Query 034587
Match_columns 90
No_of_seqs 100 out of 303
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:24:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034587.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034587hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01090 Ribosomal_S19e: Ribos 100.0 2.9E-44 6.3E-49 255.2 6.4 87 3-89 52-138 (139)
2 PTZ00095 40S ribosomal protein 100.0 3.9E-43 8.5E-48 255.9 9.0 87 3-89 77-164 (169)
3 KOG3411 40S ribosomal protein 100.0 1.3E-42 2.9E-47 246.2 8.4 88 3-90 55-142 (143)
4 PRK09333 30S ribosomal protein 100.0 2.3E-41 5E-46 242.8 8.8 86 3-89 53-138 (150)
5 COG2238 RPS19A Ribosomal prote 100.0 2E-41 4.4E-46 241.8 8.2 86 3-89 53-138 (147)
6 PF08461 HTH_12: Ribonuclease 97.7 8.5E-05 1.8E-09 46.4 5.0 63 8-79 3-66 (66)
7 PF03444 HrcA_DNA-bdg: Winged 97.6 6.9E-05 1.5E-09 49.1 3.0 57 11-81 15-75 (78)
8 TIGR02337 HpaR homoprotocatech 97.3 0.0034 7.3E-08 41.6 8.2 67 6-86 31-103 (118)
9 COG1420 HrcA Transcriptional r 97.1 0.0012 2.7E-08 52.8 6.2 65 2-78 5-75 (346)
10 PF14947 HTH_45: Winged helix- 97.1 0.0018 3.9E-08 41.0 5.6 62 6-83 9-70 (77)
11 PRK11512 DNA-binding transcrip 97.1 0.0058 1.2E-07 41.8 8.1 66 5-84 42-113 (144)
12 TIGR02702 SufR_cyano iron-sulf 97.0 0.002 4.4E-08 46.8 5.6 61 6-80 4-72 (203)
13 smart00347 HTH_MARR helix_turn 97.0 0.013 2.8E-07 36.2 8.4 71 2-86 9-85 (101)
14 PRK11050 manganese transport r 97.0 0.0062 1.3E-07 42.8 7.6 63 8-84 42-104 (152)
15 smart00529 HTH_DTXR Helix-turn 96.9 0.0029 6.3E-08 40.1 4.9 41 44-84 12-52 (96)
16 PF01638 HxlR: HxlR-like helix 96.8 0.0043 9.4E-08 39.9 5.7 65 5-83 7-77 (90)
17 PF13463 HTH_27: Winged helix 96.8 0.003 6.4E-08 37.6 4.5 58 4-75 4-68 (68)
18 COG1846 MarR Transcriptional r 96.8 0.011 2.4E-07 37.3 7.2 66 5-84 24-95 (126)
19 PRK03911 heat-inducible transc 96.6 0.0073 1.6E-07 47.3 6.4 65 2-78 2-72 (260)
20 smart00418 HTH_ARSR helix_turn 96.6 0.014 3E-07 32.9 6.2 59 8-81 2-64 (66)
21 PRK10870 transcriptional repre 96.6 0.013 2.9E-07 42.0 7.3 65 7-85 59-131 (176)
22 TIGR01889 Staph_reg_Sar staphy 96.5 0.019 4.2E-07 37.9 7.0 68 6-87 28-105 (109)
23 PRK03573 transcriptional regul 96.4 0.036 7.8E-07 37.6 8.2 65 7-85 35-106 (144)
24 smart00346 HTH_ICLR helix_turn 96.3 0.027 5.8E-07 35.1 6.5 60 3-76 5-66 (91)
25 COG3388 Predicted transcriptio 96.3 0.009 2E-07 40.9 4.6 69 3-86 14-82 (101)
26 PRK13777 transcriptional regul 96.2 0.039 8.4E-07 40.6 7.9 67 6-86 48-120 (185)
27 PRK03902 manganese transport t 96.1 0.039 8.5E-07 37.8 7.0 55 14-82 19-73 (142)
28 PF14338 Mrr_N: Mrr N-terminal 96.1 0.0089 1.9E-07 38.6 3.6 35 46-80 55-89 (92)
29 PRK00082 hrcA heat-inducible t 96.0 0.025 5.4E-07 44.8 6.5 65 2-78 5-75 (339)
30 PF05491 RuvB_C: Holliday junc 95.9 0.0043 9.3E-08 40.5 1.6 58 9-80 17-74 (76)
31 TIGR03433 padR_acidobact trans 95.7 0.023 5E-07 37.3 4.4 47 40-86 34-88 (100)
32 PF10711 DUF2513: Hypothetical 95.7 0.021 4.6E-07 37.9 4.2 47 36-82 25-80 (102)
33 COG3432 Predicted transcriptio 95.7 0.02 4.3E-07 38.8 4.0 43 41-83 41-86 (95)
34 TIGR01884 cas_HTH CRISPR locus 95.6 0.044 9.5E-07 39.8 6.1 60 2-75 142-203 (203)
35 PF09339 HTH_IclR: IclR helix- 95.6 0.028 6E-07 32.7 4.0 49 3-65 3-52 (52)
36 TIGR03338 phnR_burk phosphonat 95.5 0.023 4.9E-07 40.6 4.1 65 4-82 15-85 (212)
37 COG1693 Repressor of nif and g 95.5 0.017 3.6E-07 46.4 3.6 65 8-81 11-76 (325)
38 cd07377 WHTH_GntR Winged helix 95.4 0.1 2.2E-06 30.1 5.9 40 19-72 27-66 (66)
39 TIGR00331 hrcA heat shock gene 95.2 0.07 1.5E-06 42.2 6.4 63 4-78 3-71 (337)
40 PF13601 HTH_34: Winged helix 95.2 0.046 1E-06 34.9 4.3 61 12-86 9-76 (80)
41 PRK05638 threonine synthase; V 95.2 0.057 1.2E-06 43.6 5.8 63 7-82 375-441 (442)
42 PF12802 MarR_2: MarR family; 95.1 0.072 1.6E-06 31.0 4.8 50 2-65 4-55 (62)
43 PF03551 PadR: Transcriptional 95.1 0.021 4.5E-07 35.3 2.5 42 40-81 26-75 (75)
44 TIGR02719 repress_PhaQ poly-be 94.8 0.04 8.6E-07 39.2 3.7 44 43-86 55-106 (138)
45 PRK09834 DNA-binding transcrip 94.8 0.15 3.3E-06 38.2 6.9 62 3-78 11-74 (263)
46 TIGR02944 suf_reg_Xantho FeS a 94.7 0.19 4E-06 33.8 6.6 69 4-86 10-83 (130)
47 cd00092 HTH_CRP helix_turn_hel 94.7 0.2 4.4E-06 29.2 6.0 57 3-73 3-67 (67)
48 PF09114 MotA_activ: Transcrip 94.6 0.29 6.2E-06 33.3 7.2 73 1-86 14-86 (96)
49 COG1321 TroR Mn-dependent tran 94.4 0.071 1.5E-06 38.1 4.2 61 7-81 10-74 (154)
50 PF02082 Rrf2: Transcriptional 94.4 0.11 2.5E-06 32.7 4.6 45 17-75 25-71 (83)
51 PF01047 MarR: MarR family; I 94.3 0.13 2.7E-06 29.9 4.5 49 3-65 3-51 (59)
52 PRK11534 DNA-binding transcrip 94.2 0.08 1.7E-06 38.2 4.2 51 18-82 31-81 (224)
53 COG1802 GntR Transcriptional r 94.2 0.3 6.4E-06 35.5 7.2 52 17-82 39-90 (230)
54 TIGR02812 fadR_gamma fatty aci 94.2 0.086 1.9E-06 38.3 4.3 42 19-74 32-73 (235)
55 COG1725 Predicted transcriptio 94.2 0.083 1.8E-06 37.2 4.0 37 46-82 50-86 (125)
56 PF12840 HTH_20: Helix-turn-he 94.1 0.11 2.3E-06 31.0 3.9 46 6-65 13-58 (61)
57 cd00090 HTH_ARSR Arsenical Res 94.1 0.28 6.2E-06 28.0 5.6 63 6-84 10-75 (78)
58 PRK09990 DNA-binding transcrip 93.9 0.076 1.6E-06 39.0 3.6 45 19-77 33-77 (251)
59 COG1733 Predicted transcriptio 93.8 0.22 4.9E-06 34.2 5.6 62 8-83 28-95 (120)
60 TIGR02277 PaaX_trns_reg phenyl 93.8 0.095 2E-06 40.5 4.1 43 46-88 35-80 (280)
61 PRK11414 colanic acid/biofilm 93.6 0.11 2.5E-06 37.4 4.1 51 18-82 35-85 (221)
62 smart00345 HTH_GNTR helix_turn 93.4 0.095 2.1E-06 29.7 2.7 36 19-68 22-57 (60)
63 PRK11014 transcriptional repre 93.2 0.23 5E-06 34.1 4.9 43 17-73 25-69 (141)
64 PF12793 SgrR_N: Sugar transpo 93.0 0.11 2.3E-06 35.6 2.9 39 17-69 19-57 (115)
65 PF00392 GntR: Bacterial regul 92.9 0.12 2.7E-06 30.9 2.8 37 19-69 26-62 (64)
66 smart00420 HTH_DEOR helix_turn 92.7 0.46 1E-05 26.1 4.9 45 7-65 4-48 (53)
67 PRK09416 lstR lineage-specific 92.5 0.14 3.1E-06 36.5 3.1 43 43-85 75-121 (135)
68 PF10007 DUF2250: Uncharacteri 92.5 0.41 8.9E-06 32.0 5.1 50 6-71 10-59 (92)
69 PF13412 HTH_24: Winged helix- 92.5 0.62 1.3E-05 26.2 5.2 47 2-62 2-48 (48)
70 smart00550 Zalpha Z-DNA-bindin 92.5 0.54 1.2E-05 29.0 5.3 46 6-65 9-56 (68)
71 PRK10421 DNA-binding transcrip 92.4 0.14 3.1E-06 37.8 3.0 42 19-74 28-69 (253)
72 PRK10225 DNA-binding transcrip 92.1 0.15 3.3E-06 37.6 2.9 44 19-76 35-78 (257)
73 PRK04984 fatty acid metabolism 92.0 0.18 4E-06 36.6 3.2 41 19-73 33-73 (239)
74 PRK15090 DNA-binding transcrip 92.0 0.52 1.1E-05 35.0 5.7 58 3-74 14-72 (257)
75 PRK09464 pdhR transcriptional 91.8 0.18 3.8E-06 37.1 3.0 41 19-73 36-76 (254)
76 PRK03837 transcriptional regul 91.8 0.2 4.3E-06 36.3 3.1 42 19-74 39-80 (241)
77 PF08220 HTH_DeoR: DeoR-like h 91.7 0.56 1.2E-05 27.9 4.6 47 5-65 2-48 (57)
78 PRK08599 coproporphyrinogen II 91.7 0.63 1.4E-05 36.5 6.1 61 15-89 316-376 (377)
79 PRK11523 DNA-binding transcrip 91.6 0.19 4.1E-06 37.1 3.0 42 20-75 35-76 (253)
80 PRK09057 coproporphyrinogen II 91.5 1 2.3E-05 35.6 7.2 57 15-87 323-379 (380)
81 COG1414 IclR Transcriptional r 91.4 0.68 1.5E-05 34.8 5.8 57 3-74 4-63 (246)
82 TIGR01610 phage_O_Nterm phage 91.2 1.1 2.4E-05 29.1 6.0 50 2-65 24-81 (95)
83 PRK14165 winged helix-turn-hel 91.1 0.36 7.8E-06 36.5 4.0 55 18-86 22-79 (217)
84 TIGR00738 rrf2_super rrf2 fami 91.1 2 4.4E-05 28.4 7.3 49 16-78 24-74 (132)
85 PF06969 HemN_C: HemN C-termin 91.0 0.6 1.3E-05 27.8 4.3 52 11-76 14-65 (66)
86 PRK11569 transcriptional repre 90.8 0.87 1.9E-05 34.4 5.9 58 3-74 28-87 (274)
87 PRK10163 DNA-binding transcrip 90.6 0.97 2.1E-05 34.1 6.0 58 3-74 25-84 (271)
88 COG1695 Predicted transcriptio 90.1 0.47 1E-05 32.1 3.6 42 44-85 43-92 (138)
89 PF01726 LexA_DNA_bind: LexA D 89.9 0.43 9.3E-06 29.6 3.0 40 17-69 25-64 (65)
90 PF09382 RQC: RQC domain; Int 89.3 2.2 4.7E-05 27.4 6.1 79 2-80 3-95 (106)
91 COG3355 Predicted transcriptio 89.3 1.5 3.3E-05 31.0 5.7 59 14-86 39-111 (126)
92 TIGR02787 codY_Gpos GTP-sensin 88.8 0.46 9.9E-06 37.2 3.1 61 7-81 187-250 (251)
93 PRK07379 coproporphyrinogen II 88.7 0.59 1.3E-05 37.4 3.8 39 47-87 352-393 (400)
94 PRK05660 HemN family oxidoredu 88.6 0.76 1.6E-05 36.4 4.3 58 17-89 321-378 (378)
95 PRK11920 rirA iron-responsive 88.6 0.56 1.2E-05 33.1 3.2 47 16-76 23-71 (153)
96 PRK05628 coproporphyrinogen II 88.5 0.68 1.5E-05 36.3 3.9 38 49-87 337-374 (375)
97 TIGR02325 C_P_lyase_phnF phosp 88.5 0.55 1.2E-05 33.9 3.1 43 19-75 34-76 (238)
98 PF13814 Replic_Relax: Replica 88.4 1.4 3.1E-05 30.7 5.2 62 9-81 1-72 (191)
99 PRK08208 coproporphyrinogen II 88.3 0.45 9.6E-06 38.4 2.8 58 16-88 360-417 (430)
100 PRK05799 coproporphyrinogen II 87.8 0.88 1.9E-05 35.5 4.1 40 47-87 334-373 (374)
101 TIGR02010 IscR iron-sulfur clu 87.6 0.73 1.6E-05 31.4 3.2 46 16-75 24-71 (135)
102 PF01978 TrmB: Sugar-specific 87.6 0.8 1.7E-05 27.5 3.0 48 4-65 9-56 (68)
103 TIGR02018 his_ut_repres histid 87.3 0.64 1.4E-05 33.8 2.9 41 19-73 27-67 (230)
104 smart00419 HTH_CRP helix_turn_ 87.3 0.84 1.8E-05 24.9 2.8 35 17-65 8-42 (48)
105 COG2186 FadR Transcriptional r 87.2 0.72 1.6E-05 34.5 3.2 41 19-73 36-76 (241)
106 PRK04172 pheS phenylalanyl-tRN 87.1 1.9 4E-05 35.6 5.8 69 2-84 5-75 (489)
107 COG2524 Predicted transcriptio 87.1 0.54 1.2E-05 37.5 2.6 36 46-81 40-77 (294)
108 PRK06582 coproporphyrinogen II 86.9 3.6 7.7E-05 33.0 7.2 59 14-87 330-389 (390)
109 PRK06294 coproporphyrinogen II 86.9 0.98 2.1E-05 35.7 4.0 39 48-87 332-370 (370)
110 PRK10857 DNA-binding transcrip 86.6 2.3 4.9E-05 30.6 5.4 46 16-75 24-71 (164)
111 PRK13347 coproporphyrinogen II 86.3 1.1 2.4E-05 36.3 4.1 66 9-86 373-438 (453)
112 PRK00215 LexA repressor; Valid 85.9 3.7 8.1E-05 29.4 6.3 64 2-79 3-74 (205)
113 PF04703 FaeA: FaeA-like prote 85.7 2 4.2E-05 26.7 4.1 37 15-65 13-49 (62)
114 COG4901 Ribosomal protein S25 85.6 0.77 1.7E-05 31.8 2.4 40 17-71 59-98 (107)
115 PRK09249 coproporphyrinogen II 85.2 1.1 2.3E-05 36.3 3.5 62 15-87 378-439 (453)
116 TIGR02404 trehalos_R_Bsub treh 85.1 1 2.2E-05 32.7 3.0 41 19-73 26-66 (233)
117 PRK09764 DNA-binding transcrip 85.0 1.1 2.4E-05 32.9 3.2 43 19-75 31-73 (240)
118 PRK08898 coproporphyrinogen II 84.9 1.2 2.6E-05 35.4 3.6 58 15-87 336-393 (394)
119 COG1959 Predicted transcriptio 84.1 1.2 2.6E-05 31.4 3.0 45 17-75 25-71 (150)
120 PRK00080 ruvB Holliday junctio 84.0 1.7 3.6E-05 33.4 3.9 53 13-80 272-325 (328)
121 PRK06266 transcription initiat 83.8 3.1 6.8E-05 30.3 5.1 42 7-62 26-67 (178)
122 PRK08629 coproporphyrinogen II 83.7 3.7 7.9E-05 33.5 6.0 58 16-87 357-414 (433)
123 PRK14999 histidine utilization 83.7 1.3 2.8E-05 32.5 3.1 42 19-74 38-79 (241)
124 TIGR00538 hemN oxygen-independ 83.7 1.4 3E-05 35.7 3.5 36 50-86 403-438 (455)
125 PF14394 DUF4423: Domain of un 83.6 1.3 2.7E-05 32.1 2.9 32 43-74 53-84 (171)
126 TIGR02431 pcaR_pcaU beta-ketoa 83.6 3.8 8.3E-05 30.2 5.6 57 3-74 9-66 (248)
127 PRK13626 transcriptional regul 83.2 1.4 2.9E-05 36.4 3.3 39 17-69 23-61 (552)
128 PF01022 HTH_5: Bacterial regu 83.1 3.2 7E-05 23.4 4.0 42 7-63 6-47 (47)
129 PRK09334 30S ribosomal protein 82.8 1.5 3.2E-05 29.2 2.8 22 44-65 54-75 (86)
130 PRK10079 phosphonate metabolis 82.7 1.4 3E-05 32.3 2.9 42 19-74 37-78 (241)
131 PRK11886 bifunctional biotin-- 82.5 4.7 0.0001 31.0 5.9 58 3-74 4-62 (319)
132 PRK11402 DNA-binding transcrip 81.9 1.7 3.8E-05 31.7 3.2 43 19-75 35-77 (241)
