.. ++.+|-++||+.+|++.+.|++.+..|.+.+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 46777865 4569999999999999999999999999999
No 59
>PRK10870 transcriptional repressor MprA; Provisional
Probab=95.48 E-value=0.17 Score=39.03 Aligned_cols=71 Identities=13% Similarity=0.034 Sum_probs=53.2
Q ss_pred cccccchHHHHHHHHHHHHHcC------------CCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744 8 YVHTEVPTSLKQLSRLVVRGFY------------SIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDK 73 (157)
Q Consensus 8 ~~~~~ip~~~~~Lv~~v~R~Fy------------~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~ 73 (157)
...|..+-.+..|.+.+.|.+. ...+..||-.|.. ++.++-.|||+.++++...+-+++..|.+.|
T Consensus 20 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~l~~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG 99 (176)
T PRK10870 20 EDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG 99 (176)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4455555556666666665431 1225677777764 4579999999999999999999999999999
Q ss_pred ceeee
Q psy5744 74 IIQTR 78 (157)
Q Consensus 74 Lv~~~ 78 (157)
||...
T Consensus 100 lV~R~ 104 (176)
T PRK10870 100 WIERR 104 (176)
T ss_pred CEEec
Confidence 99975
No 60
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.43 E-value=0.049 Score=40.22 Aligned_cols=70 Identities=13% Similarity=0.189 Sum_probs=53.3
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeee-cCCCceeEEEEEEecchh
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET-GLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~-~~~gk~~~~~yw~I~y~~ 101 (157)
+-..-|+..|-+++-++-.+||+.+|+++..+++.+.+|.++|+++...-.-. ..-|.... .+.-++...
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~-a~v~v~~~~ 78 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLT-AFVEVKLER 78 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEE-EEEEEEecC
Confidence 34567899999999999999999999999999999999999999987643211 01132222 667777665
No 61
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=95.38 E-value=0.27 Score=40.10 Aligned_cols=83 Identities=12% Similarity=0.188 Sum_probs=70.0
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHH
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDV 112 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~ 112 (157)
..-+--+|+..|..|-.||++..|++...|=.+|..|+..|+|... . +....|..++.+.+++.++.++..
T Consensus 18 Ea~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~-------~--g~P~~y~av~p~~~i~~~~~~~~~ 88 (247)
T COG1378 18 EAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVI-------E--GRPKKYRAVPPEELIERIKEELQE 88 (247)
T ss_pred HHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEee-------C--CCCceEEeCCHHHHHHHHHHHHHH
Confidence 4566678888999999999999999999999999999999999854 1 244678889999999999999988
Q ss_pred HHHHHHHHHhhc
Q psy5744 113 MRKRMEMEERDA 124 (157)
Q Consensus 113 m~~~L~~~~~~~ 124 (157)
....++..+...
T Consensus 89 ~~~~~~~~~~~~ 100 (247)
T COG1378 89 LLRELESELEEL 100 (247)
T ss_pred HHHHHHHHHHHh
Confidence 777777765443
No 62
>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=95.30 E-value=0.058 Score=41.99 Aligned_cols=36 Identities=19% Similarity=0.347 Sum_probs=33.5
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+++.+||+.+|++..-||.+|..|..+|||...
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence 556899999999999999999999999999999865
No 63
>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=95.30 E-value=0.05 Score=42.66 Aligned_cols=50 Identities=12% Similarity=0.209 Sum_probs=44.8
Q ss_pred CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++....|+..|.+++.++-.+||+.+|+++..+++.|..|++.|+|...
T Consensus 141 ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 141 LSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 34556788888888888999999999999999999999999999999976
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=95.25 E-value=0.049 Score=41.37 Aligned_cols=46 Identities=15% Similarity=0.225 Sum_probs=42.4
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-.-||.+|.+++-++-.+||+.+|++..-|++-+.+|.++|++...
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~ 61 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGY 61 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence 4578999999999999999999999999999999999999999743
No 65
>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=95.25 E-value=0.09 Score=37.21 Aligned_cols=63 Identities=21% Similarity=0.288 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHcC-CCchHHHHHHHH----hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 16 SLKQLSRLVVRGFY-SIEDSLIIDMLV----RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 16 ~~~~Lv~~v~R~Fy-~~e~ivIlD~L~----~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.+-+.+...+- +.....||..|. .++.++-.+||..+++++..|-+++..|++.|+|...
T Consensus 9 ~~~~~~~~l~~~~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 9 YIKSLKRYLKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE 76 (109)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEecc
Confidence 34455555554321 233567787777 4578999999999999999999999999999999976
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.23 E-value=0.01 Score=35.96 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=18.9
Q ss_pred CeeecCCCCCccchhhhhhccCCCCcccC
Q psy5744 128 SSFKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
..|.||+||..+++.+... .+.||
T Consensus 2 ~~y~C~~CG~~~~~~~~~~-----~~~Cp 25 (46)
T PRK00398 2 AEYKCARCGREVELDEYGT-----GVRCP 25 (46)
T ss_pred CEEECCCCCCEEEECCCCC-----ceECC
Confidence 4699999999998877664 56776
No 67
>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=95.22 E-value=0.038 Score=45.15 Aligned_cols=62 Identities=18% Similarity=0.277 Sum_probs=49.2
Q ss_pred HHHHHHHHHH-cCCC-chH-HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 18 KQLSRLVVRG-FYSI-EDS-LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 18 ~~Lv~~v~R~-Fy~~-e~i-vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+..|++.+.. -|++ ++| .|++.|-. ++-+++.+||+++|++..-+|..+.+|+..|++..+.
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3455664443 3443 343 48888887 5899999999999999999999999999999999874
No 68
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=95.18 E-value=0.15 Score=39.80 Aligned_cols=86 Identities=16% Similarity=0.235 Sum_probs=62.1
Q ss_pred hHHHHHHHHHHHHHcCC-CchHHHHHHHHh-CC------------CcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744 14 PTSLKQLSRLVVRGFYS-IEDSLIIDMLVR-NP------------CMKEDDICELL-KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 14 p~~~~~Lv~~v~R~Fy~-~e~ivIlD~L~~-~~------------~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-.+-.+++.....|-= +-.+-+|++|+. .. +.|-..||..+ ||+...||+.+..|.+.|||..+
T Consensus 25 k~~ll~~l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 25 KWQLLRALKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred HHHHHHHHHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeec
Confidence 34567777776666654 446789999995 21 34568999999 99999999999999999999975
Q ss_pred EeeeecCCCce--------eEEEEEEecchhHH
Q psy5744 79 LRMETGLDGKA--------QKVNYYFINYQTFV 103 (157)
Q Consensus 79 ~~~e~~~~gk~--------~~~~yw~I~y~~~~ 103 (157)
+.|+||- ....-|=||...++
T Consensus 105 ----DS~NgkRy~~R~~~G~I~~A~GfdLsPL~ 133 (177)
T PF03428_consen 105 ----DSPNGKRYARRDRGGRIVEAFGFDLSPLI 133 (177)
T ss_pred ----cCCCCCccCccCCCCCEEeEeCcCHHHHH
Confidence 2355531 23446678865544
No 69
>PF13730 HTH_36: Helix-turn-helix domain
Probab=95.17 E-value=0.035 Score=34.21 Aligned_cols=31 Identities=16% Similarity=0.326 Sum_probs=28.7
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
+-+-+.||+.+|++.+.|++++..|++.|++
T Consensus 25 ~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 25 FPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 3579999999999999999999999999985
No 70
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=95.16 E-value=0.046 Score=45.01 Aligned_cols=48 Identities=10% Similarity=0.282 Sum_probs=43.5
Q ss_pred CchHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 31 IEDSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 31 ~e~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++..-|||+|..| |.++..||.+.+|++.-.+-++|.+|++.|+|...
T Consensus 195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~ 243 (258)
T COG2512 195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEE
Confidence 4467799999976 56999999999999999999999999999999976
No 71
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=95.12 E-value=0.062 Score=41.22 Aligned_cols=35 Identities=17% Similarity=0.181 Sum_probs=33.2
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+.++-++||+.+|++.+.++++|..|.+.|||.+.
T Consensus 24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 47999999999999999999999999999999974
No 72
>PRK14999 histidine utilization repressor; Provisional
Probab=95.11 E-value=0.1 Score=41.76 Aligned_cols=35 Identities=11% Similarity=0.232 Sum_probs=32.2
Q ss_pred Cc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 45 CM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 45 ~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+ +|.+||+.+|++...||++|..|.++|+|..++
T Consensus 35 ~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 35 RIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 35 899999999999999999999999999998763
No 73
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=95.05 E-value=0.039 Score=43.23 Aligned_cols=43 Identities=12% Similarity=0.187 Sum_probs=39.5
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++|.|-.++.++--+||.+||++.++|.+.|++|.+.|.|...
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecC
Confidence 6777777899999999999999999999999999999999754
No 74
>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=94.99 E-value=0.058 Score=35.16 Aligned_cols=34 Identities=21% Similarity=0.492 Sum_probs=32.1
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++-++||..+|++...|.++|..|+++|+|...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence 5889999999999999999999999999999864
No 75
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.96 E-value=0.06 Score=40.39 Aligned_cols=47 Identities=17% Similarity=0.268 Sum_probs=43.4
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-..-|+++|.+++-.+=.+||+.+|++...|++-+.+|.+.|++...
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 35679999999999999999999999999999999999999999854
No 76
>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=94.94 E-value=0.037 Score=43.80 Aligned_cols=34 Identities=18% Similarity=0.289 Sum_probs=31.9
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
=+|.+||+.+|++...||++|..|.++|+|..++
T Consensus 33 PsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3799999999999999999999999999999764
No 77
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=94.91 E-value=0.096 Score=41.56 Aligned_cols=36 Identities=22% Similarity=0.403 Sum_probs=33.1
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3457 79999999999999999999999999999976
No 78
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=94.88 E-value=0.098 Score=41.97 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=33.3
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4457 89999999999999999999999999999976
No 79
>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=94.86 E-value=0.1 Score=41.38 Aligned_cols=36 Identities=22% Similarity=0.403 Sum_probs=33.4
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 4568 79999999999999999999999999999976
No 80
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=94.80 E-value=0.11 Score=40.85 Aligned_cols=36 Identities=11% Similarity=0.177 Sum_probs=33.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+++.+||+.+|++..-||.+|..|..+|||...
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEe
Confidence 456899999999999999999999999999999865
No 81
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=94.80 E-value=0.061 Score=43.82 Aligned_cols=47 Identities=13% Similarity=0.320 Sum_probs=43.1
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+-.|++.|-+++.++-.|||+.++++...+|+-|..|.++|++...
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35678999988999999999999999999999999999999999764
No 82
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=94.74 E-value=0.12 Score=41.61 Aligned_cols=37 Identities=22% Similarity=0.415 Sum_probs=33.7
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+.
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4568 699999999999999999999999999998763
No 83
>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=94.73 E-value=0.058 Score=37.68 Aligned_cols=43 Identities=16% Similarity=0.323 Sum_probs=34.6
Q ss_pred HHHHHHHHh----CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 34 SLIIDMLVR----NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 34 ivIlD~L~~----~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
-.|+++|-. ..-++=++|++.|+++.++||++|..|-++|.|=
T Consensus 50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 50 DKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp HHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 345665553 3458899999999999999999999999999883
No 84
>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=94.72 E-value=0.046 Score=43.36 Aligned_cols=33 Identities=18% Similarity=0.259 Sum_probs=31.4
Q ss_pred CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+|.+||+.+|++.-.||++|..|.++|+|..++
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 699999999999999999999999999999764
No 85
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=94.68 E-value=0.063 Score=43.64 Aligned_cols=47 Identities=13% Similarity=0.260 Sum_probs=43.2
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+-.|++.|-+++.++=.|||+.+|++...+|+-|..|.+.|++...
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 45678999999999999999999999999999999999999999764
No 86
>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=94.66 E-value=0.05 Score=43.14 Aligned_cols=33 Identities=12% Similarity=0.279 Sum_probs=31.4
Q ss_pred CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+|.+||+.+|++...||++|..|.++|+|..++
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQ 59 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 899999999999999999999999999999764
No 87
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=94.64 E-value=0.05 Score=43.42 Aligned_cols=35 Identities=23% Similarity=0.379 Sum_probs=32.2
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
-=+|.+||+.+|++.-.||++|..|.++|+|..++
T Consensus 33 LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 33 IPTENELCTQYNVSRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 45799999999999999999999999999999763
No 88
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=94.57 E-value=0.1 Score=36.17 Aligned_cols=50 Identities=12% Similarity=0.210 Sum_probs=44.0
Q ss_pred CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.......++..|..++..+..+||+.+++++..+-+++.+|.+.|+|...
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~ 69 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERL 69 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence 45667788888887776666999999999999999999999999999976
No 89
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=94.56 E-value=0.05 Score=41.59 Aligned_cols=95 Identities=19% Similarity=0.239 Sum_probs=67.1
Q ss_pred HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCce---eEE------EE
Q psy5744 24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKA---QKV------NY 94 (157)
Q Consensus 24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~---~~~------~y 94 (157)
+..+|-++.|--|.|.|. .+|+|+++|.+.+|-+. ++.|..|+.-|||..+=|+-+ |.++. +.. -=
T Consensus 10 ll~~f~s~~~kkV~~~Ls-~~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP~-pG~kPeKEYhtsYs~vqaN 84 (160)
T PF09824_consen 10 LLQTFNSEVYKKVYDELS-KGWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMPE-PGEKPEKEYHTSYSKVQAN 84 (160)
T ss_pred HHHHhCCHHHHHHHHHHH-hccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccCC-CCCCchHHHHhhHhheeee
Confidence 457899999999999998 77999999999999877 999999999999998755532 32221 111 12
Q ss_pred EEecchhHHHHHH------HHHHHHHHHHHHHHhh
Q psy5744 95 YFINYQTFVNIVK------YKLDVMRKRMEMEERD 123 (157)
Q Consensus 95 w~I~y~~~~~vik------~rl~~m~~~L~~~~~~ 123 (157)
++.....+-++|. -.+..+.++|++.++.
T Consensus 85 Fqcs~~DLsdii~i~f~~deel~~~~e~i~~~v~~ 119 (160)
T PF09824_consen 85 FQCSMEDLSDIIYIAFMSDEELRDYVEKIEKEVEA 119 (160)
T ss_pred eEeeHHHHHHHHheeecCHHHHHHHHHHHHHHHHc
Confidence 3333444555543 3566666777777666
No 90
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.50 E-value=0.12 Score=38.95 Aligned_cols=44 Identities=20% Similarity=0.331 Sum_probs=38.4
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|+.++..++.++-.+||+.+++++..|++.+..|++.|+|..+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45556656788999999999999999999999999999999754
No 91
>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=94.48 E-value=0.032 Score=36.63 Aligned_cols=44 Identities=14% Similarity=0.061 Sum_probs=34.0
Q ss_pred HHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|+++|-..+ ..+.-.+|..|+++.++|.++|+.|+..|.|...
T Consensus 8 ~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 8 KILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeC
Confidence 5788888655 4556666667777799999999999999999753
No 92
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=94.45 E-value=0.06 Score=33.62 Aligned_cols=38 Identities=11% Similarity=0.188 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccC
Q psy5744 111 DVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVL 149 (157)
Q Consensus 111 ~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d 149 (157)
+.....+++.+....+... .||-|++.++......|+.
T Consensus 3 ~~~~~~~~k~i~~l~~~~~-~CPlC~r~l~~e~~~~li~ 40 (54)
T PF04423_consen 3 KSEIEELKKYIEELKEAKG-CCPLCGRPLDEEHRQELIK 40 (54)
T ss_dssp HHHHHHHHHHHHHHTT-SE-E-TTT--EE-HHHHHHHHH
T ss_pred hHHHHHHHHHHHHHhcCCC-cCCCCCCCCCHHHHHHHHH
Confidence 3344445555555556667 9999999999999887763
No 93
>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=94.44 E-value=0.34 Score=34.55 Aligned_cols=79 Identities=19% Similarity=0.343 Sum_probs=56.7
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK 107 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik 107 (157)
..|+++|.. .+.+|-++|...| +++...|=+.|..|.+.|+|... .. ++| ..+|..+.
T Consensus 11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~---~~-~~~----~~~Y~~~~-------- 74 (120)
T PF01475_consen 11 LAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI---EF-GDG----ESRYELST-------- 74 (120)
T ss_dssp HHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE---EE-TTS----EEEEEESS--------
T ss_pred HHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE---Ec-CCC----cceEeecC--------
Confidence 578999996 4689999999988 67788999999999999999975 22 233 33444442
Q ss_pred HHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhh
Q psy5744 108 YKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 108 ~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda 144 (157)
......++|..||+.+.+.+-
T Consensus 75 ----------------~~~h~h~iC~~Cg~v~~~~~~ 95 (120)
T PF01475_consen 75 ----------------CHHHHHFICTQCGKVIDLDDP 95 (120)
T ss_dssp ----------------SSSCEEEEETTTS-EEEE-GH
T ss_pred ----------------CCcceEEEECCCCCEEEecch
Confidence 234668999999999876553
No 94
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=94.43 E-value=0.44 Score=34.93 Aligned_cols=46 Identities=11% Similarity=0.208 Sum_probs=40.8
Q ss_pred hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+..||..|..+ +.++-.|||+.+|+++..|-+++..|.+.|+|...
T Consensus 33 q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 33 HWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 56778887764 56899999999999999999999999999999976
No 95
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=94.39 E-value=0.031 Score=32.25 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=20.8
Q ss_pred eeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744 129 SFKCPRCLKTFTDLEPCLLVLWCACPCKR 157 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~ 157 (157)
.+.||+|++.|...++..--+...+.|++
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~ 30 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGK 30 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCC
Confidence 46899999999988776322234788874
No 96
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=94.35 E-value=0.15 Score=40.76 Aligned_cols=37 Identities=32% Similarity=0.580 Sum_probs=33.9
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+.
T Consensus 28 G~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 28 GQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 4568 899999999999999999999999999999763
No 97
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=94.35 E-value=0.062 Score=42.94 Aligned_cols=34 Identities=24% Similarity=0.316 Sum_probs=31.7
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
=+|.+||+.+|++...||++|..|.++|+|..++
T Consensus 36 PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 36 PAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3799999999999999999999999999999764
No 98
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=94.35 E-value=0.015 Score=34.79 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=13.4
Q ss_pred eecCCCCCccchhhhhhccCCCCcccC
Q psy5744 130 FKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
|+||.||.+....|..+ +.+.|+
T Consensus 1 m~Cp~Cg~~~~~~D~~~----g~~vC~ 23 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPER----GELVCP 23 (43)
T ss_dssp ESBTTTSSSEEEEETTT----TEEEET
T ss_pred CCCcCCcCCceEEcCCC----CeEECC
Confidence 56777777665444333 455554
No 99
>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=94.29 E-value=0.13 Score=30.67 Aligned_cols=37 Identities=22% Similarity=0.316 Sum_probs=30.6
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
.-|+..|-.++-.+-.+||+.+|++...|++=+.+|+
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 4588898999999999999999999999999888875
No 100
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=94.29 E-value=0.17 Score=40.73 Aligned_cols=36 Identities=19% Similarity=0.268 Sum_probs=33.0
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus 29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~ 65 (253)
T PRK11523 29 GDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVR 65 (253)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4567 59999999999999999999999999999876
No 101
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=94.22 E-value=0.4 Score=34.24 Aligned_cols=105 Identities=15% Similarity=0.153 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHcCCCchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEE
Q psy5744 16 SLKQLSRLVVRGFYSIEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY 94 (157)
Q Consensus 16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~y 94 (157)
.++.|...+.-.=.-...|.|-..|+. .+.|.-.+|+.+++++...+|-.+..|...||++.+-. + ++|.-|-
T Consensus 6 ~l~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relv-----q-kgWvGYi 79 (113)
T COG5625 6 RLRKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELV-----Q-KGWVGYI 79 (113)
T ss_pred HHHHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHH-----h-ccceeeE
Confidence 345555555444455566888888886 45699999999999999999999999999999986522 1 3566553
Q ss_pred E-EecchhHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy5744 95 Y-FINYQTFVNIVKYKLDVMRKRMEMEERDATS 126 (157)
Q Consensus 95 w-~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~ 126 (157)
| -.....++.-|+..+.+-.+.|++..++++.
T Consensus 80 ya~~~P~k~leei~~~i~keiEelEk~~k~es~ 112 (113)
T COG5625 80 YATTPPPKPLEEIEEEIMKEIEELEKEFKNESQ 112 (113)
T ss_pred ecCCCCchHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3 3667789999999999999999998877643
No 102
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=94.15 E-value=0.18 Score=40.47 Aligned_cols=36 Identities=19% Similarity=0.337 Sum_probs=33.0
Q ss_pred CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3467 69999999999999999999999999999875
No 103
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=94.14 E-value=0.075 Score=42.51 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=32.3
Q ss_pred Cc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 45 CM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 45 ~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+ +|.+||+.+|++...||++|..|.++|+|..++
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 45 799999999999999999999999999999763
No 104
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=94.10 E-value=0.13 Score=39.05 Aligned_cols=41 Identities=17% Similarity=0.230 Sum_probs=36.7
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
++-..+.++=-|||+.||+++..|.+.+.+|.+.|+|.+..
T Consensus 18 l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 18 LLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 33357889999999999999999999999999999999863
No 105
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=93.95 E-value=0.17 Score=41.20 Aligned_cols=46 Identities=17% Similarity=0.255 Sum_probs=41.3
Q ss_pred hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++-||++|..+ +.++-.|||+.+|++...+.++|..|.+.|+|...
T Consensus 13 al~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~ 59 (263)
T PRK09834 13 GLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRS 59 (263)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 46799999865 46999999999999999999999999999999854
No 106
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=93.94 E-value=0.25 Score=38.69 Aligned_cols=46 Identities=7% Similarity=-0.046 Sum_probs=41.3
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...||-.|..++.++-.|||+.++++...+-+++.+|++.|+|...
T Consensus 47 q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 47 EHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred HHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence 4467777777889999999999999999999999999999999965
No 107
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=93.94 E-value=0.13 Score=41.93 Aligned_cols=49 Identities=8% Similarity=0.206 Sum_probs=44.2
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+..-.|++.|-.++.++=.|||+.+|++.--+|+=|..|+++|+|...+
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3456799999999999999999999999999999999999999997653
No 108
>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=93.90 E-value=0.13 Score=32.55 Aligned_cols=39 Identities=13% Similarity=0.410 Sum_probs=34.8
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
.+-++..|+.+++++=++||+.+|++.+.+|.-+..|.+
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999984
No 109
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=93.87 E-value=0.17 Score=37.35 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=34.4
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.++-.+||..+++++..|++.|.+|.+.|+|.+.
T Consensus 19 ~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 19 EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 4688899999999999999999999999999999864
No 110
>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=93.86 E-value=0.62 Score=30.90 Aligned_cols=49 Identities=14% Similarity=0.291 Sum_probs=42.2
Q ss_pred chHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744 32 EDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR 80 (157)
Q Consensus 32 e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~ 80 (157)
.+..+|..+.+ ...++--||+..+|++++.+-.++.+|.+.|||.....
T Consensus 3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 3 IQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred hHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 35667778775 45688899999999999999999999999999998755
No 111
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=93.79 E-value=0.16 Score=41.02 Aligned_cols=45 Identities=9% Similarity=0.090 Sum_probs=41.2
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-||++|..++.++=.|||+.+|++...+.++|..|.+.|+|.+.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 578999887778999999999999999999999999999999853
No 112
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=93.64 E-value=0.27 Score=34.44 Aligned_cols=49 Identities=16% Similarity=0.125 Sum_probs=41.2
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+.+.-|+-.|-+.+.=.---||..++++..+|+.+|.+|++.|||....
T Consensus 7 ~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred hhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 3355677777766777778899999999999999999999999999864
No 113
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.61 E-value=0.17 Score=40.91 Aligned_cols=45 Identities=18% Similarity=0.423 Sum_probs=40.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.--|++.|-+++.++=.|||+.+|++...+|+-|..|.+.|++..
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 345888888899999999999999999999999999999988864
No 114
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=93.59 E-value=0.17 Score=41.59 Aligned_cols=47 Identities=17% Similarity=0.254 Sum_probs=43.1
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+-.|++.|-.++.++-.|||+.+|++..-+|+=|..|+++|++...
T Consensus 18 R~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEE
Confidence 35678999988999999999999999999999999999999999854
No 115
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=93.58 E-value=0.17 Score=41.04 Aligned_cols=46 Identities=17% Similarity=0.306 Sum_probs=41.2
Q ss_pred hHHHHHHHHhCCC-cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPC-MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~-i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++-|||+|-+++. ++=.|||+.+|++...++++|..|.+.|+|.+.
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d 52 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQD 52 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEc
Confidence 4679999997644 789999999999999999999999999999864
No 116
>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=93.48 E-value=0.23 Score=32.07 Aligned_cols=43 Identities=16% Similarity=0.241 Sum_probs=36.0
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|+..|. ++.++-.+||+.+|++...|++.+..|.++|+.-..
T Consensus 4 ~il~~L~-~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 4 RLLALLA-DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 3455544 667899999999999999999999999999996543
No 117
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=93.45 E-value=0.28 Score=38.78 Aligned_cols=36 Identities=17% Similarity=0.386 Sum_probs=34.0
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...+++++||+.+|++.--||.+|..|..+|||...
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~ 72 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE 72 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec
Confidence 557999999999999999999999999999999976
No 118
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.43 E-value=0.04 Score=27.99 Aligned_cols=16 Identities=38% Similarity=0.864 Sum_probs=13.6
Q ss_pred eecCCCCCccchhhhh
Q psy5744 130 FKCPRCLKTFTDLEPC 145 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~ 145 (157)
|.||.|++.|+....+
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 7999999999977654
No 119
>PRK09954 putative kinase; Provisional
Probab=93.42 E-value=0.15 Score=43.06 Aligned_cols=44 Identities=27% Similarity=0.489 Sum_probs=40.8
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
..|+..|.+++.++=.+||+.||++...|++.|.+|+++|++..
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCC
Confidence 45889999999999999999999999999999999999999853
No 120
>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=93.39 E-value=0.13 Score=38.97 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=32.1
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+|-+|||..+|+....|-++|.+|+++|+|+..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 3789999999999999999999999999999875
No 121
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=93.35 E-value=0.11 Score=41.49 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=36.2
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-|+-+|.+.+ -.=-+|...+|+.++-|=+.|..|.++|||.++
T Consensus 19 ~Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ 61 (217)
T COG1777 19 RILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERAGLVESR 61 (217)
T ss_pred HHHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhh
Confidence 4666777655 345679999999999999999999999999985
No 122
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=93.24 E-value=0.14 Score=41.04 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=32.2
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
-=+|.+||+.+|++.-.|||+|..|.++|+|..++
T Consensus 31 LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~ 65 (236)
T COG2188 31 LPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQ 65 (236)
T ss_pred CCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEe
Confidence 34699999999999999999999999999999875
No 123
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=93.20 E-value=0.12 Score=40.29 Aligned_cols=47 Identities=11% Similarity=0.256 Sum_probs=43.1
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..-.|++.|-.++.++-+|||+.+|++..-+|+=|..|.++|+|..-
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence 45678999999999999999999999999999999999999999763
No 124
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=93.14 E-value=0.65 Score=36.40 Aligned_cols=74 Identities=12% Similarity=0.210 Sum_probs=50.5
Q ss_pred HHHHHh-CCCcCHHHHHHH----hCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHH
Q psy5744 37 IDMLVR-NPCMKEDDICEL----LKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLD 111 (157)
Q Consensus 37 lD~L~~-~~~i~dedLa~~----l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~ 111 (157)
++++.. +...+--||.+. -||.+-.|.-+|..|-+||||... . =+++.+||.+... .....+.++.
T Consensus 2 l~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E----K----iGssn~YWsFps~-~~~~~~~~~~ 72 (188)
T PF03962_consen 2 LEIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE----K----IGSSNYYWSFPSQ-AKQKRQNKLE 72 (188)
T ss_pred hHHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh----h----ccCeeEEEecChH-HHHHHHHHHH
Confidence 444443 455665565554 599999999999999999999864 2 1356889999864 4455555555
Q ss_pred HHHHHHHH
Q psy5744 112 VMRKRMEM 119 (157)
Q Consensus 112 ~m~~~L~~ 119 (157)
++.+.++.
T Consensus 73 ~l~~~~~~ 80 (188)
T PF03962_consen 73 KLQKEIEE 80 (188)
T ss_pred HHHHHHHH
Confidence 55554443
No 125
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=93.11 E-value=0.91 Score=33.96 Aligned_cols=49 Identities=8% Similarity=0.232 Sum_probs=41.9
Q ss_pred CCchHHHHHHHHhC-CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744 30 SIEDSLIIDMLVRN-PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 30 ~~e~ivIlD~L~~~-~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+.-..|+++|..+ +.+|-+||=..+ ++++-.|-++|..|.+.|||...
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~ 74 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL 74 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE
Confidence 45567899999964 679999988877 48899999999999999999965
No 126
>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=92.93 E-value=0.3 Score=31.81 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=31.2
Q ss_pred HhCC-CcCHHHHHHHhCCC-hHHHHHHHHHHhhCcceeee
Q psy5744 41 VRNP-CMKEDDICELLKFE-RKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 41 ~~~~-~i~dedLa~~l~i~-~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++| .-|-.|||+.+|++ ++-|...|..|++.|+|...
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCC
Confidence 3455 36789999999998 99999999999999999864
No 127
>PF13814 Replic_Relax: Replication-relaxation
Probab=92.92 E-value=0.31 Score=37.17 Aligned_cols=62 Identities=19% Similarity=0.247 Sum_probs=48.1
Q ss_pred HHHHhCCCcCHHHHHHHhCCChH---HHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744 38 DMLVRNPCMKEDDICELLKFERK---MLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 38 D~L~~~~~i~dedLa~~l~i~~k---~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~ 101 (157)
..|-++..+|-++|+..++.+.+ .+++.|.+|++.|+|......- +.+..+..+.|++....