133 PF01325 Fe_dep_repress: Iron 81.6 6.3 0.00014 23.8 5.1 52 3-68 4-59 (60)
134 TIGR00122 birA_repr_reg BirA b 81.5 9.1 0.0002 22.9 6.1 53 7-74 4-56 (69)
135 PRK09058 coproporphyrinogen II 81.3 2.1 4.5E-05 34.8 3.7 39 48-87 398-436 (449)
136 PF09012 FeoC: FeoC like trans 80.0 3.8 8.2E-05 24.9 3.8 40 12-65 9-48 (69)
137 TIGR00635 ruvB Holliday juncti 79.5 2.7 5.8E-05 31.4 3.5 50 15-79 253-303 (305)
138 COG2255 RuvB Holliday junction 78.9 4.3 9.3E-05 33.0 4.7 54 13-80 273-326 (332)
139 PRK08446 coproporphyrinogen II 78.9 2.8 6.1E-05 32.8 3.6 37 48-87 313-349 (350)
140 PF14277 DUF4364: Domain of un 78.6 3.4 7.4E-05 29.8 3.7 40 47-86 35-78 (163)
141 COG2188 PhnF Transcriptional r 78.5 2.4 5.2E-05 31.4 3.0 31 44-74 44-74 (236)
142 PRK09802 DNA-binding transcrip 78.2 8.2 0.00018 29.4 5.9 56 2-72 16-71 (269)
143 PF09821 AAA_assoc_C: C-termin 77.6 3 6.6E-05 28.7 3.1 31 50-81 16-46 (120)
144 TIGR00373 conserved hypothetic 76.4 7.9 0.00017 27.6 5.1 44 5-62 16-59 (158)
145 PRK13509 transcriptional repre 76.4 8.9 0.00019 28.8 5.6 49 3-65 5-53 (251)
146 PF03297 Ribosomal_S25: S25 ri 76.2 2.4 5.1E-05 29.0 2.2 35 17-65 59-93 (105)
147 TIGR02647 DNA conserved hypoth 75.9 7.3 0.00016 25.6 4.3 39 40-81 29-67 (77)
148 PF14178 YppF: YppF-like prote 75.8 6.1 0.00013 24.8 3.8 18 8-25 27-44 (60)
149 PF13730 HTH_36: Helix-turn-he 75.4 3.1 6.7E-05 23.7 2.3 18 44-61 38-55 (55)
150 PRK12423 LexA repressor; Provi 75.1 3.5 7.7E-05 29.9 3.0 36 18-66 26-61 (202)
151 COG1542 Uncharacterized conser 75.0 2.8 6.2E-05 36.0 2.8 62 7-82 429-493 (593)
152 COG0635 HemN Coproporphyrinoge 74.6 5.5 0.00012 32.4 4.3 59 15-87 352-410 (416)
153 PRK10434 srlR DNA-bindng trans 74.4 11 0.00023 28.5 5.6 55 2-71 4-58 (256)
154 COG2512 Predicted membrane-ass 73.9 3.2 6.9E-05 32.1 2.7 23 46-68 225-247 (258)
155 PF07848 PaaX: PaaX-like prote 73.4 4.1 9E-05 25.6 2.7 60 5-75 2-70 (70)
156 PRK09213 pur operon repressor; 73.2 21 0.00046 27.9 7.1 79 2-88 6-93 (271)
157 PF08222 HTH_CodY: CodY helix- 72.5 3.9 8.4E-05 25.8 2.3 21 45-65 18-38 (61)
158 TIGR00498 lexA SOS regulatory 71.4 18 0.00039 25.7 5.9 49 5-66 8-61 (199)
159 smart00344 HTH_ASNC helix_turn 71.0 14 0.0003 23.5 4.8 70 7-90 7-88 (108)
160 PF11313 DUF3116: Protein of u 70.9 6.2 0.00013 26.2 3.2 39 47-85 43-84 (85)
161 PF09681 Phage_rep_org_N: N-te 69.8 7.4 0.00016 26.9 3.5 43 17-73 53-95 (121)
162 TIGR00637 ModE_repress ModE mo 68.3 10 0.00023 24.9 3.9 34 46-79 31-71 (99)
163 PF00126 HTH_1: Bacterial regu 68.2 6.5 0.00014 23.1 2.6 31 45-76 27-60 (60)
164 PRK04424 fatty acid biosynthes 68.1 10 0.00022 27.4 4.1 48 3-64 7-54 (185)
165 TIGR01743 purR_Bsub pur operon 67.2 32 0.0007 26.8 6.9 79 2-88 4-91 (268)
166 PRK10906 DNA-binding transcrip 66.8 22 0.00048 26.8 5.8 56 2-72 4-59 (252)
167 PRK15481 transcriptional regul 66.5 7.2 0.00016 30.7 3.3 41 19-73 31-71 (431)
168 TIGR02424 TF_pcaQ pca operon t 64.7 9 0.00019 28.0 3.3 36 47-83 33-71 (300)
169 PRK10411 DNA-binding transcrip 64.5 28 0.00061 26.0 6.0 51 2-66 3-53 (240)
170 PF03836 RasGAP_C: RasGAP C-te 64.4 2.2 4.8E-05 29.7 0.0 33 47-87 8-40 (142)
171 PF07381 DUF1495: Winged helix 64.2 5.6 0.00012 26.5 2.0 28 54-81 58-89 (90)
172 PF04408 HA2: Helicase associa 64.0 5.6 0.00012 25.8 1.9 25 50-78 1-25 (102)
173 TIGR02698 CopY_TcrY copper tra 62.0 35 0.00076 23.3 5.7 54 5-69 6-59 (130)
174 PRK09791 putative DNA-binding 61.2 15 0.00032 27.0 3.9 38 46-84 34-74 (302)
175 TIGR02147 Fsuc_second hypothet 61.0 9.1 0.0002 29.7 2.9 29 44-72 152-180 (271)
176 TIGR03337 phnR transcriptional 60.7 11 0.00023 27.0 3.0 43 19-75 27-69 (231)
177 PRK10141 DNA-binding transcrip 60.5 30 0.00065 23.7 5.1 60 7-81 20-83 (117)
178 COG3327 PaaX Phenylacetic acid 60.1 14 0.0003 29.6 3.7 44 46-89 43-89 (291)
179 COG4533 ABC-type uncharacteriz 60.0 8.7 0.00019 33.2 2.8 58 17-88 23-86 (564)
180 PRK10082 cell density-dependen 59.5 12 0.00025 27.7 3.1 37 46-83 40-79 (303)
181 PHA02943 hypothetical protein; 59.0 35 0.00076 25.3 5.5 48 4-66 12-59 (165)
182 KOG1767 40S ribosomal protein 57.8 7.9 0.00017 27.0 1.8 23 43-65 72-94 (110)
183 PRK11242 DNA-binding transcrip 56.9 16 0.00035 26.4 3.5 37 46-83 30-69 (296)
184 PRK14997 LysR family transcrip 56.2 12 0.00026 27.4 2.7 36 47-83 32-70 (301)
185 TIGR03339 phn_lysR aminoethylp 55.8 19 0.0004 25.6 3.6 34 47-81 27-63 (279)
186 PF08279 HTH_11: HTH domain; 55.8 35 0.00077 19.1 4.6 48 4-65 1-50 (55)
187 smart00847 HA2 Helicase associ 55.2 10 0.00022 23.5 1.9 24 51-78 2-25 (92)
188 COG1568 Predicted methyltransf 54.9 14 0.0003 30.2 3.0 34 46-80 49-82 (354)
189 TIGR02036 dsdC D-serine deamin 54.9 26 0.00057 25.9 4.4 37 47-84 38-77 (302)
190 PF07042 TrfA: TrfA protein; 54.2 9.3 0.0002 30.2 1.9 40 17-63 231-270 (282)
191 PRK00135 scpB segregation and 54.1 51 0.0011 24.3 5.7 44 3-63 90-133 (188)
192 PRK11151 DNA-binding transcrip 54.1 21 0.00045 26.2 3.7 36 46-82 30-68 (305)
193 PRK11233 nitrogen assimilation 53.9 21 0.00045 26.4 3.7 37 46-83 30-69 (305)
194 PRK10402 DNA-binding transcrip 52.4 20 0.00043 25.8 3.3 39 46-87 184-222 (226)
195 PRK11716 DNA-binding transcrip 52.3 27 0.00059 24.5 3.9 37 47-84 7-46 (269)
196 PRK03601 transcriptional regul 52.1 20 0.00044 26.2 3.3 37 47-84 31-70 (275)
197 COG1349 GlpR Transcriptional r 51.1 44 0.00096 25.2 5.1 57 2-73 4-60 (253)
198 PRK09986 DNA-binding transcrip 50.8 22 0.00047 25.7 3.3 35 47-82 37-74 (294)
199 COG3398 Uncharacterized protei 50.8 17 0.00038 28.4 2.9 27 44-71 201-227 (240)
200 PF03965 Penicillinase_R: Peni 50.1 34 0.00073 22.5 3.9 51 6-66 6-56 (115)
201 COG2345 Predicted transcriptio 49.9 48 0.001 25.3 5.1 56 8-77 16-79 (218)
202 PRK12681 cysB transcriptional 49.7 20 0.00044 27.1 3.1 37 47-83 32-71 (324)
203 COG1654 BirA Biotin operon rep 49.7 24 0.00053 22.8 3.0 30 44-73 32-62 (79)
204 TIGR03418 chol_sulf_TF putativ 49.4 25 0.00053 25.5 3.4 36 47-83 31-69 (291)
205 PRK12680 transcriptional regul 49.4 23 0.00049 27.0 3.3 37 47-84 32-72 (327)
206 PRK09906 DNA-binding transcrip 48.7 20 0.00043 26.1 2.8 36 47-83 31-69 (296)
207 PRK11062 nhaR transcriptional 48.6 25 0.00055 25.9 3.4 37 47-84 34-73 (296)
208 PRK10632 transcriptional regul 48.5 31 0.00066 25.7 3.9 38 46-84 31-71 (309)
209 cd08768 Cdc6_C Winged-helix do 48.1 16 0.00035 22.4 2.0 45 16-65 21-66 (87)
210 PRK10094 DNA-binding transcrip 47.8 27 0.00059 26.0 3.5 36 47-83 32-70 (308)
211 PRK10837 putative DNA-binding 46.9 29 0.00062 25.0 3.4 35 47-82 33-70 (290)
212 TIGR03298 argP transcriptional 46.9 27 0.00058 25.4 3.3 36 47-84 31-69 (292)
213 PRK11013 DNA-binding transcrip 46.0 27 0.00059 25.9 3.2 37 46-83 33-72 (309)
214 PRK12684 transcriptional regul 45.9 27 0.00059 26.1 3.2 38 47-84 32-72 (313)
215 PF09202 Rio2_N: Rio2, N-termi 45.7 28 0.00061 22.5 2.9 35 45-79 38-74 (82)
216 PRK10086 DNA-binding transcrip 45.3 20 0.00044 26.6 2.5 35 47-82 44-81 (311)
217 PRK12682 transcriptional regul 44.9 33 0.00072 25.3 3.5 38 47-85 32-73 (309)
218 PRK09954 putative kinase; Prov 44.1 99 0.0021 23.8 6.2 56 1-73 1-56 (362)
219 PF04458 DUF505: Protein of un 43.8 28 0.0006 30.4 3.3 32 47-78 466-497 (591)
220 COG4754 Uncharacterized conser 43.5 25 0.00055 25.9 2.6 32 49-81 46-77 (157)
221 COG1510 Predicted transcriptio 43.5 35 0.00076 25.6 3.4 49 8-70 31-81 (177)
222 PRK06474 hypothetical protein; 43.4 89 0.0019 22.5 5.5 46 7-65 15-61 (178)
223 PRK15092 DNA-binding transcrip 43.3 32 0.00068 26.0 3.3 35 48-83 42-79 (310)
224 PF14502 HTH_41: Helix-turn-he 43.3 27 0.00058 21.0 2.3 25 44-69 19-43 (48)
225 PRK11139 DNA-binding transcrip 43.3 38 0.00083 24.7 3.6 37 46-83 35-74 (297)
226 PF02980 FokI_C: Restriction e 43.2 24 0.00052 25.6 2.5 44 39-82 76-135 (142)
227 CHL00180 rbcR LysR transcripti 43.1 37 0.00079 25.1 3.5 36 47-83 35-73 (305)
228 PRK15421 DNA-binding transcrip 43.0 34 0.00075 25.7 3.4 35 47-82 32-69 (317)
229 PF04458 DUF505: Protein of un 43.0 23 0.0005 30.9 2.7 40 43-82 327-370 (591)
230 COG1339 Transcriptional regula 43.0 27 0.00057 26.9 2.8 37 49-85 37-76 (214)
231 PF09079 Cdc6_C: CDC6, C termi 42.8 23 0.00049 22.0 2.1 44 17-65 15-59 (85)
232 PF09397 Ftsk_gamma: Ftsk gamm 42.7 27 0.00059 21.8 2.4 38 14-65 17-54 (65)
233 PRK13348 chromosome replicatio 42.2 38 0.00083 24.6 3.5 36 47-84 32-70 (294)
234 PHA00738 putative HTH transcri 41.7 80 0.0017 21.8 4.8 48 8-70 17-64 (108)
235 PRK10341 DNA-binding transcrip 41.6 41 0.00088 25.0 3.6 35 47-82 37-74 (312)
236 COG4189 Predicted transcriptio 41.1 62 0.0013 25.9 4.7 48 8-69 28-75 (308)
237 PRK05974 phosphoribosylformylg 39.7 39 0.00084 21.3 2.8 42 45-90 18-69 (80)
238 TIGR02716 C20_methyl_CrtF C-20 39.4 28 0.00061 26.2 2.5 51 15-80 21-71 (306)
239 PF09929 DUF2161: Uncharacteri 39.0 12 0.00027 26.2 0.4 58 5-79 61-118 (118)
240 PRK09508 leuO leucine transcri 38.6 60 0.0013 24.1 4.1 37 20-56 57-97 (314)
241 PF13545 HTH_Crp_2: Crp-like h 38.2 40 0.00086 19.9 2.6 22 44-65 41-62 (76)
242 PF09639 YjcQ: YjcQ protein; 38.0 33 0.00072 22.0 2.4 36 46-81 25-69 (88)
243 PF13182 DUF4007: Protein of u 38.0 23 0.0005 27.4 1.9 38 43-80 39-77 (286)
244 PRK12683 transcriptional regul 37.7 43 0.00093 25.0 3.2 36 47-83 32-71 (309)
245 COG1497 Predicted transcriptio 37.3 45 0.00098 26.4 3.3 35 49-83 43-77 (260)
246 PF03969 AFG1_ATPase: AFG1-lik 35.5 53 0.0012 26.4 3.6 47 9-59 62-111 (362)
247 PF02002 TFIIE_alpha: TFIIE al 35.2 58 0.0013 20.9 3.2 44 5-62 15-58 (105)
248 PRK11074 putative DNA-binding 34.8 65 0.0014 23.6 3.8 37 46-83 31-70 (300)
249 TIGR02802 Pal_lipo peptidoglyc 34.7 42 0.00091 21.3 2.4 24 67-90 7-30 (104)
250 PRK03635 chromosome replicatio 34.2 44 0.00095 24.5 2.7 35 47-83 32-69 (294)
251 PRK15431 ferrous iron transpor 34.1 1E+02 0.0022 20.1 4.1 41 11-65 10-50 (78)
252 PF04182 B-block_TFIIIC: B-blo 34.0 31 0.00066 21.3 1.6 20 46-65 33-52 (75)
253 TIGR01714 phage_rep_org_N phag 34.0 52 0.0011 22.8 2.9 42 17-72 51-92 (119)
254 PRK12679 cbl transcriptional r 33.9 57 0.0012 24.4 3.3 36 47-83 32-71 (316)
255 COG4344 Uncharacterized protei 33.8 31 0.00067 25.7 1.9 19 47-65 47-65 (175)
256 COG4465 CodY Pleiotropic trans 33.3 33 0.00071 27.0 2.0 21 45-65 218-238 (261)
257 PRK04214 rbn ribonuclease BN/u 33.0 50 0.0011 26.6 3.1 29 44-72 323-351 (412)
258 PF14557 AphA_like: Putative A 32.6 86 0.0019 23.5 4.0 45 43-87 44-94 (175)
259 PF10396 TrmE_N: GTP-binding p 32.5 41 0.00088 23.2 2.2 28 38-65 75-102 (114)
260 COG0583 LysR Transcriptional r 32.3 68 0.0015 22.6 3.4 37 47-84 31-70 (297)
261 PRK11482 putative DNA-binding 32.2 80 0.0017 23.7 3.9 34 47-81 59-95 (317)
262 smart00843 Ftsk_gamma This dom 32.1 44 0.00095 20.9 2.1 36 15-64 17-52 (63)
263 PRK15243 transcriptional regul 31.9 74 0.0016 24.3 3.7 37 46-83 33-72 (297)
264 PF02923 BamHI: Restriction en 31.8 20 0.00044 26.4 0.6 29 25-62 43-71 (158)
265 PF01121 CoaE: Dephospho-CoA k 31.8 37 0.0008 24.4 2.0 42 5-55 30-71 (180)
266 COG5631 Predicted transcriptio 31.4 89 0.0019 23.7 4.0 38 46-83 114-154 (199)
267 PF14357 DUF4404: Domain of un 31.2 47 0.001 21.5 2.2 18 43-60 68-85 (85)
268 PF09661 DUF2398: Protein of u 30.5 1.2E+02 0.0026 24.5 4.9 51 20-74 308-358 (368)
269 PRK09801 transcriptional activ 30.3 47 0.001 24.8 2.4 36 47-83 36-74 (310)