T Consensus 2 ~~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~--~~~~g~~~~vy~Lt~~G 66 (191)
T PF13814_consen 2 RLLARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRV--GARGGSQPYVYYLTPAG 66 (191)
T ss_pred hhHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccc--cccCCCcceEEEECHHH
Confidence 45667899999999999999998 7999999999999998764321 12234556788888654
No 128
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=92.84 E-value=0.43 Score=37.56 Aligned_cols=33 Identities=15% Similarity=0.182 Sum_probs=31.0
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+-+|||..+|+.+..|.++|.+|+++|+|...
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 578999999999999999999999999999865
No 129
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=92.81 E-value=0.23 Score=40.42 Aligned_cols=48 Identities=13% Similarity=0.293 Sum_probs=44.4
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+-.|++.|-+++.++=+|||+.+|++.-.+|+=|..|.+.|++....
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 466799999999999999999999999999999999999999999754
No 130
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=92.73 E-value=1.1 Score=33.57 Aligned_cols=49 Identities=16% Similarity=0.233 Sum_probs=44.3
Q ss_pred CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+|...-++..+-.++..|-.|||++.|=+.+.|.+.|..|.+-|+|..+
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEe
Confidence 5666778888777899999999999999999999999999999999976
No 131
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=92.71 E-value=0.066 Score=26.80 Aligned_cols=17 Identities=35% Similarity=0.749 Sum_probs=12.6
Q ss_pred eecCCCCCccchhhhhh
Q psy5744 130 FKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~ 146 (157)
|.||.|+.+|+..++..
T Consensus 1 ~~C~~C~~~~~~~~~l~ 17 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELR 17 (24)
T ss_dssp EE-SSTS-EESSHHHHH
T ss_pred CCCcCCCCcCCcHHHHH
Confidence 78999999999887654
No 132
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=92.65 E-value=0.31 Score=33.11 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=31.9
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
....+|=++||+.||++..-|-|.+..|+++|+=-
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 35689999999999999999999999999999854
No 133
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=92.55 E-value=0.19 Score=38.54 Aligned_cols=34 Identities=15% Similarity=0.347 Sum_probs=31.6
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++-++||..+|+.+..|.++|.+|+++|+|+..
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence 4677999999999999999999999999999865
No 134
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=92.54 E-value=0.19 Score=37.07 Aligned_cols=37 Identities=11% Similarity=0.175 Sum_probs=32.8
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR 80 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~ 80 (157)
..-|=.+||..+|+++|.|+|+...|+++|+|...++
T Consensus 34 kLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 34 KLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3456789999999999999999999999999998743
No 135
>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=92.51 E-value=0.61 Score=33.02 Aligned_cols=62 Identities=16% Similarity=0.215 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHcCCCchHHHHHHHHhC--C------CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 17 LKQLSRLVVRGFYSIEDSLIIDMLVRN--P------CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~~--~------~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+|+..+.++=......-|+.++.|. | .|+..++|+.+|++...|.+.+..|.+.|++...
T Consensus 18 aNelld~l~~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 18 ANELLDALLRADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRD 87 (100)
T ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 345556665544444445777777764 2 6999999999999999999999999999999654
No 136
>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=92.50 E-value=0.23 Score=33.98 Aligned_cols=47 Identities=15% Similarity=0.252 Sum_probs=36.6
Q ss_pred chHHHHHHH---Hh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 32 EDSLIIDML---VR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L---~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++.-|+.++ .+ |++|+.+.|+...|++...+.+.|..|...+||.+.
T Consensus 7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~ 57 (82)
T PF09202_consen 7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRR 57 (82)
T ss_dssp HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCcccc
Confidence 344444444 44 689999999999999999999999999999999984
No 137
>PRK09462 fur ferric uptake regulator; Provisional
Probab=92.38 E-value=1.6 Score=32.40 Aligned_cols=78 Identities=13% Similarity=0.239 Sum_probs=56.9
Q ss_pred hHHHHHHHHhC--CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744 33 DSLIIDMLVRN--PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI 105 (157)
Q Consensus 33 ~ivIlD~L~~~--~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v 105 (157)
-..|++.|..+ +.+|-++|-+.+ +++...|=++|..|.+.|||... +. ++|.. +|-++
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~---~~-~~~~~----~y~~~------- 83 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH---NF-EGGKS----VFELT------- 83 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE---Ec-CCCcE----EEEeC-------
Confidence 46799999853 589999998888 57889999999999999999865 22 23321 22221
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchh
Q psy5744 106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDL 142 (157)
Q Consensus 106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~l 142 (157)
....-..++|..||+.+.+.
T Consensus 84 -----------------~~~~H~H~iC~~Cg~i~~i~ 103 (148)
T PRK09462 84 -----------------QQHHHDHLICLDCGKVIEFS 103 (148)
T ss_pred -----------------CCCCCCceEECCCCCEEEeC
Confidence 01234579999999998874
No 138
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=92.29 E-value=0.47 Score=37.55 Aligned_cols=33 Identities=21% Similarity=0.359 Sum_probs=31.0
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++-++||..+|+.+..|-++|.+|+++|+|...
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence 678999999999999999999999999999864
No 139
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=92.28 E-value=0.32 Score=32.44 Aligned_cols=42 Identities=19% Similarity=0.321 Sum_probs=32.4
Q ss_pred HHHHHHH--hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 35 LIIDMLV--RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 35 vIlD~L~--~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
+|+|.|- .++..+=.+|+...|++.+.+.++|..|.+.|||+
T Consensus 7 Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 7 IIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK 50 (77)
T ss_dssp HHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee
Confidence 4555554 27889999999999999999999999999999994
No 140
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=92.25 E-value=0.12 Score=27.41 Aligned_cols=17 Identities=41% Similarity=0.958 Sum_probs=13.8
Q ss_pred cCCCCeeecCCCCCccc
Q psy5744 124 ATSRSSFKCPRCLKTFT 140 (157)
Q Consensus 124 ~~~~~~Y~Cp~C~~~Ys 140 (157)
-++...|.||.|+++|+
T Consensus 9 H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HSSSSSEEESSSSEEES
T ss_pred cCCCCCCCCCCCcCeeC
Confidence 34556799999999986
No 141
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=92.19 E-value=0.33 Score=40.55 Aligned_cols=43 Identities=16% Similarity=0.187 Sum_probs=38.6
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
.-|++.|..+..++-.+||+.+|++..-|++.+..|.+.|++-
T Consensus 7 ~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i 49 (319)
T PRK11886 7 LQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDI 49 (319)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 4578888777889999999999999999999999999999943
No 142
>PRK11569 transcriptional repressor IclR; Provisional
Probab=92.19 E-value=0.39 Score=39.31 Aligned_cols=44 Identities=5% Similarity=0.198 Sum_probs=40.5
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
+-||++|.+ ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~ 75 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQ 75 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 679999986 46799999999999999999999999999999974
No 143
>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=92.19 E-value=0.93 Score=30.87 Aligned_cols=45 Identities=22% Similarity=0.367 Sum_probs=38.8
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...|+..|.. +..+=.||.+.+ |++++.+.+-|..|.++|||...
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcc
Confidence 3567777774 889999999999 99999999999999999999865
No 144
>PHA02768 hypothetical protein; Provisional
Probab=92.16 E-value=0.057 Score=34.33 Aligned_cols=20 Identities=15% Similarity=0.567 Sum_probs=17.3
Q ss_pred CeeecCCCCCccchhhhhhc
Q psy5744 128 SSFKCPRCLKTFTDLEPCLL 147 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~lda~~L 147 (157)
-+|.||.||++|+..+++..
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~ 23 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMIT 23 (55)
T ss_pred cccCcchhCCeeccHHHHHH
Confidence 47999999999999998753
No 145
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.09 E-value=0.12 Score=29.77 Aligned_cols=28 Identities=14% Similarity=0.369 Sum_probs=20.6
Q ss_pred eeecCCCCCccchhhhhhccCC-CCcccCC
Q psy5744 129 SFKCPRCLKTFTDLEPCLLVLW-CACPCKR 157 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~L~d~-~~F~C~~ 157 (157)
...||+|+++|...|.. |-.. ....|++
T Consensus 2 ~i~Cp~C~~~y~i~d~~-ip~~g~~v~C~~ 30 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEK-IPPKGRKVRCSK 30 (36)
T ss_pred EEECCCCCCEEeCCHHH-CCCCCcEEECCC
Confidence 35799999999999887 4443 3677763
No 146
>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=92.09 E-value=0.4 Score=38.46 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=40.2
Q ss_pred hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
.+-||++|-. .+.++=.|||+.+|++...+.++|..|.+.|+|.
T Consensus 11 al~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 11 GLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3679999886 5679999999999999999999999999999996
No 147
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=91.92 E-value=0.23 Score=37.97 Aligned_cols=34 Identities=15% Similarity=0.246 Sum_probs=31.6
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence 3689999999999999999999999999999854
No 148
>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=91.85 E-value=0.26 Score=38.79 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=31.7
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
=+|.+||+.+|++.-.+|++|..|.++|+|..++
T Consensus 26 PsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 26 PSERDLGERFNTTRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC
Confidence 3799999999999999999999999999999764
No 149
>PRK13824 replication initiation protein RepC; Provisional
Probab=91.78 E-value=1.1 Score=39.18 Aligned_cols=104 Identities=12% Similarity=0.110 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHcCC-CchHHHHHHHHh-CC------------CcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeE
Q psy5744 15 TSLKQLSRLVVRGFYS-IEDSLIIDMLVR-NP------------CMKEDDICELL-KFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~-~e~ivIlD~L~~-~~------------~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
-.+-.+++.....|-= +-.+-|||+|+. ++ +-|-..|+..+ ||+...||+.|..|.+.|||..+
T Consensus 38 w~l~r~l~~a~~~lGl~~~~l~vL~aLlsf~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGLI~rr- 116 (404)
T PRK13824 38 WKLFRDLCEARALLGVSDRALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIRR- 116 (404)
T ss_pred HHHHHHHHHHHHhcCCChhHHHHHHHHHhhCCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEee-
Confidence 3456666666666544 446789999994 33 34567899985 99999999999999999999965
Q ss_pred eeeecCCCce--------eEEEEEEecchhH--------------------HHHHHHHHHHHHHHHHHHHh
Q psy5744 80 RMETGLDGKA--------QKVNYYFINYQTF--------------------VNIVKYKLDVMRKRMEMEER 122 (157)
Q Consensus 80 ~~e~~~~gk~--------~~~~yw~I~y~~~--------------------~~vik~rl~~m~~~L~~~~~ 122 (157)
+ .||||- ....-|=||...+ ...++.++-.++..|.+.+.
T Consensus 117 --D-SpNGKRyarr~~~G~i~~AfGfDLsPL~~R~~El~~~A~~~~ae~~~~r~lr~~it~~rRdi~~li~ 184 (404)
T PRK13824 117 --D-SPNGKRYARKGRGGEIEEAFGFDLAPLLARAEEFEALAEQVAAERKALRRLRERLTLCRRDIAKLIE 184 (404)
T ss_pred --c-CCCCcccceeCCCCceeeeeccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 356532 1234555665332 44556666666665555443
No 150
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.59 E-value=0.12 Score=29.93 Aligned_cols=27 Identities=22% Similarity=0.472 Sum_probs=19.5
Q ss_pred eecCCCCCccchhhhhhccC-CCCcccCC
Q psy5744 130 FKCPRCLKTFTDLEPCLLVL-WCACPCKR 157 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~L~d-~~~F~C~~ 157 (157)
-.||+|+++|...|.. |-. .....|++
T Consensus 3 i~CP~C~~~f~v~~~~-l~~~~~~vrC~~ 30 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-LPAGGRKVRCPK 30 (37)
T ss_pred EECCCCCceEEcCHHH-cccCCcEEECCC
Confidence 4799999999988876 333 34777764
No 151
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=91.43 E-value=0.075 Score=29.65 Aligned_cols=20 Identities=30% Similarity=0.426 Sum_probs=7.5
Q ss_pred ecCCCCCccchhhhhhccCCCCcccC
Q psy5744 131 KCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
.||.|+..|+. .|...|.||
T Consensus 4 ~Cp~C~se~~y------~D~~~~vCp 23 (30)
T PF08274_consen 4 KCPLCGSEYTY------EDGELLVCP 23 (30)
T ss_dssp --TTT-----E------E-SSSEEET
T ss_pred CCCCCCCccee------ccCCEEeCC
Confidence 47777777776 444566665
No 152
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=91.43 E-value=0.25 Score=39.84 Aligned_cols=33 Identities=18% Similarity=0.419 Sum_probs=31.2
Q ss_pred CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+|.+||+.+|++...||.+|..|..+|||..++
T Consensus 36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~r~ 68 (241)
T COG2186 36 SERELAERFGVSRTVVREALKRLEAKGLVEIRQ 68 (241)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecC
Confidence 499999999999999999999999999999874
No 153
>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=91.42 E-value=0.51 Score=30.76 Aligned_cols=44 Identities=18% Similarity=0.340 Sum_probs=36.2
Q ss_pred HHHHHHHhC-CCcCHHHHHHHh---CCCh--HHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRN-PCMKEDDICELL---KFER--KMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~-~~i~dedLa~~l---~i~~--k~vRkiL~~L~~d~Lv~~~ 78 (157)
.||+.|-.+ +.++-.+|++.+ |.+. ..||+.|..|.++|++...
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc
Confidence 578888864 679999999999 4554 7899999999999988743
No 154
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=91.17 E-value=0.5 Score=37.96 Aligned_cols=36 Identities=8% Similarity=0.099 Sum_probs=33.4
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+..+|-.+||+.+++++..+.++|..|++.|+|...
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 456899999999999999999999999999999865
No 155
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=91.09 E-value=2.9 Score=27.16 Aligned_cols=75 Identities=11% Similarity=0.260 Sum_probs=55.9
Q ss_pred HHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744 18 KQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI 97 (157)
Q Consensus 18 ~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I 97 (157)
..-+..+..+.-++.-..|+..|.+....+-.+|+..++++...+...|..|.+.|+|..+ . +|+. .+|.+
T Consensus 12 ~~~~~~~~~~l~~~~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~--~----~~~~---~~~~l 82 (110)
T COG0640 12 SEEVAEILKALADPTRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELR--R----EGRL---RLYRL 82 (110)
T ss_pred hHHHHHHHHHhCCHHHHHHHHHHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEE--e----cccE---EEEec
Confidence 3344455556666667778888876667889999999999999999999999999999973 1 2212 56667
Q ss_pred cchh
Q psy5744 98 NYQT 101 (157)
Q Consensus 98 ~y~~ 101 (157)
+...
T Consensus 83 ~~~~ 86 (110)
T COG0640 83 ADEK 86 (110)
T ss_pred CcHH
Confidence 7655
No 156
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=90.98 E-value=0.86 Score=37.46 Aligned_cols=49 Identities=22% Similarity=0.343 Sum_probs=44.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
-+-|+..|.+.+.+.=.+||+.+|+++..+-.-+..|++.||+..++++
T Consensus 25 Rv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~k 73 (308)
T COG4189 25 RVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVK 73 (308)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeec
Confidence 4778999999999999999999999999999999999999999988654
No 157
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=90.85 E-value=0.67 Score=37.88 Aligned_cols=44 Identities=14% Similarity=0.121 Sum_probs=40.0
Q ss_pred HHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 34 SLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 34 ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
+-||++|-.+ +.++=.|||+.+|++...+.++|..|.+.|+|.+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 5789998865 5799999999999999999999999999999965
No 158
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=90.72 E-value=0.37 Score=37.78 Aligned_cols=34 Identities=12% Similarity=0.293 Sum_probs=31.8
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+|-++||..+|+....|.++|.+|+++|+|...
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 3788999999999999999999999999999965
No 159
>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=90.72 E-value=0.34 Score=37.56 Aligned_cols=45 Identities=9% Similarity=0.166 Sum_probs=36.8
Q ss_pred HHHHHHHHh----CC-CcCHHHHHHHhCCC-hHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVR----NP-CMKEDDICELLKFE-RKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~----~~-~i~dedLa~~l~i~-~k~vRkiL~~L~~d~Lv~~~ 78 (157)
--|+++|.. ++ ..+-.|||+.+|++ ..-+++.|..|.+.|+|...
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 345666653 22 37789999999999 99999999999999999865
No 160
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=90.39 E-value=0.78 Score=32.02 Aligned_cols=68 Identities=12% Similarity=0.307 Sum_probs=46.9
Q ss_pred CCCCcccccch-HHHHHHHHHHHHHcCCC----c------------hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHH
Q psy5744 4 SDEGYVHTEVP-TSLKQLSRLVVRGFYSI----E------------DSLIIDMLVRNPCMKEDDICELLKFERKMLRARI 66 (157)
Q Consensus 4 ~~~~~~~~~ip-~~~~~Lv~~v~R~Fy~~----e------------~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL 66 (157)
..-+.+.+.|+ .++.+.|+.+.+-+|.+ + ...++|..+.+..=...--|..|||+...+||-|
T Consensus 13 ~s~~~t~~~~~~~plRdsV~~~L~~Y~~~L~G~~v~~lY~mVL~evE~PLL~~vM~~~~gNQtrAa~mLGinR~TLRKKL 92 (98)
T COG2901 13 VSTPNSQDQITQKPLRDSVKQALKNYFADLNGQDVNDLYEMVLAEVEQPLLDMVMQYTRGNQTRAALMLGINRGTLRKKL 92 (98)
T ss_pred ccccccCCccccccHHHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhHHHHHHHHHhcccHHHHHHHHcccHHHHHHHH
Confidence 34456677777 77888877777777653 2 3457777776544456677889999999999854
Q ss_pred HHHhhCcc
Q psy5744 67 STLKNDKI 74 (157)
Q Consensus 67 ~~L~~d~L 74 (157)
++.||
T Consensus 93 ---kqygl 97 (98)
T COG2901 93 ---KKYGL 97 (98)
T ss_pred ---HHhCC
Confidence 44444
No 161
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=90.35 E-value=0.43 Score=32.36 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=28.1
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+||+.+|+++.-+++++..|.+.|+|...
T Consensus 3 ~ela~~l~is~stvs~~l~~L~~~glI~r~ 32 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKLEKDGLVEYE 32 (96)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence 489999999999999999999999999865
No 162
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=90.35 E-value=1.2 Score=34.98 Aligned_cols=50 Identities=22% Similarity=0.325 Sum_probs=39.4
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI 97 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I 97 (157)
..++-++||+.|+++.+.||+.+..|.+-|++..+..- +.-||. .++|.+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~--~~~~~~--~~~~~~ 226 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHY--GVTGRP--VYRYRL 226 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeec--cCCCCC--Ceeeec
Confidence 67899999999999999999999999999999876432 234444 455544
No 163
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=90.30 E-value=1.3 Score=34.45 Aligned_cols=67 Identities=9% Similarity=0.052 Sum_probs=54.6
Q ss_pred cchHHHHHHHHHHHHHcCCCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 12 EVPTSLKQLSRLVVRGFYSIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 12 ~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++-+.+-..+-..++.|.-+..|--+-+++- .+.++-+||++.+||+...|-..+.+|.+-+||...
T Consensus 6 qak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 6 QAKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred HHHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 3445566666667777877887776666663 578999999999999999999999999999999875
No 164
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=90.21 E-value=1.1 Score=34.86 Aligned_cols=52 Identities=15% Similarity=0.298 Sum_probs=40.1
Q ss_pred HHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCcee
Q psy5744 36 IIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQ 90 (157)
Q Consensus 36 IlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~ 90 (157)
|+..+. .+ ..+-.+||+.||++.+.|++.+..|...|+++....= +.-||..
T Consensus 167 Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~--~~~grp~ 220 (225)
T PRK10046 167 VRKLFK-EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH--GKVGRPQ 220 (225)
T ss_pred HHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec--CCCCCcC
Confidence 455444 33 4789999999999999999999999999999976432 2345554
No 165
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=90.13 E-value=0.16 Score=26.76 Aligned_cols=17 Identities=41% Similarity=0.823 Sum_probs=15.2
Q ss_pred eecCCCCCccchhhhhh
Q psy5744 130 FKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~ 146 (157)
|.|+.|++.|+..++..
T Consensus 2 ~~C~~C~~~F~~~~~l~ 18 (27)
T PF13912_consen 2 FECDECGKTFSSLSALR 18 (27)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCccCCccCChhHHH
Confidence 89999999999988764
No 166
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=89.93 E-value=0.56 Score=33.50 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=37.7
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
|.+-..+..++|-..||..+||+...-|++|..|++.|.|.-..
T Consensus 50 i~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvs 93 (107)
T COG4901 50 IRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVS 93 (107)
T ss_pred HHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeec
Confidence 34444456799999999999999999999999999999998763
No 167
>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=89.67 E-value=0.99 Score=30.21 Aligned_cols=47 Identities=26% Similarity=0.360 Sum_probs=40.0
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHH--hhCcceeee
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTL--KNDKIIQTR 78 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L--~~d~Lv~~~ 78 (157)
..-.|+++|-+-+..+-++|++.+|+++-.+|-.|.-+ +..||.-..
T Consensus 11 Kqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s 59 (72)
T PF11994_consen 11 KQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTITS 59 (72)
T ss_pred HHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEe
Confidence 34678899888888899999999999999999999988 666776543
No 168
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=89.53 E-value=8 Score=29.72 Aligned_cols=98 Identities=13% Similarity=0.098 Sum_probs=64.7
Q ss_pred HHHcCCCc-hHHHHHHHHhC-CCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeeeEe-----eee----c-------
Q psy5744 25 VRGFYSIE-DSLIIDMLVRN-PCMKEDDICELL--KFERKMLRARISTLKNDKIIQTRLR-----MET----G------- 84 (157)
Q Consensus 25 ~R~Fy~~e-~ivIlD~L~~~-~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~~~-----~e~----~------- 84 (157)
...||+.= |.+|..++--. +.-..+.||+.+ +++..++|+.|..|.+-||++.... .+. +
T Consensus 17 ~~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~a 96 (171)
T PF14394_consen 17 EFEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEA 96 (171)
T ss_pred HHHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHH
Confidence 34455554 45555544433 344899999999 9999999999999999999986321 000 0
Q ss_pred --------------------CCCceeEEEEEEecchhHHHHHHHHHHHHHHHHHHHHhh
Q psy5744 85 --------------------LDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123 (157)
Q Consensus 85 --------------------~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~ 123 (157)
++.|..+...--|+ +.-..-|+..|...++++-...+.
T Consensus 97 vr~~h~q~~~lA~~al~~~p~~~R~~s~~T~~vs-~~~~~ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 97 VRSYHKQMLELAQEALDRVPPEERDFSGLTMSVS-REDYEKIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred HHHHHHHHHHHHHHHHHhCCccccceeeeEEEeC-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 12133334455666 345566777888888888877666
No 169
>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=89.17 E-value=0.44 Score=31.27 Aligned_cols=29 Identities=14% Similarity=0.193 Sum_probs=22.8
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhC
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKND 72 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d 72 (157)
..-++++||+.|||+.++|+.++.....-
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~~~~ 47 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQASRRP 47 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHHSCC
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhCCCC
Confidence 46789999999999999999999876543
No 170
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=88.71 E-value=0.72 Score=39.15 Aligned_cols=37 Identities=14% Similarity=0.310 Sum_probs=34.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+..++-.|||++||++.-.|++.|.+.++.|+|+-.-
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i 60 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISI 60 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEe
Confidence 4589999999999999999999999999999999763
No 171
>PRK05638 threonine synthase; Validated
Probab=88.63 E-value=1.5 Score=38.48 Aligned_cols=60 Identities=20% Similarity=0.288 Sum_probs=47.3
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhC--CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLK--FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~--i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~ 101 (157)
...||..|. ++.++=.||++.++ ++...|++.|..|+++|||..+.+ +|+ +.||.|+-..
T Consensus 373 r~~IL~~L~-~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~-----~g~---~~~Y~Lt~~g 434 (442)
T PRK05638 373 KLEILKILS-EREMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYR-----KGR---RVYYKLTEKG 434 (442)
T ss_pred HHHHHHHHh-hCCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeec-----CCC---cEEEEECcHH
Confidence 466887766 55789999999998 899999999999999999987511 232 5588888543
No 172
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=88.43 E-value=0.3 Score=28.19 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=14.7
Q ss_pred eeecCCCCCccchhhhhh
Q psy5744 129 SFKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~ 146 (157)
.|.|+.||..|+.....+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~ 22 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS 22 (41)
T ss_pred EEEcCCCCCEEEEEEecC
Confidence 689999999998776543
No 173
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=88.38 E-value=8 Score=28.25 Aligned_cols=105 Identities=14% Similarity=0.181 Sum_probs=72.0
Q ss_pred CCCCCcccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeee
Q psy5744 3 TSDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRME 82 (157)
Q Consensus 3 ~~~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e 82 (157)
|.+.+.++++....+.++++. .=..-.-...+-+|....+++--+|....|+-+-+|--++..|++.|-|..+. +
T Consensus 2 ~~~~~~~l~E~e~~~ie~L~~---lgi~R~vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~--e 76 (124)
T COG4738 2 MEDNDMVLTEKEYEIIELLRI---LGIPRNVATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDERE--E 76 (124)
T ss_pred CcccccccchhHHHHHHHHHH---cCCCchHHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccchHH--h
Confidence 344555666666666555543 33333334455566667899999999999999999999999999999999873 3
Q ss_pred ecCCCceeEEEEEEec--chhHHHHHHHHHHHH
Q psy5744 83 TGLDGKAQKVNYYFIN--YQTFVNIVKYKLDVM 113 (157)
Q Consensus 83 ~~~~gk~~~~~yw~I~--y~~~~~vik~rl~~m 113 (157)
. ..|+++...+|.+. .+.|++.+-..+.+=
T Consensus 77 K-KkGKGRPik~Y~Lt~~~~eIvs~iee~~~ke 108 (124)
T COG4738 77 K-KKGKGRPIKLYRLTVPFDEIVSEIEEEIIKE 108 (124)
T ss_pred c-ccCCCCCceEEEecCcHHHHHHHHHHHHHHH
Confidence 3 25677777777754 555665555444433
No 174
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=88.37 E-value=1.5 Score=30.93 Aligned_cols=78 Identities=12% Similarity=0.174 Sum_probs=59.9
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeee-ecCCCceeEEEEEEecchhHHHHHHHHH
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRME-TGLDGKAQKVNYYFINYQTFVNIVKYKL 110 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e-~~~~gk~~~~~yw~I~y~~~~~vik~rl 110 (157)
.|+.|++.+++++.+-=--|+..+||+--.||=-|..|++.++++..+.-- .+++ ...++.-++-++
T Consensus 15 RHl~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~~iI~PS~~GAi~td~------------~~e~ie~i~~dl 82 (101)
T COG3388 15 RHLSVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQENIISPSRQGAILTDD------------FPEFIEEIIGDL 82 (101)
T ss_pred HHHHHHHHHHHhCCceeEeechhcCCchhhhhhhhhhhhhcCccCccccCCccCcc------------HHHHHHHHHHHH
Confidence 388999999998877777899999999999999999999999998653110 1223 246777777888
Q ss_pred HHHHHHHHHHH
Q psy5744 111 DVMRKRMEMEE 121 (157)
Q Consensus 111 ~~m~~~L~~~~ 121 (157)
.++.++.++-.
T Consensus 83 ~ei~e~~~~i~ 93 (101)
T COG3388 83 SEINEEAENIE 93 (101)
T ss_pred HHHHHHHHHHH
Confidence 77777666543
No 175
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=88.29 E-value=1 Score=31.09 Aligned_cols=37 Identities=3% Similarity=0.089 Sum_probs=34.4
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
....||-..|++++++...--|++|..|.+.|+++..
T Consensus 38 ~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 38 KEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred cCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 4578999999999999999999999999999999865
No 176
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=88.23 E-value=1.5 Score=39.14 Aligned_cols=47 Identities=9% Similarity=0.134 Sum_probs=41.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
..-||..|-.++.++-.+||+.+|++...|-+++..|...|||....
T Consensus 8 e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~ 54 (489)
T PRK04172 8 EKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEE 54 (489)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEe
Confidence 45677787777889999999999999999999999999999999763
No 177
>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=88.19 E-value=1.5 Score=29.79 Aligned_cols=35 Identities=14% Similarity=0.217 Sum_probs=32.8
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
...|.-.+||+.+++++--||-.+..|++.|||..
T Consensus 21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 21 GEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 46799999999999999999999999999999974
No 178
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=88.06 E-value=0.9 Score=27.14 Aligned_cols=31 Identities=13% Similarity=0.160 Sum_probs=19.5
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
..+..++|+.+|++.+.|++++....+.|+-
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~ 47 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEGLE 47 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccccc
Confidence 7899999999999999999999988887764
No 179
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=87.66 E-value=7.3 Score=26.97 Aligned_cols=80 Identities=11% Similarity=0.133 Sum_probs=51.9
Q ss_pred HHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HH
Q psy5744 34 SLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FV 103 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~ 103 (157)
..||-.|. .+.++=-+|++.+ .++...+-.+|.+|+++|+|...... . ++ ...+.+|.|.-.. ..
T Consensus 7 ~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~-~-~~--~~~rk~y~iT~~Gr~~l 81 (100)
T TIGR03433 7 LLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGE-S-EN--NRRAKFYRLTAAGRKQL 81 (100)
T ss_pred HHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeee-c-CC--CCCceEEEECHHHHHHH
Confidence 45565555 4567777777775 68888999999999999999986222 1 22 2335788888532 34
Q ss_pred HHHHHHHHHHHHHHH
Q psy5744 104 NIVKYKLDVMRKRME 118 (157)
Q Consensus 104 ~vik~rl~~m~~~L~ 118 (157)
+....+...+.+.+.
T Consensus 82 ~~~~~~~~~~~~~i~ 96 (100)
T TIGR03433 82 AAETESWARLSAAIA 96 (100)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444444444444444
No 180
>PRK12423 LexA repressor; Provisional
Probab=87.59 E-value=1.5 Score=34.33 Aligned_cols=33 Identities=18% Similarity=0.345 Sum_probs=30.5
Q ss_pred cCHHHHHHHhCC-ChHHHHHHHHHHhhCcceeee
Q psy5744 46 MKEDDICELLKF-ERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 46 i~dedLa~~l~i-~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-|..|||+.+|+ ++.-+|+.|..|.+.|+|...
T Consensus 26 Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 26 PSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence 599999999995 889999999999999999874
No 181
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=87.41 E-value=1.9 Score=36.01 Aligned_cols=44 Identities=23% Similarity=0.390 Sum_probs=37.3
Q ss_pred HHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 36 IIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 36 IlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
++-.|-+.+. +..-+|.+++|++...|-.+|..|++.|+|+.++
T Consensus 9 lir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rrk 54 (321)
T COG3888 9 LIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRK 54 (321)
T ss_pred HHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeee
Confidence 3444555444 8999999999999999999999999999999875
No 182
>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=87.19 E-value=1 Score=27.95 Aligned_cols=32 Identities=13% Similarity=0.250 Sum_probs=24.2
Q ss_pred HHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHH
Q psy5744 35 LIIDMLVRN--PCMKEDDICELLKFERKMLRARI 66 (157)
Q Consensus 35 vIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL 66 (157)
-+|..|... ..++=.+||+.+|+++.+|||=|
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 456666654 46999999999999999999854
No 183
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=87.15 E-value=3.7 Score=29.84 Aligned_cols=48 Identities=19% Similarity=0.245 Sum_probs=41.7
Q ss_pred CCchHHHHHHHHhCCCcCHHHHHHHhC-CChHHHHHHHHHHhhCcceeee
Q psy5744 30 SIEDSLIIDMLVRNPCMKEDDICELLK-FERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 30 ~~e~ivIlD~L~~~~~i~dedLa~~l~-i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+.=.++|+-.|.. +...=.+|...++ |+++.+-+-|..|+++|||...
T Consensus 22 ~kW~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~ 70 (120)
T COG1733 22 GKWTLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERV 70 (120)
T ss_pred CccHHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEee
Confidence 3345778877775 8889999999998 9999999999999999999976
No 184
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=86.94 E-value=1.5 Score=36.97 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=40.8
Q ss_pred HHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 20 LSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 20 Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|+-.+++.+|.+ .++-.|||++||++.-.|-|+|..=++.|+|+-.
T Consensus 17 l~~~vA~lYY~~-------------g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 17 LVARIAWFYYHD-------------GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred HHHHHHHHHHhc-------------CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEE
Confidence 566777777755 7899999999999999999999999999999875
No 185
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.74 E-value=0.53 Score=28.41 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=16.2
Q ss_pred eeecCCCCCccchhhhhhccCCCCcccC
Q psy5744 129 SFKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
.|+|..||..++.. +.....||
T Consensus 2 ~Y~C~~Cg~~~~~~------~~~~irC~ 23 (44)
T smart00659 2 IYICGECGRENEIK------SKDVVRCR 23 (44)
T ss_pred EEECCCCCCEeecC------CCCceECC
Confidence 69999999998865 23456665
No 186
>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=86.68 E-value=2.3 Score=31.18 Aligned_cols=46 Identities=9% Similarity=0.161 Sum_probs=37.8
Q ss_pred hHHHHHHHHhCCCcCHHHHHHH----hCCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICEL----LKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~----l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..-||..|-.++.++=.||.+. .|+..+-|+.+|..|.+.|+|..+
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 4568888887777887775554 489999999999999999999754
No 187
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=86.43 E-value=1.7 Score=37.79 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=32.1
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
.+.++.++|++.++++...++++|..|.+.|+|.
T Consensus 308 g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~ 341 (412)
T PRK04214 308 GKALDVDEIRRLEPMGYDELGELLCELARIGLLR 341 (412)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE
Confidence 3578999999999999999999999999999997
No 188
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=86.43 E-value=0.47 Score=25.11 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=9.9
Q ss_pred CCCeeecCCCCC
Q psy5744 126 SRSSFKCPRCLK 137 (157)
Q Consensus 126 ~~~~Y~Cp~C~~ 137 (157)
....|.||+||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 367899999984
No 189
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.40 E-value=8.1 Score=29.39 Aligned_cols=97 Identities=13% Similarity=0.162 Sum_probs=66.1
Q ss_pred HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCC-ceeE--EE-------
Q psy5744 24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDG-KAQK--VN------- 93 (157)
Q Consensus 24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~g-k~~~--~~------- 93 (157)
+.++|-++-+-.++++|. .||+|--+|.+..|- +-|+.|..|+..|++...=+. +.+| +... ++
T Consensus 17 ifh~~~set~rKl~~aLs-tgW~T~~eiee~iG~---eg~RaL~iLkkagmlEtqWr~--p~~G~kPeKeYHtsYt~Vqi 90 (170)
T COG4860 17 IFHAADSETKRKLLLALS-TGWITLPEIEEKIGK---EGRRALLILKKAGMLETQWRT--PSNGQKPEKEYHTSYTNVQI 90 (170)
T ss_pred HHHHcccHHHHHHHHHHh-hcceeHHHHHHHhch---hhHHHHHHHHhhcchhheeec--cCCCCCchhhhhhheeeEEE
Confidence 457888888899999988 889999999999994 557799999999999876443 2233 2111 11
Q ss_pred EEEecchhHHHHHH------HHHHHHHHHHHHHHhhcCC
Q psy5744 94 YYFINYQTFVNIVK------YKLDVMRKRMEMEERDATS 126 (157)
Q Consensus 94 yw~I~y~~~~~vik------~rl~~m~~~L~~~~~~~~~ 126 (157)
=+++....+.|+|- -.+....++|+..++....
T Consensus 91 Nf~~Sl~dL~dii~~~f~sdeev~ey~~ei~~l~e~g~t 129 (170)
T COG4860 91 NFMGSLSDLADIIYAAFLSDEEVKEYEDEIKALMEEGNT 129 (170)
T ss_pred EEEEeHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCCc
Confidence 23444566666653 3455566667776665433
No 190
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=86.40 E-value=1.9 Score=35.44 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=39.5
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR 80 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~ 80 (157)
++...-.+++.++..|||..||+.+.-|--.+..|.++|+|..+-|
T Consensus 15 IL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR 60 (260)
T COG1497 15 ILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGR 60 (260)
T ss_pred HHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCC
Confidence 3444445789999999999999999999999999999999987543
No 191
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=86.38 E-value=0.29 Score=35.40 Aligned_cols=25 Identities=20% Similarity=0.550 Sum_probs=21.7
Q ss_pred HHHHHhhcCCCCeeecCCCCCccch
Q psy5744 117 MEMEERDATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 117 L~~~~~~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
++.+..++....||.|.+||.+|.+
T Consensus 88 ~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 88 LQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred eehhccCCCceEEEEecccCCEeec
Confidence 5677788889999999999999875
No 192
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=86.31 E-value=2.8 Score=32.93 Aligned_cols=44 Identities=9% Similarity=0.160 Sum_probs=35.0
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ 100 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~ 100 (157)
|.|+..-||=.+.|.-+|+.|-+||+|+.+ . =+++.+||.+...
T Consensus 32 EkLGSKK~IVl~tVKd~lQqlVDDgvV~~E----K----~GtsN~YWsF~s~ 75 (209)
T COG5124 32 EKLGSKKQIVLMTVKDLLQQLVDDGVVSVE----K----CGTSNIYWSFKSQ 75 (209)
T ss_pred HHhccccccHHHHHHHHHHHHhhcCceeee----e----eccceeEEecchH
Confidence 556677788889999999999999999965 2 1255889998864
No 193
>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=86.05 E-value=1.7 Score=29.51 Aligned_cols=37 Identities=11% Similarity=0.301 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
+.++..|.....++-++||..+|.+..+|+.+|..+-
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 4466666666789999999999999999999998774
No 194
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.70 E-value=0.41 Score=29.69 Aligned_cols=20 Identities=20% Similarity=0.424 Sum_probs=15.2
Q ss_pred CCCeeecCCCCCccchhhhh
Q psy5744 126 SRSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~lda~ 145 (157)
....|+|-+||+.++.+.+.
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~ 22 (49)
T COG1996 3 AMMEYKCARCGREVELDQET 22 (49)
T ss_pred ceEEEEhhhcCCeeehhhcc
Confidence 35689999999999555444
No 195
>PHA02591 hypothetical protein; Provisional
Probab=85.42 E-value=2 Score=29.23 Aligned_cols=41 Identities=20% Similarity=0.203 Sum_probs=30.3
Q ss_pred HHcCCCc--hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 26 RGFYSIE--DSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 26 R~Fy~~e--~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
|-|.+.+ -+-+.-.|. ...+|-++||..||++.+.||+.|.
T Consensus 39 ryfi~~~dd~~~vA~eL~-eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 39 RYFVESEDDLISVTHELA-RKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred EEEEeccchHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4555533 334444444 5578999999999999999999985
No 196
>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=85.10 E-value=2.2 Score=25.38 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=22.1
Q ss_pred HHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 37 IDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 37 lD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
+-.|...| ++-.+||+.+|++...|.++|.
T Consensus 14 i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 33455577 9999999999999999999875
No 197
>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=85.01 E-value=1.4 Score=32.15 Aligned_cols=55 Identities=9% Similarity=0.177 Sum_probs=41.2
Q ss_pred HHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 20 LSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 20 Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.++.+ ...++.+.++ .+-..++|.||..++-+...||.+|..|.+-|||..-
T Consensus 30 ~lkLll~s-~n~~G~L~~~---~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~ 84 (119)
T TIGR01714 30 WLKLLLLS-LNDGGCIYLN---ELAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKK 84 (119)
T ss_pred HHHHHHHH-hcCCCEEEEc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34555555 5555554443 2335689999999999999999999999999999853
No 198
>PHA00626 hypothetical protein
Probab=84.89 E-value=0.53 Score=30.03 Aligned_cols=16 Identities=13% Similarity=0.237 Sum_probs=14.1
Q ss_pred CCeeecCCCCCccchh
Q psy5744 127 RSSFKCPRCLKTFTDL 142 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~l 142 (157)
+..|+||.||-.||-+
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 5789999999999864
No 199
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=84.82 E-value=0.64 Score=28.83 Aligned_cols=9 Identities=67% Similarity=1.364 Sum_probs=5.7
Q ss_pred eeecCCCCC
Q psy5744 129 SFKCPRCLK 137 (157)
Q Consensus 129 ~Y~Cp~C~~ 137 (157)
.|.||-|++
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 456666666
No 200
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=84.80 E-value=2.5 Score=31.30 Aligned_cols=43 Identities=7% Similarity=0.122 Sum_probs=38.4
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|+++.=.||-+|-.|++..+|.+.+.+++.+..|.+.|-|-.+
T Consensus 17 IvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 17 IVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence 6666566999999999999999999999999999999988654
No 201
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=84.71 E-value=0.58 Score=24.76 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=14.9
Q ss_pred eecCCCCCccchhhhhh
Q psy5744 130 FKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~ 146 (157)
|.|+.|++.|+...+..
T Consensus 2 ~~C~~C~k~f~~~~~~~ 18 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLK 18 (27)
T ss_dssp CBBTTTTBBBSSHHHHH
T ss_pred CCcccCCCCcCCHHHHH
Confidence 78999999999988765
No 202
>KOG2907|consensus
Probab=84.38 E-value=0.5 Score=34.27 Aligned_cols=27 Identities=22% Similarity=0.668 Sum_probs=20.6
Q ss_pred HHHHHHHhhcCCCCeeecCCCCCccch
Q psy5744 115 KRMEMEERDATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 115 ~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
..++-|-.+|....||.||+|+.+|+.
T Consensus 88 ~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 88 HTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred hhhhcccccCCceEEEEcCccceeeec
Confidence 345556667777889999999998875
No 203
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=84.37 E-value=1.6 Score=39.03 Aligned_cols=59 Identities=17% Similarity=0.400 Sum_probs=47.8
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ 100 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~ 100 (157)
+-.++.++..++.+|-.+|++.+|++.+.+++.|..|...|++++. ++.| .-+|||...
T Consensus 404 ~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~-----g~~~----~g~~~v~~~ 462 (467)
T COG2865 404 QEKILELIKENGKVTARELREILGISSETIRRRIANLVKRGLLKQL-----GSSG----RGTWYVKGE 462 (467)
T ss_pred HHHHHHHHhhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHh-----CcCC----CCcEEecCC
Confidence 3567777778899999999999999999999999999999999864 2222 346777654
No 204
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=84.21 E-value=2.2 Score=32.95 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhh
Q psy5744 106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~ 146 (157)
+..+-.++-+++.++++ ++..|+||.||...-- ++..
T Consensus 114 ~Ek~H~~~~~~~Le~~~---~~~~~vC~vCGy~~~g-e~P~ 150 (166)
T COG1592 114 AEKRHAEMFRGLLERLE---EGKVWVCPVCGYTHEG-EAPE 150 (166)
T ss_pred HHHHHHHHHHHHHHhhh---cCCEEEcCCCCCcccC-CCCC
Confidence 33444444455555443 4449999999977665 5543
No 205
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=84.12 E-value=0.81 Score=37.28 Aligned_cols=35 Identities=20% Similarity=0.286 Sum_probs=33.1
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
|+.+|=+|.|+.+|+++|.+|++++.|++.|.+..
T Consensus 28 hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeR 62 (269)
T COG5340 28 HKIITIRDVAETLEVAPNTLRELASRLEKKGWLER 62 (269)
T ss_pred CceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhh
Confidence 68999999999999999999999999999999864
No 206
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=84.10 E-value=0.76 Score=28.06 Aligned_cols=15 Identities=27% Similarity=0.804 Sum_probs=12.1
Q ss_pred eeecCCCCCccchhh
Q psy5744 129 SFKCPRCLKTFTDLE 143 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~ld 143 (157)
.|.|+.||.+|..+.
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ 19 (52)
T ss_pred EEEeCCCCCEeEEEE
Confidence 588999998888763
No 207
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=84.06 E-value=0.33 Score=28.62 Aligned_cols=21 Identities=14% Similarity=0.445 Sum_probs=16.5
Q ss_pred HHhhcCCCCeeecCCCCCccc
Q psy5744 120 EERDATSRSSFKCPRCLKTFT 140 (157)
Q Consensus 120 ~~~~~~~~~~Y~Cp~C~~~Ys 140 (157)
+-.++....+|+|.+|+.+|.
T Consensus 19 RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 19 RSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCeEEEEeCCCCCEeC
Confidence 344666778999999999875
No 208
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=83.91 E-value=3.5 Score=37.04 Aligned_cols=49 Identities=8% Similarity=0.110 Sum_probs=42.1
Q ss_pred hHHHHHHHHhCCC-cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744 33 DSLIIDMLVRNPC-MKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 33 ~ivIlD~L~~~~~-i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
..-||..|..++. ++-++||+.+|++...|..++..|...|+|....+.
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~ 54 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIK 54 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence 3567788876664 899999999999999999999999999999987544
No 209
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=83.84 E-value=0.95 Score=27.20 Aligned_cols=28 Identities=29% Similarity=0.462 Sum_probs=17.4
Q ss_pred CCCCeeecCCCCCccchhhhhhccCCCCcccC
Q psy5744 125 TSRSSFKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 125 ~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
.=..+++||.||.+ .+..|-+...|.|.
T Consensus 14 RW~~g~~CP~Cg~~----~~~~~~~~~~~~C~ 41 (46)
T PF12760_consen 14 RWPDGFVCPHCGST----KHYRLKTRGRYRCK 41 (46)
T ss_pred cCCCCCCCCCCCCe----eeEEeCCCCeEECC
Confidence 34556899999985 33333334566664
No 210
>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=83.79 E-value=1.6 Score=29.75 Aligned_cols=36 Identities=6% Similarity=0.059 Sum_probs=32.4
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
+.+..|++.|.. +.++=.|||+..|++...|++.|.
T Consensus 6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 6 ERVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 356789999999 999999999999999999999773
No 211
>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=83.77 E-value=7.2 Score=25.31 Aligned_cols=40 Identities=23% Similarity=0.347 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744 56 KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY 99 (157)
Q Consensus 56 ~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y 99 (157)
.++...|-.+|.+|.++|+|....... ++ ...+.+|.|.-
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~--~~--~~~rk~Y~iT~ 67 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEE--GN--GRPRKYYRITE 67 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEE--TT--SSEEEEEEESH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeecc--CC--CCCCEEEEECH
Confidence 577889999999999999999884432 23 35567888764
No 212
>PHA00616 hypothetical protein
Probab=83.69 E-value=0.27 Score=29.80 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=11.1
Q ss_pred eecCCCCCccchh
Q psy5744 130 FKCPRCLKTFTDL 142 (157)
Q Consensus 130 Y~Cp~C~~~Ys~l 142 (157)
|.||+||..|...
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 8899999998754
No 213
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=83.21 E-value=7.3 Score=30.42 Aligned_cols=30 Identities=10% Similarity=0.169 Sum_probs=27.7
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
++-+|||..+|+....|.++|.+|++.|+.
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~~~gl~ 203 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALASHGVH 203 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHhCCeE
Confidence 457899999999999999999999999974
No 214
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=83.13 E-value=4.1 Score=24.13 Aligned_cols=28 Identities=11% Similarity=0.334 Sum_probs=24.6
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
+.++..++|+.+|++.+.|+..+..+..
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4579999999999999999999987654
No 215
>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=83.11 E-value=2.5 Score=34.85 Aligned_cols=44 Identities=9% Similarity=0.018 Sum_probs=39.0
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.-|.|.|- .+..|-++||+.+|+++.-++++|..|..-|++...
T Consensus 13 Lglfd~L~-~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~ 56 (306)
T TIGR02716 13 LDLFSHMA-EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLE 56 (306)
T ss_pred cCcHHHHh-cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEec
Confidence 34788876 578999999999999999999999999999999853
No 216
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=83.04 E-value=2.2 Score=28.52 Aligned_cols=41 Identities=20% Similarity=0.314 Sum_probs=33.9
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
.....++..|+.++.++=+++|+.++++...+++.+..+.+
T Consensus 16 s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 16 SLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp SHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44678898999899999999999999999999999998875
No 217
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=82.99 E-value=0.36 Score=30.92 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=14.2
Q ss_pred hcCCCCeeecCCCCCccch
Q psy5744 123 DATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 123 ~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
......++.||+|+.-|..
T Consensus 11 ~RDGE~~lrCPRC~~~FR~ 29 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRR 29 (65)
T ss_pred ccCCceeeeCCchhHHHHH
Confidence 3345679999999987753
No 218
>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=82.55 E-value=2.6 Score=27.07 Aligned_cols=35 Identities=14% Similarity=0.321 Sum_probs=28.9
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+.+.-..+|.+.|+....+-.+|.+|+..|++.++
T Consensus 3 g~lvas~iAd~~GiTRSvIVNALRKleSaGvIesr 37 (61)
T PF08222_consen 3 GRLVASKIADRVGITRSVIVNALRKLESAGVIESR 37 (61)
T ss_dssp EEE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred ceehHHHHHHHhCccHHHHHHHHHHHHhcCceeec
Confidence 34667789999999999999999999999999976
No 219
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=82.53 E-value=1.6 Score=30.43 Aligned_cols=26 Identities=31% Similarity=0.612 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHhhcCCCCeeecCCCCCcc
Q psy5744 109 KLDVMRKRMEMEERDATSRSSFKCPRCLKTF 139 (157)
Q Consensus 109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Y 139 (157)
.+.++.++++.... ..|.||.||+.=
T Consensus 20 slRK~vkkie~~q~-----~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 20 SLRKRVKKIEISQH-----AKYTCPFCGKTS 45 (90)
T ss_dssp HHHHHHHHHHHHHH-----S-BEESSSSSSE
T ss_pred HHHHHHHHHHHHHh-----CCCcCCCCCCce
Confidence 35566666666553 479999998753
No 220
>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=82.46 E-value=3.3 Score=29.35 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=39.4
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
...||+.|-.++.++=.||.+.++ +..+.|+.+|..|.+.|+|+..
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence 467999999887899999988885 5699999999999999999975
No 221
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=82.40 E-value=3.6 Score=28.37 Aligned_cols=39 Identities=13% Similarity=0.206 Sum_probs=31.0
Q ss_pred HHHHHHHhCCCcCHHHHH--HHhCCChHHHHHHHHHHhhCc
Q psy5744 35 LIIDMLVRNPCMKEDDIC--ELLKFERKMLRARISTLKNDK 73 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa--~~l~i~~k~vRkiL~~L~~d~ 73 (157)
.++|.|+.++.+++||.- ..-.-++..+|+++.-+..-|
T Consensus 19 plLD~Ll~n~~it~E~y~~V~a~~T~qdkmRkLld~v~akG 59 (85)
T cd08324 19 CLVDNLLKNDYFSTEDAEIVCACPTQPDKVRKILDLVQSKG 59 (85)
T ss_pred HHHHHHhccCCccHHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence 589999999999988754 445889999999998655443
No 222
>KOG3623|consensus
Probab=82.38 E-value=0.88 Score=42.69 Aligned_cols=35 Identities=26% Similarity=0.573 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccch
Q psy5744 102 FVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 102 ~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
.-.+.||| ..|++-++--.+..-|.||+|++|||-
T Consensus 287 CgKAFKfK-----HHLKEHlRIHSGEKPfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 287 CGKAFKFK-----HHLKEHLRIHSGEKPFECPNCKKRFSH 321 (1007)
T ss_pred cchhhhhH-----HHHHhhheeecCCCCcCCccccccccc
Confidence 33455555 457888888888899999999999974
No 223
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=82.07 E-value=4.6 Score=36.37 Aligned_cols=49 Identities=18% Similarity=0.320 Sum_probs=41.9
Q ss_pred hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744 33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
...||..|-. .+.++-++||+.+|++...|..++..|...|+|....+.
T Consensus 8 e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~ 57 (494)
T PTZ00326 8 ENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKK 57 (494)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence 3457777776 467889999999999999999999999999999987543
No 224
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=81.93 E-value=0.84 Score=24.08 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=11.5
Q ss_pred eecCCCCCccchhhh
Q psy5744 130 FKCPRCLKTFTDLEP 144 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda 144 (157)
..||.||++|...-.
T Consensus 3 ~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 3 VPCPICGRKFNPDRL 17 (25)
T ss_pred CcCCCCCCEECHHHH
Confidence 469999999965543
No 225
>PRK00215 LexA repressor; Validated
Probab=81.65 E-value=4.1 Score=31.62 Aligned_cols=34 Identities=12% Similarity=0.241 Sum_probs=31.5
Q ss_pred CcCHHHHHHHhCC-ChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKF-ERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i-~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+-.|||+.+|+ +..-+.++|..|.+.|+|...
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeC
Confidence 5789999999999 999999999999999999754
No 226
>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=81.63 E-value=2.3 Score=28.52 Aligned_cols=33 Identities=12% Similarity=0.112 Sum_probs=29.4
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
...+|=.|||+.||++.+.|+..+..+.+.|.+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 367899999999999999999999998877654
No 227
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=81.56 E-value=6.9 Score=31.65 Aligned_cols=43 Identities=14% Similarity=0.304 Sum_probs=36.8
Q ss_pred HHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|+++|-. ....|-|++|+.+|++.-.+||.|..|...+++..+
T Consensus 163 i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 163 VREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence 4444442 467999999999999999999999999999999876
No 228
>PRK13239 alkylmercury lyase; Provisional
Probab=81.41 E-value=3 Score=33.34 Aligned_cols=38 Identities=8% Similarity=0.156 Sum_probs=33.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
++-|+..|.+...++-++||..+|.+..+|+++|..|-
T Consensus 24 ~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 24 LVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 46688888877889999999999999999999999875
No 229
>PF13518 HTH_28: Helix-turn-helix domain
Probab=81.37 E-value=4.9 Score=23.75 Aligned_cols=41 Identities=12% Similarity=0.211 Sum_probs=33.1
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|+.... ++. +=.++|..+|++...|++.+....+.|+..-.
T Consensus 5 iv~~~~-~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~ 45 (52)
T PF13518_consen 5 IVELYL-EGE-SVREIAREFGISRSTVYRWIKRYREGGIEGLK 45 (52)
T ss_pred HHHHHH-cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhc
Confidence 444444 455 99999999999999999999999998875443
No 230
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=81.19 E-value=1.1 Score=25.12 Aligned_cols=14 Identities=29% Similarity=0.736 Sum_probs=9.1
Q ss_pred eecCCCCCccchhh
Q psy5744 130 FKCPRCLKTFTDLE 143 (157)
Q Consensus 130 Y~Cp~C~~~Ys~ld 143 (157)
|+|+.||-.|+..+
T Consensus 2 ~~C~~CGy~y~~~~ 15 (33)
T cd00350 2 YVCPVCGYIYDGEE 15 (33)
T ss_pred EECCCCCCEECCCc
Confidence 67777776666544
No 231
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=81.18 E-value=4.1 Score=31.22 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=39.6
Q ss_pred CCchHHHHHHHHhC----C--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 30 SIEDSLIIDMLVRN----P--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 30 ~~e~ivIlD~L~~~----~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|....-|+-+|+.+ + .++..+||+.+|++...|.+.+..|.+.+++...
T Consensus 54 g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~ 108 (165)
T PF05732_consen 54 GNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI 108 (165)
T ss_pred chhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence 44556666666643 2 4789999999999999999999999999999753
No 232
>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=81.09 E-value=2.5 Score=27.27 Aligned_cols=23 Identities=30% Similarity=0.322 Sum_probs=21.2
Q ss_pred CCCcCHHHHHHHhCCChHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRAR 65 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRki 65 (157)
+|.++--|||+.||++.+.||+=
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 68999999999999999999974
No 233
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.01 E-value=0.79 Score=34.04 Aligned_cols=17 Identities=24% Similarity=0.530 Sum_probs=12.5
Q ss_pred CCeeecCCCCCccchhh
Q psy5744 127 RSSFKCPRCLKTFTDLE 143 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~ld 143 (157)
...|.|+.||..|+..+
T Consensus 68 p~~~~C~~CG~~~~~~~ 84 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKE 84 (135)
T ss_pred ceEEECCCCCCEEeccc
Confidence 35678888888887764
No 234
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=80.91 E-value=2.3 Score=36.54 Aligned_cols=36 Identities=14% Similarity=0.173 Sum_probs=32.4
Q ss_pred CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.-+ ++.+||+.+|++...||+++..|..+|+|..+.
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~ 63 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQG 63 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 445 789999999999999999999999999998753
No 235
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.49 E-value=6.4 Score=36.97 Aligned_cols=73 Identities=19% Similarity=0.271 Sum_probs=55.3
Q ss_pred CCCcccccchHHHHHHHHHHHHHcCCCc------------------------------------hHHHHHHHHhCCCcCH
Q psy5744 5 DEGYVHTEVPTSLKQLSRLVVRGFYSIE------------------------------------DSLIIDMLVRNPCMKE 48 (157)
Q Consensus 5 ~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e------------------------------------~ivIlD~L~~~~~i~d 48 (157)
.++.+...+|+.+...+...-. ||... ..+|++.+-.+.+++=
T Consensus 547 sp~~~~~~lP~~l~p~le~f~~-~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~ 625 (773)
T COG5647 547 SPEEVSIRLPKELVPILEGFKK-FYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTF 625 (773)
T ss_pred CccccccCCChHHHHHHHHHHH-HHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeH
Confidence 4567777888877776666543 33322 2335555456789999
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|+|.+.++++..++-.+|+.|...+++.-.
T Consensus 626 eei~e~T~l~~~dl~~~L~sl~~ak~~~l~ 655 (773)
T COG5647 626 EEILELTKLSTDDLKRVLQSLSCAKLVVLL 655 (773)
T ss_pred HHHHhhcCCChhhHHHHHHHHHhhheeeec
Confidence 999999999999999999999999998765
No 236
>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=80.28 E-value=1.7 Score=28.68 Aligned_cols=35 Identities=9% Similarity=0.125 Sum_probs=25.9
Q ss_pred CCcCHHHH---HHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCMKEDDI---CELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i~dedL---a~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++++=-+| .+.+|++.+-+|-.|..|..+|++...
T Consensus 19 ~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~ 56 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESE 56 (70)
T ss_dssp S-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeee
Confidence 45555544 455699999999999999999999976
No 237
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=80.12 E-value=1.1 Score=33.60 Aligned_cols=14 Identities=29% Similarity=0.819 Sum_probs=11.8
Q ss_pred CCCeeecCCCCCcc
Q psy5744 126 SRSSFKCPRCLKTF 139 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Y 139 (157)
...||.||.||+-|
T Consensus 121 ~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 121 YDEFWRCPGCGKIY 134 (147)
T ss_pred CCeEEECCCCCCEe
Confidence 45699999999987
No 238
>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=79.78 E-value=4 Score=29.21 Aligned_cols=37 Identities=16% Similarity=0.275 Sum_probs=34.5
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
....||--.||++++++..--|++|..|.+.|++...