270 PF14629 ORC4_C: Origin recogn 30.1 56 0.0012 23.3 2.7 36 41-76 149-185 (203)
271 PRK04158 transcriptional repre 30.1 29 0.00063 27.3 1.2 21 45-65 215-235 (256)
272 PRK09391 fixK transcriptional 30.0 60 0.0013 23.4 2.8 18 47-64 195-212 (230)
273 TIGR03350 type_VI_ompA type VI 29.9 45 0.00098 22.4 2.1 23 68-90 38-60 (137)
274 PF03180 Lipoprotein_9: NLPA l 29.7 41 0.0009 25.5 2.0 23 50-72 111-133 (237)
275 PF03428 RP-C: Replication pro 28.6 48 0.0011 24.3 2.2 21 44-64 84-104 (177)
276 PF05402 PqqD: Coenzyme PQQ sy 28.4 50 0.0011 19.3 1.9 50 5-62 19-68 (68)
277 COG1386 scpB Chromosome segreg 28.2 2.2E+02 0.0049 20.9 5.6 56 9-81 98-157 (184)
278 COG0735 Fur Fe2+/Zn2+ uptake r 28.2 64 0.0014 22.4 2.6 26 43-68 53-78 (145)
279 COG3398 Uncharacterized protei 28.0 1.6E+02 0.0034 23.2 4.9 49 8-70 106-154 (240)
280 PF03849 Tfb2: Transcription f 27.6 1.3E+02 0.0027 24.3 4.5 45 8-65 36-80 (366)
281 PRK11057 ATP-dependent DNA hel 27.3 1.1E+02 0.0024 25.9 4.3 74 7-80 418-503 (607)
282 KOG4068 Uncharacterized conser 27.2 68 0.0015 24.0 2.7 27 40-66 63-89 (174)
283 PF05732 RepL: Firmicute plasm 26.9 82 0.0018 22.6 3.1 31 44-74 88-118 (165)
284 PF06399 GFRP: GTP cyclohydrol 26.8 47 0.001 22.1 1.6 14 48-61 52-65 (83)
285 TIGR00625 tfb2 Transcription f 26.8 58 0.0013 27.4 2.6 31 49-79 156-187 (448)
286 TIGR03703 plsB glycerol-3-phos 26.7 1.6E+02 0.0034 26.5 5.3 49 35-87 743-791 (799)
287 cd07153 Fur_like Ferric uptake 26.6 45 0.00099 21.3 1.6 49 8-65 6-55 (116)
288 PRK13239 alkylmercury lyase; P 26.4 1.9E+02 0.0042 21.8 5.1 47 7-71 26-72 (206)
289 PF07574 SMC_Nse1: Nse1 non-SM 26.4 55 0.0012 23.8 2.1 31 46-76 167-197 (200)
290 PF00727 IL4: Interleukin 4 Th 26.2 43 0.00093 23.5 1.4 12 4-15 47-58 (117)
291 COG1724 Predicted RNA binding 25.8 67 0.0014 20.5 2.1 16 48-63 9-24 (66)
292 PF08183 SpoV: Stage V sporula 25.8 42 0.00092 17.8 1.0 17 41-57 9-25 (26)
293 PF03849 Tfb2: Transcription f 25.6 41 0.00089 27.1 1.4 30 50-79 157-187 (366)
294 TIGR02928 orc1/cdc6 family rep 25.5 1.6E+02 0.0035 22.3 4.6 44 16-64 306-350 (365)
295 COG1485 Predicted ATPase [Gene 25.5 80 0.0017 26.1 3.1 49 7-59 63-114 (367)
296 PF06044 DRP: Dam-replacing fa 25.5 63 0.0014 25.5 2.4 20 47-66 229-248 (254)
297 PF10264 Stork_head: Winged he 24.5 1.1E+02 0.0024 20.0 3.1 53 16-74 28-80 (80)
298 cd00772 ProRS_core Prolyl-tRNA 24.3 1.5E+02 0.0032 22.4 4.2 37 50-86 5-42 (264)
299 PF12052 VGCC_beta4Aa_N: Volta 23.8 48 0.001 19.5 1.1 13 47-59 28-40 (42)
300 PF13518 HTH_28: Helix-turn-he 23.5 1.4E+02 0.0029 16.1 4.3 39 12-65 8-46 (52)
301 PF13835 DUF4194: Domain of un 23.5 1.7E+02 0.0036 20.3 4.1 57 6-66 80-145 (166)
302 PRK10676 DNA-binding transcrip 23.0 1.3E+02 0.0027 23.0 3.6 34 47-80 47-87 (263)
303 PF08604 Nup153: Nucleoporin N 22.6 51 0.0011 28.4 1.5 13 46-58 197-209 (519)
304 COG3710 CadC DNA-binding winge 22.6 54 0.0012 23.1 1.4 30 45-74 75-105 (148)
305 COG1710 Uncharacterized protei 22.4 48 0.001 23.8 1.1 27 30-60 52-78 (139)
306 PF08784 RPA_C: Replication pr 22.3 76 0.0016 20.2 2.0 33 17-63 65-97 (102)
307 PRK09967 putative outer membra 22.2 73 0.0016 22.6 2.0 23 67-89 59-81 (160)
308 PRK10802 peptidoglycan-associa 22.1 1E+02 0.0022 22.2 2.8 31 59-90 69-99 (173)
309 PRK13918 CRP/FNR family transc 22.1 1.1E+02 0.0024 21.0 2.9 38 44-84 162-199 (202)
310 cd04911 ACT_AKiii-YclM-BS_1 AC 22.1 76 0.0016 20.3 1.9 21 45-65 15-36 (76)
311 COG2885 OmpA Outer membrane pr 21.9 76 0.0017 22.4 2.1 23 68-90 91-113 (190)
312 TIGR00302 phosphoribosylformyl 21.8 1E+02 0.0022 19.3 2.5 15 76-90 55-69 (80)
313 PF02887 PK_C: Pyruvate kinase 21.8 64 0.0014 21.1 1.6 34 32-65 58-94 (117)
314 cd06590 RNaseH_typeII_bacteria 21.7 1E+02 0.0022 22.5 2.7 33 2-36 142-174 (208)
315 smart00351 PAX Paired Box doma 21.6 2.6E+02 0.0057 18.7 4.8 39 16-68 32-70 (125)
316 PRK11169 leucine-responsive tr 21.1 2.6E+02 0.0057 19.4 4.7 70 7-90 18-101 (164)
317 smart00479 EXOIII exonuclease 21.0 1.6E+02 0.0034 19.4 3.4 49 6-57 117-165 (169)
318 PF03004 Transposase_24: Plant 20.9 1.6E+02 0.0035 19.6 3.5 59 29-88 24-93 (141)
319 COG1059 Thermostable 8-oxoguan 20.5 1.5E+02 0.0032 22.9 3.4 33 47-82 149-181 (210)
320 PF05427 FIBP: Acidic fibrobla 20.5 45 0.00097 27.4 0.7 19 68-86 108-126 (361)
321 smart00190 IL4_13 Interleukins 20.3 2.9E+02 0.0064 19.9 4.8 41 4-44 72-116 (138)
322 COG3177 Fic family protein [Fu 20.2 1.1E+02 0.0025 24.1 3.0 29 42-70 315-343 (348)
323 PRK06423 phosphoribosylformylg 20.0 1.1E+02 0.0024 18.8 2.3 23 68-90 39-63 (73)
No 1
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=100.00 E-value=2.9e-44 Score=255.21 Aligned_cols=87 Identities=52% Similarity=0.954 Sum_probs=79.1
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+||||||||||++||+||++|+++|||+||||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+|
T Consensus 52 ~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~i 131 (139)
T PF01090_consen 52 IRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRI 131 (139)
T ss_dssp HHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHH
T ss_pred eeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999989999999999999999
Q ss_pred HHHhhcC
Q 034587 83 AGRIVVA 89 (90)
Q Consensus 83 A~~v~~~ 89 (90)
|.+|+++
T Consensus 132 A~~v~~~ 138 (139)
T PF01090_consen 132 AGQVAKE 138 (139)
T ss_dssp HHHHHHH
T ss_pred HHHHHHc
Confidence 9999864
No 2
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=100.00 E-value=3.9e-43 Score=255.94 Aligned_cols=87 Identities=33% Similarity=0.604 Sum_probs=84.0
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchHhhHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRDLDQ 81 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~lD~ 81 (90)
+||||||||||++||+||++|++.|||+||||++|+||++|||+|||+||||||++|||++++ ++||+|||+||+|||+
T Consensus 77 iRaASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~ 156 (169)
T PTZ00095 77 IRCAAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANA 156 (169)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHH
Confidence 699999999999999999999999999999999999999999999999999999999999996 4899999999999999
Q ss_pred HHHHhhcC
Q 034587 82 VAGRIVVA 89 (90)
Q Consensus 82 iA~~v~~~ 89 (90)
||.+|+++
T Consensus 157 iA~~v~~~ 164 (169)
T PTZ00095 157 FARQVTIR 164 (169)
T ss_pred HHHHHHHH
Confidence 99999753
No 3
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-42 Score=246.25 Aligned_cols=88 Identities=56% Similarity=0.999 Sum_probs=86.0
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
.|||||+||||+++|+||+.|+++|||+||||++|+||+.+||+|+|++||+||++||||++|++||+||++||+|||+|
T Consensus 55 tRaASiaRhiylR~~~gvg~~~KiYGg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrI 134 (143)
T KOG3411|consen 55 TRAASIARHIYLRGPVGVGALTKIYGGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRI 134 (143)
T ss_pred HHHHHHHHHHHhccccchhHHHHHhcccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC
Q 034587 83 AGRIVVAP 90 (90)
Q Consensus 83 A~~v~~~~ 90 (90)
|++|.+++
T Consensus 135 a~~i~~~~ 142 (143)
T KOG3411|consen 135 AGQIREEQ 142 (143)
T ss_pred HHHHHhcc
Confidence 99998764
No 4
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=100.00 E-value=2.3e-41 Score=242.84 Aligned_cols=86 Identities=40% Similarity=0.663 Sum_probs=83.7
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+||||||||||++||+||++|++.||++||||++|+||++|||+|||++|||||++|||++++ +||+|||+||++||+|
T Consensus 53 ~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~i 131 (150)
T PRK09333 53 VRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNL 131 (150)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHH
Confidence 699999999999999999999999999999999999999999999999999999999999998 8999999999999999
Q ss_pred HHHhhcC
Q 034587 83 AGRIVVA 89 (90)
Q Consensus 83 A~~v~~~ 89 (90)
|.+|+++
T Consensus 132 A~~i~~~ 138 (150)
T PRK09333 132 AAEVKKE 138 (150)
T ss_pred HHHHHHH
Confidence 9999753
No 5
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-41 Score=241.84 Aligned_cols=86 Identities=40% Similarity=0.677 Sum_probs=83.9
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+|||||||||||+||+||++|++.|||+||||++|+||.+|||+|+|++|||||++|||++++ +||+|||+||++||+|
T Consensus 53 ~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~ 131 (147)
T COG2238 53 VRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRI 131 (147)
T ss_pred HHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHH
Confidence 699999999999999999999999999999999999999999999999999999999999999 7999999999999999
Q ss_pred HHHhhcC
Q 034587 83 AGRIVVA 89 (90)
Q Consensus 83 A~~v~~~ 89 (90)
|.+|+++
T Consensus 132 a~ei~ee 138 (147)
T COG2238 132 ATEIKEE 138 (147)
T ss_pred HHHHHHH
Confidence 9999764
No 6
>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=97.73 E-value=8.5e-05 Score=46.44 Aligned_cols=63 Identities=21% Similarity=0.221 Sum_probs=50.6
Q ss_pred HHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587 8 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL 79 (90)
Q Consensus 8 i~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l 79 (90)
||+.|+-. +|+|=..|+....-. | ..-|-.-+|.-|.+||+.||+++...+||.||++|...|
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~---g------~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR---G------EELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc---C------hhhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence 67777765 689999999877653 2 223446799999999999999988788999999998764
No 7
>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=97.57 E-value=6.9e-05 Score=49.15 Aligned_cols=57 Identities=25% Similarity=0.514 Sum_probs=46.8
Q ss_pred HHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcchHhhHHH
Q 034587 11 KIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 11 klYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G~~~lD~ 81 (90)
..|++ .|||=..+....+- |..-||+.++.||++|||++. +.+||+-|++|-+.+++
T Consensus 15 ~~Y~~~~~PVgSk~ia~~l~~--------------s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 15 ELYIETGEPVGSKTIAEELGR--------------SPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred HHHHhcCCCcCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence 35775 69999999987542 236899999999999999964 46999999999998864
No 8
>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=97.25 E-value=0.0034 Score=41.56 Aligned_cols=67 Identities=13% Similarity=0.111 Sum_probs=52.9
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL 79 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l 79 (90)
..|+..|+-++++.+..|++..|-.+ +-+-.+++.||+.|||+..+ .+.| .||++|+..+
T Consensus 31 ~~iL~~l~~~~~~t~~ela~~~~~~~--------------~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~ 96 (118)
T TIGR02337 31 WRILRILAEQGSMEFTQLANQACILR--------------PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALY 96 (118)
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCc--------------hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHH
Confidence 45777788888899999999877654 35678999999999999654 3444 6999999999
Q ss_pred HHHHHHh
Q 034587 80 DQVAGRI 86 (90)
Q Consensus 80 D~iA~~v 86 (90)
+++....