T Consensus 56 ~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 56 KMKLITPSVLSERLKINGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp TSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEE
T ss_pred cCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEE
Confidence 3568999999999999999999999999999999876
No 239
>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=79.76 E-value=4.6 Score=34.32 Aligned_cols=86 Identities=13% Similarity=0.230 Sum_probs=39.8
Q ss_pred CCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeee-----------cCCCceeEEEEEE
Q psy5744 30 SIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET-----------GLDGKAQKVNYYF 96 (157)
Q Consensus 30 ~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~-----------~~~gk~~~~~yw~ 96 (157)
+++..+|.+++-. +..|-=.||...+|++.+.|.|+|..|+..+||+...-... .|+ +..+==-||
T Consensus 83 ~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~l~Ps-~eiTGG~wy 161 (327)
T PF05158_consen 83 SDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYDLEPS-EEITGGPWY 161 (327)
T ss_dssp SCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESSS-------------
T ss_pred CHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEccCCcC-cccCCCCcc
Confidence 3445677777664 56788999999999999999999999999999998642211 122 111122566
Q ss_pred ecc---hhHHHHHHHHHHHHHHH
Q psy5744 97 INY---QTFVNIVKYKLDVMRKR 116 (157)
Q Consensus 97 I~y---~~~~~vik~rl~~m~~~ 116 (157)
-|- ..|+++++..+.+..++
T Consensus 162 ~d~e~D~efi~~l~~~~~~~i~~ 184 (327)
T PF05158_consen 162 TDGEFDTEFIDVLREQCLRFIQQ 184 (327)
T ss_dssp -----------------------
T ss_pred cCCcccHHHHHHHHHHHHHHHHh
Confidence 552 45777777766655443
No 240
>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=79.75 E-value=7.6 Score=27.12 Aligned_cols=53 Identities=9% Similarity=0.165 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 16 SLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
.....+..++..+ ++..--|+.... -...+..+||+.+|++.+.|++.+.+..
T Consensus 99 ~~~~~l~~~l~~L-~~~~~~ii~~~~-~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 99 EEREALREALEKL-PEREREVLVLRY-LEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred HHHHHHHHHHHhC-CHHHHHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445555566655 444444443332 2468999999999999999999988654
No 241
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=79.71 E-value=1.4 Score=26.05 Aligned_cols=26 Identities=23% Similarity=0.533 Sum_probs=17.6
Q ss_pred eeecCCCCCccchhhhhhccCCCCcccC
Q psy5744 129 SFKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
.|.|+.||..|..+.-.+ +...-.||
T Consensus 5 ey~C~~Cg~~fe~~~~~~--~~~~~~CP 30 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS--EDDPVPCP 30 (42)
T ss_pred EEEeCCCCCEEEEEEEcC--CCCCCcCC
Confidence 689999999998764332 33455555
No 242
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=79.70 E-value=2.2 Score=29.85 Aligned_cols=25 Identities=32% Similarity=0.712 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744 109 KLDVMRKRMEMEERDATSRSSFKCPRCLKT 138 (157)
Q Consensus 109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~ 138 (157)
.+.++.++|+... ...|.||.|++.
T Consensus 20 slRK~v~kie~~q-----~a~y~CpfCgk~ 44 (91)
T TIGR00280 20 KLRRQVKKIEIQQ-----KAKYVCPFCGKK 44 (91)
T ss_pred HHHHHHHHHHHHH-----hcCccCCCCCCC
Confidence 3556666666655 347999999864
No 243
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=79.58 E-value=1.7 Score=35.89 Aligned_cols=46 Identities=20% Similarity=0.304 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhhcCCCCee-----------------ecCCCCCccchhhhhhccCCCCcccCC
Q psy5744 110 LDVMRKRMEMEERDATSRSSF-----------------KCPRCLKTFTDLEPCLLVLWCACPCKR 157 (157)
Q Consensus 110 l~~m~~~L~~~~~~~~~~~~Y-----------------~Cp~C~~~Ys~lda~~L~d~~~F~C~~ 157 (157)
+.+--..|-++++..++...| .||.||..+...+.. .|...|.|..
T Consensus 184 Ls~~G~~l~~~Ie~~T~iPtYYyLyrv~g~~~~~e~~r~CP~Cg~~W~L~~pl--h~iFdFKCD~ 246 (258)
T PF10071_consen 184 LSKRGRDLCKRIEKLTGIPTYYYLYRVGGESLASEQARKCPSCGGDWRLKEPL--HDIFDFKCDP 246 (258)
T ss_pred HHHHHHHHHHHHHHHhCCCeEEEEEEccCcchHHhhCCCCCCCCCccccCCch--hhceeccCCc
Confidence 334445566677777777766 799999999887765 5667888863
No 244
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.10 E-value=5.4 Score=23.42 Aligned_cols=36 Identities=17% Similarity=0.364 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
.-++..+ . ..++..+||+.+|++...|++.+..+.+
T Consensus 9 ~~i~~~~-~-~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 9 REVLRLL-A-EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HHHHHHH-H-cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3445443 2 3479999999999999999999887643
No 245
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=78.94 E-value=2.2 Score=26.45 Aligned_cols=35 Identities=20% Similarity=0.145 Sum_probs=27.6
Q ss_pred HHHHHHHhCC--CcCHHHHHHHhC----CChHHHHHHHHHH
Q psy5744 35 LIIDMLVRNP--CMKEDDICELLK----FERKMLRARISTL 69 (157)
Q Consensus 35 vIlD~L~~~~--~i~dedLa~~l~----i~~k~vRkiL~~L 69 (157)
-|.|+|.++| .+|-.||+..+. -++..+++++..|
T Consensus 10 gI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 10 GIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp THHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 4889999865 899999999999 4455778888776
No 246
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.78 E-value=6.3 Score=32.05 Aligned_cols=56 Identities=23% Similarity=0.245 Sum_probs=46.4
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY 99 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y 99 (157)
-|++.|..+++.+--+||..+|++...|+=.+.+|++-|++... + .| ..+-|+||.
T Consensus 178 ~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~---~---~G---r~iiy~in~ 233 (240)
T COG3398 178 AIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPED---R---EG---RSIIYSINP 233 (240)
T ss_pred HHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCccc---c---cC---ceEEEEeCH
Confidence 37888888899999999999999999999999999999999853 1 22 245677774
No 247
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=78.51 E-value=3.8 Score=30.17 Aligned_cols=46 Identities=15% Similarity=0.290 Sum_probs=33.8
Q ss_pred hCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHH
Q psy5744 55 LKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKL 110 (157)
Q Consensus 55 l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl 110 (157)
++++-=+|=++|..|+.-|+|+.. =+|..+||+++-+.+ .-++.-+
T Consensus 36 l~vpNL~Vik~mqSL~Srg~Vke~---------f~WrhyYw~LT~eGi-eyLR~yL 81 (124)
T PTZ00034 36 LNVPNLHVMMLMRSLKSRGLVKEQ---------FAWQHYYYYLTDEGI-EYLRTYL 81 (124)
T ss_pred cCCccHHHHHHHHccccCCceEEE---------EeeEEEEEEEchHHH-HHHHHHh
Confidence 367777899999999999999843 258899999996543 3444333
No 248
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=78.49 E-value=14 Score=29.00 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=40.2
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
.+-++..+..++.+|-.||++..|++. ..++..|.+.|||...-+.
T Consensus 92 aLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~ 137 (188)
T PRK00135 92 ALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRK 137 (188)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcC
Confidence 667888888899999999999999997 8899999999999865333
No 249
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=78.48 E-value=3.4 Score=29.12 Aligned_cols=39 Identities=13% Similarity=0.276 Sum_probs=31.7
Q ss_pred hCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744 55 LKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF 102 (157)
Q Consensus 55 l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~ 102 (157)
++++-=+|-+++..|+.-|+|+.. =+|..+||+++-+.+
T Consensus 33 l~vpNL~V~k~mqSL~SrgyVke~---------faWrh~Yw~LT~eGI 71 (95)
T PF03501_consen 33 LNVPNLHVIKAMQSLKSRGYVKEQ---------FAWRHYYWYLTNEGI 71 (95)
T ss_dssp TSSBHHHHHHHHHHHHHCTSEEEE---------ECTTEEEEEE-HHHH
T ss_pred cCCCcHHHHHHHhcccchhhhcCe---------ecceEEEEEEcchhH
Confidence 488888999999999999999843 258899999997654
No 250
>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=78.00 E-value=4.7 Score=29.43 Aligned_cols=34 Identities=6% Similarity=0.042 Sum_probs=31.8
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
...++|+||..++-+...|+.+|..|.+-|||..
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~ 85 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEI 85 (121)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3678999999999999999999999999999985
No 251
>KOG3433|consensus
Probab=77.99 E-value=2.3 Score=33.49 Aligned_cols=61 Identities=8% Similarity=0.149 Sum_probs=42.5
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHHHHHH
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRME 118 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~~L~ 118 (157)
|-|+..-||-...|..+|+.|.+||+|... . =+.+.|||-+..+. +...+.++..+.+.|.
T Consensus 31 EKlG~kKgIv~~tvKdvLQsLvDD~lV~~e----K----IgtSnyywsfps~a-~~~~ks~~qeLe~~L~ 91 (203)
T KOG3433|consen 31 EKLGSKKGIVWQTVKDVLQSLVDDGLVIKE----K----IGTSNYYWSFPSEA-ICDRKSVLQELESQLA 91 (203)
T ss_pred HHhCCccceehhHHHHHHHHHhccchHHHH----H----hcccccccccchHH-HHHHHHHHHHHHHHHH
Confidence 445555688888999999999999999854 2 12557899998754 4445555555544444
No 252
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.92 E-value=0.89 Score=34.67 Aligned_cols=21 Identities=38% Similarity=0.558 Sum_probs=17.1
Q ss_pred CeeecCCCCCccchhhhhhcc
Q psy5744 128 SSFKCPRCLKTFTDLEPCLLV 148 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~lda~~L~ 148 (157)
.+|.||.||.+|+..|-..++
T Consensus 27 ~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 27 RRRECLACGKRFTTFERVELV 47 (154)
T ss_pred eeeeccccCCcceEeEeccCc
Confidence 359999999999998866554
No 253
>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=77.82 E-value=6.3 Score=23.49 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=21.8
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
....|-.|||+.+|++...|+++...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 56789999999999999999887763
No 254
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=77.56 E-value=4.8 Score=32.61 Aligned_cols=43 Identities=14% Similarity=0.160 Sum_probs=38.4
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDK 73 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~ 73 (157)
+.+-.|++.|-+++.++=.|||+.+|++.--+|+=|..|++.+
T Consensus 7 eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 7 ERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 3456799999999999999999999999999999999999543
No 255
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=77.52 E-value=2.7 Score=29.27 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744 109 KLDVMRKRMEMEERDATSRSSFKCPRCLKT 138 (157)
Q Consensus 109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~ 138 (157)
.+.++.++|+... ...|.||.|++.
T Consensus 21 slRK~v~kie~~q-----~a~y~CpfCgk~ 45 (90)
T PRK03976 21 KIRKRVADIEEKM-----RAKHVCPVCGRP 45 (90)
T ss_pred HHHHHHHHHHHHH-----hcCccCCCCCCC
Confidence 3556666666655 347999999754
No 256
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=77.41 E-value=1.3 Score=22.55 Aligned_cols=17 Identities=29% Similarity=0.594 Sum_probs=14.4
Q ss_pred eecCCCCCccchhhhhh
Q psy5744 130 FKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~ 146 (157)
|.|+-|+++|+...+..
T Consensus 1 ~~C~~C~~~f~s~~~~~ 17 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLR 17 (25)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCCCCCCcCCHHHHH
Confidence 78999999999887654
No 257
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=77.37 E-value=2.5 Score=29.45 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744 110 LDVMRKRMEMEERDATSRSSFKCPRCLKT 138 (157)
Q Consensus 110 l~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~ 138 (157)
+.++.++||... ..-|.||.|++.
T Consensus 22 lRK~v~kie~~q-----~a~y~CpfCgk~ 45 (90)
T PTZ00255 22 LRKQIKKIEISQ-----HAKYFCPFCGKH 45 (90)
T ss_pred HHHHHHHHHHHH-----hCCccCCCCCCC
Confidence 455666666654 447999999853
No 258
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=77.32 E-value=1.3 Score=24.49 Aligned_cols=17 Identities=29% Similarity=0.931 Sum_probs=10.5
Q ss_pred CCeeecCCCCCccchhh
Q psy5744 127 RSSFKCPRCLKTFTDLE 143 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~ld 143 (157)
..-|.||+|+..|=+++
T Consensus 11 ~~kY~Cp~C~~~~CSl~ 27 (30)
T PF04438_consen 11 PAKYRCPRCGARYCSLA 27 (30)
T ss_dssp EESEE-TTT--EESSHH
T ss_pred CCEEECCCcCCceeCcE
Confidence 45799999999986654
No 259
>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=77.13 E-value=41 Score=27.87 Aligned_cols=91 Identities=10% Similarity=0.089 Sum_probs=60.5
Q ss_pred hHHHHHHHHh-CCCcCHHHHHHHhC--CChHHHHHHHHHHhhCcceeeeE-----eeee---------------------
Q psy5744 33 DSLIIDMLVR-NPCMKEDDICELLK--FERKMLRARISTLKNDKIIQTRL-----RMET--------------------- 83 (157)
Q Consensus 33 ~ivIlD~L~~-~~~i~dedLa~~l~--i~~k~vRkiL~~L~~d~Lv~~~~-----~~e~--------------------- 83 (157)
|.+|..++.- .+.-.-++||+.++ |+..+|+..|..|.+-||++..- +.+.
T Consensus 124 ~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l 203 (271)
T TIGR02147 124 NSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEVIPLAVRQYQKQMI 203 (271)
T ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCccchHHHHHHHHHHH
Confidence 4444444432 34556778999999 99999999999999999997521 1100
Q ss_pred ----------cCCCceeEEEEEEecchhHHHHHHHHHHHHHHHHHHHHhhc
Q psy5744 84 ----------GLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDA 124 (157)
Q Consensus 84 ----------~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~ 124 (157)
.++.|..+...--|+- .-..-|+.+|...++++-...+..
T Consensus 204 ~lA~~al~~~p~~eR~~S~lT~~i~~-~~~~~i~~~i~~fRk~i~~i~~~~ 253 (271)
T TIGR02147 204 DLAKEALDALPPSERDVSTVTFGISE-EAYKEIVKKIQEFRKEVLAIATKD 253 (271)
T ss_pred HHHHHHHHhCCccccccceeeEecCH-HHHHHHHHHHHHHHHHHHHHHhcC
Confidence 0222444445566774 455667778888888887655543
No 260
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=77.05 E-value=15 Score=26.43 Aligned_cols=54 Identities=15% Similarity=0.194 Sum_probs=40.7
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF 102 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~ 102 (157)
.++=+|||+.+.-+.+.+|.+|.+|.+.|.+...-. . .-| ..+.--|.++.+.+
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg--~-GRG-~~S~L~~l~~~~~~ 72 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWITWQPG--R-GRG-NRSQLTFLKSPEEL 72 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCC--C-CCC-CCCeeEEeeCHHHH
Confidence 588999999999999999999999999999998622 1 122 23344566665443
No 261
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=76.79 E-value=7 Score=26.87 Aligned_cols=38 Identities=18% Similarity=0.173 Sum_probs=32.7
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCCh-----HHHHHHHHHHhhCc
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFER-----KMLRARISTLKNDK 73 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~-----k~vRkiL~~L~~d~ 73 (157)
|+|.|...+.++++|..+...-.. ++.+++|..|..-|
T Consensus 21 l~d~L~q~~VLt~~d~EeI~~~~t~~~r~~ka~~LLdiL~~rG 63 (86)
T cd08785 21 LTPYLRQCKVLDEQDEEEVLSSPRLPIRANRTGRLLDILATRG 63 (86)
T ss_pred HHHHHHhcCCCCHHHHHHHhCCCccccHHHHHHHHHHHHHhcC
Confidence 899999999999999999998766 88999999887544
No 262
>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=76.78 E-value=11 Score=21.38 Aligned_cols=40 Identities=18% Similarity=0.288 Sum_probs=29.3
Q ss_pred CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
.++...++.++. ...++-.++|+.+|++...|++.+....
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 333444454443 3568999999999999999999988654
No 263
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=76.34 E-value=0.98 Score=26.37 Aligned_cols=19 Identities=16% Similarity=0.364 Sum_probs=15.1
Q ss_pred hhcCCCCeeecCCCCCccc
Q psy5744 122 RDATSRSSFKCPRCLKTFT 140 (157)
Q Consensus 122 ~~~~~~~~Y~Cp~C~~~Ys 140 (157)
.++....+|.|..||.+|.
T Consensus 21 aDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 21 ADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp SSSSSEEEEEESSSTEEEE
T ss_pred CCCCCeEEEEeCCCCCeeC
Confidence 4556677999999999874
No 264
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=76.28 E-value=1.7 Score=24.55 Aligned_cols=16 Identities=19% Similarity=0.303 Sum_probs=13.3
Q ss_pred CCCCeeecCCCCCccc
Q psy5744 125 TSRSSFKCPRCLKTFT 140 (157)
Q Consensus 125 ~~~~~Y~Cp~C~~~Ys 140 (157)
++...++|+.||..|.
T Consensus 17 ~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSFP 32 (33)
T ss_pred ecCCeEEcccCCcEee
Confidence 4677899999999875
No 265
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=76.26 E-value=7.6 Score=24.53 Aligned_cols=35 Identities=20% Similarity=0.330 Sum_probs=31.6
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
++|.|+.++.+|---+|+.+|+.+.-..+++..|-
T Consensus 4 Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg 38 (54)
T PF11972_consen 4 LIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELG 38 (54)
T ss_pred HHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhh
Confidence 68999999999999999999999999999886554
No 266
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=75.35 E-value=2.5 Score=25.88 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=12.9
Q ss_pred eecCCCCCccchhhhh
Q psy5744 130 FKCPRCLKTFTDLEPC 145 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~ 145 (157)
|+|+.|+..|+...-.
T Consensus 2 y~C~~CgyvYd~~~Gd 17 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGD 17 (47)
T ss_dssp EEETTTSBEEETTTBB
T ss_pred cCCCCCCEEEcCCcCC
Confidence 8899999888877654
No 267
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=75.24 E-value=1.5 Score=33.85 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=13.1
Q ss_pred cCCCCeeecCCCCCcc
Q psy5744 124 ATSRSSFKCPRCLKTF 139 (157)
Q Consensus 124 ~~~~~~Y~Cp~C~~~Y 139 (157)
.....+|.||+||+.|
T Consensus 125 ~~~~~f~~C~~CgkiY 140 (165)
T COG1656 125 RNYEEFYRCPKCGKIY 140 (165)
T ss_pred hcccceeECCCCcccc
Confidence 3456799999999988
No 268
>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=75.18 E-value=4 Score=32.50 Aligned_cols=44 Identities=11% Similarity=0.266 Sum_probs=38.5
Q ss_pred hHHHHHHH--HhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 33 DSLIIDML--VRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 33 ~ivIlD~L--~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
+..|++.+ -..+.+|..+||..+|++....+..|..+.++|++-
T Consensus 176 ~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 176 QSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 56688887 557899999999999999999999999999999985
No 269
>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=75.08 E-value=11 Score=24.64 Aligned_cols=44 Identities=7% Similarity=0.107 Sum_probs=36.1
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-++++.+.++-+|-.-|-..++|--+.--+++..|+++|+|+..
T Consensus 10 ~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~ 53 (65)
T PF09397_consen 10 EAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPA 53 (65)
T ss_dssp HHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE--
T ss_pred HHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCC
Confidence 35566677889999999999999999999999999999999965
No 270
>smart00355 ZnF_C2H2 zinc finger.
Probab=74.93 E-value=1.5 Score=21.71 Aligned_cols=16 Identities=31% Similarity=0.876 Sum_probs=12.5
Q ss_pred eecCCCCCccchhhhh
Q psy5744 130 FKCPRCLKTFTDLEPC 145 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~ 145 (157)
|.|+.|+..|+.....
T Consensus 1 ~~C~~C~~~f~~~~~l 16 (26)
T smart00355 1 YRCPECGKVFKSKSAL 16 (26)
T ss_pred CCCCCCcchhCCHHHH
Confidence 6799999998765543
No 271
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=74.93 E-value=4 Score=33.41 Aligned_cols=31 Identities=16% Similarity=0.114 Sum_probs=27.7
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+.+..+|++++++=.+++.|+++|+++|-+
T Consensus 20 ~~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPR 50 (259)
T smart00437 20 QEASRKLGFSAKKTMQIAQKLYEKGLITYPR 50 (259)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHhCCeeEecC
Confidence 3567788999999999999999999999973
No 272
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=74.89 E-value=10 Score=31.94 Aligned_cols=95 Identities=12% Similarity=0.126 Sum_probs=63.5
Q ss_pred CCchHHHHHHHH---h-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744 30 SIEDSLIIDMLV---R-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI 105 (157)
Q Consensus 30 ~~e~ivIlD~L~---~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v 105 (157)
+++..-||.++- | +.+++.+.|.+..+|+.+++...|.+|...|||++++.. .. ++..||==.|+=.+-..
T Consensus 12 ~~~D~rlLraiE~~mR~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l~lv~r~~~~---y~--Gy~lT~~GyD~LAL~~l 86 (304)
T COG0478 12 SKEDFRLLRAIEGGMRSHEWVPLELIKKRARMDEEELLYRLKRLDKLKLVSRRTIS---YE--GYQLTFSGYDALALHAL 86 (304)
T ss_pred CHHHHHHHHHHHhcccccccccHHHHHHHcCCCHHHHHHHHHHHHhcCceeccCCc---ce--eEEEEecchhHHHHHHH
Confidence 455666666654 4 689999999999999999999999999999999974221 12 24444433443222222
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCeeec
Q psy5744 106 VKYKLDVMRKRMEMEERDATSRSSFKC 132 (157)
Q Consensus 106 ik~rl~~m~~~L~~~~~~~~~~~~Y~C 132 (157)
. .+.+.+.|-..+.-..+...|.|
T Consensus 87 ~---~r~~ve~iG~~IGvGKEsdVY~~ 110 (304)
T COG0478 87 V---KRGIVEAIGTKIGVGKESDVYVA 110 (304)
T ss_pred H---HcChHHhhccccccCccceEEEE
Confidence 2 23344555566666677778887
No 273
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=74.48 E-value=5.7 Score=31.18 Aligned_cols=45 Identities=11% Similarity=0.036 Sum_probs=39.3
Q ss_pred CchHHHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 31 IEDSLIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 31 ~e~ivIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
+.+--|++.|..++ .++=++||+.+|+++..||+=|..|...|.=
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~~ 62 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGKR 62 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCCC
Confidence 33567899999888 9999999999999999999999999887753
No 274
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=74.46 E-value=6.3 Score=32.87 Aligned_cols=36 Identities=19% Similarity=0.326 Sum_probs=33.9
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+..++-+|+|+.+|.++-.||-.++.|+.-|||...
T Consensus 23 ~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegv 58 (294)
T COG2524 23 KRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGV 58 (294)
T ss_pred CCCcchHHHHHHHccCcchHHHHHHHHHhcCccccc
Confidence 468999999999999999999999999999999875
No 275
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=74.43 E-value=1.6 Score=29.75 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=15.9
Q ss_pred HHHHHHHHHHH-HhhcCCCCeeecCCCCCccc
Q psy5744 110 LDVMRKRMEME-ERDATSRSSFKCPRCLKTFT 140 (157)
Q Consensus 110 l~~m~~~L~~~-~~~~~~~~~Y~Cp~C~~~Ys 140 (157)
--.|-+++.-. +.--+|-.+|.||.||.++.
T Consensus 45 ~~~~~~~~~vpilGvVENMs~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 45 AIDMFRKLNVPILGVVENMSYFVCPHCGERIY 76 (81)
T ss_dssp HHHHHHCTT-EEEEEEECT-EEE-TTT--EEE
T ss_pred HHHHHHhcCCCcEEEEECCCccCCCCCCCeec
Confidence 33444555554 33445667999999998865
No 276
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=74.40 E-value=4.6 Score=32.60 Aligned_cols=38 Identities=11% Similarity=0.274 Sum_probs=34.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhC-cceeeeEe
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKND-KIIQTRLR 80 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d-~Lv~~~~~ 80 (157)
.+.+|.+|||-+||+++..|++-+..+.+. |.+-..+.
T Consensus 103 gglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG 141 (220)
T PF07900_consen 103 GGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRG 141 (220)
T ss_pred CCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCC
Confidence 578999999999999999999999999998 98877643
No 277
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=73.86 E-value=1.3 Score=31.81 Aligned_cols=16 Identities=38% Similarity=0.810 Sum_probs=9.6
Q ss_pred CeeecCCCCCccchhh
Q psy5744 128 SSFKCPRCLKTFTDLE 143 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~ld 143 (157)
.--+||.||++|=.|-
T Consensus 8 tKR~Cp~CG~kFYDLn 23 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN 23 (108)
T ss_pred CcccCCCCcchhccCC
Confidence 3446777777765443
No 278
>PF14353 CpXC: CpXC protein
Probab=73.67 E-value=3.3 Score=29.90 Aligned_cols=33 Identities=27% Similarity=0.269 Sum_probs=20.6
Q ss_pred HHHHHhhcCCCCeeecCCCCCccchhhhhhccCC
Q psy5744 117 MEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLW 150 (157)
Q Consensus 117 L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~ 150 (157)
+++++- ..+--.|.||.||.++...--.-..|+
T Consensus 27 l~e~il-~g~l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 27 LKEKIL-DGSLFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred HHHHHH-cCCcCEEECCCCCCceecCCCEEEEcC
Confidence 444443 335668999999999975433333354
No 279
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=73.64 E-value=2.2 Score=24.14 Aligned_cols=17 Identities=24% Similarity=0.399 Sum_probs=12.1
Q ss_pred eeecCCCCCccchhhhh
Q psy5744 129 SFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~ 145 (157)
.|+|+.||..|...++.
T Consensus 2 ~~~C~~CG~i~~g~~~p 18 (34)
T cd00729 2 VWVCPVCGYIHEGEEAP 18 (34)
T ss_pred eEECCCCCCEeECCcCC
Confidence 58888888877765543
No 280
>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=73.32 E-value=6.6 Score=33.40 Aligned_cols=42 Identities=12% Similarity=0.243 Sum_probs=36.3
Q ss_pred HHHHH-hCCCcCHHHHHHH--hCCChHHHHHHHHHHhhCcceeee
Q psy5744 37 IDMLV-RNPCMKEDDICEL--LKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 37 lD~L~-~~~~i~dedLa~~--l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
++..+ .++.++=.+||+. +|+++-.+|+-+..|++.|++..-
T Consensus 12 V~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 12 VEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred HHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCC
Confidence 33334 4688999999999 999999999999999999999764
No 281
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=73.30 E-value=6.6 Score=23.62 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=19.6
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
-..++-.|||+.+|++.+.|+..+..
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45789999999999999999998874
No 282
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=73.30 E-value=6.7 Score=28.56 Aligned_cols=47 Identities=17% Similarity=0.129 Sum_probs=37.1
Q ss_pred ccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh
Q psy5744 9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL 55 (157)
Q Consensus 9 ~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l 55 (157)
.+...++.+.+-||+|+|.+--++..--+..|+|...++.++|.+-+
T Consensus 47 dL~~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTRg~~it~~~l~~fI 93 (115)
T PF08328_consen 47 DLDENWEVLAEPIQTVMRRYGIPNPYEKLKELTRGKKITKEDLREFI 93 (115)
T ss_dssp HHCT-GGGGHHHHHHHHHHTT-SSHHHHHHHHHTTS---HHHHHHHH
T ss_pred HHHHCHHHHHHHHHHHHHHcCCCCHHHHHHHHHcCCCCCHHHHHHHH
Confidence 35667788999999999999999999999999998899999988765
No 283
>PLN02839 nudix hydrolase
Probab=73.18 E-value=2.7 Score=36.44 Aligned_cols=33 Identities=21% Similarity=0.503 Sum_probs=25.1
Q ss_pred HHHHHHHHHHH-cCCC-chHHHHHHHHhCCCcCHH
Q psy5744 17 LKQLSRLVVRG-FYSI-EDSLIIDMLVRNPCMKED 49 (157)
Q Consensus 17 ~~~Lv~~v~R~-Fy~~-e~ivIlD~L~~~~~i~de 49 (157)
+.+++..+... |+-+ -++||+|+|+|||.++.|
T Consensus 321 v~EV~~~l~~~~~fKpn~aLViiDFLiRhG~Itpe 355 (372)
T PLN02839 321 VAQVANVIRKTSFFKANCSLVIIDFLFRHGFIRPE 355 (372)
T ss_pred HHHHHHHHHcCCCCCcccHHHHHHHHHHcCCCCCC
Confidence 56666666653 5544 579999999999999866
No 284
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=73.07 E-value=2.7 Score=23.85 Aligned_cols=15 Identities=20% Similarity=0.651 Sum_probs=10.6
Q ss_pred CCeeecCCCCCccch
Q psy5744 127 RSSFKCPRCLKTFTD 141 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~ 141 (157)
+..+.||+|++....
T Consensus 2 ~~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 2 SPYVECPNCGRPVAA 16 (33)
T ss_dssp S-EEE-TTTSSEEEG
T ss_pred CCeEECCCCcCCcch
Confidence 568999999997654
No 285
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=73.04 E-value=1.3 Score=33.75 Aligned_cols=18 Identities=33% Similarity=0.608 Sum_probs=16.3
Q ss_pred ecCCCCCccchhhhhhcc
Q psy5744 131 KCPRCLKTFTDLEPCLLV 148 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~ 148 (157)
.||.||.+||+.|-..|.
T Consensus 30 eC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 30 ECLECGERFTTFERAELR 47 (156)
T ss_pred cccccccccchhheeeec
Confidence 599999999999988876
No 286
>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=72.58 E-value=8.3 Score=23.74 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=28.3
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
..-|+..+. ...+..+||..+|++.+.|+..+..+..
T Consensus 8 E~~vl~~l~--~G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 8 ELEVLRLLA--QGMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp HHHHHHHHH--TTS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHH--hcCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 455666666 3578999999999999999988876653
No 287
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=72.23 E-value=8.6 Score=19.59 Aligned_cols=20 Identities=20% Similarity=0.144 Sum_probs=17.4
Q ss_pred cCHHHHHHHhCCChHHHHHH
Q psy5744 46 MKEDDICELLKFERKMLRAR 65 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRki 65 (157)
.+-.++|+.+|+..+.+.+.
T Consensus 22 ~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 22 ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 48999999999999888765
No 288
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=71.57 E-value=9.7 Score=28.98 Aligned_cols=46 Identities=7% Similarity=0.121 Sum_probs=36.7
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCC-------ChH-------HHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKF-------ERK-------MLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i-------~~k-------~vRkiL~~L~~d~Lv~~~ 78 (157)
+.-|+-.+..++.+-=..|+...|. +.. .+|++|+.|++.|||...
T Consensus 55 ~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~ 114 (150)
T PRK09333 55 AASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKT 114 (150)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeC
Confidence 4556667766778888899999998 333 499999999999999853
No 289
>PF14502 HTH_41: Helix-turn-helix domain
Probab=71.16 E-value=10 Score=23.37 Aligned_cols=33 Identities=12% Similarity=0.188 Sum_probs=30.2
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-+=+|+++++++..=-|..+|..|++++-|+-.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKLE 39 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEee
Confidence 356899999999999999999999999999866
No 290
>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=71.14 E-value=10 Score=27.53 Aligned_cols=49 Identities=18% Similarity=0.328 Sum_probs=42.2
Q ss_pred CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.++|+--|++. .+. ..|=-|||..++++...+|-++..|.+.|+|..+.
T Consensus 41 l~pE~~~Il~l-C~~-~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~ 89 (114)
T PF05331_consen 41 LGPEHRAILEL-CRR-PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRA 89 (114)
T ss_pred CCHHHHHHHHH-HCC-CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeC
Confidence 45677777765 434 89999999999999999999999999999999874
No 291
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=70.90 E-value=11 Score=25.16 Aligned_cols=37 Identities=11% Similarity=0.276 Sum_probs=33.9
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
....++=++||+.++++..++..++..+-.+|.++-+
T Consensus 57 ~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ 93 (105)
T PF01399_consen 57 PYSSISISEIAKALQLSEEEVESILIDLISNGLIKAK 93 (105)
T ss_dssp C-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEE
T ss_pred HhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEE
Confidence 4678999999999999999999999999999999965
No 292
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=70.59 E-value=8.2 Score=32.86 Aligned_cols=37 Identities=8% Similarity=0.179 Sum_probs=33.7
Q ss_pred hCCCcCHHHHHHH--hCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICEL--LKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~--l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.++=.+||+. +|+++-.+|.-+..|++.|++..-
T Consensus 22 ~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 22 TGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred cCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCC
Confidence 4688999999977 999999999999999999999854
No 293
>KOG2462|consensus
Probab=70.44 E-value=2.3 Score=35.36 Aligned_cols=29 Identities=24% Similarity=0.523 Sum_probs=22.6
Q ss_pred HHHHHHHHhhcCCCCeeecCCCCCccchh
Q psy5744 114 RKRMEMEERDATSRSSFKCPRCLKTFTDL 142 (157)
Q Consensus 114 ~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~l 142 (157)
|.+|..-++-=.+..-|.|++|+++|+..
T Consensus 228 RSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 228 RSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred hHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 55667777777788899999999999753
No 294
>PF13551 HTH_29: Winged helix-turn helix
Probab=70.01 E-value=9.5 Score=25.96 Aligned_cols=35 Identities=11% Similarity=0.130 Sum_probs=30.2
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.|..+-.++|..+|++...|.+.+....+.|+-.-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l 44 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGL 44 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHH
Confidence 44447999999999999999999999999996543
No 295
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=69.84 E-value=2.1 Score=24.67 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=10.8
Q ss_pred eecCCCCCccchh
Q psy5744 130 FKCPRCLKTFTDL 142 (157)
Q Consensus 130 Y~Cp~C~~~Ys~l 142 (157)
.+||.||+.|-..
T Consensus 2 r~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 2 RICPKCGRIYHIE 14 (36)
T ss_dssp EEETTTTEEEETT
T ss_pred cCcCCCCCccccc
Confidence 5899999999753
No 296
>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=69.37 E-value=16 Score=29.65 Aligned_cols=28 Identities=11% Similarity=0.181 Sum_probs=23.6
Q ss_pred CCcCHHHHHHHhCCChHHHH----HHHHHHhh
Q psy5744 44 PCMKEDDICELLKFERKMLR----ARISTLKN 71 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vR----kiL~~L~~ 71 (157)
..+|-.+||+.||++...|+ ++|.+|++
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999 66666664
No 297
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=69.21 E-value=18 Score=24.59 Aligned_cols=43 Identities=19% Similarity=0.206 Sum_probs=39.3
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|=|+|-.++-++-.+||..+++++.-|+-.|..|...|-|...
T Consensus 7 lRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 4577778999999999999999999999999999999999865
No 298
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=68.89 E-value=6.6 Score=24.31 Aligned_cols=29 Identities=14% Similarity=0.227 Sum_probs=20.3
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.++...-++-.+||+.+|++...+.+++.
T Consensus 4 ~~m~~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 4 ELMAERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HHHHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 44544456999999999999999998887
No 299
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=68.87 E-value=2.1 Score=30.87 Aligned_cols=22 Identities=9% Similarity=0.184 Sum_probs=14.0
Q ss_pred hhcCCCCeeecCCCCCccchhh
Q psy5744 122 RDATSRSSFKCPRCLKTFTDLE 143 (157)
Q Consensus 122 ~~~~~~~~Y~Cp~C~~~Ys~ld 143 (157)
.-+.-.....|+.||..|+..+
T Consensus 63 ~I~~~p~~~~C~~Cg~~~~~~~ 84 (115)
T TIGR00100 63 NIEDEPVECECEDCSEEVSPEI 84 (115)
T ss_pred EEEeeCcEEEcccCCCEEecCC
Confidence 3334455677888887776654
No 300
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=68.75 E-value=31 Score=22.81 Aligned_cols=33 Identities=18% Similarity=0.374 Sum_probs=25.0
Q ss_pred HHHHHHhCCCh---HHHHHHHHHHhhCcceeeeEee
Q psy5744 49 DDICELLKFER---KMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 49 edLa~~l~i~~---k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
.+||+.+|+++ ..++.+|..|...|||..+...
T Consensus 26 ~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~~~ 61 (85)
T PF09079_consen 26 EELCESLGVDPLSYRRFSDYLSELEMLGLIESERKG 61 (85)
T ss_dssp HHHHHHTTS----HHHHHHHHHHHHHTTSEEEEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEeec
Confidence 46788877654 5888899999999999987443
No 301
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=68.66 E-value=2.1 Score=27.94 Aligned_cols=9 Identities=44% Similarity=1.401 Sum_probs=7.3
Q ss_pred eecCCCCCc
Q psy5744 130 FKCPRCLKT 138 (157)
Q Consensus 130 Y~Cp~C~~~ 138 (157)
|+||+||.+
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 789999764
No 302
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=68.52 E-value=16 Score=23.90 Aligned_cols=41 Identities=20% Similarity=0.215 Sum_probs=31.7
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCC--hHHHHHHHHHHhhCc
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFE--RKMLRARISTLKNDK 73 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~--~k~vRkiL~~L~~d~ 73 (157)
.--|+|.|...+.++++|.....+.. .+.+|++|..|...|
T Consensus 18 ~~~ild~L~~~~vlt~~e~e~I~~~~t~~~k~~~LLd~l~~kg 60 (85)
T PF00619_consen 18 LDDILDHLLSRGVLTEEEYEEIRSEPTRQDKARKLLDILKRKG 60 (85)
T ss_dssp HHHHHHHHHHTTSSSHHHHHHHHTSSSHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHccCChHHHHHHHHHHHHHHC
Confidence 34589999999999999998888643 447888888776443
No 303
>PRK10220 hypothetical protein; Provisional
Probab=68.51 E-value=3.1 Score=29.99 Aligned_cols=19 Identities=32% Similarity=0.910 Sum_probs=15.3
Q ss_pred CCCeeecCCCCCccchhhh
Q psy5744 126 SRSSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~lda 144 (157)
+..-|+||.|+..|+..++
T Consensus 17 d~~~~vCpeC~hEW~~~~~ 35 (111)
T PRK10220 17 DNGMYICPECAHEWNDAEP 35 (111)
T ss_pred CCCeEECCcccCcCCcccc
Confidence 4567999999999988773
No 304
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=68.48 E-value=19 Score=25.39 Aligned_cols=52 Identities=10% Similarity=-0.045 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHH
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARI 66 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL 66 (157)
+...+.+....|..-+...-.=+..+.....++..++|+.+|+++..+.+..
T Consensus 48 ~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e 99 (127)
T TIGR03830 48 KRNSAALADFYRKVDGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYE 99 (127)
T ss_pred HHHHHHHHHHHHHccCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3333333333333333322223344444568999999999999998887764
No 305
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=68.45 E-value=14 Score=25.38 Aligned_cols=38 Identities=8% Similarity=0.029 Sum_probs=30.2
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCC--ChHHHHHHHHHHhhC
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKF--ERKMLRARISTLKND 72 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i--~~k~vRkiL~~L~~d 72 (157)
.|+|.|+..|.+|+++.....+. ...+.+++|..|..-
T Consensus 24 ~v~~~L~~~gvlt~~~~~~I~~~~t~~~k~~~Lld~L~~R 63 (90)
T cd08332 24 ELLIHLLQKDILTDSMAESIMAKPTSFSQNVALLNLLPKR 63 (90)
T ss_pred HHHHHHHHcCCCCHHHHHHHHcCCCcHHHHHHHHHHHHHh
Confidence 48999999999999998877654 566788888876643
No 306
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.22 E-value=2.7 Score=28.48 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=18.9
Q ss_pred CeeecCCCCCccchhhhhhccCCCCcccC
Q psy5744 128 SSFKCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
-.|.|..|+.+|+...++. |+..-.||
T Consensus 11 Y~Y~c~~cg~~~dvvq~~~--ddplt~ce 37 (82)
T COG2331 11 YSYECTECGNRFDVVQAMT--DDPLTTCE 37 (82)
T ss_pred eEEeecccchHHHHHHhcc--cCccccCh
Confidence 3688999999988877765 44444454
No 307
>KOG0402|consensus
Probab=68.18 E-value=3.7 Score=28.30 Aligned_cols=31 Identities=23% Similarity=0.494 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhh
Q psy5744 110 LDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 110 l~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~ 145 (157)
|.+|.++|+... ...|.|+.||+.=---+|.
T Consensus 22 Lrk~vKkiei~Q-----haky~CsfCGK~~vKR~Av 52 (92)
T KOG0402|consen 22 LRKMVKKIEIQQ-----HAKYTCSFCGKKTVKRKAV 52 (92)
T ss_pred HHHHHHHHHHHH-----hhhhhhhhcchhhhhhhce
Confidence 456666666544 4579999999864444443
No 308
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=67.69 E-value=6.5 Score=33.86 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=27.7
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+....+|++++++=+++++|++.|+|+|-+
T Consensus 94 ~~a~~~~g~s~~~tl~iaQ~LYe~glISYPR 124 (381)
T cd00186 94 QEASSKLGFSAKKTMQIAQKLYEAGLITYPR 124 (381)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHcCCeeeecC
Confidence 3567788999999999999999999999973
No 309
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.64 E-value=6.1 Score=27.42 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=9.5
Q ss_pred CCeeecCCCCCc
Q psy5744 127 RSSFKCPRCLKT 138 (157)
Q Consensus 127 ~~~Y~Cp~C~~~ 138 (157)
.+-|.||.|+++
T Consensus 33 ~~~~~Cp~C~~~ 44 (89)
T COG1997 33 RAKHVCPFCGRT 44 (89)
T ss_pred hcCCcCCCCCCc
Confidence 347899999887
No 310
>PF06806 DUF1233: Putative excisionase (DUF1233); InterPro: IPR009634 This family consists of several putative phage and prophage excisionase proteins of around 80 residues in length.; PDB: 2KVV_A.
Probab=67.48 E-value=4.5 Score=27.04 Aligned_cols=28 Identities=7% Similarity=0.119 Sum_probs=16.5
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHH
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARI 66 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL 66 (157)
.|..+.+|+++-|...+|+.++.++++=
T Consensus 3 qi~p~~WV~e~~L~a~tGls~~~I~~yR 30 (72)
T PF06806_consen 3 QIFPNKWVTEELLMAITGLSPGTIKRYR 30 (72)
T ss_dssp ------EE-HHHHHHHH---HHHHHHHH
T ss_pred ccChhhhhhHHHHHHHHCCCHHHHHHHH
Confidence 4556889999999999999999998773
No 311
>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=66.82 E-value=17 Score=23.70 Aligned_cols=45 Identities=13% Similarity=0.107 Sum_probs=37.7
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
=.|-.+|-.++.+|=.+|++.+|++.+++-.+++=|.+++=|...
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~ 55 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFE 55 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEE
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEE
Confidence 356777777899999999999999999999999988877777655
No 312
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.40 E-value=3.1 Score=25.69 Aligned_cols=8 Identities=50% Similarity=1.107 Sum_probs=6.4
Q ss_pred ecCCCCCc
Q psy5744 131 KCPRCLKT 138 (157)
Q Consensus 131 ~Cp~C~~~ 138 (157)
.||+||..
T Consensus 22 fCP~Cg~~ 29 (50)
T PRK00432 22 FCPRCGSG 29 (50)
T ss_pred cCcCCCcc
Confidence 59999875
No 313
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=66.34 E-value=14 Score=25.75 Aligned_cols=42 Identities=14% Similarity=0.161 Sum_probs=34.5
Q ss_pred hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
-+...|.++. .+.++=.|.|+.|||.++.+.+.|. +.|++-.
T Consensus 11 Ka~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr---~~g~l~~ 53 (111)
T PF03374_consen 11 KAEFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLR---EKGWLYR 53 (111)
T ss_pred hhHHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHH---hCCceEE
Confidence 3567888885 6899999999999999988887765 4777766
No 314
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=66.18 E-value=7.6 Score=27.87 Aligned_cols=37 Identities=22% Similarity=0.401 Sum_probs=20.8
Q ss_pred HHHHHHHHHHH--HHHhhcCCC----CeeecCCCCCccchhhh
Q psy5744 108 YKLDVMRKRME--MEERDATSR----SSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 108 ~rl~~m~~~L~--~~~~~~~~~----~~Y~Cp~C~~~Ys~lda 144 (157)
.||.++.++|+ ..-+...++ ....|..|++.|.++..
T Consensus 27 ~Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~fg~l~~ 69 (118)
T PF02318_consen 27 ERIRKLKQELQKEKMRREALGNSQKYGERHCARCGKPFGFLFN 69 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-BCSCTST
T ss_pred HHHHHHHHHHHHHHHHhhccccccccCCcchhhhCCcccccCC
Confidence 46677777772 222222233 56689999999876543
No 315
>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=66.08 E-value=5.2 Score=35.60 Aligned_cols=68 Identities=16% Similarity=0.235 Sum_probs=48.5
Q ss_pred ccchHHHHHHHHHHHHHcCCCc--------------------------------hHHHHHHHHhCCCcCHHHHHHHhCCC
Q psy5744 11 TEVPTSLKQLSRLVVRGFYSIE--------------------------------DSLIIDMLVRNPCMKEDDICELLKFE 58 (157)
Q Consensus 11 ~~ip~~~~~Lv~~v~R~Fy~~e--------------------------------~ivIlD~L~~~~~i~dedLa~~l~i~ 58 (157)
..+|+.+...+......+-... +..||.++-.+..+|-++|++.+|++
T Consensus 468 ~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~ 547 (588)
T PF00888_consen 468 IKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGIS 547 (588)
T ss_dssp ----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---
T ss_pred ccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcC
Confidence 5788888888877655442221 45667666667889999999999999
Q ss_pred hHHHHHHHHHHhhCcceeee
Q psy5744 59 RKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 59 ~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..++++.|..|...|++...
T Consensus 548 ~~~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 548 EEELKRALKSLVKSKILILL 567 (588)
T ss_dssp HHHHHHHHHCCCTTTTCSEE
T ss_pred HHHHHHHHHHHHhCCcceee
Confidence 99999999999999999865
No 316
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=65.90 E-value=2.9 Score=24.23 Aligned_cols=10 Identities=60% Similarity=1.251 Sum_probs=7.4
Q ss_pred ecCCCCCccc
Q psy5744 131 KCPRCLKTFT 140 (157)
Q Consensus 131 ~Cp~C~~~Ys 140 (157)
.||+|++.|-
T Consensus 4 ~CprC~kg~H 13 (36)
T PF14787_consen 4 LCPRCGKGFH 13 (36)
T ss_dssp C-TTTSSSCS
T ss_pred cCcccCCCcc
Confidence 4999999874
No 317
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=65.71 E-value=2.3 Score=32.26 Aligned_cols=18 Identities=33% Similarity=0.724 Sum_probs=15.4
Q ss_pred ecCCCCCccchhhhhhcc
Q psy5744 131 KCPRCLKTFTDLEPCLLV 148 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~ 148 (157)
.|+.||++||+.|-..+.
T Consensus 30 eC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 30 ECLECHERFTTFERAELL 47 (147)
T ss_pred cCCccCCccceeeecccc
Confidence 599999999999877654
No 318
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=65.46 E-value=15 Score=27.25 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=32.7
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.++-.+||..+|.....+.+++..|.++|++....
T Consensus 171 ~~~~~~ia~~~g~~~~~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 171 PLTHKDLAEYLGLSRETVSRILKELRKDGLISVRG 205 (214)
T ss_pred cCCHHHHHHHhCCchhhHHHHHHHHHhCCcEeeCC
Confidence 68999999999999999999999999999998753
No 319
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=65.23 E-value=33 Score=25.01 Aligned_cols=37 Identities=16% Similarity=0.272 Sum_probs=29.4
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
..-|+.+|..+ ++-++||+.++++.+.|+..+..|.+
T Consensus 142 E~~il~~l~~g--~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 142 ERQVAEKLAQG--MAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred HHHHHHHHHCC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34467666643 79999999999999999888887765
No 320
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=65.07 E-value=19 Score=24.20 Aligned_cols=38 Identities=18% Similarity=0.304 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELL--KFERKMLRARISTLKN 71 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~ 71 (157)
--|+|.|+..+.+++++..... +-++.+.|+++..|..
T Consensus 18 ~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar~Lld~l~~ 57 (82)
T cd08330 18 DPILDKLHGKKVITQEQYSEVRAEKTNQEKMRKLFSFVRS 57 (82)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHHHHHHHHHc
Confidence 4589999998999999887766 5556788888886654
No 321
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=64.90 E-value=32 Score=26.24 Aligned_cols=58 Identities=16% Similarity=0.287 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHHc-CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 12 EVPTSLKQLSRLVVRGF-YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 12 ~ip~~~~~Lv~~v~R~F-y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
+.|+.+..+-..+.+.. .+++..-++.... -..+|-+|||+.||++.+.|++-+...+
T Consensus 118 ~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~-~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 118 PSPEELLELEEALERLLALDPRQRRVVELRF-FEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CCHHHHHHHHHHHHHHHccCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555544444444322 4455555555533 3467999999999999999999988765
No 322
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=64.89 E-value=4.4 Score=25.09 Aligned_cols=13 Identities=15% Similarity=0.567 Sum_probs=10.3
Q ss_pred eecCCCCCccchh
Q psy5744 130 FKCPRCLKTFTDL 142 (157)
Q Consensus 130 Y~Cp~C~~~Ys~l 142 (157)
|+|+.||-.|+..
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7888888888765
No 323
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=64.84 E-value=5.9 Score=22.23 Aligned_cols=11 Identities=18% Similarity=0.603 Sum_probs=8.7
Q ss_pred eecCCCCCccc
Q psy5744 130 FKCPRCLKTFT 140 (157)
Q Consensus 130 Y~Cp~C~~~Ys 140 (157)
|+|..||+..+
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 78888988887
No 324
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=64.78 E-value=6.5 Score=34.06 Aligned_cols=30 Identities=17% Similarity=0.135 Sum_probs=23.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhC-cceeee
Q psy5744 49 DDICELLKFERKMLRARISTLKND-KIIQTR 78 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d-~Lv~~~ 78 (157)
.+.+..+|++++++-.+++.|+++ |+|+|-
T Consensus 125 ~~a~k~~g~s~~~tl~iaQ~LYE~~g~ISYP 155 (403)
T PF01131_consen 125 KEASKKLGFSAKETLDIAQKLYEKHGLISYP 155 (403)
T ss_dssp HHHHHHH---HHHHHHHHHHHHHTTTSBS-S
T ss_pred HHHHHHhhhhHHHHHHHHHHHHhhhheeeee
Confidence 456788999999999999999997 999997
No 325
>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=64.60 E-value=13 Score=28.25 Aligned_cols=36 Identities=17% Similarity=0.363 Sum_probs=27.3
Q ss_pred HHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhC
Q psy5744 36 IIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKND 72 (157)
Q Consensus 36 IlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d 72 (157)
++++++. ...++-++||+.++ +..+++++|..|.++
T Consensus 2 ~iEAlLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~ 39 (159)
T PF04079_consen 2 IIEALLFASGEPVSIEELAEILG-SEDEVEEALEELQEE 39 (159)
T ss_dssp HHHHHHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHH
T ss_pred hhHhhHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHH
Confidence 4566663 45699999999999 999999999998764
No 326
>smart00753 PAM PCI/PINT associated module.
Probab=64.49 E-value=30 Score=22.75 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=34.2
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.++=++||+.++++..++-..+..+-.+|.+.-+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEE
Confidence 3788999999999999999999999999999999765
No 327
>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=64.49 E-value=30 Score=22.75 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=34.2
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++.++=++||+.++++..++-..+..+-.+|.+.-+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEE
Confidence 3788999999999999999999999999999999765
No 328
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=64.19 E-value=2.9 Score=24.00 Aligned_cols=16 Identities=13% Similarity=0.521 Sum_probs=10.3
Q ss_pred CeeecCCCCCccchhh
Q psy5744 128 SSFKCPRCLKTFTDLE 143 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~ld 143 (157)
++--|+.||-+|+..+
T Consensus 20 ~~isC~~CGPr~~i~~ 35 (35)
T PF07503_consen 20 QFISCTNCGPRYSIID 35 (35)
T ss_dssp TT--BTTCC-SCCCES
T ss_pred cCccCCCCCCCEEEeC
Confidence 3457999999999754
No 329
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=64.09 E-value=21 Score=25.13 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHH
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICEL 54 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~ 54 (157)
+.....++.++..|++...--++-+|+.+..++++||+++
T Consensus 70 e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~~ls~~el~~L 109 (115)
T PF03965_consen 70 EYLAQELRQFLDRLFDGSIPQLVAALVESEELSPEELEEL 109 (115)
T ss_dssp HHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-S-HHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCCCHHHHHHH
Confidence 4577889999999999888888888898889999999865
No 330
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=63.96 E-value=20 Score=24.99 Aligned_cols=64 Identities=16% Similarity=0.293 Sum_probs=46.8
Q ss_pred HHHHHHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHH
Q psy5744 35 LIIDMLVRNPCMKEDDICELL--KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDV 112 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~ 112 (157)
+|+|.|+.++.+|+++....- +-...+++++|..|..- ||. -|+.|+++++. .-.
T Consensus 25 ~v~~~L~~~gIlT~~~~e~I~a~~T~~~k~~~LLdiLp~R-----------G~~-----------AF~~F~~aL~e-~~~ 81 (94)
T cd08327 25 LVIQYLYQEGILTESHVEEIESQTTSRRKTMKLLDILPSR-----------GPK-----------AFHAFLDSLEE-FPW 81 (94)
T ss_pred HHHHHHHhCCCCCHHHHHHHHccCChHHHHHHHHHHHHhh-----------Chh-----------HHHHHHHHHHH-HHH
Confidence 588999999999999888766 45566888888876532 233 14679999976 777
Q ss_pred HHHHHHHHH
Q psy5744 113 MRKRMEMEE 121 (157)
Q Consensus 113 m~~~L~~~~ 121 (157)
+.++|.+..
T Consensus 82 l~~~l~~~~ 90 (94)
T cd08327 82 VRDKLLKLR 90 (94)
T ss_pred HHHHHHHHH
Confidence 777776643
No 331
>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=63.95 E-value=19 Score=26.21 Aligned_cols=40 Identities=15% Similarity=0.225 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHH
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICEL 54 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~ 54 (157)
+-....++.++..||+....-++-+|+.+..++++||.++
T Consensus 71 e~~~~~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L 110 (130)
T TIGR02698 71 EAVENAAQELFSRICSRKVGAVIADLIEESPLSQTDIEKL 110 (130)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHH
Confidence 3457788999988999888888888888888999998764
No 332
>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=63.49 E-value=9.4 Score=30.05 Aligned_cols=43 Identities=12% Similarity=0.234 Sum_probs=33.9
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.++++-.+.++.=+|||..+|+...++-.-+..|..+|.++=.
T Consensus 104 Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv 146 (188)
T PF09756_consen 104 FINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGV 146 (188)
T ss_dssp HHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE
T ss_pred HHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceee
Confidence 4566667899999999999999999999999999999999865
No 333
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=63.39 E-value=1.7 Score=23.63 Aligned_cols=10 Identities=50% Similarity=1.252 Sum_probs=3.6
Q ss_pred ecCCCCCccc
Q psy5744 131 KCPRCLKTFT 140 (157)
Q Consensus 131 ~Cp~C~~~Ys 140 (157)
.||+|+....
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 4666665533
No 334
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=63.26 E-value=11 Score=22.45 Aligned_cols=26 Identities=12% Similarity=0.206 Sum_probs=20.6
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
...+|-.|+|+.+|+++..|.+++.-
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 45789999999999999999988763
No 335
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=62.87 E-value=19 Score=24.40 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=33.7
Q ss_pred HHHHHHHHh-CCCcCHHH--HHHHhCCChHHHHHHHHHHhhCcc
Q psy5744 34 SLIIDMLVR-NPCMKEDD--ICELLKFERKMLRARISTLKNDKI 74 (157)
Q Consensus 34 ivIlD~L~~-~~~i~ded--La~~l~i~~k~vRkiL~~L~~d~L 74 (157)
..+++.... .+.+.+++ ||...|.+.++-++++..|-+.+.
T Consensus 26 ~~Ll~~~~~~~~plp~d~~~Lar~~~~s~~~~~~a~~~ll~~f~ 69 (88)
T PF07120_consen 26 MRLLDLYYDTEGPLPDDDKRLARICGCSTKEWRKALDFLLREFF 69 (88)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHhCC
Confidence 445666665 68899766 999999999999999998888776
No 336
>PRK14136 recX recombination regulator RecX; Provisional
Probab=62.71 E-value=20 Score=30.36 Aligned_cols=60 Identities=18% Similarity=0.186 Sum_probs=42.6
Q ss_pred HHHHHHHHHHcCCCchH-HHHHHHHhCCCcCHHHHHHHh---CCChHHHHHHHHHHhhCcceee
Q psy5744 18 KQLSRLVVRGFYSIEDS-LIIDMLVRNPCMKEDDICELL---KFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 18 ~~Lv~~v~R~Fy~~e~i-vIlD~L~~~~~i~dedLa~~l---~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.+|.+.+.+.-|+++.| -||+.|..++++.|+.-|+.+ .+..+--++|-+.|.+.||-..
T Consensus 180 ~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rIrqELrQKGId~e 243 (309)
T PRK14136 180 AELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARIVSELKRHAVGDA 243 (309)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHHHHHHHHcCCCHH
Confidence 45555666655555554 489999999999999988866 2333456778888888888543
No 337
>PRK10736 hypothetical protein; Provisional
Probab=62.70 E-value=16 Score=31.81 Aligned_cols=43 Identities=9% Similarity=-0.012 Sum_probs=36.6
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|++.|- ...++-|+|+..+|++..++-.+|..|+-.|+|...
T Consensus 312 ~v~~~l~-~~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 312 ELLANVG-DEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred HHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEc
Confidence 4555543 456889999999999999999999999999999853
No 338
>PRK07758 hypothetical protein; Provisional
Probab=62.65 E-value=12 Score=26.35 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=28.1
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcc
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKI 74 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~L 74 (157)
.++++||...-|+-+|-++.|-.+|.+.||
T Consensus 63 ~~te~ELl~iknlGkKSL~EIkekL~E~GL 92 (95)
T PRK07758 63 KYSEKEILKLHGMGPASLPKLRKALEESGL 92 (95)
T ss_pred cCCHHHHHHccCCCHHHHHHHHHHHHHcCC
Confidence 678999999999999999999999999886
No 339
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=62.60 E-value=20 Score=21.25 Aligned_cols=31 Identities=16% Similarity=0.219 Sum_probs=24.5
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
|+..+. +. .+-.++|..+|++.+.|++++..
T Consensus 20 i~~~~~-~~-~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 20 ILKLLR-ES-RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHh-hc-CCHHHHHHHHCCCHHHHHHHHHh
Confidence 444444 33 68999999999999999999864
No 340
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=62.57 E-value=9.5 Score=23.29 Aligned_cols=23 Identities=9% Similarity=0.212 Sum_probs=17.5
Q ss_pred cCHHHHHHHhCCChHHHHHHHHH
Q psy5744 46 MKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
++=.|||+.+|+++++|=+.|.+
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~ 26 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFK 26 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-H
T ss_pred eEHHHHHHHHCcCHHHHHHHHHH
Confidence 44568999999999998777743
No 341
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=62.51 E-value=22 Score=22.99 Aligned_cols=42 Identities=12% Similarity=0.203 Sum_probs=31.2
Q ss_pred chHHHHHHHHhCCCcCHHHHHHHhCC--ChHHHHHHHHHHhhCc
Q psy5744 32 EDSLIIDMLVRNPCMKEDDICELLKF--ERKMLRARISTLKNDK 73 (157)
Q Consensus 32 e~ivIlD~L~~~~~i~dedLa~~l~i--~~k~vRkiL~~L~~d~ 73 (157)
..--|+|.|...+.++.+|.....+- .....|++|..|...|
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~~~~~~k~~~Lld~l~~kg 57 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSESTRQDKARKLLDILPRKG 57 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcCCChHHHHHHHHHHHHhcC
Confidence 34458999998999999988877644 4567788887776543
No 342
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=62.50 E-value=15 Score=28.79 Aligned_cols=38 Identities=18% Similarity=0.348 Sum_probs=31.3
Q ss_pred HHHHHHHh--CCC-cCHHHHHHHhCCChHHHHHHHHHHhhC
Q psy5744 35 LIIDMLVR--NPC-MKEDDICELLKFERKMLRARISTLKND 72 (157)
Q Consensus 35 vIlD~L~~--~~~-i~dedLa~~l~i~~k~vRkiL~~L~~d 72 (157)
-++++++. ... ++-++||+.+|++..+|+.+|..|.++
T Consensus 7 ~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~ 47 (188)
T PRK00135 7 SIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEK 47 (188)
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45677774 333 999999999999999999999999654
No 343
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=62.50 E-value=2.3 Score=29.61 Aligned_cols=20 Identities=20% Similarity=0.582 Sum_probs=14.0
Q ss_pred hhcCCCCeeecCCCCCccch
Q psy5744 122 RDATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 122 ~~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
.++....+|+|..|+.+|..