T Consensus 97 ~~~~~~~ 103 (118)
T TIGR02337 97 ASLSPQI 103 (118)
T ss_pred HHhhHHH
Confidence 9886654
No 9
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=97.15 E-value=0.0012 Score=52.84 Aligned_cols=65 Identities=26% Similarity=0.371 Sum_probs=53.2
Q ss_pred hhhHHHHHHHH---hhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587 2 SELVTSMARKI---YLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG 75 (90)
Q Consensus 2 ~~r~ASi~Rkl---Yl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G 75 (90)
..|-..|||-| |+. -|||=.+|.+.|+- .-|..-||+.+++||++|+++|.. -.||+.|++|
T Consensus 5 ~~Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l------------~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~G 72 (346)
T COG1420 5 DERQRLILRAIVEDYLATGEPVGSKTLSEKYNL------------DLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKG 72 (346)
T ss_pred hHHHHHHHHHHHHHHHhcCCccchHHHHHHhCC------------CCCchhHHHHHHHHHHCCCccCccccCCcCCcHhH
Confidence 45677777764 775 59999999998863 245678999999999999999776 4799999999
Q ss_pred Hhh
Q 034587 76 QRD 78 (90)
Q Consensus 76 ~~~ 78 (90)
-+.
T Consensus 73 yr~ 75 (346)
T COG1420 73 YRY 75 (346)
T ss_pred HHH
Confidence 764
No 10
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.13 E-value=0.0018 Score=40.99 Aligned_cols=62 Identities=15% Similarity=0.241 Sum_probs=43.6
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHH
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+.||.-+- .++.....+.. .++=+-+.+...|+.|++.|+|++. ++.-.||++|...|+.+-
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHHH
Confidence 44555544 67777766663 3345668999999999999999774 578999999999999874
No 11
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.07 E-value=0.0058 Score=41.83 Aligned_cols=66 Identities=14% Similarity=0.152 Sum_probs=52.1
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD 78 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~ 78 (90)
-..|+..|+-.+++....|+...+-.+ +-+=.+++.||+.|||++.+ .++| .||++|+..
T Consensus 42 q~~vL~~l~~~~~~t~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~ 107 (144)
T PRK11512 42 QFKVLCSIRCAACITPVELKKVLSVDL--------------GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAI 107 (144)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHH
Confidence 356788888888889999999877754 46777899999999999654 4455 589999999
Q ss_pred HHHHHH
Q 034587 79 LDQVAG 84 (90)
Q Consensus 79 lD~iA~ 84 (90)
++++..
T Consensus 108 ~~~~~~ 113 (144)
T PRK11512 108 CEQCHQ 113 (144)
T ss_pred HHHHHH
Confidence 887643
No 12
>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=97.00 E-value=0.002 Score=46.77 Aligned_cols=61 Identities=15% Similarity=0.251 Sum_probs=49.9
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCCe-----eeCcchHh
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQR 77 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~GR-----~lT~~G~~ 77 (90)
-+|+.-|.-.+++.+..|+...|-. ..-++..|+.||+.|||+..+ ..|| .||++|..
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis--------------~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~ 69 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAIS--------------PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGRE 69 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhh
Confidence 3577778778999999999988764 258999999999999998762 3578 99999987
Q ss_pred hHH
Q 034587 78 DLD 80 (90)
Q Consensus 78 ~lD 80 (90)
.+.
T Consensus 70 ~~~ 72 (203)
T TIGR02702 70 QFP 72 (203)
T ss_pred hcc
Confidence 553
No 13
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.97 E-value=0.013 Score=36.20 Aligned_cols=71 Identities=17% Similarity=0.225 Sum_probs=54.8
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC------CeeeCcch
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSG 75 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~------GR~lT~~G 75 (90)
+.-.-.|+..|+..+++.+..+....+-. ..-+...|+.|++.|||+...++ .-.||++|
T Consensus 9 ~~~~~~il~~l~~~~~~~~~~la~~~~~s--------------~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g 74 (101)
T smart00347 9 TPTQFLVLRILYEEGPLSVSELAKRLGVS--------------PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEG 74 (101)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhH
Confidence 34455688888889999999999876532 13478999999999999866532 35699999
Q ss_pred HhhHHHHHHHh
Q 034587 76 QRDLDQVAGRI 86 (90)
Q Consensus 76 ~~~lD~iA~~v 86 (90)
...++.+...+
T Consensus 75 ~~~~~~~~~~~ 85 (101)
T smart00347 75 RELIEELLEAR 85 (101)
T ss_pred HHHHHHHHHHH
Confidence 99998877654
No 14
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.95 E-value=0.0062 Score=42.85 Aligned_cols=63 Identities=16% Similarity=0.191 Sum_probs=51.7
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
|++.++-.+++.+..|+..++-.+ +-+...|++||+.|||...+.+|-.||++|+..+..+..
T Consensus 42 I~~~l~~~~~~t~~eLA~~l~is~--------------stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~ 104 (152)
T PRK11050 42 IADLIAEVGEARQVDIAARLGVSQ--------------PTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE 104 (152)
T ss_pred HHHHHHhcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence 445555668899999999887643 689999999999999998777789999999998776653
No 15
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.85 E-value=0.0029 Score=40.08 Aligned_cols=41 Identities=22% Similarity=0.398 Sum_probs=35.7
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
+.+-+..+|+.||+.|||++.++++-.||++|+...+.+..
T Consensus 12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~ 52 (96)
T smart00529 12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLR 52 (96)
T ss_pred ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHH
Confidence 34679999999999999999987799999999998877654
No 16
>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=96.85 E-value=0.0043 Score=39.90 Aligned_cols=65 Identities=12% Similarity=0.178 Sum_probs=50.0
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC------CeeeCcchHhh
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRD 78 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~------GR~lT~~G~~~ 78 (90)
+..|++.|+. ||...+.|.+.- ...|.+++-.-|..||+.|+|++.... -..||++|+++
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l 72 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKEL 72 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHH
T ss_pred HHHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHH
Confidence 4678888888 888888888744 345678999999999999999876422 37899999998
Q ss_pred HHHHH
Q 034587 79 LDQVA 83 (90)
Q Consensus 79 lD~iA 83 (90)
++-+.
T Consensus 73 ~~~l~ 77 (90)
T PF01638_consen 73 LPVLE 77 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 87654
No 17
>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=96.83 E-value=0.003 Score=37.57 Aligned_cols=58 Identities=19% Similarity=0.284 Sum_probs=41.8
Q ss_pred hHHHHHHHHh-hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587 4 LVTSMARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG 75 (90)
Q Consensus 4 r~ASi~RklY-l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G 75 (90)
.-..||+.|+ -+++.....|+...+-.+ .-+..++++|++.|||++.+ ..+| .|||+|
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~--------------~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAERLGISK--------------STVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHHHTT--H--------------HHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHccCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 4457889999 778999999999887643 46679999999999997654 3455 578877
No 18
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=96.80 E-value=0.011 Score=37.35 Aligned_cols=66 Identities=20% Similarity=0.333 Sum_probs=50.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD 78 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~ 78 (90)
-..++..||..++.+...|+...+-.+ +-+=.+++.||+.|||+..+ .++| .||++|+..
T Consensus 24 q~~~L~~l~~~~~~~~~~la~~l~i~~--------------~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~ 89 (126)
T COG1846 24 QYQVLLALYEAGGITVKELAERLGLDR--------------STVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGREL 89 (126)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHH
Confidence 356777888887776677777666543 56778899999999998555 3455 799999999
Q ss_pred HHHHHH
Q 034587 79 LDQVAG 84 (90)
Q Consensus 79 lD~iA~ 84 (90)
+.++..
T Consensus 90 ~~~~~~ 95 (126)
T COG1846 90 LEQLLP 95 (126)
T ss_pred HHHhcc
Confidence 988755
No 19
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=96.62 E-value=0.0073 Score=47.26 Aligned_cols=65 Identities=17% Similarity=0.280 Sum_probs=51.0
Q ss_pred hhhHHHHHHH---Hhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587 2 SELVTSMARK---IYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG 75 (90)
Q Consensus 2 ~~r~ASi~Rk---lYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G 75 (90)
..|--.|++. -|+. .|||=..|.+.|+-. -|.+-||+.++.||++|++++.. ..||+.|.+|
T Consensus 2 ~~R~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l~------------~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~g 69 (260)
T PRK03911 2 LNKKDLLLDSIIQTYLQDNEPIGSNELKSLMNLK------------ISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKA 69 (260)
T ss_pred chHHHHHHHHHHHHHhccCCccCHHHHHHHcCCC------------CCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHH
Confidence 3455556664 4775 599999999988753 35578999999999999998665 4799999999
Q ss_pred Hhh
Q 034587 76 QRD 78 (90)
Q Consensus 76 ~~~ 78 (90)
-+.
T Consensus 70 yr~ 72 (260)
T PRK03911 70 MKN 72 (260)
T ss_pred HHH
Confidence 864
No 20
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.62 E-value=0.014 Score=32.91 Aligned_cols=59 Identities=19% Similarity=0.260 Sum_probs=43.5
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC---CeeeCc-chHhhHHH
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS-SGQRDLDQ 81 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~-~G~~~lD~ 81 (90)
|+..|+ .+++.+..+...+|- |..-++.+|++|++.|||+...++ .-.+|+ .|...++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~i--------------s~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGL--------------SQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 566777 889999999999973 235799999999999999966532 233666 55555543
No 21
>PRK10870 transcriptional repressor MprA; Provisional
Probab=96.61 E-value=0.013 Score=42.01 Aligned_cols=65 Identities=17% Similarity=0.193 Sum_probs=47.7
Q ss_pred HHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCee----eCcchHhh
Q 034587 7 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQRD 78 (90)
Q Consensus 7 Si~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~----lT~~G~~~ 78 (90)
.||..||-. +++.+..|+...+-.+ +-+=.+++.||+.|||++.+ +++|. ||++|+..
T Consensus 59 ~iL~~L~~~~~~~it~~eLa~~l~l~~--------------~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~ 124 (176)
T PRK10870 59 MALITLESQENHSIQPSELSCALGSSR--------------TNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEF 124 (176)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHH
Confidence 455566542 3566678887776543 46677899999999999654 56777 99999999
Q ss_pred HHHHHHH
Q 034587 79 LDQVAGR 85 (90)
Q Consensus 79 lD~iA~~ 85 (90)
++++-..
T Consensus 125 ~~~i~~~ 131 (176)
T PRK10870 125 LREVLPP 131 (176)
T ss_pred HHHHHHH
Confidence 9997543
No 22
>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=96.48 E-value=0.019 Score=37.89 Aligned_cols=68 Identities=10% Similarity=0.098 Sum_probs=51.4
Q ss_pred HHHHHHHh----hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCee----eCcch
Q 034587 6 TSMARKIY----LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSG 75 (90)
Q Consensus 6 ASi~RklY----l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~----lT~~G 75 (90)
-.||..|| -.+++....|+..-+-.+ +-+=.++..||+.|||++.+ ++.|. ||++|
T Consensus 28 ~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~--------------stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G 93 (109)
T TIGR01889 28 LLILYYLGKLENNEGKLTLKEIIKEILIKQ--------------SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQ 93 (109)
T ss_pred HHHHHHHHhhhccCCcCcHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHH
Confidence 34677777 346788888888766543 45667899999999999655 44552 99999
Q ss_pred HhhHHHHHHHhh
Q 034587 76 QRDLDQVAGRIV 87 (90)
Q Consensus 76 ~~~lD~iA~~v~ 87 (90)
+..++.+..++-
T Consensus 94 ~~~~~~~~~~~~ 105 (109)
T TIGR01889 94 RSKIESLISEIE 105 (109)
T ss_pred HHHHHHHHHHHH
Confidence 999999887763
No 23
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.41 E-value=0.036 Score=37.60 Aligned_cols=65 Identities=14% Similarity=0.139 Sum_probs=47.4
Q ss_pred HHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587 7 SMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL 79 (90)
Q Consensus 7 Si~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l 79 (90)
.+|..|+-. ++..+..|+...|-.+ +-+=.+++.||+.|||++.+ ++.| .||++|+..+
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~~~~--------------~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~ 100 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIGIEQ--------------PSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLI 100 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCh--------------hhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHH
Confidence 456666654 3567778887776643 35668999999999999665 3455 4999999999
Q ss_pred HHHHHH
Q 034587 80 DQVAGR 85 (90)
Q Consensus 80 D~iA~~ 85 (90)
+.+...
T Consensus 101 ~~~~~~ 106 (144)
T PRK03573 101 SEVEAV 106 (144)
T ss_pred HHHHHH
Confidence 886544
No 24
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.30 E-value=0.027 Score=35.08 Aligned_cols=60 Identities=20% Similarity=0.267 Sum_probs=49.0
Q ss_pred hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchH
Q 034587 3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ 76 (90)
Q Consensus 3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~ 76 (90)
.|+-.|+..|.-. +++++..+....|-. .+-++..|+.||+.|||+.++ ++...+++...
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~--------------~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~ 66 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLS--------------KSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence 4778899988887 799999999988653 368999999999999999875 34567877544
No 25
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=96.29 E-value=0.009 Score=40.93 Aligned_cols=69 Identities=22% Similarity=0.268 Sum_probs=56.9
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+|--+|+..+-=.+|+|+..|+..-|- |+|. +|+.|.=||+.++|.-.. .|=++|+.+-.+++++
T Consensus 14 ~RHl~Vl~~v~eeqPiGI~klS~~TGm-------p~HK-------VRYSLRVLEq~~iI~PS~-~GAi~td~~~e~ie~i 78 (101)
T COG3388 14 KRHLSVLKVVLEEQPIGIIKLSDETGM-------PEHK-------VRYSLRVLEQENIISPSR-QGAILTDDFPEFIEEI 78 (101)
T ss_pred HHHHHHHHHHHHhCCceeEeechhcCC-------chhh-------hhhhhhhhhhcCccCccc-cCCccCccHHHHHHHH
Confidence 344566666777899999999998886 6563 799999999999997664 6999999999999988
Q ss_pred HHHh
Q 034587 83 AGRI 86 (90)
Q Consensus 83 A~~v 86 (90)
..++
T Consensus 79 ~~dl 82 (101)
T COG3388 79 IGDL 82 (101)
T ss_pred HHHH
Confidence 7664
No 26
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=96.19 E-value=0.039 Score=40.62 Aligned_cols=67 Identities=12% Similarity=0.142 Sum_probs=50.0
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe----eeCcchHhhH
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDL 79 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR----~lT~~G~~~l 79 (90)
..||-.||-.+++....|++..+-.+ +-+=.+++.||+.|||+.. +++.| .||++|+..+
T Consensus 48 ~~iL~~L~~~~~itq~eLa~~l~l~~--------------sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~ 113 (185)
T PRK13777 48 HHILWIAYHLKGASISEIAKFGVMHV--------------STAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELL 113 (185)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHCCCH--------------hhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 35777788888888899988554421 2456699999999999854 44455 3999999999
Q ss_pred HHHHHHh
Q 034587 80 DQVAGRI 86 (90)
Q Consensus 80 D~iA~~v 86 (90)
+++...+
T Consensus 114 ~~l~~~~ 120 (185)
T PRK13777 114 LETMEEY 120 (185)
T ss_pred HHHHHHH
Confidence 9876543
No 27
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.08 E-value=0.039 Score=37.84 Aligned_cols=55 Identities=13% Similarity=0.107 Sum_probs=42.9
Q ss_pred hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-.+++-+..|+...+-.+ .-+...|+.||+.|||+....++=.||++|+.....+
T Consensus 19 ~~~~~~~~ela~~l~vs~--------------~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 19 EKGYARVSDIAEALSVHP--------------SSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred cCCCcCHHHHHHHhCCCh--------------hHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 357788888888666532 4677789999999999866667899999998876655
No 28
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=96.07 E-value=0.0089 Score=38.64 Aligned_cols=35 Identities=26% Similarity=0.352 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
.-++++++-|.++|+|++...|--.||++|++.|.