T Consensus 83 adE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 83 ADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred CCCCcEEEEEeCCCCCeeEe
Confidence 45666678888888877654
No 344
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=62.11 E-value=4.1 Score=26.39 Aligned_cols=21 Identities=14% Similarity=0.401 Sum_probs=16.4
Q ss_pred hhcCCCCeeecCCCCCccchh
Q psy5744 122 RDATSRSSFKCPRCLKTFTDL 142 (157)
Q Consensus 122 ~~~~~~~~Y~Cp~C~~~Ys~l 142 (157)
+.+......+||.||+.|-..
T Consensus 46 ~~~i~eg~L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 46 EVEIVEGELICPECGREYPIR 66 (68)
T ss_dssp TEETTTTEEEETTTTEEEEEE
T ss_pred cccccCCEEEcCCCCCEEeCC
Confidence 356677899999999999643
No 345
>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=62.10 E-value=43 Score=23.85 Aligned_cols=39 Identities=18% Similarity=0.008 Sum_probs=28.2
Q ss_pred CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
+..-.|+-+.. -..++-+|||+.+|++...|+..+....
T Consensus 116 ~~~r~il~l~~-~~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 116 EQCRKIFILSR-FEGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44444444323 3578999999999999999988887543
No 346
>PHA02998 RNA polymerase subunit; Provisional
Probab=62.09 E-value=2.6 Score=33.02 Aligned_cols=24 Identities=21% Similarity=0.434 Sum_probs=18.2
Q ss_pred HHHHhhcCCCCeeecCCCCCccch
Q psy5744 118 EMEERDATSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 118 ~~~~~~~~~~~~Y~Cp~C~~~Ys~ 141 (157)
+.|-.+|....||.|..||.+|..
T Consensus 160 QTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 160 QTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred eeccCCCCceEEEEcCCCCCccCC
Confidence 345557777889999999988864
No 347
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=62.01 E-value=4 Score=21.82 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=8.2
Q ss_pred eecCCCCCccc
Q psy5744 130 FKCPRCLKTFT 140 (157)
Q Consensus 130 Y~Cp~C~~~Ys 140 (157)
=.||.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35888888774
No 348
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=61.81 E-value=15 Score=21.73 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=22.3
Q ss_pred HhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 41 VRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 41 ~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.....++-+++|..+|+++..|.++..
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 335678999999999999988888763
No 349
>PF12728 HTH_17: Helix-turn-helix domain
Probab=61.68 E-value=12 Score=22.22 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=31.2
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK 107 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik 107 (157)
++|=+|+|+.||++.+.+++.+. .|-+... + . |+ -|+++...+...++
T Consensus 1 ~lt~~e~a~~l~is~~tv~~~~~----~g~i~~~-~--~---g~-----~~~~~~~~l~~~~~ 48 (51)
T PF12728_consen 1 YLTVKEAAELLGISRSTVYRWIR----QGKIPPF-K--I---GR-----KWRIPKSDLDRWLE 48 (51)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH----cCCCCeE-E--e---CC-----EEEEeHHHHHHHHH
Confidence 36778999999999999887774 4544332 1 1 11 26677666665554
No 350
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=61.64 E-value=9.6 Score=26.49 Aligned_cols=25 Identities=12% Similarity=0.074 Sum_probs=22.8
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
...+|.+++|..||++..+|.++|.
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3578999999999999999999997
No 351
>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=61.63 E-value=22 Score=23.09 Aligned_cols=44 Identities=9% Similarity=0.151 Sum_probs=38.8
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-++++.+..+..|=.-|-..+++--|.-.+++..|+++|+|+..
T Consensus 9 ~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~ 52 (63)
T smart00843 9 EAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPA 52 (63)
T ss_pred HHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCC
Confidence 35666677888899999999999999999999999999999965
No 352
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=61.23 E-value=22 Score=25.92 Aligned_cols=38 Identities=13% Similarity=0.154 Sum_probs=24.0
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeee
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET 83 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~ 83 (157)
.-..+|..||..+|++..+||+.-.. .|+.-.....++
T Consensus 70 ~~GFsD~~IA~l~~~~e~~vr~~R~~---~~i~p~yk~VDT 107 (123)
T PF02787_consen 70 RLGFSDRQIARLWGVSEEEVRELRKE---HGIVPVYKMVDT 107 (123)
T ss_dssp HTT--HHHHHHHHTS-HHHHHHHHHH---HT---EEEE--S
T ss_pred HcCCCHHHHHhccCCCHHHHHHHHHH---cCCceeeeeecC
Confidence 45799999999999999999988765 467766655543
No 353
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=61.07 E-value=4.4 Score=29.17 Aligned_cols=18 Identities=28% Similarity=0.754 Sum_probs=14.1
Q ss_pred CCCeeecCCCCCccchhh
Q psy5744 126 SRSSFKCPRCLKTFTDLE 143 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~ld 143 (157)
+...|+||.|+..|+..+
T Consensus 16 dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 16 DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCeeECccccccccccc
Confidence 455789999999997665
No 354
>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=60.61 E-value=17 Score=23.97 Aligned_cols=44 Identities=11% Similarity=0.172 Sum_probs=32.5
Q ss_pred HHHHHHHh----CCCcCHHHHHH-HhCCChHHHHHHHHHHhhCcceeee
Q psy5744 35 LIIDMLVR----NPCMKEDDICE-LLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 35 vIlD~L~~----~~~i~dedLa~-~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.|++.|-. ..-..=.|+++ ....++++|.++++.|-++|-+.|-
T Consensus 5 ~Ile~L~~k~~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yW 53 (67)
T PF08679_consen 5 KILEFLEAKKKKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLEYW 53 (67)
T ss_dssp HHHHHHSSCCCHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhccCCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEE
Confidence 46677652 23455677887 7799999999999999999999886
No 355
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=60.47 E-value=3.3 Score=28.46 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=14.3
Q ss_pred ecCCCCCccchhhhhh
Q psy5744 131 KCPRCLKTFTDLEPCL 146 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~ 146 (157)
.|+.||..|+..||.+
T Consensus 10 ~C~~CG~d~~~~~adD 25 (86)
T PF06170_consen 10 RCPHCGLDYSHARADD 25 (86)
T ss_pred cccccCCccccCCcCc
Confidence 5999999999999864
No 356
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=60.39 E-value=8 Score=30.99 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=20.0
Q ss_pred ecCCCCCccchhhhhhccCCCCcccC
Q psy5744 131 KCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
-||.||+.+-+.++ |+|-..|.|.
T Consensus 220 ~CPsC~k~Wqlk~~--i~d~fhfkcd 243 (256)
T COG5595 220 CCPSCGKDWQLKNP--IFDTFHFKCD 243 (256)
T ss_pred CCCcccccceeccc--hhhheeeecc
Confidence 49999999998876 5577899986
No 357
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=60.25 E-value=21 Score=20.94 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
...+..|. ..-++--+||..||.++.-|.+.|.
T Consensus 10 R~~I~~l~-~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 10 RNQIEALL-EQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHH-CS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHH-HcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 34455555 4458999999999999999988764
No 358
>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=60.23 E-value=28 Score=28.29 Aligned_cols=60 Identities=7% Similarity=0.075 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHcCCCchHH--HHHHHHh---CCCcCHHHHHHHhCCChHHHHHHHH-HHhhCccee
Q psy5744 17 LKQLSRLVVRGFYSIEDSL--IIDMLVR---NPCMKEDDICELLKFERKMLRARIS-TLKNDKIIQ 76 (157)
Q Consensus 17 ~~~Lv~~v~R~Fy~~e~iv--IlD~L~~---~~~i~dedLa~~l~i~~k~vRkiL~-~L~~d~Lv~ 76 (157)
++..+..+...+.+..+.- .+.+++. .+..+=+++|..||.++..++.++. .|-+.+|+.
T Consensus 222 v~~~l~~l~~~~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 222 ALKALEMLMIDELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc
Confidence 3333333333334444333 6665553 5568899999999999999999999 699999994
No 359
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=59.84 E-value=25 Score=29.48 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=40.4
Q ss_pred CCchHHHHHHHHh-CCCc------CHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 30 SIEDSLIIDMLVR-NPCM------KEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 30 ~~e~ivIlD~L~~-~~~i------~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
++.+=+|++.|.. +|.| +.|||-+..||+.....++|+.|...|+|..
T Consensus 224 ~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q 278 (287)
T COG2996 224 DEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ 278 (287)
T ss_pred hhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE
Confidence 3456678888885 4554 4899999999999999999999999999985
No 360
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=59.80 E-value=38 Score=26.35 Aligned_cols=55 Identities=16% Similarity=0.216 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHcCCCchHHHHHHHH----hCCCc--CHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 17 LKQLSRLVVRGFYSIEDSLIIDMLV----RNPCM--KEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~----~~~~i--~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
-.+|...+.-.+.++....|...|+ .+|++ +.++||..+|++.++|.++|..|..
T Consensus 18 ~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ~ 78 (194)
T PF04963_consen 18 YEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIAEELGVSEEEVEKALELLQS 78 (194)
T ss_dssp -HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 3556666666677766555555555 46775 4789999999999999999887754
No 361
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=59.74 E-value=36 Score=23.85 Aligned_cols=34 Identities=24% Similarity=0.317 Sum_probs=26.8
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
|+..|+ ++.+|-.+||+.+|++...|-+.=..|+
T Consensus 47 i~~~Ll-~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 47 IVNELL-NGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHHHHH-hCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 444444 5789999999999999998887766665
No 362
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=59.32 E-value=26 Score=23.82 Aligned_cols=39 Identities=21% Similarity=0.211 Sum_probs=30.1
Q ss_pred HHHHHHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhhCc
Q psy5744 35 LIIDMLVRNPCMKEDDICELL--KFERKMLRARISTLKNDK 73 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~ 73 (157)
.|+|.|+.++.+++++..+.. +-...+.+++|..|..-|
T Consensus 20 ~v~~~L~~~~Vlt~~~~e~I~~~~tr~~q~~~LLd~L~~RG 60 (84)
T cd08326 20 YLWDHLLSRGVFTPDMIEEIQAAGSRRDQARQLLIDLETRG 60 (84)
T ss_pred HHHHHHHhcCCCCHHHHHHHHcCCCHHHHHHHHHHHHHhcC
Confidence 499999999999998777766 445568888888776543
No 363
>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=59.28 E-value=19 Score=26.92 Aligned_cols=39 Identities=18% Similarity=0.293 Sum_probs=28.6
Q ss_pred cCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 28 FYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 28 Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
|..+...-|+.+ +...+|-++||+.+|++..-|+++...
T Consensus 6 ~Lte~qr~VL~L--r~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 6 FLTERQIKVLEL--REKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 344445556655 356789999999999999988865553
No 364
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=59.12 E-value=15 Score=20.92 Aligned_cols=30 Identities=10% Similarity=0.183 Sum_probs=22.9
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+++-+|+|+.+|++...+++.+. +|.+...
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~~~----~g~i~~~ 30 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRLIH----EGELPAY 30 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH----cCCCCeE
Confidence 36778999999999988887763 5665543
No 365
>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=59.08 E-value=41 Score=20.92 Aligned_cols=41 Identities=10% Similarity=0.255 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 16 SLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
+.+-|..-+-.+||+. -..++=+|||+.||++..-+-..|.
T Consensus 5 Q~e~L~~A~~~GYfd~-----------PR~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 5 QREILKAAYELGYFDV-----------PRRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred HHHHHHHHHHcCCCCC-----------CCcCCHHHHHHHhCCCHHHHHHHHH
Confidence 3444445555566654 1357889999999999986554444
No 366
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=58.51 E-value=7.1 Score=24.95 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=15.6
Q ss_pred CCCCeeecCCCCCccchhhhh
Q psy5744 125 TSRSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 125 ~~~~~Y~Cp~C~~~Ys~lda~ 145 (157)
.....|.||.||..+.-+...
T Consensus 42 ~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 42 RSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred cccceEEcCCCCCEECcHHHH
Confidence 456689999999987766543
No 367
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=58.50 E-value=31 Score=25.13 Aligned_cols=25 Identities=16% Similarity=0.302 Sum_probs=22.5
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
..++-++||+.+|++.+.|++.+.+
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999988775
No 368
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=58.42 E-value=30 Score=26.33 Aligned_cols=46 Identities=9% Similarity=0.158 Sum_probs=39.7
Q ss_pred hHHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-..|++.|.. .+.+|-++|...| +++...|=+.|..|.+.|||...
T Consensus 28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 28 RLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 4679999886 4689999999888 57888999999999999999755
No 369
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=57.94 E-value=19 Score=23.03 Aligned_cols=29 Identities=10% Similarity=0.141 Sum_probs=23.8
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.++....++-+++|+.+|++...|.+++.
T Consensus 12 ~~~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 12 EFLEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 44555678999999999999988888765
No 370
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=57.90 E-value=85 Score=24.16 Aligned_cols=55 Identities=9% Similarity=0.031 Sum_probs=35.0
Q ss_pred chHHHHHHHHHHHHHcCCCchHHHHHHHH----hCCCcCHHH---HHHHhCCChHHHHHHHHH
Q psy5744 13 VPTSLKQLSRLVVRGFYSIEDSLIIDMLV----RNPCMKEDD---ICELLKFERKMLRARIST 68 (157)
Q Consensus 13 ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~----~~~~i~ded---La~~l~i~~k~vRkiL~~ 68 (157)
.++...+-+..++..+-. ..-.+|.+|. ..|+++++. +|+.||++..+|..++..
T Consensus 16 ~~~~~~~~i~~ii~~~~~-~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~gVatF 77 (169)
T PRK07571 16 SGDKRFKVLEATMKRNQY-RQDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATF 77 (169)
T ss_pred CcHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHHHHH
Confidence 334333344555555533 3333444443 369999876 799999999999887764
No 371
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=57.81 E-value=38 Score=25.71 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=24.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
-..++-++||+.+|++++.|+..+....
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3579999999999999999998888654
No 372
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.61 E-value=4.1 Score=30.02 Aligned_cols=18 Identities=33% Similarity=0.582 Sum_probs=15.0
Q ss_pred CCeeecCCCCCccchhhh
Q psy5744 127 RSSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~lda 144 (157)
.+-|+|+.|+++|+.+.-
T Consensus 51 ~qRyrC~~C~~tf~~~~~ 68 (129)
T COG3677 51 HQRYKCKSCGSTFTVETG 68 (129)
T ss_pred ccccccCCcCcceeeecc
Confidence 678999999999987643
No 373
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=57.58 E-value=4.4 Score=29.01 Aligned_cols=25 Identities=16% Similarity=0.133 Sum_probs=14.9
Q ss_pred HhhcCCCCeeecCCCCCccchhhhh
Q psy5744 121 ERDATSRSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 121 ~~~~~~~~~Y~Cp~C~~~Ys~lda~ 145 (157)
+.-+.-.....|+.||..|+..+-.
T Consensus 62 L~Ie~~p~~~~C~~Cg~~~~~~~~~ 86 (113)
T PF01155_consen 62 LEIEEVPARARCRDCGHEFEPDEFD 86 (113)
T ss_dssp EEEEEE--EEEETTTS-EEECHHCC
T ss_pred EEEEecCCcEECCCCCCEEecCCCC
Confidence 3334445577899999998876643
No 374
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=57.47 E-value=14 Score=26.34 Aligned_cols=47 Identities=9% Similarity=0.083 Sum_probs=39.2
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCC--hHHHHHHHHHHhhCcceeeeEee
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFE--RKMLRARISTLKNDKIIQTRLRM 81 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~--~k~vRkiL~~L~~d~Lv~~~~~~ 81 (157)
.+++.+....++|=-|||+..|++ .++|-++|..|.++-.+--++..
T Consensus 13 ~vv~~IP~GkV~TYGdIA~laG~p~~ARqVG~il~~l~~~s~lPWhRVv 61 (103)
T COG3695 13 DVVAAIPEGKVSTYGDIAKLAGLPRAARQVGRILKHLPEGSDLPWHRVV 61 (103)
T ss_pred HHHHhCCCCceeeHHHHHHHhCCChhHHHHHHHHhhCCCCCCCChhhee
Confidence 355566667789999999999999 99999999999998887776544
No 375
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=57.41 E-value=22 Score=31.46 Aligned_cols=41 Identities=10% Similarity=0.115 Sum_probs=35.5
Q ss_pred HHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 37 IDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 37 lD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+-.+++.+..+--|||+.+|+++-.|-+.|..| .|+|..+.
T Consensus 5 ~~~~L~~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~ 45 (442)
T PRK09775 5 LTTLLLQGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRFG 45 (442)
T ss_pred HHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEec
Confidence 445566899999999999999999999999999 78887653
No 376
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=57.24 E-value=25 Score=23.20 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=22.1
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.+.+...+|-.|+|+.+|+++..|-+++.
T Consensus 25 ~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 25 ELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 34557789999999999999999999885
No 377
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.15 E-value=5.2 Score=23.54 Aligned_cols=17 Identities=24% Similarity=0.462 Sum_probs=13.6
Q ss_pred eecCCCCCccchhhhhh
Q psy5744 130 FKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 130 Y~Cp~C~~~Ys~lda~~ 146 (157)
=.||.||-.|+...+.+
T Consensus 14 ~~C~~CgM~Y~~~~~eD 30 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPED 30 (41)
T ss_pred cCCCCCCCEECCCCHHH
Confidence 48999999999876543
No 378
>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=57.12 E-value=4.2 Score=30.86 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=14.3
Q ss_pred eeecCCCCCccchhhhhhc
Q psy5744 129 SFKCPRCLKTFTDLEPCLL 147 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~L 147 (157)
+|.||.||..-...|=..+
T Consensus 128 ~F~Cp~Cg~~L~~~dn~~~ 146 (158)
T TIGR00373 128 NFTCPRCGAMLDYLDNSEA 146 (158)
T ss_pred CCcCCCCCCEeeeccCHHH
Confidence 8999999998666654433
No 379
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=57.10 E-value=5.3 Score=25.78 Aligned_cols=11 Identities=27% Similarity=1.020 Sum_probs=8.7
Q ss_pred CCeeecCCCCC
Q psy5744 127 RSSFKCPRCLK 137 (157)
Q Consensus 127 ~~~Y~Cp~C~~ 137 (157)
...|+||+||-
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 55799999984
No 380
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=56.90 E-value=50 Score=26.59 Aligned_cols=33 Identities=12% Similarity=0.132 Sum_probs=25.2
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLKNDKII 75 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv 75 (157)
+..-++++||+.||++..+++.+.........+
T Consensus 127 gr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~ 159 (256)
T PRK07408 127 GRQPTDQEIAQALDISLEEWQEIKLALQNRTPL 159 (256)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCc
Confidence 456789999999999999999987543333333
No 381
>smart00114 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
Probab=56.78 E-value=23 Score=23.70 Aligned_cols=39 Identities=21% Similarity=0.278 Sum_probs=28.8
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChH--HHHHHHHHHhhCc
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERK--MLRARISTLKNDK 73 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k--~vRkiL~~L~~d~ 73 (157)
-|+|.|+.++++++++....-..+.. +.|+++..|..-|
T Consensus 24 ~vld~L~~~~Vlt~~e~e~i~~~~t~~~~~~~Lld~l~~kG 64 (88)
T smart00114 24 GLLDYLVEKNVLTEKEIEAIKAATTKLRDKRELVDSLQKRG 64 (88)
T ss_pred HHHHHHHHcCCCCHHHHHHHHccCChHHHHHHHHHHHHhHh
Confidence 58999999999999998888765543 4566666555443
No 382
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=56.69 E-value=12 Score=34.28 Aligned_cols=30 Identities=13% Similarity=0.233 Sum_probs=26.9
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+....+|++++++-++++.|++.|+++|-
T Consensus 282 ~~a~~~~g~s~~~tl~iaQ~LYe~g~ISYP 311 (618)
T TIGR01057 282 REAYRIFGFSPKKTQSIAQELYEEALISYP 311 (618)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHhcCceeec
Confidence 345668899999999999999999999996
No 383
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=56.67 E-value=7.2 Score=24.47 Aligned_cols=14 Identities=21% Similarity=0.681 Sum_probs=10.1
Q ss_pred cCCCCeeecCCCCC
Q psy5744 124 ATSRSSFKCPRCLK 137 (157)
Q Consensus 124 ~~~~~~Y~Cp~C~~ 137 (157)
+.....|+||.||.
T Consensus 39 ~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 39 EFEEIQYRCPYCGA 52 (54)
T ss_pred cCCceEEEcCCCCC
Confidence 34555899999985
No 384
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=56.43 E-value=19 Score=32.52 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=32.0
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
..-|++.| .++++|-.+||+.+|++.+.||+=+..|.+
T Consensus 6 ~~~iL~~L-~~~~~t~~~LA~~l~VS~RTIr~dI~~in~ 43 (584)
T PRK09863 6 ELKIVDLL-EQQDRSGGELAQQLGVSRRTIVRDIAYINF 43 (584)
T ss_pred HHHHHHHH-HcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45677777 468999999999999999999999997743
No 385
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=56.33 E-value=5.1 Score=25.41 Aligned_cols=13 Identities=31% Similarity=0.595 Sum_probs=10.8
Q ss_pred ecCCCCCccchhh
Q psy5744 131 KCPRCLKTFTDLE 143 (157)
Q Consensus 131 ~Cp~C~~~Ys~ld 143 (157)
-||.||++|++.+
T Consensus 41 gCPfC~~~~~~~~ 53 (55)
T PF14447_consen 41 GCPFCGTPFEFDD 53 (55)
T ss_pred CCCCCCCcccCCC
Confidence 4999999998765
No 386
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.15 E-value=8.8 Score=22.99 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=11.5
Q ss_pred CCeeecCCCCCccch
Q psy5744 127 RSSFKCPRCLKTFTD 141 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~ 141 (157)
+..|+||.||..+..
T Consensus 18 ~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 18 KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCEEECCcCCCeEEC
Confidence 358999999976543
No 387
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=56.13 E-value=29 Score=29.19 Aligned_cols=42 Identities=14% Similarity=0.155 Sum_probs=33.7
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-+|++.|.+ ++.+|-+||+..+||...+ ++..|...+++++.
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~i~~~D---ii~tL~~l~~l~~~ 253 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATGIRGED---IVSTLQSLNLIKYW 253 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHH---HHHHHHHCCcEEEE
Confidence 468888876 4689999999999999999 56666677888753
No 388
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.93 E-value=15 Score=25.60 Aligned_cols=24 Identities=13% Similarity=0.254 Sum_probs=22.3
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.-+|++++|..||+..-.|-++|+
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Confidence 468999999999999999999996
No 389
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=55.75 E-value=52 Score=24.65 Aligned_cols=28 Identities=14% Similarity=0.033 Sum_probs=24.7
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
-...|-++||+.||++.+.|+..+....
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~~~l~r~r 190 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSIDNALQRVK 190 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4689999999999999999998888665
No 390
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=55.69 E-value=7 Score=28.03 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=9.4
Q ss_pred CCCeeecCCCCCccchh
Q psy5744 126 SRSSFKCPRCLKTFTDL 142 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~l 142 (157)
-.....|+.||..|...
T Consensus 67 vp~~~~C~~Cg~~~~~~ 83 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIH 83 (113)
T ss_pred eCcEEEcccCCCEEecC
Confidence 34455666666555544
No 391
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.63 E-value=37 Score=24.34 Aligned_cols=25 Identities=8% Similarity=-0.121 Sum_probs=22.2
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
..+|-+|||+.+|++.+.|+..+..
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999988774
No 392
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=55.61 E-value=43 Score=22.77 Aligned_cols=57 Identities=16% Similarity=0.252 Sum_probs=37.2
Q ss_pred cCHHHHHHHhCCChHHHHHHHHHHhhC------cceeeeEeeeecCCCceeEEEEEEecchhHH
Q psy5744 46 MKEDDICELLKFERKMLRARISTLKND------KIIQTRLRMETGLDGKAQKVNYYFINYQTFV 103 (157)
Q Consensus 46 i~dedLa~~l~i~~k~vRkiL~~L~~d------~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~ 103 (157)
++=-+||+.+|..-+.|-+.+..+.++ +.+........ .+|.+....+|.++-+.+.
T Consensus 2 ~tS~~IAe~~gk~H~~Vlr~I~~~~~~~~~~~~~~~~f~~~~~y-~~~~gr~~~~y~Ltk~g~~ 64 (93)
T PF09669_consen 2 TTSREIAEMFGKRHKNVLRDIRKLIEKECSPEFGQLNFFIESKY-KDGQGRSYPCYLLTKDGFT 64 (93)
T ss_pred CCHHHHHHHHCccHHHHHHHHHHHHhhhcchhhhhccCcceeee-ECCCCcEeEEEEEccChhh
Confidence 455789999999999888888888866 23323111111 1234555778889876654
No 393
>KOG2165|consensus
Probab=55.60 E-value=22 Score=33.47 Aligned_cols=47 Identities=17% Similarity=0.275 Sum_probs=39.4
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+.+|+-.....+..|=|||++.+||+..-+|+-|...-.+|++....
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~ 650 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEP 650 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCC
Confidence 55555555556678999999999999999999999999999997653
No 394
>KOG1088|consensus
Probab=55.55 E-value=16 Score=26.80 Aligned_cols=76 Identities=13% Similarity=0.164 Sum_probs=42.5
Q ss_pred hCCChHHHHHHHHHHhhCcceeeeEeee--ecCCCceeEEEEEEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeec
Q psy5744 55 LKFERKMLRARISTLKNDKIIQTRLRME--TGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKC 132 (157)
Q Consensus 55 l~i~~k~vRkiL~~L~~d~Lv~~~~~~e--~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~C 132 (157)
+.+++.-++.++.++.=..++...+..+ +-|+++. .-|-- --..+..++|++.= +-.+ ..-..+|
T Consensus 35 vEFnPdFl~~m~~kidW~All~~A~~l~~~~lP~~kP---e~~~e----~de~~Lr~lHhlLl--e~~v----~EG~l~C 101 (124)
T KOG1088|consen 35 VEFNPDFLIRMLPKIDWSALLEAARSLGNTELPDEKP---EKLVE----DDEEFLRKLHHLLL--EIDV----IEGELVC 101 (124)
T ss_pred eecChHHHHHhhhhccHHHHHHHHHHhccccCCCCCc---ccccc----ccHHHHHHHHHHHh--hhhh----ccceEec
Confidence 5667777777776655444443322111 1133322 11111 24577778888873 3333 2336899
Q ss_pred CCCCCccchhh
Q psy5744 133 PRCLKTFTDLE 143 (157)
Q Consensus 133 p~C~~~Ys~ld 143 (157)
|.||+.|..-+
T Consensus 102 petG~vfpI~~ 112 (124)
T KOG1088|consen 102 PETGRVFPISD 112 (124)
T ss_pred CCCCcEeeccc
Confidence 99999998655
No 395
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=55.51 E-value=6.1 Score=22.87 Aligned_cols=17 Identities=24% Similarity=0.743 Sum_probs=13.1
Q ss_pred CCCCeeecCCCCCccch
Q psy5744 125 TSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 125 ~~~~~Y~Cp~C~~~Ys~ 141 (157)
.+...++||.||-.|-.
T Consensus 28 ~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 28 ENVPALVCPQCGEEYLD 44 (46)
T ss_pred eCCCccccccCCCEeeC
Confidence 35678899999988743
No 396
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=55.33 E-value=6.8 Score=27.25 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=18.5
Q ss_pred CCCCeeecCCCCCccchhhhhh
Q psy5744 125 TSRSSFKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 125 ~~~~~Y~Cp~C~~~Ys~lda~~ 146 (157)
.+.+-.+|+.||-.|-..++..
T Consensus 31 knVPa~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 31 KETPSISCSHCGMEYQDDTTVK 52 (89)
T ss_pred ecCCcccccCCCcEeecHHHHH
Confidence 3678899999999998887754
No 397
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=54.46 E-value=29 Score=25.49 Aligned_cols=37 Identities=22% Similarity=0.363 Sum_probs=28.9
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
.+.|+..|..+ ++-++||+.|+++.+.|+..+..+..
T Consensus 154 e~~vl~~l~~g--~s~~eIa~~l~~s~~tv~~~~~~~~~ 190 (210)
T PRK09935 154 EVTILRYLVSG--LSNKEIADQLLLSNKTVSAHKSNIYG 190 (210)
T ss_pred HHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34566555533 89999999999999999988887764
No 398
>KOG0978|consensus
Probab=54.25 E-value=8.3 Score=36.12 Aligned_cols=40 Identities=23% Similarity=0.448 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHH------HHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhc
Q psy5744 100 QTFVNIVKYKLDV------MRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLL 147 (157)
Q Consensus 100 ~~~~~vik~rl~~------m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L 147 (157)
..--|+|.-+=.+ |...++.+.+. ||.||+.|...|+-.+
T Consensus 651 ~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRK--------CP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 651 TRWKDAVITKCGHVFCEECVQTRYETRQRK--------CPKCNAAFGANDVHRI 696 (698)
T ss_pred CchhhHHHHhcchHHHHHHHHHHHHHhcCC--------CCCCCCCCCccccccc
Confidence 3344555444443 45556666654 9999999999998654
No 399
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=54.24 E-value=54 Score=25.93 Aligned_cols=26 Identities=8% Similarity=0.137 Sum_probs=22.4
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
...-++++||+.||++..+++.++..
T Consensus 101 g~~pt~~eia~~l~~~~~~v~~~~~~ 126 (238)
T TIGR02393 101 GREPTDEELAERMGMPAEKVREIKKI 126 (238)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34678999999999999999998663
No 400
>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=53.89 E-value=72 Score=23.99 Aligned_cols=45 Identities=18% Similarity=0.311 Sum_probs=39.2
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELL--KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-+|+++|.. |...+--||..-| ++..-.|-++|..|.++|.+...
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K 51 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEK 51 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeee
Confidence 368888886 7789999999988 68999999999999999999865
No 401
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=53.87 E-value=66 Score=26.10 Aligned_cols=33 Identities=6% Similarity=0.094 Sum_probs=25.2
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
..-++++||+.||++..+|+.++..-..-..++
T Consensus 142 ~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~S 174 (264)
T PRK07122 142 RAPTASELAAELGMDREEVVEGLVAGSAYNTLS 174 (264)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCc
Confidence 456899999999999999999887543333333
No 402
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=53.63 E-value=6.9 Score=28.19 Aligned_cols=19 Identities=21% Similarity=0.667 Sum_probs=14.1
Q ss_pred CCCeeecCCCCCccchhhh
Q psy5744 126 SRSSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~lda 144 (157)
+...|+||.|...++..++
T Consensus 17 d~~~~~cpec~~ew~~~~~ 35 (112)
T COG2824 17 DGGQLICPECAHEWNENEA 35 (112)
T ss_pred cCceEeCchhccccccccc
Confidence 3447889999999985553
No 403
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=53.62 E-value=65 Score=27.10 Aligned_cols=72 Identities=22% Similarity=0.267 Sum_probs=44.4
Q ss_pred HHHHHHHHhC-----CCcCHHHHH-------HHhCCCh---HHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744 34 SLIIDMLVRN-----PCMKEDDIC-------ELLKFER---KMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN 98 (157)
Q Consensus 34 ivIlD~L~~~-----~~i~dedLa-------~~l~i~~---k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~ 98 (157)
-.++-++.+. +.++-.++. +.+|+++ +.+..+|..|...|||...+.. .|+....+.+.++
T Consensus 299 k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~~~~----~g~~g~~~~~~~~ 374 (394)
T PRK00411 299 KLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYSG----KGGRGRTRLISLS 374 (394)
T ss_pred HHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEEEec----CCCCCCeEEEEec
Confidence 3455555531 345555555 5689977 9999999999999999876322 2333334555677
Q ss_pred chhHHHHHHHHHH
Q psy5744 99 YQTFVNIVKYKLD 111 (157)
Q Consensus 99 y~~~~~vik~rl~ 111 (157)
++. +.|...+.
T Consensus 375 ~~~--~~~~~~~~ 385 (394)
T PRK00411 375 YDP--EDVLERLL 385 (394)
T ss_pred CCH--HHHHHHHH
Confidence 653 34444443
No 404
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=53.29 E-value=51 Score=26.37 Aligned_cols=28 Identities=11% Similarity=0.142 Sum_probs=23.9
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
+..-++++||+.||++..+++.++....
T Consensus 134 ~~~pt~~elA~~l~~~~e~v~~~~~~~~ 161 (254)
T TIGR02850 134 SKEPTVSEIAKELKVPQEEVVFALDAIQ 161 (254)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHhcC
Confidence 3567899999999999999999987653
No 405
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=52.75 E-value=28 Score=19.34 Aligned_cols=25 Identities=12% Similarity=0.246 Sum_probs=20.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
...++-.++|..+|++...+.+.+.
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4468899999999999988877644
No 406
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.67 E-value=6.1 Score=24.88 Aligned_cols=16 Identities=31% Similarity=0.758 Sum_probs=12.4
Q ss_pred eeecCCCCCccchhhh
Q psy5744 129 SFKCPRCLKTFTDLEP 144 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda 144 (157)
.+.||.||..+...+.
T Consensus 2 ~~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 2 QFECPDCGAEIELENP 17 (54)
T ss_pred ccCCCCCCCEEecCCC
Confidence 4689999998877554
No 407
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=52.61 E-value=61 Score=23.97 Aligned_cols=50 Identities=12% Similarity=0.129 Sum_probs=32.4
Q ss_pred HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
..+...+..+=+.+-.++.-.. -..++-++||+.||++.+.|+..+....
T Consensus 128 ~~l~~~l~~L~~~~r~v~~l~~--~~g~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T TIGR02948 128 DTIQQEIQALPPKYRMVIVLKY--MEDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred HHHHHHHHhCCHHHhHHhhhHH--hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444455555333333332212 2468999999999999999999887543
No 408
>PRK00118 putative DNA-binding protein; Validated
Probab=52.55 E-value=27 Score=24.84 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=24.1
Q ss_pred hCCCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 42 RNPCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
..+.+|-.+||+.+|++++-|.+.+...
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3568999999999999999998888743
No 409
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=52.54 E-value=25 Score=19.39 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=19.9
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARI 66 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL 66 (157)
..-++-.++|+.+|++...+.+.+
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 446799999999999998887654
No 410
>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=52.54 E-value=32 Score=27.84 Aligned_cols=55 Identities=13% Similarity=0.172 Sum_probs=42.8
Q ss_pred CCCcccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCCh
Q psy5744 5 DEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFER 59 (157)
Q Consensus 5 ~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~ 59 (157)
+++..+|--|..+..++--.+-+..+.-.+..+-.++....=++||+.+.||++.
T Consensus 161 ~~~~~spvsP~~~~Ni~iaf~~Gl~~~igiafl~e~lD~tIKs~edie~~l~lPv 215 (226)
T COG3944 161 EASPSSPVSPKVMRNIVIAFLAGLAGAIGIAFLLEYLDKTIKSEEDIEEVLDLPV 215 (226)
T ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhCCce
Confidence 3335778888888888777777777777777666667678889999999999873
No 411
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. 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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=52.03 E-value=30 Score=30.52 Aligned_cols=57 Identities=14% Similarity=0.267 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHcCCCchH----HHHHHHHhCCCcC--HHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 15 TSLKQLSRLVVRGFYSIEDS----LIIDMLVRNPCMK--EDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~i----vIlD~L~~~~~i~--dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
....+|...+.-.+.+++.. .|++.|=.+|+++ .++||..+|++..+|.++|..+..
T Consensus 77 sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~~ve~~l~~iq~ 139 (429)
T TIGR02395 77 SLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADELEVSEEEVEKVLELIQR 139 (429)
T ss_pred CHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 44567888887777776643 4555555678876 799999999999999998876553
No 412
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=51.95 E-value=8 Score=28.00 Aligned_cols=11 Identities=27% Similarity=0.923 Sum_probs=9.2
Q ss_pred eeecCCCCCcc
Q psy5744 129 SFKCPRCLKTF 139 (157)
Q Consensus 129 ~Y~Cp~C~~~Y 139 (157)
.|.||.||..-
T Consensus 74 EyyCP~Cgt~l 84 (112)
T PF08882_consen 74 EYYCPGCGTQL 84 (112)
T ss_pred EEECCCCccee
Confidence 78999999754
No 413
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.78 E-value=45 Score=26.13 Aligned_cols=46 Identities=17% Similarity=0.230 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChH----HHHHHHHHHhh
Q psy5744 15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERK----MLRARISTLKN 71 (157)
Q Consensus 15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k----~vRkiL~~L~~ 71 (157)
.+++-|..-...+||+.+ .-++=.|||+.|||+.. .+|++..+|-+
T Consensus 159 rQ~~vL~~A~~~GYFd~P-----------R~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 159 RQLEVLRLAYKMGYFDYP-----------RRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred HHHHHHHHHHHcCCCCCC-----------ccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 334444444455555541 24678999999999987 56666666543
No 414
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=51.76 E-value=51 Score=24.41 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=23.4
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
-...+-++||+.+|++.+.|+..+..-
T Consensus 150 ~~~~s~~eIA~~lgis~~~v~~~l~Ra 176 (187)
T PRK09641 150 IEDLSLKEISEILDLPVGTVKTRIHRG 176 (187)
T ss_pred hhCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 368899999999999999999887743
No 415
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=51.75 E-value=7.4 Score=25.03 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=8.1
Q ss_pred CCeeecCCCCC
Q psy5744 127 RSSFKCPRCLK 137 (157)
Q Consensus 127 ~~~Y~Cp~C~~ 137 (157)
...|.||.||-
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 45788888874
No 416
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=51.74 E-value=30 Score=28.36 Aligned_cols=44 Identities=14% Similarity=0.239 Sum_probs=35.9
Q ss_pred HHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 36 IIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 36 IlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
++|-|.. +..-||++||+.||++..++..++......++++...
T Consensus 115 ~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~ 160 (247)
T COG1191 115 AIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDE 160 (247)
T ss_pred HHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhh
Confidence 4455552 3478999999999999999999999998888888754
No 417
>PRK05776 DNA topoisomerase I; Provisional
Probab=51.74 E-value=15 Score=34.18 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=26.7
Q ss_pred HHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 50 DICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 50 dLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
+.+..+|+++++.=++.+.|++.|||+|-+
T Consensus 286 ~As~~lg~sa~ktm~iAQ~LYe~glISYPR 315 (670)
T PRK05776 286 EAARIYGFSPYKTQSIAEDLYLDGLISYPR 315 (670)
T ss_pred HHHhhcCCCHHHHHHHHHHHHhcCceecCC
Confidence 345788999999999999999999999973
No 418
>PRK04217 hypothetical protein; Provisional
Probab=51.67 E-value=28 Score=25.03 Aligned_cols=27 Identities=4% Similarity=0.137 Sum_probs=23.0
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
...++-++||+.+|++...|++.+...
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356799999999999999988887743
No 419
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.57 E-value=12 Score=26.80 Aligned_cols=44 Identities=16% Similarity=0.359 Sum_probs=30.4
Q ss_pred cchhHHHHHHHHHHHHHHHHH-HHHhhc-CCCCeeecCCCCCccch
Q psy5744 98 NYQTFVNIVKYKLDVMRKRME-MEERDA-TSRSSFKCPRCLKTFTD 141 (157)
Q Consensus 98 ~y~~~~~vik~rl~~m~~~L~-~~~~~~-~~~~~Y~Cp~C~~~Ys~ 141 (157)
|-+..-++|.--+.+.-++|. ..+.+- .+.-++.||.||.-+..
T Consensus 16 dV~s~ddAi~iAiseagk~Ln~~~LdyV~ie~G~t~CP~Cg~~~e~ 61 (115)
T COG1885 16 DVESVDDAINIAISEAGKRLNKPDLDYVEIEVGSTSCPKCGEPFES 61 (115)
T ss_pred ccccHHHHHHHHHHHHHHHhccCCCCeEEEecccccCCCCCCccce
Confidence 445667777777788888887 445443 34457799999987753
No 420
>PRK06835 DNA replication protein DnaC; Validated
Probab=51.42 E-value=28 Score=29.54 Aligned_cols=39 Identities=18% Similarity=0.314 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcCCC-----CeeecCCCCCc
Q psy5744 100 QTFVNIVKYKLDVMRKRMEMEERDATSR-----SSFKCPRCLKT 138 (157)
Q Consensus 100 ~~~~~vik~rl~~m~~~L~~~~~~~~~~-----~~Y~Cp~C~~~ 138 (157)
+..+..+|.++..+.++-..-+....-. ..|.||.|+-+
T Consensus 64 ~~~~~~l~~~~~~l~~~~~~lL~~~g~~~dyl~~~y~Cp~C~dt 107 (329)
T PRK06835 64 EETLKELKEKITDLRVKKAELLVSNGYPPDYLEMKYTCPKCKDT 107 (329)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCChhhcCCCCCCCCCCCC
Confidence 3588899999999988888777654433 56899999755
No 421
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=51.32 E-value=60 Score=23.56 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=22.6
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
..++-++||+.+|++.+.|+..+..-
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra 151 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARA 151 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 67899999999999999988877643
No 422
>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=51.27 E-value=16 Score=22.72 Aligned_cols=35 Identities=17% Similarity=0.380 Sum_probs=29.8
Q ss_pred CCcCHHHHHHHh---CCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCMKEDDICELL---KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i~dedLa~~l---~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..+.-++|...+ +++.+.+..+|..|.++|.+...
T Consensus 16 ~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 16 PGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVE 53 (59)
T ss_dssp S-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEE
T ss_pred cCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeE
Confidence 357889999888 89999999999999999999864
No 423
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.05 E-value=6.9 Score=34.50 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=14.4
Q ss_pred hhcCCCCeeecCCCCCccchhhhh
Q psy5744 122 RDATSRSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 122 ~~~~~~~~Y~Cp~C~~~Ys~lda~ 145 (157)
+..-.+ +|.||+||.++...+-.
T Consensus 361 ~S~G~~-g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 361 KSAGRN-GFRCKKCGTRARETLIK 383 (421)
T ss_pred hhcCCC-CcccccccccCCccccc
Confidence 333344 78888888877665443
No 424
>smart00351 PAX Paired Box domain.
Probab=50.81 E-value=30 Score=24.94 Aligned_cols=35 Identities=11% Similarity=0.076 Sum_probs=31.2
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+..+-.+||+.+|++...|.+++.+..+.|.+..+
T Consensus 32 ~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk 66 (125)
T smart00351 32 NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPG 66 (125)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCc
Confidence 45688999999999999999999999999987753
No 425
>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=50.72 E-value=24 Score=25.72 Aligned_cols=28 Identities=18% Similarity=0.242 Sum_probs=24.0
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
-..++-+|||+.+|++.+.|+..+..-.
T Consensus 124 ~~g~s~~eIA~~lgis~~tV~~~l~ra~ 151 (162)
T TIGR02983 124 YEDLSEAQVAEALGISVGTVKSRLSRAL 151 (162)
T ss_pred HhcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3478999999999999999998887544
No 426
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=50.69 E-value=7.5 Score=24.23 Aligned_cols=15 Identities=33% Similarity=0.977 Sum_probs=7.8
Q ss_pred CCeeecCCCCCccch
Q psy5744 127 RSSFKCPRCLKTFTD 141 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~ 141 (157)
...|.||+|+.-|=.
T Consensus 19 ~~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCI 33 (51)
T ss_dssp -EEE--TTTT--B-H
T ss_pred CCeEECCCCCCcccc
Confidence 578999999998854
No 427
>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=50.35 E-value=83 Score=22.54 Aligned_cols=27 Identities=15% Similarity=0.116 Sum_probs=23.1
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
..++-++||+.+|++.+.|+..+....
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 578999999999999999988776543
No 428
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=50.26 E-value=25 Score=21.30 Aligned_cols=32 Identities=19% Similarity=0.338 Sum_probs=24.5
Q ss_pred CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
.+|+|||++++|.+.. -+-+..|...|+--..
T Consensus 2 fLT~~El~elTG~k~~--~~Q~~~L~~~Gi~~~~ 33 (47)
T PF13986_consen 2 FLTDEELQELTGYKRP--SKQIRWLRRNGIPFVV 33 (47)
T ss_pred CCCHHHHHHHHCCCCH--HHHHHHHHHCCCeeEE
Confidence 4799999999998754 4556678888886654
No 429
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=50.25 E-value=35 Score=25.77 Aligned_cols=33 Identities=12% Similarity=0.186 Sum_probs=23.5
Q ss_pred CCChHHHHHHHHHHhhCcceeeeE-eeeecCCCc
Q psy5744 56 KFERKMLRARISTLKNDKIIQTRL-RMETGLDGK 88 (157)
Q Consensus 56 ~i~~k~vRkiL~~L~~d~Lv~~~~-~~e~~~~gk 88 (157)
+=+.+.+|++|+.|++.|+|.... ..--.|+|+
T Consensus 92 ~gsgsI~RkilqqLE~~G~V~k~~~GR~ltp~Gr 125 (147)
T COG2238 92 KGSGSIIRKVLQQLEKAGLVEKTPKGRVLTPKGR 125 (147)
T ss_pred cCCchHHHHHHHHHHHCCceeecCCCceeCccch
Confidence 345678999999999999998764 111236663
No 430
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.14 E-value=7.4 Score=20.05 Aligned_cols=11 Identities=36% Similarity=0.893 Sum_probs=8.3
Q ss_pred ecCCCCCccch
Q psy5744 131 KCPRCLKTFTD 141 (157)
Q Consensus 131 ~Cp~C~~~Ys~ 141 (157)
.||+||+....
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 49999987653
No 431
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=50.08 E-value=8.7 Score=32.19 Aligned_cols=25 Identities=20% Similarity=0.159 Sum_probs=16.5
Q ss_pred eeecCCCCCccch---hhhhhccCCCCc
Q psy5744 129 SFKCPRCLKTFTD---LEPCLLVLWCAC 153 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~---lda~~L~d~~~F 153 (157)
.++||.|+.-|-. +-...|+|++.|
T Consensus 46 ~~vc~~c~~h~rl~areRi~~L~D~gsF 73 (292)
T PRK05654 46 LNVCPKCGHHMRISARERLDLLLDEGSF 73 (292)
T ss_pred CCCCCCCCCCeeCCHHHHHHHHccCCcc
Confidence 4799999987753 334445676555
No 432
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=49.83 E-value=21 Score=31.22 Aligned_cols=43 Identities=14% Similarity=0.058 Sum_probs=35.1
Q ss_pred HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744 34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76 (157)
Q Consensus 34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~ 76 (157)
..+|+.|-- .|.-+=.|||+++|++...+-.++.+|.+.||++
T Consensus 343 ~~~l~~L~~~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 343 MAMLWVLNYSDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHhccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 456777664 6889999999999999999999999999999985
No 433
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=49.71 E-value=31 Score=30.67 Aligned_cols=58 Identities=21% Similarity=0.230 Sum_probs=43.4
Q ss_pred hHHHHHHHHHHHHHcCCCchH----HHHHHHHhCCCc--CHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 14 PTSLKQLSRLVVRGFYSIEDS----LIIDMLVRNPCM--KEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 14 p~~~~~Lv~~v~R~Fy~~e~i----vIlD~L~~~~~i--~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
|....+|...+.-.+.+++.. .|++.|=.+|++ +.++||..+|++..+|.++|..|..
T Consensus 101 ~sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ~ 164 (455)
T PRK05932 101 ESLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAESLGVELDEVEAVLKRIQS 164 (455)
T ss_pred CCHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 344567788877777776643 456665567887 5699999999999999998886653
No 434
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=49.71 E-value=97 Score=23.40 Aligned_cols=57 Identities=16% Similarity=0.242 Sum_probs=36.0
Q ss_pred ccchHHHHHHHHHHHHHcCCCchHHHHHHH---Hh-CCCcCHH---HHHHHhCCChHHHHHHHHHH
Q psy5744 11 TEVPTSLKQLSRLVVRGFYSIEDSLIIDML---VR-NPCMKED---DICELLKFERKMLRARISTL 69 (157)
Q Consensus 11 ~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L---~~-~~~i~de---dLa~~l~i~~k~vRkiL~~L 69 (157)
|+-|....++- .+...+ ....-.+|.+| -+ .|+++++ .||+.||+++.+|..++..-
T Consensus 2 ~~~~~~~~~i~-~ii~~y-~~~~~~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~~vatFY 65 (156)
T PRK05988 2 PDEPWDAARIA-AIIAEH-KHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFY 65 (156)
T ss_pred CCchhHHHHHH-HHHHHc-CCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence 44565566544 344433 33333344444 33 6999976 57999999999999887643
No 435
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=49.48 E-value=41 Score=23.27 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=28.5
Q ss_pred HHHHHHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhhCc
Q psy5744 35 LIIDMLVRNPCMKEDDICELL--KFERKMLRARISTLKNDK 73 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~ 73 (157)
-|+|.|+..+.+++++....- +-...+.|+++..|..-|
T Consensus 27 ~ilD~Ll~~~Vlt~ee~e~I~~~~t~~~qAr~Lld~l~~KG 67 (94)
T cd08329 27 PILDSLLSANVITEQEYDVIKQKTQTPLQARELIDTVLVKG 67 (94)
T ss_pred HHHHHHHHcCCCCHHHHHHHHcCCChHHHHHHHHHHHHhhh
Confidence 389999999999999886655 334567777777665443
No 436
>PHA00542 putative Cro-like protein
Probab=49.36 E-value=47 Score=22.13 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=21.6
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
...++-.+||+.+|++...|.+++.
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 3458999999999999999988875
No 437
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=49.25 E-value=37 Score=24.17 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=26.4
Q ss_pred HHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 39 MLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
.+-.++.++-.|||+.+|++..-|-..|. .-|+...
T Consensus 65 ~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lk---rlg~t~K 100 (119)
T PF01710_consen 65 LVEENPDATLRELAERLGVSPSTIWRALK---RLGITRK 100 (119)
T ss_pred HHHHCCCcCHHHHHHHcCCCHHHHHHHHH---HcCchhc
Confidence 33458899999999999998877765554 4466544
No 438
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=49.23 E-value=22 Score=29.43 Aligned_cols=37 Identities=14% Similarity=0.171 Sum_probs=29.8
Q ss_pred CCCcCHHH---HHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 43 NPCMKEDD---ICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 43 ~~~i~ded---La~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+.|+=-+ +.+.+|++..-||.+|..|..+|+|....
T Consensus 15 gg~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~ 54 (280)
T TIGR02277 15 GGAIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQSER 54 (280)
T ss_pred CCceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEEeee
Confidence 45566544 55667999999999999999999998753
No 439
>COG5602 SIN3 Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=49.11 E-value=40 Score=32.81 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHcCCCch-HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 17 LKQLSRLVVRGFYSIED-SLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 17 ~~~Lv~~v~R~Fy~~e~-ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
-+.+++.|.+..|+.|| -.|+|+|.++..++---+-++|+++.++.|..-..
T Consensus 605 S~sIyKkvik~VY~KEhA~eile~L~k~P~vt~PiVlkRLk~Kd~EWR~~kRe 657 (1163)
T COG5602 605 SKSIYKKVIKKVYDKEHAPEILEALLKKPHVTIPIVLKRLKMKDEEWRSCKRE 657 (1163)
T ss_pred cHHHHHHHHHHHhchhhHHHHHHHHHhCCCcchHHHHHHHHHhhHHHHHHHHH
Confidence 47789999999999995 57999999999999999999999999888876543
No 440
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=49.02 E-value=34 Score=22.38 Aligned_cols=44 Identities=14% Similarity=0.128 Sum_probs=32.1
Q ss_pred CchHHHHHHHHhC----CCcCHHHHHHHhCCChHHHHHHHHHHhhCcc
Q psy5744 31 IEDSLIIDMLVRN----PCMKEDDICELLKFERKMLRARISTLKNDKI 74 (157)
Q Consensus 31 ~e~ivIlD~L~~~----~~i~dedLa~~l~i~~k~vRkiL~~L~~d~L 74 (157)
+..-.|.+.++.| ..++-.|||+..|+++.-|-+.+.+|-=.|+
T Consensus 16 ~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 16 PTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGF 63 (77)
T ss_dssp HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCH
T ss_pred HHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCH
Confidence 4456677888865 3689999999999999999999998865554
No 441
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=48.82 E-value=8.2 Score=20.47 Aligned_cols=19 Identities=16% Similarity=0.373 Sum_probs=14.7
Q ss_pred ecCCCCCccchhhhhhccC
Q psy5744 131 KCPRCLKTFTDLEPCLLVL 149 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~d 149 (157)
.||-|++..+.....+-+|
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 5999999997776666555
No 442
>KOG3233|consensus
Probab=48.68 E-value=20 Score=30.05 Aligned_cols=85 Identities=11% Similarity=0.209 Sum_probs=56.5
Q ss_pred HHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeee-----------cCCCceeEEEEEEecc-
Q psy5744 34 SLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET-----------GLDGKAQKVNYYFINY- 99 (157)
Q Consensus 34 ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~-----------~~~gk~~~~~yw~I~y- 99 (157)
-+|.+++-. +..+.-.+|-.+.+++..+|+|+|..|+..+||+...-+.. .|+ ...+==-||-|=
T Consensus 87 k~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKsv~n~~~KvYmLy~leP~-~elTGG~WytDqd 165 (297)
T KOG3233|consen 87 KLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKSVKNSRKKVYMLYDLEPD-SELTGGTWYTDQD 165 (297)
T ss_pred HHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEEeccccc-ccccCCccccccc
Confidence 345545443 34678889999999999999999999999999987532211 133 111112567542
Q ss_pred --hhHHHHHHHHHHHHHHHHHH
Q psy5744 100 --QTFVNIVKYKLDVMRKRMEM 119 (157)
Q Consensus 100 --~~~~~vik~rl~~m~~~L~~ 119 (157)
-.++++++....+..+.=..
T Consensus 166 lDvEfIe~L~~~c~~fl~~~~~ 187 (297)
T KOG3233|consen 166 LDVEFIEVLKQICVRFLESKRF 187 (297)
T ss_pred ccHHHHHHHHHHHHHHHHhccc
Confidence 35888888888777654333
No 443
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=48.36 E-value=37 Score=21.17 Aligned_cols=32 Identities=16% Similarity=0.132 Sum_probs=25.7
Q ss_pred HHHHhCCCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 38 DMLVRNPCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 38 D~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
+-|-.+=-++-+|-|..||+..-.+.+++..+
T Consensus 8 ~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 8 EDLSQYFHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred HHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 44444556888999999999999999999754
No 444
>KOG1994|consensus
Probab=48.28 E-value=15 Score=30.00 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=15.8
Q ss_pred eeecCCCCCccchhhhhh
Q psy5744 129 SFKCPRCLKTFTDLEPCL 146 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda~~ 146 (157)
.|.|-.||..|+..+++-
T Consensus 239 h~YC~fCG~~y~~~edl~ 256 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLY 256 (268)
T ss_pred ceEEEEeccccCCHHHHH
Confidence 678999999999998863
No 445
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=48.25 E-value=27 Score=25.89 Aligned_cols=26 Identities=12% Similarity=0.195 Sum_probs=22.8
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
-..++-++||+.||++.+.|+..+..
T Consensus 133 ~~~~s~~EIA~~lgis~~tV~~~l~R 158 (173)
T PRK12522 133 YEQYSYKEMSEILNIPIGTVKYRLNY 158 (173)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46789999999999999999888763
No 446
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=48.21 E-value=7.4 Score=22.52 Aligned_cols=19 Identities=16% Similarity=0.392 Sum_probs=11.1
Q ss_pred CCCeeecCCCCCccchhhh
Q psy5744 126 SRSSFKCPRCLKTFTDLEP 144 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~lda 144 (157)
...+|+|..||.-....++
T Consensus 3 ~~~~YkC~~CGniVev~~~ 21 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEVVHD 21 (36)
T ss_dssp TTEEEE-TTT--EEEEEE-
T ss_pred cccEEEccCCCCEEEEEEC
Confidence 4579999999988755444
No 447
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=48.18 E-value=64 Score=27.61 Aligned_cols=26 Identities=12% Similarity=0.183 Sum_probs=22.7
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
...-|.++||+.||++..+|+.++..
T Consensus 230 gr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 230 GREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 34678999999999999999999763
No 448
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.07 E-value=6.8 Score=28.48 Aligned_cols=9 Identities=22% Similarity=0.338 Sum_probs=8.0
Q ss_pred ecCCCCCcc
Q psy5744 131 KCPRCLKTF 139 (157)
Q Consensus 131 ~Cp~C~~~Y 139 (157)
+||.||++|
T Consensus 28 VsPytG~s~ 36 (129)
T COG4530 28 VSPYTGKSY 36 (129)
T ss_pred ccCcccccc
Confidence 889999988
No 449
>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=47.74 E-value=27 Score=27.53 Aligned_cols=42 Identities=10% Similarity=0.160 Sum_probs=30.6
Q ss_pred HHHHHHHHhC-C--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRN-P--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~-~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-+|+..|..+ + .++=+||++.+||...+|-.+|. ..+++++.
T Consensus 136 ~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~---~l~~l~~~ 180 (188)
T PF01853_consen 136 RVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQ---QLGMLKYY 180 (188)
T ss_dssp HHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHH---HTT-EEEE
T ss_pred HHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHH---HCCCEEEE
Confidence 4688888864 3 49999999999999998766555 55677765
No 450
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.67 E-value=7.6 Score=28.03 Aligned_cols=22 Identities=14% Similarity=0.342 Sum_probs=13.6
Q ss_pred HhhcCCCCeeecCCCCCccchh
Q psy5744 121 ERDATSRSSFKCPRCLKTFTDL 142 (157)
Q Consensus 121 ~~~~~~~~~Y~Cp~C~~~Ys~l 142 (157)
+.-+.-...+.|+.||..|+..
T Consensus 63 L~Ie~vp~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 63 LDIVDEKVELECKDCSHVFKPN 84 (117)
T ss_pred EEEEecCCEEEhhhCCCccccC
Confidence 3344455567788888666554
No 451
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=47.39 E-value=40 Score=26.35 Aligned_cols=37 Identities=16% Similarity=0.349 Sum_probs=0.0
Q ss_pred HHHHHHh--CCCcCHHHHHHHhCC-ChHHHHHHHHHHhhC
Q psy5744 36 IIDMLVR--NPCMKEDDICELLKF-ERKMLRARISTLKND 72 (157)
Q Consensus 36 IlD~L~~--~~~i~dedLa~~l~i-~~k~vRkiL~~L~~d 72 (157)
++.+++- ...+|.++||+.+|+ +...+..+|..|+.+
T Consensus 12 ~vEall~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~ 51 (184)
T COG1386 12 LIEALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEE 51 (184)
T ss_pred HHHHHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHh
No 452
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=47.27 E-value=33 Score=21.26 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=19.1
Q ss_pred CCcCHHHHHHHhCCChH-HHHHHHHHHh
Q psy5744 44 PCMKEDDICELLKFERK-MLRARISTLK 70 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k-~vRkiL~~L~ 70 (157)
..+++++|. .+|+... .-++++..+.