T Consensus 55 ~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 55 NRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA 89 (92)
T ss_pred HhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence 46899999999999999877777999999999874
No 29
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=96.01 E-value=0.025 Score=44.77 Aligned_cols=65 Identities=23% Similarity=0.368 Sum_probs=49.8
Q ss_pred hhhHHHHHHH---Hhh--cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587 2 SELVTSMARK---IYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG 75 (90)
Q Consensus 2 ~~r~ASi~Rk---lYl--~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G 75 (90)
+.|--.|+.. .|+ ..|+|...|.+.|+-. -|..-||+-+..||++|++++.- ..||+.|.+|
T Consensus 5 ~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~------------~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kG 72 (339)
T PRK00082 5 DERQREILRAIVEDYIATGEPVGSKTLSKRYGLG------------VSSATIRNDMADLEELGLLEKPHTSSGRIPTDKG 72 (339)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCC------------CChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHH
Confidence 4555566652 455 5799999999875542 24478999999999999998655 4699999999
Q ss_pred Hhh
Q 034587 76 QRD 78 (90)
Q Consensus 76 ~~~ 78 (90)
-+.
T Consensus 73 YR~ 75 (339)
T PRK00082 73 YRY 75 (339)
T ss_pred HHH
Confidence 774
No 30
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=95.93 E-value=0.0043 Score=40.54 Aligned_cols=58 Identities=21% Similarity=0.273 Sum_probs=37.0
Q ss_pred HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
+...|-.||||+.+|+..-|-.+ ..|.=.+===|-..|+|++.+ .||++|++|.+.|.
T Consensus 17 l~~~f~ggPvGl~tlA~~l~ed~-------------~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~l~ 74 (76)
T PF05491_consen 17 LIENFKGGPVGLDTLAAALGEDK-------------ETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEHLG 74 (76)
T ss_dssp HHHCSTTS-B-HHHHHHHTTS-H-------------HHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHHTT
T ss_pred HHHHcCCCCeeHHHHHHHHCCCH-------------hHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHHhC
Confidence 34445578999999998666532 112222222466789999998 59999999987663
No 31
>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=95.68 E-value=0.023 Score=37.27 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=35.0
Q ss_pred cccCchhHHHHHHHHHHhCCccccc--C-CCC-----eeeCcchHhhHHHHHHHh
Q 034587 40 FCKSSGAIARHILQQLQNMNIIDIE--P-KGG-----RRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 40 ~~~asg~iiR~~LqqLE~~glV~k~--~-~~G-----R~lT~~G~~~lD~iA~~v 86 (90)
+..-+-+-+=.+|..||+.|||+.. + .++ -.||++|+..++......
T Consensus 34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~ 88 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW 88 (100)
T ss_pred ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 3344445688899999999999973 2 223 259999999999887654
No 32
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=95.68 E-value=0.021 Score=37.87 Aligned_cols=47 Identities=23% Similarity=0.226 Sum_probs=38.0
Q ss_pred CCCccccCchhHHHHHHHHHHhCCcccccCCCC---------eeeCcchHhhHHHH
Q 034587 36 RPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---------RRITSSGQRDLDQV 82 (90)
Q Consensus 36 ~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---------R~lT~~G~~~lD~i 82 (90)
.+..+..-+-..+-+-+++|+++|||+...... ..||.+|..+||.|
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~I 80 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAI 80 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHh
Confidence 455666667779999999999999998665322 48999999999986
No 33
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=95.65 E-value=0.02 Score=38.76 Aligned_cols=43 Identities=19% Similarity=0.232 Sum_probs=34.2
Q ss_pred ccCchhHHHHHHHHHHhCCcccccCCC---CeeeCcchHhhHHHHH
Q 034587 41 CKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA 83 (90)
Q Consensus 41 ~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~~G~~~lD~iA 83 (90)
++=+=.+.+++++.|++.|++++...+ .-.||++|.+++..+-
T Consensus 41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 344457999999999999988877643 3579999999987653
No 34
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=95.64 E-value=0.044 Score=39.76 Aligned_cols=60 Identities=13% Similarity=0.142 Sum_probs=47.5
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCcch
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSG 75 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~~G 75 (90)
+.+-..|+..|.-++++.+..++...|-. .+-++..|+.||+.|||+..++ ..-.||++|
T Consensus 142 s~~~~~IL~~l~~~g~~s~~eia~~l~is--------------~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 142 SREELKVLEVLKAEGEKSVKNIAKKLGKS--------------LSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 45666788888877899999999988753 3578999999999999998763 234578776
No 35
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=95.58 E-value=0.028 Score=32.72 Aligned_cols=49 Identities=18% Similarity=0.259 Sum_probs=41.1
Q ss_pred hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.|+..|+.-|.-.+ ++++..++..-|-.+ +-+..+|+.|++.|||+++|
T Consensus 3 ~ral~iL~~l~~~~~~~t~~eia~~~gl~~--------------stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 3 ERALRILEALAESGGPLTLSEIARALGLPK--------------STVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHHCHHCTBSCEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCcCeecCc
Confidence 57888999888865 479999999888754 68899999999999999875
No 36
>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=95.51 E-value=0.023 Score=40.57 Aligned_cols=65 Identities=17% Similarity=0.224 Sum_probs=48.6
Q ss_pred hHHHHHHHHhhcCC------CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587 4 LVTSMARKIYLRQG------LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR 77 (90)
Q Consensus 4 r~ASi~RklYl~g~------vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~ 77 (90)
.++..++.-=+.|. +.-..|+..||- |..-+|.+|+.||..|||+..|..|-.+++-...
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV--------------SRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~ 80 (212)
T TIGR03338 15 LVQDEIERAILSGELPPGAKLNESDIAARLGV--------------SRGPVREAFRALEEAGLVRNEKNRGVFVREISLA 80 (212)
T ss_pred HHHHHHHHHHHcCCCCCCCEecHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence 34444555444442 445678888886 4479999999999999999999889999887777
Q ss_pred hHHHH
Q 034587 78 DLDQV 82 (90)
Q Consensus 78 ~lD~i 82 (90)
++..+
T Consensus 81 ~~~ei 85 (212)
T TIGR03338 81 EADEI 85 (212)
T ss_pred HHHHH
Confidence 66554
No 37
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=95.49 E-value=0.017 Score=46.38 Aligned_cols=65 Identities=20% Similarity=0.234 Sum_probs=48.1
Q ss_pred HHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587 8 MARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 8 i~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
|||=|.=.+ |+|-...+..--- ||+. =+---+|+=||-||+.||+.|+--.||.||++|-+.|.+
T Consensus 11 Il~il~esd~plgak~Ia~el~k---RGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~ 76 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELRK---RGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR 76 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHHh---cccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence 445454444 7887766655422 2332 222469999999999999999988999999999999998
No 38
>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=95.37 E-value=0.1 Score=30.14 Aligned_cols=40 Identities=18% Similarity=0.299 Sum_probs=31.6
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
.+..|+..||- |...++.+|+.|++.|||+..+..|-.||
T Consensus 27 ~~~~la~~~~i--------------s~~~v~~~l~~L~~~G~i~~~~~~~~~l~ 66 (66)
T cd07377 27 SERELAEELGV--------------SRTTVREALRELEAEGLVERRPGRGTFVA 66 (66)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 37788887765 34789999999999999987776666654
No 39
>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=95.21 E-value=0.07 Score=42.21 Aligned_cols=63 Identities=22% Similarity=0.255 Sum_probs=48.7
Q ss_pred hHHHHHH-----HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcchHh
Q 034587 4 LVTSMAR-----KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQR 77 (90)
Q Consensus 4 r~ASi~R-----klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~ 77 (90)
|--.|++ .+--.+|+|+..|.+.|+-. -|..-||.-+.+||+.|++++.-. .||.-|.+|-+
T Consensus 3 R~~~il~aIV~~~l~~~~pv~s~~l~~~~~~~------------vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR 70 (337)
T TIGR00331 3 RQRKILKAIVEEYIKTGQPVGSKTLLEKYNLG------------LSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYR 70 (337)
T ss_pred HHHHHHHHHHHHHHhcCCCcCHHHHHhhcCCC------------CChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHH
Confidence 4445554 33335899999999986542 345789999999999999987654 59999999987
Q ss_pred h
Q 034587 78 D 78 (90)
Q Consensus 78 ~ 78 (90)
.
T Consensus 71 ~ 71 (337)
T TIGR00331 71 Y 71 (337)
T ss_pred H
Confidence 6
No 40
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=95.16 E-value=0.046 Score=34.94 Aligned_cols=61 Identities=13% Similarity=0.336 Sum_probs=40.3
Q ss_pred HhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC-----eeeCcchHhhHHHHHH
Q 034587 12 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG-----RRITSSGQRDLDQVAG 84 (90)
Q Consensus 12 lYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G-----R~lT~~G~~~lD~iA~ 84 (90)
||-.+.+-...|+..-|- +.+-+..-|+.||++|+|+..+ .++ -.||++|++.+++.-.
T Consensus 9 L~~~~~~~f~~L~~~l~l--------------t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~ 74 (80)
T PF13601_consen 9 LYANEEATFSELKEELGL--------------TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA 74 (80)
T ss_dssp HHHHSEEEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred HhhcCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence 333455555555554433 4467888999999999998554 333 2699999999987665
Q ss_pred Hh
Q 034587 85 RI 86 (90)
Q Consensus 85 ~v 86 (90)
.+
T Consensus 75 ~L 76 (80)
T PF13601_consen 75 AL 76 (80)
T ss_dssp HH
T ss_pred HH
Confidence 44
No 41
>PRK05638 threonine synthase; Validated
Probab=95.16 E-value=0.057 Score=43.62 Aligned_cols=63 Identities=16% Similarity=0.282 Sum_probs=48.1
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCee----eCcchHhhHHHH
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR----ITSSGQRDLDQV 82 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~----lT~~G~~~lD~i 82 (90)
.||..|. +++.-+..|.+..+. .-|...+...|+.||++|||+...+.||+ ||++|+..+..+
T Consensus 375 ~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 375 EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL 441 (442)
T ss_pred HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence 4666665 568889999998874 13667999999999999999854223444 999999998764
No 42
>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=95.12 E-value=0.072 Score=31.00 Aligned_cols=50 Identities=16% Similarity=0.214 Sum_probs=41.9
Q ss_pred hhhHHHHHHHHhhcCC--CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 2 SELVTSMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~--vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
+.--..||..|+-.++ +.+..|+...+-.+ +-+-.+++.||+.|||++.+
T Consensus 4 t~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~--------------~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 4 TPSQFRVLMALARHPGEELTQSELAERLGISK--------------STVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp THHHHHHHHHHHHSTTSGEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEeC
Confidence 4445789999999998 99999999888754 57888999999999999766
No 43
>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=95.08 E-value=0.021 Score=35.32 Aligned_cols=42 Identities=29% Similarity=0.409 Sum_probs=32.2
Q ss_pred cccCchhHHHHHHHHHHhCCcccccCC---CC-----eeeCcchHhhHHH
Q 034587 40 FCKSSGAIARHILQQLQNMNIIDIEPK---GG-----RRITSSGQRDLDQ 81 (90)
Q Consensus 40 ~~~asg~iiR~~LqqLE~~glV~k~~~---~G-----R~lT~~G~~~lD~ 81 (90)
+..-+-+-+=.+|+.||+.|||+.... +| -.||++|+..|.+
T Consensus 26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 345567788999999999999985542 12 4699999998863
No 44
>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=94.84 E-value=0.04 Score=39.18 Aligned_cols=44 Identities=20% Similarity=0.317 Sum_probs=33.1
Q ss_pred CchhHHHHHHHHHHhCCccccc---CCCCe-----eeCcchHhhHHHHHHHh
Q 034587 43 SSGAIARHILQQLQNMNIIDIE---PKGGR-----RITSSGQRDLDQVAGRI 86 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~---~~~GR-----~lT~~G~~~lD~iA~~v 86 (90)
.+-+-+=.+|+.||+.|||+.. ..+|| .||+.|+..++....+.
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w 106 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF 106 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence 3445677899999999999853 22344 49999999888876653
No 45
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=94.80 E-value=0.15 Score=38.19 Aligned_cols=62 Identities=18% Similarity=0.194 Sum_probs=50.7
Q ss_pred hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchHhh
Q 034587 3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD 78 (90)
Q Consensus 3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~ 78 (90)
.|+..||+-|.-.+ ++++..|.+..|-.| +-+..+|+.|++.|||++++ ++...||++....
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~k--------------stv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHR--------------TTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence 47888998887654 599999999997654 68999999999999999886 4567888877543
No 46
>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=94.73 E-value=0.19 Score=33.83 Aligned_cols=69 Identities=14% Similarity=0.203 Sum_probs=50.3
Q ss_pred hHHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcch-Hhh
Q 034587 4 LVTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSG-QRD 78 (90)
Q Consensus 4 r~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G-~~~ 78 (90)
.|-.++..|.-. +++.+..|+..+|-. .+.++++|+.|++.|||+.. +.+|..|.... +-.
T Consensus 10 yal~~l~~la~~~~~~~s~~eia~~l~is--------------~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it 75 (130)
T TIGR02944 10 YATLVLTTLAQNDSQPYSAAEIAEQTGLN--------------APTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDIT 75 (130)
T ss_pred HHHHHHHHHHhCCCCCccHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccC
Confidence 455566666654 478999999988874 47999999999999999854 35777777655 334
Q ss_pred HHHHHHHh
Q 034587 79 LDQVAGRI 86 (90)
Q Consensus 79 lD~iA~~v 86 (90)
+++|...+
T Consensus 76 ~~~v~~~l 83 (130)
T TIGR02944 76 VADIVKAV 83 (130)
T ss_pred HHHHHHHH
Confidence 66666554
No 47
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=94.71 E-value=0.2 Score=29.24 Aligned_cols=57 Identities=18% Similarity=0.240 Sum_probs=39.6
Q ss_pred hhHHHHHHHHhh--------cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 3 ELVTSMARKIYL--------RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 3 ~r~ASi~RklYl--------~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.|.|..+-.++- .+++....|+...|- |..-+..+|++|++.|||+..+.+.-.|||
T Consensus 3 ~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 3 ERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred hHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 355555554443 245777777777765 346789999999999999988645566664
No 48
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=94.65 E-value=0.29 Score=33.35 Aligned_cols=73 Identities=16% Similarity=0.130 Sum_probs=55.0
Q ss_pred ChhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 1 MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 1 ~~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
+|+.+|+|+=+||-+.=+..+.++-.-. ...+-..+-+=++-|-+-|||||.-| |-++|..|+..+-
T Consensus 14 lsE~~~~ilI~v~Kk~Fit~~ev~e~l~------------~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~ 80 (96)
T PF09114_consen 14 LSENAANILIQVAKKNFITASEVREALA------------TEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIII 80 (96)
T ss_dssp S-HHHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHH
T ss_pred hhHHHHHHHHHHHHHccCCHHHHHHHHH------------HHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHH
Confidence 4678999999999998888888887432 23334566666899999999999975 7999999999999
Q ss_pred HHHHHh
Q 034587 81 QVAGRI 86 (90)
Q Consensus 81 ~iA~~v 86 (90)
++|.--
T Consensus 81 ~AA~l~ 86 (96)
T PF09114_consen 81 QAAELW 86 (96)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 988643
No 49
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=94.44 E-value=0.071 Score=38.13 Aligned_cols=61 Identities=18% Similarity=0.355 Sum_probs=47.2
Q ss_pred HHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587 7 SMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 7 Si~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
.-+..||. .+++.++.++..-+= .| +-+-..|+.|++.|||+..+.+|=.||++|.+.--.