T Consensus 37 ~~l~~~~L~-~lGI~~~~~r~kll~~i~ 63 (66)
T PF07647_consen 37 LQLTEEDLK-ELGITNLGHRRKLLSAIQ 63 (66)
T ss_dssp TTSCHHHHH-HTTTTHHHHHHHHHHHHH
T ss_pred hhCCHHHHH-HcCCCCHHHHHHHHHHHH
Confidence 378999997 9999655 4466666554
No 453
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=47.15 E-value=22 Score=34.02 Aligned_cols=29 Identities=17% Similarity=0.054 Sum_probs=26.7
Q ss_pred HHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 50 DICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 50 dLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+.+..+|+++++.=++.++||+.|||+|-
T Consensus 279 ~As~klg~s~~~tm~~aQ~LYE~glITYp 307 (859)
T PRK07561 279 EASRKLGFSVKKTMRIAQRLYEAGYITYM 307 (859)
T ss_pred HHHHhcCCCHHHHHHHHHHHHhCCeEEec
Confidence 45678999999999999999999999997
No 454
>KOG3993|consensus
Probab=47.10 E-value=8.6 Score=34.10 Aligned_cols=14 Identities=36% Similarity=1.101 Sum_probs=12.2
Q ss_pred CCeeecCCCCCccc
Q psy5744 127 RSSFKCPRCLKTFT 140 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys 140 (157)
...|.||.|++.|+
T Consensus 293 ~vEYrCPEC~KVFs 306 (500)
T KOG3993|consen 293 HVEYRCPECDKVFS 306 (500)
T ss_pred EeeecCCccccccc
Confidence 45899999999987
No 455
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=47.01 E-value=9.4 Score=31.91 Aligned_cols=25 Identities=16% Similarity=0.082 Sum_probs=15.1
Q ss_pred eeecCCCCCccch---hhhhhccCCCCc
Q psy5744 129 SFKCPRCLKTFTD---LEPCLLVLWCAC 153 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~---lda~~L~d~~~F 153 (157)
.++||.|+.-|-. +-...|+|++.|
T Consensus 45 ~~vc~~c~~h~rl~areRi~~L~D~gsF 72 (285)
T TIGR00515 45 LEVCPKCDHHMRMDARERIESLLDEGSF 72 (285)
T ss_pred CCCCCCCCCcCcCCHHHHHHHceeCCee
Confidence 4899999876642 223334565544
No 456
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.97 E-value=11 Score=24.43 Aligned_cols=16 Identities=19% Similarity=0.571 Sum_probs=13.0
Q ss_pred CCCeeecCCCCCccch
Q psy5744 126 SRSSFKCPRCLKTFTD 141 (157)
Q Consensus 126 ~~~~Y~Cp~C~~~Ys~ 141 (157)
+..+=+||-|+++|..
T Consensus 45 ~~gev~CPYC~t~y~l 60 (62)
T COG4391 45 DEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCcEecCccccEEEe
Confidence 4556789999999975
No 457
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=46.91 E-value=11 Score=23.21 Aligned_cols=18 Identities=28% Similarity=0.800 Sum_probs=14.6
Q ss_pred CCeeecCCCCCccchhhhh
Q psy5744 127 RSSFKCPRCLKTFTDLEPC 145 (157)
Q Consensus 127 ~~~Y~Cp~C~~~Ys~lda~ 145 (157)
..+| |..|..+|+.++.=
T Consensus 4 k~GY-CE~C~~ky~~l~~H 21 (49)
T PF07535_consen 4 KPGY-CENCRVKYDDLEEH 21 (49)
T ss_pred CCcc-CccccchhhhHHHH
Confidence 4566 99999999988763
No 458
>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=46.75 E-value=32 Score=21.11 Aligned_cols=32 Identities=19% Similarity=0.171 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
+-|+..+- .|. +-.+||..+|++...|+.|+-
T Consensus 13 ~~iI~~~e-~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 13 LEIIKRLE-EGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHH-CTT--HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHH-cCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 44666643 444 999999999999999999986
No 459
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=46.73 E-value=41 Score=28.75 Aligned_cols=52 Identities=17% Similarity=0.169 Sum_probs=39.1
Q ss_pred HHHHHHHHHcCCCc--------------------hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 19 QLSRLVVRGFYSIE--------------------DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 19 ~Lv~~v~R~Fy~~e--------------------~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
.++..+.+.|.... |+++|=..+.+-.+.=++||..|+|+++.+..+...|-
T Consensus 273 ~v~~~ll~~Ft~~~~~~~~~~~~~s~~~~dkLl~~il~LaL~id~f~~d~~~L~~dLkl~~~~l~~~~r~LG 344 (385)
T PF06870_consen 273 IVIDKLLDRFTESSSSSGSRSYQISKTMKDKLLTYILALALHIDNFSVDITDLARDLKLSPKKLTQYFRELG 344 (385)
T ss_dssp HHHHHHHHHHSEE-------BEE--HHHHHHHHHHHHHHHHHHTTTEEEHHHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHHHccCcccCCCCcCcccCHHHHHHHHHHHHHHHHHhcCcccChHHHHHHhCCCHHHHHHHHHHhC
Confidence 45677888888871 67777665655567789999999999999999988764
No 460
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=46.52 E-value=31 Score=19.38 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=20.8
Q ss_pred CHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744 47 KEDDICELLKFERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
+-.|+|+.+|++...|++... +|.+..
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~----~g~~~~ 28 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK----EGKLKA 28 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH----cCCCCc
Confidence 567999999999888887665 566643
No 461
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=46.47 E-value=20 Score=27.67 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=23.2
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHH
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRAR 65 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRki 65 (157)
.|..+=- ...+|-+|||++|+.+.+.||++
T Consensus 83 ~Ir~ARE-~~G~SqedLA~ki~ek~svI~~i 112 (165)
T COG1813 83 RIREARE-KRGLSQEDLAAKLKEKVSVIRRI 112 (165)
T ss_pred HHHHHHH-HcCCCHHHHHHHhcccHHHHHHH
Confidence 4444422 45789999999999999988876
No 462
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=46.42 E-value=49 Score=19.93 Aligned_cols=34 Identities=9% Similarity=0.321 Sum_probs=26.3
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
.++..+. .| .+..+||..+|++.+.|+..+..+.
T Consensus 11 ~v~~l~~-~G-~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 11 EILRLVA-QG-KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred HHHHHHH-CC-CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444433 44 8999999999999999998887664
No 463
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=46.42 E-value=77 Score=23.65 Aligned_cols=48 Identities=10% Similarity=0.025 Sum_probs=31.6
Q ss_pred HHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 20 LSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 20 Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
.+......+=.....+++-. .-..++-+|||+.+|++.+.|+..++.-
T Consensus 126 ~l~~~l~~L~~~~r~i~~l~--~~~~~s~~eIA~~lgis~~tV~~~l~ra 173 (182)
T PRK12537 126 KIHRCLEQLEPARRNCILHA--YVDGCSHAEIAQRLGAPLGTVKAWIKRS 173 (182)
T ss_pred HHHHHHHhCCHHHHHHHHHH--HHcCCCHHHHHHHHCCChhhHHHHHHHH
Confidence 44455554444433333322 2357899999999999999998877743
No 464
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=46.37 E-value=1.2e+02 Score=26.79 Aligned_cols=64 Identities=2% Similarity=-0.056 Sum_probs=40.4
Q ss_pred CcccccchHHHHHHHHHHHHHcC---CCchH-HHHHHHHh-CCCcCHHH---HHHHhCCChHHHHHHHHHHh
Q psy5744 7 GYVHTEVPTSLKQLSRLVVRGFY---SIEDS-LIIDMLVR-NPCMKEDD---ICELLKFERKMLRARISTLK 70 (157)
Q Consensus 7 ~~~~~~ip~~~~~Lv~~v~R~Fy---~~e~i-vIlD~L~~-~~~i~ded---La~~l~i~~k~vRkiL~~L~ 70 (157)
|-.++...+....-++.++..|- ...++ -+|..+-+ +|||+++. +|+.|||+.-+|..+...-.
T Consensus 9 ~p~~f~f~~e~~~~i~~ii~~yp~~~~~salIplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~eVATFYt 80 (400)
T PRK12373 9 QPDSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVLEVATFYT 80 (400)
T ss_pred CCccccCCHHHHHHHHHHHHHCCCccCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHHhh
Confidence 43334444445555666776663 22333 34444443 79999875 79999999999998876443
No 465
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=46.27 E-value=39 Score=24.85 Aligned_cols=45 Identities=11% Similarity=0.215 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeee
Q psy5744 34 SLIIDMLVRNPCMKEDDICELL----KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
-.||++|=.++..|=+||-+.+ .+....|+-+|+.|...|+|+.+
T Consensus 9 ~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~ 57 (123)
T COG3682 9 WEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRK 57 (123)
T ss_pred HHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhh
Confidence 4689999999999987777666 46788999999999999999965
No 466
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=46.19 E-value=10 Score=24.75 Aligned_cols=20 Identities=30% Similarity=0.484 Sum_probs=13.7
Q ss_pred hcCCCCeeecCCCCCc-cchh
Q psy5744 123 DATSRSSFKCPRCLKT-FTDL 142 (157)
Q Consensus 123 ~~~~~~~Y~Cp~C~~~-Ys~l 142 (157)
...+.+.=+||.||.. ||..
T Consensus 12 ~l~~~d~e~CP~Cgs~~~te~ 32 (64)
T COG2093 12 RLTPEDTEICPVCGSTDLTEE 32 (64)
T ss_pred ccCCCCCccCCCCCCcccchh
Confidence 3445556679999998 5544
No 467
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=46.17 E-value=24 Score=32.77 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=27.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhC-cceeeeE
Q psy5744 49 DDICELLKFERKMLRARISTLKND-KIIQTRL 79 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d-~Lv~~~~ 79 (157)
.+.+..+|++++++=++.++|++. |||+|-+
T Consensus 291 ~~as~~~g~s~~~tm~iAQ~LYE~~glITYpR 322 (660)
T TIGR01056 291 EDANKRFGISAKRTLDIAQKLYETHKLITYPR 322 (660)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHhCCEEEEec
Confidence 356678899999999999999998 9999973
No 468
>PRK01381 Trp operon repressor; Provisional
Probab=46.00 E-value=61 Score=22.93 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=26.5
Q ss_pred HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
|+..|+ .|.+|-.+||+.+|++.-.|-+--+.|+.
T Consensus 47 I~~~L~-~g~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 47 IVEELL-RGELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred HHHHHH-cCCcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 444544 67899999999999998877776666653
No 469
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=45.98 E-value=39 Score=20.47 Aligned_cols=28 Identities=4% Similarity=-0.012 Sum_probs=24.3
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
....+.++||...|++...+.++.....
T Consensus 17 R~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 17 RLNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HcCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 4578999999999999999999887654
No 470
>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=45.93 E-value=53 Score=21.85 Aligned_cols=36 Identities=19% Similarity=0.247 Sum_probs=29.6
Q ss_pred hCCCcCHHHHHHHhC-CChHHHHHHHHHHhhCcceee
Q psy5744 42 RNPCMKEDDICELLK-FERKMLRARISTLKNDKIIQT 77 (157)
Q Consensus 42 ~~~~i~dedLa~~l~-i~~k~vRkiL~~L~~d~Lv~~ 77 (157)
..+.++=+|....++ ++.+.++++-..|...|+|.+
T Consensus 50 ~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~INf 86 (86)
T PF04433_consen 50 PNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLINF 86 (86)
T ss_dssp TTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSSSS
T ss_pred CCCcccHHHHHHHccccCHHHHHHHHHHHHHcCccCC
Confidence 367899999999998 999999999999999999863
No 471
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=45.62 E-value=8.9 Score=22.62 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=10.3
Q ss_pred cCCCCCccchhhhhhccCC----CCccc
Q psy5744 132 CPRCLKTFTDLEPCLLVLW----CACPC 155 (157)
Q Consensus 132 Cp~C~~~Ys~lda~~L~d~----~~F~C 155 (157)
||.|+. -|..+++++ +.+.|
T Consensus 6 CP~CGG----~DrFri~~d~~~~G~~~C 29 (40)
T PF08273_consen 6 CPICGG----KDRFRIFDDKDGRGTWIC 29 (40)
T ss_dssp -TTTT-----TTTEEEETT----S-EEE
T ss_pred CCCCcC----ccccccCcCcccCCCEEC
Confidence 788876 455665554 45555
No 472
>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=45.60 E-value=14 Score=26.41 Aligned_cols=22 Identities=32% Similarity=0.289 Sum_probs=19.5
Q ss_pred CCCcCHHHHHHHhCCChHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRA 64 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRk 64 (157)
-..+|-+|||+.||++.+-|+|
T Consensus 121 ~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 121 FEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HcCCCHHHHHHHHCcCHHhhcC
Confidence 4578999999999999998875
No 473
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=45.57 E-value=6.8 Score=33.72 Aligned_cols=22 Identities=23% Similarity=0.505 Sum_probs=16.1
Q ss_pred ecCCCCCccchhhhhhccCCCCcccC
Q psy5744 131 KCPRCLKTFTDLEPCLLVLWCACPCK 156 (157)
Q Consensus 131 ~Cp~C~~~Ys~lda~~L~d~~~F~C~ 156 (157)
-|.+|.++||..||.+ ....||
T Consensus 248 AC~rC~t~y~le~A~~----~~wrCp 269 (403)
T COG1379 248 ACSRCYTRYSLEEAKS----LRWRCP 269 (403)
T ss_pred HHHHhhhccCcchhhh----hcccCc
Confidence 4888888888888887 444554
No 474
>PRK00441 argR arginine repressor; Provisional
Probab=45.51 E-value=45 Score=25.05 Aligned_cols=43 Identities=16% Similarity=0.337 Sum_probs=35.6
Q ss_pred hHHHHHHHHhCCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744 33 DSLIIDMLVRNPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 33 ~ivIlD~L~~~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
+-.|++.|-.++..+-+||++.| ++++-.+|+-|..| ++++..
T Consensus 6 ~~~I~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L---~lvKv~ 53 (149)
T PRK00441 6 HAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKEL---KLIKVL 53 (149)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHc---CcEEeE
Confidence 44677887789999999999998 99999999987766 588754
No 475
>PRK12496 hypothetical protein; Provisional
Probab=45.50 E-value=11 Score=28.82 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=11.6
Q ss_pred eeecCCCCCccchh
Q psy5744 129 SFKCPRCLKTFTDL 142 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~l 142 (157)
.|.|+.|++.|...
T Consensus 127 ~~~C~gC~~~~~~~ 140 (164)
T PRK12496 127 RKVCKGCKKKYPED 140 (164)
T ss_pred eEECCCCCccccCC
Confidence 48999999999643
No 476
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=45.41 E-value=45 Score=23.88 Aligned_cols=36 Identities=11% Similarity=0.181 Sum_probs=26.9
Q ss_pred HHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 36 IIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 36 IlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
+++.+-. ...++-++||+.+|+++..+.+.+..-..
T Consensus 14 ~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 14 ILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 4444443 35689999999999999999988875443
No 477
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=45.38 E-value=1e+02 Score=22.42 Aligned_cols=50 Identities=8% Similarity=-0.013 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHcCCCchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 17 LKQLSRLVVRGFYSIEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
.+..|..+... .+++.--|+....- ....++++||..+|++...+++.-.
T Consensus 72 ~~~~I~~~l~~-Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~ 122 (134)
T TIGR01636 72 NRDAIENCLNE-ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRN 122 (134)
T ss_pred HHHHHHHHHHh-CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34455555555 35555555555442 3347999999999999999877654
No 478
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=45.37 E-value=29 Score=19.16 Aligned_cols=18 Identities=6% Similarity=0.043 Sum_probs=13.3
Q ss_pred HHHHhCCChHHHHHHHHH
Q psy5744 51 ICELLKFERKMLRARIST 68 (157)
Q Consensus 51 La~~l~i~~k~vRkiL~~ 68 (157)
-|..+|++..++|..|..
T Consensus 11 eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 11 EAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHTT--HHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHh
Confidence 478899999999998864
No 479
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=45.11 E-value=43 Score=25.21 Aligned_cols=91 Identities=11% Similarity=0.147 Sum_probs=55.0
Q ss_pred HHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHH------
Q psy5744 40 LVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVM------ 113 (157)
Q Consensus 40 L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m------ 113 (157)
+..-+.+|.++++.....=.+++......+.+ ...++.+++..+-+.+=..+..|
T Consensus 27 ~~~~~elT~eEl~lv~~ylkRDl~~~a~~~~~-------------------~~~~~~~~~~lie~slw~~L~~ItDkTqv 87 (146)
T PF07295_consen 27 LVAAGELTREELALVSAYLKRDLEEFARYYEE-------------------LREWLSPDLQLIEESLWDELSSITDKTQV 87 (146)
T ss_pred HHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH-------------------hhhhccccHHHHHHHHHHHHHhhhchhHH
Confidence 34457888888888888878888877777776 01223344444444443333333
Q ss_pred -----HHHHHHHHh----hcCCCCeeecCCCCCccchhhhhhccC
Q psy5744 114 -----RKRMEMEER----DATSRSSFKCPRCLKTFTDLEPCLLVL 149 (157)
Q Consensus 114 -----~~~L~~~~~----~~~~~~~Y~Cp~C~~~Ys~lda~~L~d 149 (157)
.+.++..-. .....-.|+|.+||..-.+..+..|..
T Consensus 88 Ew~el~~d~~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~~ 132 (146)
T PF07295_consen 88 EWAELAQDLEHHGVYHSGEVVGPGTLVCENCGHEVELTHPERLPP 132 (146)
T ss_pred HHHHHHHHHHhcCCeecCcEecCceEecccCCCEEEecCCCcCCC
Confidence 333333211 112334789999999999988877654
No 480
>PRK07726 DNA topoisomerase III; Provisional
Probab=44.98 E-value=24 Score=32.80 Aligned_cols=31 Identities=16% Similarity=0.040 Sum_probs=27.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhC-cceeeeE
Q psy5744 49 DDICELLKFERKMLRARISTLKND-KIIQTRL 79 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d-~Lv~~~~ 79 (157)
.+.+..+|++++++=++++.|++. |+++|-+
T Consensus 288 ~~a~~~~g~s~~~tl~iaQ~LYE~~glITYPR 319 (658)
T PRK07726 288 IDANKRFGLSAKETLDIAQSLYETHKLITYPR 319 (658)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHhcCEEEecC
Confidence 456678899999999999999997 9999973
No 481
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=44.96 E-value=42 Score=27.76 Aligned_cols=50 Identities=14% Similarity=0.227 Sum_probs=41.4
Q ss_pred cCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 28 FYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 28 Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
|.++.---|+-+ +..|.-+=+||-..+++++..+-.-|.+|.+.|||...
T Consensus 10 f~SekRk~lLll-L~egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~ 59 (260)
T COG4742 10 FLSEKRKDLLLL-LKEGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE 59 (260)
T ss_pred HccHHHHHHHHH-HHhCCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEec
Confidence 555554445544 44689999999999999999999999999999999875
No 482
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=44.78 E-value=48 Score=24.85 Aligned_cols=38 Identities=11% Similarity=0.224 Sum_probs=27.1
Q ss_pred CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
.++...-|+.+ +...+|-.+||+.||++...|..+...
T Consensus 7 Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 7 LTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34445555544 356799999999999999777666653
No 483
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.72 E-value=33 Score=24.93 Aligned_cols=26 Identities=15% Similarity=0.050 Sum_probs=22.0
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
...+|-++||+.||++.+.|+..|..
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l~R 145 (160)
T PRK09642 120 LEEKSYQEIALQEKIEVKTVEMKLYR 145 (160)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45789999999999999999776653
No 484
>PRK07219 DNA topoisomerase I; Validated
Probab=44.71 E-value=24 Score=33.69 Aligned_cols=31 Identities=10% Similarity=0.025 Sum_probs=27.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744 49 DDICELLKFERKMLRARISTLKNDKIIQTRL 79 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~ 79 (157)
.+.+..+|+++++.=++++.|++.|||+|-+
T Consensus 291 ~~a~~~~g~sa~~tm~iaQ~LYe~glITYpR 321 (822)
T PRK07219 291 REASKIFGISPKRAMEIAEKLYTAGYISYPR 321 (822)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHhCCceeccC
Confidence 3556788999999999999999999999973
No 485
>PHA01976 helix-turn-helix protein
Probab=44.25 E-value=41 Score=20.84 Aligned_cols=25 Identities=0% Similarity=-0.009 Sum_probs=20.7
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
..-+|-+++|+.+|+++..|.++..
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4568999999999999888877643
No 486
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=44.23 E-value=41 Score=23.38 Aligned_cols=43 Identities=12% Similarity=0.096 Sum_probs=36.2
Q ss_pred cCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhC
Q psy5744 28 FYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKND 72 (157)
Q Consensus 28 Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d 72 (157)
|.+...+-++.++.+++-++ .-|+.||+++.-+-+.+..|++.
T Consensus 1 ~~~~~~l~~~~av~~~gSis--~AA~~L~iS~stvs~~I~~LE~~ 43 (99)
T TIGR00637 1 FADPRRVALLKAIARMGSIS--QAAKDAGISYKSAWDYIRAMNNL 43 (99)
T ss_pred CCCHHHHHHHHHHHHhCCHH--HHHHHHCCCHHHHHHHHHHHHHH
Confidence 66777888888988877654 57999999999999999999864
No 487
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=44.22 E-value=36 Score=27.74 Aligned_cols=60 Identities=15% Similarity=0.242 Sum_probs=45.9
Q ss_pred HHHHHHHH-HcCCCc-hH-HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744 19 QLSRLVVR-GFYSIE-DS-LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR 78 (157)
Q Consensus 19 ~Lv~~v~R-~Fy~~e-~i-vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~ 78 (157)
..|++++- .-|++- ++ -|++-|-. .|-+.-.-||.+.||....+--+|.+|+..|.+.++
T Consensus 174 t~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSR 237 (261)
T COG4465 174 TVVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 237 (261)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeec
Confidence 45555555 344442 22 26666665 477899999999999999999999999999999987
No 488
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=44.19 E-value=69 Score=26.27 Aligned_cols=24 Identities=4% Similarity=-0.054 Sum_probs=21.4
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARIS 67 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~ 67 (157)
..+|-.+||+.+|++...||++..
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 578999999999999999997765
No 489
>PRK10403 transcriptional regulator NarP; Provisional
Probab=44.02 E-value=52 Score=23.99 Aligned_cols=36 Identities=14% Similarity=0.302 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN 71 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~ 71 (157)
.-|+..+.. .++-++||+.+|++.+.|+..+..+.+
T Consensus 159 ~~vl~~~~~--g~s~~~ia~~l~~s~~tv~~~~~~i~~ 194 (215)
T PRK10403 159 LDVLHELAQ--GLSNKQIASVLNISEQTVKVHIRNLLR 194 (215)
T ss_pred HHHHHHHHC--CCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 345655543 288899999999999988888887764
No 490
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=43.93 E-value=65 Score=22.02 Aligned_cols=35 Identities=23% Similarity=0.196 Sum_probs=27.6
Q ss_pred HHHHHHhCCCcCHHHHHHHhC--CChHHHHHHHHHHh
Q psy5744 36 IIDMLVRNPCMKEDDICELLK--FERKMLRARISTLK 70 (157)
Q Consensus 36 IlD~L~~~~~i~dedLa~~l~--i~~k~vRkiL~~L~ 70 (157)
++|.|...+.++.+|..+... -..++.+++|..|.
T Consensus 21 l~d~L~s~~ILt~~d~EeI~~~~t~~~qa~~LLdiL~ 57 (84)
T cd08810 21 HFDYLRSKRILTRDDCEEISCRTTSRKQAGKLLDILA 57 (84)
T ss_pred HHHHHHHcCCCCHHHHHHHhccCCcHHHHHHHHHHHh
Confidence 899999889999888887774 44557777887766
No 491
>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=43.83 E-value=35 Score=25.33 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=22.8
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744 43 NPCMKEDDICELLKFERKMLRARIST 68 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~ 68 (157)
-..+|-+|||+.||++.+.|+..+..
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 148 FAGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46799999999999999998887764
No 492
>PHA02325 hypothetical protein
Probab=43.80 E-value=10 Score=24.87 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=8.6
Q ss_pred ecCCCCCccc
Q psy5744 131 KCPRCLKTFT 140 (157)
Q Consensus 131 ~Cp~C~~~Ys 140 (157)
+||.|++++-
T Consensus 5 ~CPkC~A~Wl 14 (72)
T PHA02325 5 ICPKCGARWL 14 (72)
T ss_pred ccCccCCEeE
Confidence 7999999874
No 493
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=43.67 E-value=28 Score=31.97 Aligned_cols=30 Identities=17% Similarity=0.137 Sum_probs=27.3
Q ss_pred HHHHHHhCCChHHHHHHHHHHhhC-cceeee
Q psy5744 49 DDICELLKFERKMLRARISTLKND-KIIQTR 78 (157)
Q Consensus 49 edLa~~l~i~~k~vRkiL~~L~~d-~Lv~~~ 78 (157)
.+-+..+|++++.+=.+.++||+. |+|+|-
T Consensus 267 q~As~~lgfs~kktm~iAQ~LYE~~glITYp 297 (570)
T COG0550 267 QEASRKLGFSAKKTMDIAQKLYEGHGLITYP 297 (570)
T ss_pred HHHHHhCCCCHHHHHHHHHHHhcCCCcEEec
Confidence 456788999999999999999997 999996
No 494
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=43.63 E-value=1.2e+02 Score=24.47 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=22.1
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
..-++++||+.+|++..+|+.++..-
T Consensus 125 r~pt~~eiA~~l~i~~~~v~~~~~~~ 150 (257)
T PRK05911 125 KEPTDGELCEYLNISQQELSGWFSSA 150 (257)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence 45679999999999999999987643
No 495
>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=43.59 E-value=1.4e+02 Score=22.31 Aligned_cols=63 Identities=10% Similarity=0.209 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCcCHHHHHHHh------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744 34 SLIIDMLVRNPCMKEDDICELL------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT 101 (157)
Q Consensus 34 ivIlD~L~~~~~i~dedLa~~l------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~ 101 (157)
..||-.|. .+.+.=-+|.+.+ .++.-.|-.+|.+|+++|+|...... . +. ...+.||.|.-..
T Consensus 27 ~~IL~~L~-~~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~-~-~~--gp~RK~Y~LTe~G 95 (138)
T TIGR02719 27 PFLLLCLK-DWNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDT-S-AE--GPAKRIYSLTDAG 95 (138)
T ss_pred HHHHHHHc-cCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeee-c-CC--CCCcEEEEECHHH
Confidence 44555544 3445555555443 46667899999999999999876322 2 22 3457899898644
No 496
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=43.58 E-value=39 Score=25.26 Aligned_cols=28 Identities=4% Similarity=0.100 Sum_probs=23.7
Q ss_pred CCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744 43 NPCMKEDDICELLKFERKMLRARISTLK 70 (157)
Q Consensus 43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~ 70 (157)
...++-++||+.||++.+.|+..++.-.
T Consensus 142 ~~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (186)
T PRK05602 142 YQGLSNIEAAAVMDISVDALESLLARGR 169 (186)
T ss_pred hcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 3588999999999999999988877543
No 497
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=43.58 E-value=41 Score=19.07 Aligned_cols=26 Identities=15% Similarity=0.160 Sum_probs=19.8
Q ss_pred CCcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744 44 PCMKEDDICELLKFERKMLRARISTL 69 (157)
Q Consensus 44 ~~i~dedLa~~l~i~~k~vRkiL~~L 69 (157)
..++=+|||..+|+++..++++..+.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45888999999999999999988754
No 498
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=43.37 E-value=11 Score=22.58 Aligned_cols=14 Identities=43% Similarity=0.679 Sum_probs=11.0
Q ss_pred CeeecCCCCCccch
Q psy5744 128 SSFKCPRCLKTFTD 141 (157)
Q Consensus 128 ~~Y~Cp~C~~~Ys~ 141 (157)
..=+||.||+-||-
T Consensus 7 p~K~C~~C~rpf~W 20 (42)
T PF10013_consen 7 PSKICPVCGRPFTW 20 (42)
T ss_pred CCCcCcccCCcchH
Confidence 34579999999874
No 499
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=43.27 E-value=15 Score=19.90 Aligned_cols=16 Identities=44% Similarity=0.675 Sum_probs=12.6
Q ss_pred eeecCCCCCccchhhh
Q psy5744 129 SFKCPRCLKTFTDLEP 144 (157)
Q Consensus 129 ~Y~Cp~C~~~Ys~lda 144 (157)
.|.|.-|++.|+...+
T Consensus 3 ~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 3 GFYCKLCNVTFTDEIS 18 (35)
T ss_pred CeEccccCCccCCHHH
Confidence 4779999999995444
No 500
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=43.02 E-value=69 Score=21.84 Aligned_cols=36 Identities=11% Similarity=0.176 Sum_probs=27.0
Q ss_pred HHHHHHHhCCCcCHHHHHHHhCC--ChHHHHHHHHHHh
Q psy5744 35 LIIDMLVRNPCMKEDDICELLKF--ERKMLRARISTLK 70 (157)
Q Consensus 35 vIlD~L~~~~~i~dedLa~~l~i--~~k~vRkiL~~L~ 70 (157)
-|+|.|+..+.+++++....-.- ...+.|++|..|-
T Consensus 18 ~ild~L~~~gvlt~~~~e~I~~~~t~~~qa~~Lld~L~ 55 (86)
T cd08323 18 YIMDHMISDGVLTLDEEEKVKSKATQKEKAVMLINMIL 55 (86)
T ss_pred HHHHHHHhcCCCCHHHHHHHHcCCChHHHHHHHHHHHH
Confidence 38999999899998888776644 3457777777654
Done!