T Consensus 10 dYL~~Iy~l~~~~~~~~~~diA~~L~V------sp--------~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 10 DYLETIYELLEEKGFARTKDIAERLKV------SP--------PSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKE 74 (154)
T ss_pred HHHHHHHHHHhccCcccHHHHHHHhCC------Cc--------HHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHH
Confidence 34556662 477888888886543 34 467789999999999999999999999999865443
No 50
>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=94.36 E-value=0.11 Score=32.66 Aligned_cols=45 Identities=24% Similarity=0.346 Sum_probs=35.4
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG 75 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G 75 (90)
++.+..|+..++-. -..+++++++|++.|+|+..+ .||-.|+..-
T Consensus 25 ~~s~~eiA~~~~i~--------------~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 25 PVSSKEIAERLGIS--------------PSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred CCCHHHHHHHHCcC--------------HHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 48899999988874 368999999999999998554 5788887643
No 51
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=94.33 E-value=0.13 Score=29.89 Aligned_cols=49 Identities=18% Similarity=0.280 Sum_probs=40.3
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.--..+|..||-.+++.+..|....+-. .+-+-.++++||+.|||++.+
T Consensus 3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~--------------~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 3 PSQFRILRILYENGGITQSELAEKLGIS--------------RSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEecc
Confidence 3446789999999999999999988774 356778999999999998554
No 52
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=94.24 E-value=0.08 Score=38.21 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=41.5
Q ss_pred CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+-...|+..||-. ...+|.+|+.||..|||+..|..|-.+++--..++..+
T Consensus 31 L~e~eLae~lgVS--------------RtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei 81 (224)
T PRK11534 31 LRMSLLTSRYALG--------------VGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDI 81 (224)
T ss_pred CCHHHHHHHHCCC--------------hHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHHH
Confidence 4567889988874 47899999999999999999988888887766665543
No 53
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=94.22 E-value=0.3 Score=35.54 Aligned_cols=52 Identities=19% Similarity=0.348 Sum_probs=46.1
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
++....|+..||-.. ..||.+|+.|+..|||+..|..|-.+++--.++++.+
T Consensus 39 ~l~e~~La~~~gvSr--------------tPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei 90 (230)
T COG1802 39 RLSEEELAEELGVSR--------------TPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI 90 (230)
T ss_pred CccHHHHHHHhCCCC--------------ccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence 578899999999853 5799999999999999999999999999888888774
No 54
>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=94.18 E-value=0.086 Score=38.30 Aligned_cols=42 Identities=14% Similarity=0.229 Sum_probs=35.9
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.-..|+..||- |..-+|.+|+.||..|||+..+..|-.+++-
T Consensus 32 sE~~La~~lgV--------------SRtpVREAL~~Le~eGlV~~~~~~G~~V~~~ 73 (235)
T TIGR02812 32 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNNF 73 (235)
T ss_pred CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence 56678888876 4589999999999999999999889888873
No 55
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=94.17 E-value=0.083 Score=37.18 Aligned_cols=37 Identities=22% Similarity=0.343 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
.-+.++.|.||..|+|++....|..+|++++..+|..
T Consensus 50 nTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~ 86 (125)
T COG1725 50 NTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQL 86 (125)
T ss_pred HHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHH
Confidence 5789999999999999988888999999999877653
No 56
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=94.07 E-value=0.11 Score=30.98 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=39.2
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
..|++.|-..+|..++.|....|-. -+-+.+=|+.||++|||+...
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~~~--------------~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELGIS--------------QSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEec
Confidence 4688888889999999999999743 367899999999999999775
No 57
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=94.07 E-value=0.28 Score=27.98 Aligned_cols=63 Identities=16% Similarity=0.183 Sum_probs=46.9
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHH
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQV 82 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~i 82 (90)
.-|+..++-.+ +.+..+.+..|-. ..-++..|++|++.|||..... .-..+|+ |...++.+
T Consensus 10 ~~il~~l~~~~-~~~~ei~~~~~i~--------------~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~ 73 (78)
T cd00090 10 LRILRLLLEGP-LTVSELAERLGLS--------------QSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALL 73 (78)
T ss_pred HHHHHHHHHCC-cCHHHHHHHHCcC--------------HhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHH
Confidence 45666666655 8999999877542 3578999999999999986542 2457898 88888876
Q ss_pred HH
Q 034587 83 AG 84 (90)
Q Consensus 83 A~ 84 (90)
..
T Consensus 74 ~~ 75 (78)
T cd00090 74 ES 75 (78)
T ss_pred HH
Confidence 53
No 58
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=93.91 E-value=0.076 Score=38.96 Aligned_cols=45 Identities=18% Similarity=0.129 Sum_probs=37.3
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR 77 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~ 77 (90)
.-..|+..||- |...+|.+|+.||..|||+..+..|-.+++-...
T Consensus 33 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~ 77 (251)
T PRK09990 33 SERRLCEKLGF--------------SRSALREGLTVLRGRGIIETAQGRGSFVARLNRV 77 (251)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence 45688888886 4589999999999999999999888888766544
No 59
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=93.85 E-value=0.22 Score=34.21 Aligned_cols=62 Identities=19% Similarity=0.282 Sum_probs=46.9
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC------CCCeeeCcchHhhHHH
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRRITSSGQRDLDQ 81 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~------~~GR~lT~~G~~~lD~ 81 (90)
|++++.- |+.--+.|++.-++ =|.+++=.-|++||+.|+|++.. +-...||+.|+++..-
T Consensus 28 Il~~L~~-g~~RF~eL~r~i~~-------------Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~v 93 (120)
T COG1733 28 ILRDLFD-GPKRFNELRRSIGG-------------ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPV 93 (120)
T ss_pred HHHHHhc-CCCcHHHHHHHccc-------------cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHH
Confidence 5666665 77777777775554 45578888999999999998765 3478899999998765
Q ss_pred HH
Q 034587 82 VA 83 (90)
Q Consensus 82 iA 83 (90)
+.
T Consensus 94 l~ 95 (120)
T COG1733 94 LL 95 (120)
T ss_pred HH
Confidence 43
No 60
>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=93.82 E-value=0.095 Score=40.50 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHHHHHhhc
Q 034587 46 AIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRIVV 88 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~iA~~v~~ 88 (90)
..+|.+|.-|++.|||+.... ....||++|++.++..+..|+.
T Consensus 35 ~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~ 80 (280)
T TIGR02277 35 RLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD 80 (280)
T ss_pred chHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence 579999999999999987653 5778999999999998887764
No 61
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=93.65 E-value=0.11 Score=37.41 Aligned_cols=51 Identities=22% Similarity=0.311 Sum_probs=39.9
Q ss_pred CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+-...|+..||-. ...+|.+|+.||..|||+..+..|-.+++--..++..+
T Consensus 35 L~e~~La~~lgVS--------------RtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei 85 (221)
T PRK11414 35 LITKNLAEQLGMS--------------ITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI 85 (221)
T ss_pred cCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence 4456788988874 46899999999999999999887877776665555543
No 62
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.45 E-value=0.095 Score=29.66 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=28.8
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 68 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G 68 (90)
.+..|+..||- |..-+|.+|++|++.|+|+..+.+|
T Consensus 22 s~~~la~~~~v--------------s~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 22 SERELAAQLGV--------------SRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCe
Confidence 67777887765 4478999999999999998776443
No 63
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.24 E-value=0.23 Score=34.10 Aligned_cols=43 Identities=21% Similarity=0.310 Sum_probs=34.6
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCc
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITS 73 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~ 73 (90)
++.+..|+..||-. ...+|++|++|++.|||+..+. ||-.|+.
T Consensus 25 ~~s~~~ia~~~~is--------------~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 25 MTSISEVTEVYGVS--------------RNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred ccCHHHHHHHHCcC--------------HHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 57788899888874 4699999999999999997763 4666654
No 64
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=92.97 E-value=0.11 Score=35.61 Aligned_cols=39 Identities=26% Similarity=0.399 Sum_probs=32.6
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
++.+..|+..+....| -.|.+|++|++.|||+-.|..||
T Consensus 19 ~vtl~elA~~l~cS~R--------------n~r~lLkkm~~~gWi~W~pg~GR 57 (115)
T PF12793_consen 19 EVTLDELAELLFCSRR--------------NARTLLKKMQEEGWITWQPGRGR 57 (115)
T ss_pred ceeHHHHHHHhCCCHH--------------HHHHHHHHHHHCCCeeeeCCCCC
Confidence 4788888888777553 58999999999999999997666
No 65
>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=92.88 E-value=0.12 Score=30.92 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=29.8
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
....|+..||- |...+|.+|+.|++.|||+..+..|-
T Consensus 26 s~~~la~~~~v--------------sr~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 26 SERELAERYGV--------------SRTTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp -HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred CHHHHHHHhcc--------------CCcHHHHHHHHHHHCCcEEEECCceE
Confidence 77788888876 45799999999999999998886553
No 66
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.74 E-value=0.46 Score=26.06 Aligned_cols=45 Identities=13% Similarity=0.182 Sum_probs=36.2
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.|+..+.-++++.+..|+..++-. -.-++..|+.|++.|||+...
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s--------------~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVS--------------EMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEee
Confidence 466666667889999999998542 256899999999999998765
No 67
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=92.53 E-value=0.14 Score=36.53 Aligned_cols=43 Identities=14% Similarity=0.170 Sum_probs=32.8
Q ss_pred CchhHHHHHHHHHHhCCcccccCC----CCeeeCcchHhhHHHHHHH
Q 034587 43 SSGAIARHILQQLQNMNIIDIEPK----GGRRITSSGQRDLDQVAGR 85 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~~----~GR~lT~~G~~~lD~iA~~ 85 (90)
.+-+-|=-+|+.||+.|||+.... .=..||++|+..|+....+
T Consensus 75 ~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~ 121 (135)
T PRK09416 75 GNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN 121 (135)
T ss_pred CCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence 344567789999999999986432 2346999999999987653
No 68
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=92.51 E-value=0.41 Score=32.02 Aligned_cols=50 Identities=18% Similarity=0.187 Sum_probs=39.4
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 71 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l 71 (90)
=-|+.|+|--||--...+++.. ...-.-++.+|..||++|||+... |..|
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~--g~~i 59 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE--GKTI 59 (92)
T ss_pred HHHHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec--Cccc
Confidence 3588999999988888888765 334468999999999999999875 4444
No 69
>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=92.51 E-value=0.62 Score=26.21 Aligned_cols=47 Identities=13% Similarity=0.167 Sum_probs=37.3
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
+..--.|+.-|+-+|++.+..++...|-. .+-+.+.|++|++.|||+
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is--------------~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGIS--------------RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCcCcC
Confidence 34445678888889999999999988864 468999999999999985
No 70
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.46 E-value=0.54 Score=28.98 Aligned_cols=46 Identities=9% Similarity=-0.005 Sum_probs=39.0
Q ss_pred HHHHHHHhhcCC--CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 6 TSMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 6 ASi~RklYl~g~--vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
..|+..|.-+|+ +....|++.-|=.+ +.++..|..||+.|+|++..
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~--------------~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPK--------------KEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecC
Confidence 357777777877 99999999988754 58999999999999999865
No 71
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=92.35 E-value=0.14 Score=37.75 Aligned_cols=42 Identities=19% Similarity=0.135 Sum_probs=35.3
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.-..|+..||= |...+|.+|+.||..|||+..+..|-.+++-
T Consensus 28 sE~eLae~~gV--------------SRtpVREAL~~Le~~GlV~~~~~~G~~V~~~ 69 (253)
T PRK10421 28 AERQLAMQLGV--------------SRNSLREALAKLVSEGVLLSRRGGGTFIRWR 69 (253)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence 35678888886 4579999999999999999888888888764
No 72
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=92.06 E-value=0.15 Score=37.58 Aligned_cols=44 Identities=11% Similarity=0.186 Sum_probs=36.6
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ 76 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 76 (90)
....|+..||= |...+|.+|+.||..|||+..+..|-.+++...
T Consensus 35 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~ 78 (257)
T PRK10225 35 PEREIAEMLDV--------------TRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG 78 (257)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence 46689998887 457999999999999999999877888876543
No 73
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=92.01 E-value=0.18 Score=36.60 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=34.7
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.-..|+..||- |...+|.+|+.||..|||+..+..|-.+++
T Consensus 33 sE~eLae~~gV--------------SRt~VReAL~~L~~eGlv~~~~g~G~~V~~ 73 (239)
T PRK04984 33 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN 73 (239)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence 45678888876 558999999999999999999887877765
No 74
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.98 E-value=0.52 Score=35.02 Aligned_cols=58 Identities=14% Similarity=0.139 Sum_probs=47.2
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcc
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~ 74 (90)
.|+-.||.-|.-.+++++..|++.=|-.| +-+..+|+.|++.|||+.++. +...|+++
T Consensus 14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~k--------------stv~Rll~tL~~~G~l~~~~~~~~Y~lG~~ 72 (257)
T PRK15090 14 LKVFGILQALGEEREIGITELSQRVMMSK--------------STVYRFLQTMKTLGYVAQEGESEKYSLTLK 72 (257)
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence 47788898888778899999999888754 688999999999999998763 44556554
No 75
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=91.85 E-value=0.18 Score=37.08 Aligned_cols=41 Identities=17% Similarity=0.225 Sum_probs=33.9
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.-..|+..||- |...+|.+|+.||..|||+..+..|-.+++
T Consensus 36 sE~eLa~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~ 76 (254)
T PRK09464 36 PERELAKQFDV--------------SRPSLREAIQRLEAKGLLLRRQGGGTFVQS 76 (254)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence 45668888876 457999999999999999998877866665
No 76
>PRK03837 transcriptional regulator NanR; Provisional
Probab=91.76 E-value=0.2 Score=36.30 Aligned_cols=42 Identities=17% Similarity=0.298 Sum_probs=34.7
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
....|+..||= |...+|.+|+.||..|||+..+..|-.+++-
T Consensus 39 ~E~~Lae~~gV--------------SRt~VREAL~~L~~eGlv~~~~~~G~~V~~~ 80 (241)
T PRK03837 39 SERELMAFFGV--------------GRPAVREALQALKRKGLVQISHGERARVSRP 80 (241)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence 56678888886 5589999999999999999988767766653
No 77
>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=91.75 E-value=0.56 Score=27.95 Aligned_cols=47 Identities=15% Similarity=0.184 Sum_probs=40.4
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
-..|+..|--++.+.+..|+..||-. -.-||.=|+.||+.|+|.+.-
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS--------------~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVS--------------EMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEc
Confidence 34677888889999999999999764 368999999999999998875
No 78
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=91.72 E-value=0.63 Score=36.45 Aligned_cols=61 Identities=18% Similarity=0.317 Sum_probs=46.5
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhcC
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 89 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~~ 89 (90)
..++-...+...||.. -.......+++|++.||++.+. +.=+||++|+-..|.|+..++-+
T Consensus 316 ~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~~~ 376 (377)
T PRK08599 316 KSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFLLD 376 (377)
T ss_pred hCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHhhh
Confidence 4566667777776642 1245677889999999999764 46789999999999999987643
No 79
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=91.64 E-value=0.19 Score=37.06 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=34.7
Q ss_pred hhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587 20 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 75 (90)
Q Consensus 20 V~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G 75 (90)
-..|+..||= |...+|.+|+.||..|||+..+..|-.+++.-
T Consensus 35 E~eLae~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~ 76 (253)
T PRK11523 35 ERFIADEKNV--------------SRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ 76 (253)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence 4578888876 45799999999999999999987777776643
No 80
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=91.49 E-value=1 Score=35.60 Aligned_cols=57 Identities=21% Similarity=0.352 Sum_probs=44.5
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
..++-...+...||-.- ....|+.|++.||++.+.++.=+||++|+.++|.|+..++
T Consensus 323 ~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~ 379 (380)
T PRK09057 323 REGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA 379 (380)
T ss_pred hCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence 45677789999888531 1247999999999986543246899999999999999875
No 81
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=91.43 E-value=0.68 Score=34.81 Aligned_cols=57 Identities=16% Similarity=0.254 Sum_probs=45.5
Q ss_pred hhHHHHHHHHhhcCCC--chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC-eeeCcc
Q 034587 3 ELVTSMARKIYLRQGL--GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl~g~v--GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G-R~lT~~ 74 (90)
.|+..||.-|.- +|. ++..|.+.-|-.| +=++.+|+.|++.|||+.+++.| ..|+++
T Consensus 4 ~ral~iL~~l~~-~~~~l~l~ela~~~glpk--------------sT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~ 63 (246)
T COG1414 4 ERALAILDLLAE-GPGGLSLAELAERLGLPK--------------STVHRLLQTLVELGYVEQDPEDGRYRLGPR 63 (246)
T ss_pred HHHHHHHHHHHh-CCCCCCHHHHHHHhCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEeehHH
Confidence 578889988887 454 4999999888754 67899999999999999998654 455543
No 82
>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=91.16 E-value=1.1 Score=29.15 Aligned_cols=50 Identities=14% Similarity=0.038 Sum_probs=36.8
Q ss_pred hhhHHHHHHHHh--------hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 2 SELVTSMARKIY--------LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 2 ~~r~ASi~RklY--------l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
+.|-|++|-.|. ...++.-..|+...|-. ..-+-.+|++||+.|||+...
T Consensus 24 ~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~s--------------r~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 24 SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLS--------------RTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeeeec
Confidence 456677766665 45677777777777764 246888999999999998654
No 83
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=91.08 E-value=0.36 Score=36.53 Aligned_cols=55 Identities=24% Similarity=0.170 Sum_probs=41.5
Q ss_pred CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHHHHHh
Q 034587 18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~iA~~v 86 (90)
+..+.|++..+- |..-+-..|+.||+.|||+.... .--.||++|+..+++.....
T Consensus 22 IS~~eLA~~L~i--------------S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~ 79 (217)
T PRK14165 22 ISSSEFANHTGT--------------SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADY 79 (217)
T ss_pred cCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHH
Confidence 446678776654 44678889999999999986642 24579999999998877553
No 84
>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=91.07 E-value=2 Score=28.45 Aligned_cols=49 Identities=20% Similarity=0.308 Sum_probs=39.3
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcchHhh
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRD 78 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G~~~ 78 (90)
+|+.+..|+..++-. ...++.+|+.|++.|||... ..+|-.|+......
T Consensus 24 ~~~s~~eia~~~~i~--------------~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i 74 (132)
T TIGR00738 24 GPVSVKEIAERQGIS--------------RSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI 74 (132)
T ss_pred CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC
Confidence 388999999988774 47999999999999999854 34678888776544
No 85
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=91.00 E-value=0.6 Score=27.76 Aligned_cols=52 Identities=21% Similarity=0.425 Sum_probs=36.1
Q ss_pred HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587 11 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ 76 (90)
Q Consensus 11 klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 76 (90)
.+=+..++-+..+...||.. --......|+.|++.|||+.+. +.=++|++|+
T Consensus 14 ~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~ 65 (66)
T PF06969_consen 14 GLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR 65 (66)
T ss_dssp HHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred HHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence 34445678888888888864 1234578899999999998885 5778999996
No 86
>PRK11569 transcriptional repressor IclR; Provisional
Probab=90.80 E-value=0.87 Score=34.36 Aligned_cols=58 Identities=10% Similarity=0.099 Sum_probs=46.3
Q ss_pred hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcc
Q 034587 3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~ 74 (90)
.|+-.||+-|-- .+|+++..|.+.=|-.| +-+..+|+.|++.|||+.+++ +...|.+.
T Consensus 28 ~ral~IL~~l~~~~~~~~lseia~~lglpk--------------sTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 87 (274)
T PRK11569 28 TRGLKLLEWIAESNGSVALTELAQQAGLPN--------------STTHRLLTTMQQQGFVRQVGELGHWAIGAH 87 (274)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence 477888888876 46899999999888765 689999999999999998864 33455544
No 87
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=90.55 E-value=0.97 Score=34.12 Aligned_cols=58 Identities=12% Similarity=0.051 Sum_probs=46.6
Q ss_pred hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC-eeeCcc
Q 034587 3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G-R~lT~~ 74 (90)
.|+-+||+-|.-. +++++..|++.-|-.| +-+..+|+.|++.|||+.++..| ..|++.
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpk--------------Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 84 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLPL--------------STTFRLLKVLQAADFVYQDSQLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence 4788999999764 5799999999988865 67899999999999999886433 345543
No 88
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=90.07 E-value=0.47 Score=32.08 Aligned_cols=42 Identities=21% Similarity=0.344 Sum_probs=31.7
Q ss_pred chhHHHHHHHHHHhCCcccccC--CC------CeeeCcchHhhHHHHHHH
Q 034587 44 SGAIARHILQQLQNMNIIDIEP--KG------GRRITSSGQRDLDQVAGR 85 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~--~~------GR~lT~~G~~~lD~iA~~ 85 (90)
|-+.|=-+|+.||+.|||+... .+ --.||++|+..|.+...+
T Consensus 43 s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~ 92 (138)
T COG1695 43 SPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREE 92 (138)
T ss_pred CCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHH
Confidence 3345667899999999998642 22 237999999999987654
No 89
>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=89.95 E-value=0.43 Score=29.62 Aligned_cols=40 Identities=20% Similarity=0.216 Sum_probs=30.6
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
|..|..++..+|- .|-+-+..-|++||+.|+|+.++...|
T Consensus 25 ~Pt~rEIa~~~g~-------------~S~~tv~~~L~~Le~kG~I~r~~~~~R 64 (65)
T PF01726_consen 25 PPTVREIAEALGL-------------KSTSTVQRHLKALERKGYIRRDPGKAR 64 (65)
T ss_dssp ---HHHHHHHHTS-------------SSHHHHHHHHHHHHHTTSEEEGCCSCC
T ss_pred CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCcCccCCCCCCC
Confidence 5688888887776 356789999999999999999885443
No 90
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=89.29 E-value=2.2 Score=27.41 Aligned_cols=79 Identities=16% Similarity=0.155 Sum_probs=52.6
Q ss_pred hhhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCcc------cc---CchhHHHHHHHHHHhCCcccccCC----C
Q 034587 2 SELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHF------CK---SSGAIARHILQQLQNMNIIDIEPK----G 67 (90)
Q Consensus 2 ~~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~------~~---asg~iiR~~LqqLE~~glV~k~~~----~ 67 (90)
+.-|..|++=|+- .+.+|...+..++-|.++......++ -. =+..-++.++++|...|+++.... .
T Consensus 3 T~~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~ 82 (106)
T PF09382_consen 3 TEEAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYP 82 (106)
T ss_dssp HHHHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTE
T ss_pred HHHHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCccccc
Confidence 3445666666665 57899999999999999887544333 11 144589999999999999965542 1
Q ss_pred CeeeCcchHhhHH
Q 034587 68 GRRITSSGQRDLD 80 (90)
Q Consensus 68 GR~lT~~G~~~lD 80 (90)
-=.+|++|++.|.
T Consensus 83 ~l~~~~~~~~~l~ 95 (106)
T PF09382_consen 83 YLKLTPKGKELLN 95 (106)
T ss_dssp EEEE-GGGHHHHC
T ss_pred EEEECHHHHHHHC
Confidence 3468999998875
No 91
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.27 E-value=1.5 Score=30.96 Aligned_cols=59 Identities=25% Similarity=0.326 Sum_probs=45.8
Q ss_pred hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCCe-----------eeCcchHhhH
Q 034587 14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----------RITSSGQRDL 79 (90)
Q Consensus 14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~GR-----------~lT~~G~~~l 79 (90)
-+||..|..|+..-+- +.+-+-++||.|.++|+|++.+ ++|| .++.+..++|
T Consensus 39 ~~~~~tvdelae~lnr--------------~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l 104 (126)
T COG3355 39 ENGPLTVDELAEILNR--------------SRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL 104 (126)
T ss_pred hcCCcCHHHHHHHHCc--------------cHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence 4899999999987654 3478899999999999998654 3444 2566778888
Q ss_pred HHHHHHh
Q 034587 80 DQVAGRI 86 (90)
Q Consensus 80 D~iA~~v 86 (90)
|..+.++
T Consensus 105 ~~w~~~~ 111 (126)
T COG3355 105 DEWYDKM 111 (126)
T ss_pred HHHHHHH
Confidence 8888776
No 92
>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=88.80 E-value=0.46 Score=37.18 Aligned_cols=61 Identities=11% Similarity=0.151 Sum_probs=46.7
Q ss_pred HHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-C-CCeeeCcchHhhHHH
Q 034587 7 SMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-K-GGRRITSSGQRDLDQ 81 (90)
Q Consensus 7 Si~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~-~GR~lT~~G~~~lD~ 81 (90)
.|++.|=- +|-+.-..|+..+|= |.+.+|.+++.||++|+|+..+ . .|-.+.+....++|.
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGV--------------SRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e 250 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGI--------------TRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE 250 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence 35555544 356666777777764 5589999999999999999888 5 488888888888875
No 93
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=88.75 E-value=0.59 Score=37.35 Aligned_cols=39 Identities=23% Similarity=0.296 Sum_probs=32.8
Q ss_pred HHHHHHHHHHhCCcccccCCCCe--eeCc-chHhhHHHHHHHhh
Q 034587 47 IARHILQQLQNMNIIDIEPKGGR--RITS-SGQRDLDQVAGRIV 87 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~~GR--~lT~-~G~~~lD~iA~~v~ 87 (90)
.....|++|++.||++.+ +++ +||+ +|.-++|.|+.+++
T Consensus 352 ~~~~~l~~l~~~gll~~~--~~~~~~lT~~~G~~~~~~i~~~~~ 393 (400)
T PRK07379 352 QILQCLQPYFQQGWVELE--GDRRLRLTDPEGFLFSNTVLASLF 393 (400)
T ss_pred HHHHHHHHHHHCCCEEEe--CCeEEEECchHHhHHHHHHHHHHH
Confidence 456778999999999865 355 8995 99999999999875
No 94
>PRK05660 HemN family oxidoreductase; Provisional
Probab=88.65 E-value=0.76 Score=36.42 Aligned_cols=58 Identities=14% Similarity=0.123 Sum_probs=42.5
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhcC
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 89 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~~ 89 (90)
++-+..+...||.. + -. ....++.|++.||++.+. +-=+||++|+-++|.|+..++.+
T Consensus 321 G~~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~~~~~~ 378 (378)
T PRK05660 321 AAPRADFEAYTGLP------E-------SV-IRPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLELFLAE 378 (378)
T ss_pred CCCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHHHHhcC
Confidence 45556666666642 1 11 356889999999998664 34678999999999999988753
No 95
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=88.58 E-value=0.56 Score=33.12 Aligned_cols=47 Identities=23% Similarity=0.329 Sum_probs=37.3
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchH
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ 76 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~ 76 (90)
.++.+..++..++-. ...++++||+|.++|||+... +||-.|+..-.
T Consensus 23 ~~~s~~eIA~~~~is--------------~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~ 71 (153)
T PRK11920 23 KLSRIPEIARAYGVS--------------ELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAA 71 (153)
T ss_pred CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHH
Confidence 357788888877663 479999999999999998655 57989986554
No 96
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=88.52 E-value=0.68 Score=36.33 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=32.7
Q ss_pred HHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 49 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 49 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
...|++|++.|++..+. +.=+||++|+-.+|.|+..++
T Consensus 337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 374 (375)
T PRK05628 337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVRDLL 374 (375)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHHHHh
Confidence 57899999999998764 357899999999999998764
No 97
>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=88.47 E-value=0.55 Score=33.92 Aligned_cols=43 Identities=12% Similarity=0.183 Sum_probs=34.9
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 75 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G 75 (90)
.-..|+..||- |..-+|++|+.|++.|+|+.....|-.+++..
T Consensus 34 sE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~~ 76 (238)
T TIGR02325 34 AEMQLAERFGV--------------NRHTVRRAIAALVERGLLRAEQGRGTFVAARR 76 (238)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEECCCc
Confidence 44577787776 45799999999999999999887788887553
No 98
>PF13814 Replic_Relax: Replication-relaxation
Probab=88.42 E-value=1.4 Score=30.68 Aligned_cols=62 Identities=23% Similarity=0.289 Sum_probs=46.4
Q ss_pred HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-----C-----eeeCcchHhh
Q 034587 9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----G-----RRITSSGQRD 78 (90)
Q Consensus 9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-----G-----R~lT~~G~~~ 78 (90)
|+-||-...+....|...+....+.. .-++..|++|++.|+|+..... | -.||++|.+.
T Consensus 1 L~~L~~~r~lt~~Qi~~l~~~~~~~~-----------~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~ 69 (191)
T PF13814_consen 1 LRLLARHRFLTTDQIARLLFPSSKSE-----------RTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARL 69 (191)
T ss_pred ChhHHHhcCcCHHHHHHHHcCCCcch-----------HHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHH
Confidence 34566677888888888887754321 1789999999999999866531 2 2699999998
Q ss_pred HHH
Q 034587 79 LDQ 81 (90)
Q Consensus 79 lD~ 81 (90)
++.
T Consensus 70 l~~ 72 (191)
T PF13814_consen 70 LAD 72 (191)
T ss_pred HHh
Confidence 874
No 99
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=88.31 E-value=0.45 Score=38.35 Aligned_cols=58 Identities=22% Similarity=0.351 Sum_probs=43.5
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhc
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV 88 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~ 88 (90)
.++-...+...||.. + .. .-..|++|++.|||+.+. +.=+||++|+-..|.|+.+++.
T Consensus 360 ~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~ 417 (430)
T PRK08208 360 QGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFIS 417 (430)
T ss_pred CCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcC
Confidence 466667777777742 1 12 335789999999998764 3458999999999999998864
No 100
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=87.79 E-value=0.88 Score=35.55 Aligned_cols=40 Identities=5% Similarity=0.200 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 47 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
.....|+.|++.||++.+. +.=+||++|+-++|.|+.+++
T Consensus 334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 373 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMSDFL 373 (374)
T ss_pred HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHHHHh
Confidence 3556689999999998664 346889999999999998864
No 101
>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=87.58 E-value=0.73 Score=31.45 Aligned_cols=46 Identities=13% Similarity=0.265 Sum_probs=36.5
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cCCCCeeeCcch
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG 75 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~~~GR~lT~~G 75 (90)
+++.+..++..++- +...++++|++|.++|||+. .+.||-.|+..-
T Consensus 24 ~~~s~~~ia~~~~i--------------p~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~ 71 (135)
T TIGR02010 24 GPVTLADISERQGI--------------SLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA 71 (135)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH
Confidence 47899999987776 34799999999999999974 335788887643
No 102
>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=87.57 E-value=0.8 Score=27.50 Aligned_cols=48 Identities=10% Similarity=0.063 Sum_probs=38.8
Q ss_pred hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.=+.|...|--+|+..+..+++.-|-. .+-+..+|+.|++.|||+..+
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~l~i~--------------~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEELGIS--------------RSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHHHTSS--------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEc
Confidence 345566666668999999999877764 368999999999999999876
No 103
>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=87.34 E-value=0.64 Score=33.78 Aligned_cols=41 Identities=15% Similarity=0.239 Sum_probs=34.2
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
+-..|+..||- |..-+|++|+.|++.|+|.+.+..|-.+++
T Consensus 27 sE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~ 67 (230)
T TIGR02018 27 SEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAE 67 (230)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEcc
Confidence 56678888886 457999999999999999998877777654
No 104
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=87.33 E-value=0.84 Score=24.85 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=26.9
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
|+.+..++..+|-. ..-+..+|++|++.|||+...
T Consensus 8 ~~s~~~la~~l~~s--------------~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 8 PLTRQEIAELLGLT--------------RETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred ccCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEeC
Confidence 55666677766653 357899999999999998764
No 105
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=87.17 E-value=0.72 Score=34.52 Aligned_cols=41 Identities=17% Similarity=0.366 Sum_probs=31.9
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
+-..|+..||= |..++|-+|+.||..|||+.-+..|=.+++
T Consensus 36 ~EreLae~fgV--------------SR~~vREAl~~L~a~Glve~r~G~Gt~V~~ 76 (241)
T COG2186 36 SERELAERFGV--------------SRTVVREALKRLEAKGLVEIRQGSGTFVRP 76 (241)
T ss_pred CHHHHHHHHCC--------------CcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence 35567777775 457999999999999999987765655554
No 106
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.14 E-value=1.9 Score=35.61 Aligned_cols=69 Identities=7% Similarity=0.067 Sum_probs=52.8
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCcchHhhH
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDL 79 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~~G~~~l 79 (90)
+.--..||..|+-.+++....|+...|-.+ +-+-.++..||+.|||+...+ .--.||++|++.+
T Consensus 5 t~~e~~vL~~L~~~~~~s~~eLA~~l~l~~--------------~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~ 70 (489)
T PRK04172 5 HPNEKKVLKALKELKEATLEELAEKLGLPP--------------EAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYA 70 (489)
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHhCcCH--------------HHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHH
Confidence 344567899998889999999998776532 345566889999999986652 3457999999999
Q ss_pred HHHHH
Q 034587 80 DQVAG 84 (90)
Q Consensus 80 D~iA~ 84 (90)
+++.-
T Consensus 71 ~~g~p 75 (489)
T PRK04172 71 EEGLP 75 (489)
T ss_pred HhcCH
Confidence 87543
No 107
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=87.09 E-value=0.54 Score=37.49 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHhCCcccccC--CCCeeeCcchHhhHHH
Q 034587 46 AIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ 81 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~lD~ 81 (90)
+-+|+.+|.|..+||||-.| +||.+-|.+.-..|+.
T Consensus 40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~i 77 (294)
T COG2524 40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSI 77 (294)
T ss_pred chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhcc
Confidence 47999999999999999666 7999999998877753
No 108
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=86.91 E-value=3.6 Score=32.99 Aligned_cols=59 Identities=15% Similarity=0.284 Sum_probs=43.8
Q ss_pred hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHH-HHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIA-RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~ii-R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
+..++-+..+...||-.- -... ...|++|++.||++. . +.=.||++|+-+.|.|+.+++
T Consensus 330 ~~~Gl~~~~~~~~~g~~~-------------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~~~~ 389 (390)
T PRK06582 330 LSKGINISTLEQKLNTKL-------------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVPRLI 389 (390)
T ss_pred hhCCCCHHHHHHHHCcCH-------------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHHHHh
Confidence 346677778888887421 0111 467889999999987 3 457899999999999998864
No 109
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=86.88 E-value=0.98 Score=35.69 Aligned_cols=39 Identities=10% Similarity=0.146 Sum_probs=32.6
Q ss_pred HHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 48 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 48 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
....+++|++.||++.+. +.=.||++|+-++|.|+.+++
T Consensus 332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~~~~ 370 (370)
T PRK06294 332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAEEIM 370 (370)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHhC
Confidence 557789999999998764 356899999999999998753
No 110
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=86.65 E-value=2.3 Score=30.56 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=37.4
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cCCCCeeeCcch
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG 75 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~~~GR~lT~~G 75 (90)
+|+.+..++..++-. ...++++|++|.++|||+. .++||..|...-
T Consensus 24 ~~vs~~eIA~~~~ip--------------~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p 71 (164)
T PRK10857 24 GPVPLADISERQGIS--------------LSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA 71 (164)
T ss_pred CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH
Confidence 478999999988763 4799999999999999984 456788886553
No 111
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=86.31 E-value=1.1 Score=36.32 Aligned_cols=66 Identities=18% Similarity=0.208 Sum_probs=46.1
Q ss_pred HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHh
Q 034587 9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v 86 (90)
+-.|-....+-...+...||-. +..+. -....|++|++.|||+.+. +.=+||++|+-.+|.|+..+
T Consensus 373 ~~~L~~~~~ld~~~~~~~~g~~------~~~~~-----~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~f 438 (453)
T PRK13347 373 IETLMCNFPVDLAAIAARHGFF------ARYFL-----DELARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAAAF 438 (453)
T ss_pred HHHHHhhCCcCHHHHHHHHCCC------HHHHH-----HHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHH
Confidence 3334445566777888888743 11110 1245789999999999764 35689999999999999854
No 112
>PRK00215 LexA repressor; Validated
Probab=85.94 E-value=3.7 Score=29.38 Aligned_cols=64 Identities=16% Similarity=0.159 Sum_probs=44.2
Q ss_pred hhhHHHHHHHHh---hc--CCCchhHHHHHhcC-CCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe--eeCc
Q 034587 2 SELVTSMARKIY---LR--QGLGVGSFRRIYGG-SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR--RITS 73 (90)
Q Consensus 2 ~~r~ASi~RklY---l~--g~vGV~~Lr~~YGg-~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR--~lT~ 73 (90)
+.+-..|+..|. .+ .+..+..|+...|- .+ +-+-..|+.||+.|||+..++..| .|++
T Consensus 3 t~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~--------------~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~ 68 (205)
T PRK00215 3 TKRQQEILDFIRDHIEETGYPPSRREIADALGLRSP--------------SAVHEHLKALERKGFIRRDPGRSRAIEVAA 68 (205)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCh--------------HHHHHHHHHHHHCCCEEeCCCCcceEEecc
Confidence 344556666665 22 35789999998886 32 467789999999999998886554 3555
Q ss_pred chHhhH
Q 034587 74 SGQRDL 79 (90)
Q Consensus 74 ~G~~~l 79 (90)
.|+..+
T Consensus 69 ~~~~~~ 74 (205)
T PRK00215 69 PAQLEL 74 (205)
T ss_pred cccccc
Confidence 555443
No 113
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=85.71 E-value=2 Score=26.73 Aligned_cols=37 Identities=22% Similarity=0.185 Sum_probs=29.3
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
++|+-...++...|=. -.-+|+.|++||+.|.|++.|
T Consensus 13 ~~p~~T~eiA~~~gls--------------~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 13 NGPLKTREIADALGLS--------------IYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp TS-EEHHHHHHHHTS---------------HHHHHHHHHHHHHCTSEEEES
T ss_pred CCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEEEec
Confidence 6777777777777653 367999999999999999877
No 114
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=85.59 E-value=0.77 Score=31.85 Aligned_cols=40 Identities=23% Similarity=0.384 Sum_probs=30.7
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 71 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l 71 (90)
-|.+..|...||- +++|.|.+|..||+.|+|.... ++|+.
T Consensus 59 ~VTpy~la~r~gI--------------~~SvAr~vLR~LeeeGvv~lvs-knrR~ 98 (107)
T COG4901 59 VVTPYVLASRYGI--------------NGSVARIVLRHLEEEGVVQLVS-KNRRQ 98 (107)
T ss_pred eecHHHHHHHhcc--------------chHHHHHHHHHHHhCCceeeec-cCccc
Confidence 3566667777765 4789999999999999998775 35554
No 115
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=85.16 E-value=1.1 Score=36.33 Aligned_cols=62 Identities=15% Similarity=0.233 Sum_probs=42.2
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
..++-...+...||.. +...-...+ ..|++|++.|||+.+. +.=+||++|+-.+|.|+..+.
T Consensus 378 ~~gl~~~~~~~~fg~~---------~~~~~~~~~-~~l~~l~~~gll~~~~-~~~~lT~~G~~~~d~i~~~f~ 439 (453)
T PRK09249 378 NFELDFAAIEAAFGID---------FAEYFAEEL-ERLAPLEADGLVELDE-NGITVTPKGRLLVRNIAMAFD 439 (453)
T ss_pred cCCcCHHHHHHHHCCC---------HHHHHHHHH-HHHHHHHHCCCEEEEC-CEEEECccchHHHHHHHHHHH
Confidence 3455566777777742 110011111 2478999999999775 457899999999999998653
No 116
>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=85.09 E-value=1 Score=32.70 Aligned_cols=41 Identities=20% Similarity=0.221 Sum_probs=33.6
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.=..|+..||- |...+|.+|+.|++.|+|+.....|-.+++
T Consensus 26 sE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~G~GTfV~~ 66 (233)
T TIGR02404 26 SEHELMDQYGA--------------SRETVRKALNLLTEAGYIQKIQGKGSIVLN 66 (233)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence 34567777776 457999999999999999998877877764
No 117
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=84.99 E-value=1.1 Score=32.91 Aligned_cols=43 Identities=19% Similarity=0.281 Sum_probs=34.4
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 75 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G 75 (90)
.-..|+..||- |..-+|.+|+.|++.|+|.+.+..|-.+++..
T Consensus 31 sE~eL~~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~~ 73 (240)
T PRK09764 31 TESALQTEFGV--------------SRVTVRQALRQLVEQQILESIQGSGTYVKEER 73 (240)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEcccc
Confidence 44677777775 45799999999999999998887777776554
No 118
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=84.91 E-value=1.2 Score=35.45 Aligned_cols=58 Identities=19% Similarity=0.189 Sum_probs=41.9
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
..++=...+...||-. ..-+-..|+.|++.|||+.+. +.=+||++|+-++|.|+.+++
T Consensus 336 ~~Gld~~~f~~~~g~~--------------~~~~~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d~i~~~~~ 393 (394)
T PRK08898 336 TDGVPAHLFQERTGLP--------------LAAIEPQLAAAEQRGLLERDH-TRIRPTPLGQRFLNDLQELFL 393 (394)
T ss_pred hCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEEC-CEEEEChhHhHHHHHHHHHHh
Confidence 3455566777666631 012345889999999998664 234799999999999998875
No 119
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=84.12 E-value=1.2 Score=31.40 Aligned_cols=45 Identities=18% Similarity=0.256 Sum_probs=36.3
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG 75 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G 75 (90)
++-+..++..+|-. -..++++|++|.++|+|+... +||-+|...-
T Consensus 25 ~~s~~~IA~~~~is--------------~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~ 71 (150)
T COG1959 25 PVSSAEIAERQGIS--------------PSYLEKILSKLRKAGLVKSVRGKGGGYRLARPP 71 (150)
T ss_pred cccHHHHHHHhCcC--------------HHHHHHHHHHHHHcCCEEeecCCCCCccCCCCh
Confidence 57788888877763 379999999999999998554 6899987654
No 120
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=83.95 E-value=1.7 Score=33.41 Aligned_cols=53 Identities=17% Similarity=0.298 Sum_probs=39.9
Q ss_pred hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHH-HHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 13 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 13 Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~Lq-qLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
|-.+|+|+..++..-|-... -+-..+. .|-+.|+|+..+ .||++|++|.+.|.
T Consensus 272 ~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~~~~ 325 (328)
T PRK00080 272 FGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTP-RGRVATPKAYEHLG 325 (328)
T ss_pred cCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCC-chHHHHHHHHHHhC
Confidence 34578999999888776432 2333344 888999998776 69999999998875
No 121
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=83.81 E-value=3.1 Score=30.33 Aligned_cols=42 Identities=14% Similarity=0.170 Sum_probs=36.3
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
-|+..|.-+|++..+.|+..-|-+. .-+|++|+.|++.|||.
T Consensus 26 ~Vl~~L~~~g~~tdeeLA~~Lgi~~--------------~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALIKKGEVTDEEIAEQTGIKL--------------NTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeE
Confidence 4677777789999999999887754 68999999999999998
No 122
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=83.75 E-value=3.7 Score=33.48 Aligned_cols=58 Identities=17% Similarity=0.167 Sum_probs=44.3
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
+.+-...+...||.. --......|++|++.||++.+. +-=.||++|+-.+|.|..+++
T Consensus 357 ~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~f~ 414 (433)
T PRK08629 357 GRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKEFY 414 (433)
T ss_pred CCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHHH
Confidence 566667777777742 1234667889999999998764 345899999999999998875
No 123
>PRK14999 histidine utilization repressor; Provisional
Probab=83.74 E-value=1.3 Score=32.46 Aligned_cols=42 Identities=14% Similarity=0.103 Sum_probs=35.0
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.-..|+..||- |..-+|++|+.|++.|+|.+.+..|--+++.
T Consensus 38 sE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~GkGTfV~~~ 79 (241)
T PRK14999 38 SEAELVAQYGF--------------SRMTINRALRELTDEGWLVRLQGVGTFVAEP 79 (241)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCcEEEECCC
Confidence 56778888886 4579999999999999999888778777654
No 124
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=83.72 E-value=1.4 Score=35.68 Aligned_cols=36 Identities=19% Similarity=0.407 Sum_probs=30.5
Q ss_pred HHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHh
Q 034587 50 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 50 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v 86 (90)
..|++|++.|||+.+. +.=+||++|+-.+|.|+.++
T Consensus 403 ~~l~~l~~~gll~~~~-~~~~lT~~G~~~~~~i~~~f 438 (455)
T TIGR00538 403 ELLKPLEEDGLLDVDE-KGIEVTPKGRLLIRNIAMVF 438 (455)
T ss_pred HHHHHHHhCCCEEEEC-CEEEECcCChHHHHHHHHHH
Confidence 3578999999999764 46789999999999999875
No 125
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=83.60 E-value=1.3 Score=32.06 Aligned_cols=32 Identities=22% Similarity=0.253 Sum_probs=26.1
Q ss_pred CchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 43 SSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
-+-.=+|.+|+-|+++|+|+++.+|.-..|.+
T Consensus 53 is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~ 84 (171)
T PF14394_consen 53 ISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDK 84 (171)
T ss_pred CCHHHHHHHHHHHHHCCCeEECCCCcEEEecc
Confidence 34567999999999999999998766666664
No 126
>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=83.55 E-value=3.8 Score=30.15 Aligned_cols=57 Identities=16% Similarity=0.110 Sum_probs=45.2
Q ss_pred hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.|+-.||.-|-- .+|+++..|++.-|-.| +-+..+|+.|++.|||+++. +...|+++
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglpk--------------sT~~RlL~tL~~~G~l~~~~-~~Y~lG~~ 66 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLTR--------------AAARRFLLTLVELGYVTSDG-RLFWLTPR 66 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeCC-CEEEecHH
Confidence 467788887764 57899999999888755 67899999999999999864 44556554
No 127
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=83.15 E-value=1.4 Score=36.40 Aligned_cols=39 Identities=18% Similarity=0.343 Sum_probs=33.1
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
.+.+..|+....+..| -+|.+|++|++.|||+-.|..||
T Consensus 23 ~~~l~~la~~l~cs~R--------------~~~~~l~~~~~~gwl~w~~~~GR 61 (552)
T PRK13626 23 ETTLNELAELLNCSRR--------------HMRTLLNTMQQRGWLTWQAEAGR 61 (552)
T ss_pred eeeHHHHHHHhcCChh--------------HHHHHHHHHHHCCCeeeecCCCC
Confidence 5788888888877654 58999999999999999997676
No 128
>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=83.08 E-value=3.2 Score=23.43 Aligned_cols=42 Identities=17% Similarity=0.243 Sum_probs=32.6
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 63 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k 63 (90)
.|+..|.- +|..+..|+...|-. -+.+.+=|..|+++|+|++
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s--------------~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLS--------------QSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHh-CCCchhhHHHhcccc--------------chHHHHHHHHHHHCcCeeC
Confidence 34444443 889999999988874 3788999999999999975
No 129
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=82.77 E-value=1.5 Score=29.18 Aligned_cols=22 Identities=14% Similarity=0.373 Sum_probs=18.9
Q ss_pred chhHHHHHHHHHHhCCcccccC
Q 034587 44 SGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~ 65 (90)
.+|+.|.+|++||+-|+|.-..
T Consensus 54 ~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 54 KISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred hHHHHHHHHHHHHHCCCEEEEe
Confidence 4789999999999999996543
No 130
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=82.71 E-value=1.4 Score=32.31 Aligned_cols=42 Identities=12% Similarity=0.071 Sum_probs=33.0
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
+=..|+..||- |..-+|++|++|++.|+|+.....|-.+++.
T Consensus 37 sE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~ 78 (241)
T PRK10079 37 AEQQLAARYEV--------------NRHTLRRAIDQLVEKGWVQRRQGVGVLVLMR 78 (241)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEecC
Confidence 34567777765 5579999999999999999888778777543
No 131
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=82.46 E-value=4.7 Score=30.96 Aligned_cols=58 Identities=14% Similarity=0.047 Sum_probs=44.8
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCc-ccccCCCCeeeCcc
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITSS 74 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~gl-V~k~~~~GR~lT~~ 74 (90)
.|...|++-|.-..++....|+..+|-. .+-++..++.|++.|+ |...+..|-.|.+.
T Consensus 4 ~r~~~il~~L~~~~~~s~~~LA~~lgvs--------------r~tV~~~l~~L~~~G~~i~~~~~~Gy~L~~~ 62 (319)
T PRK11886 4 TVMLQLLSLLADGDFHSGEQLGEELGIS--------------RAAIWKHIQTLEEWGLDIFSVKGKGYRLAEP 62 (319)
T ss_pred cHHHHHHHHHHcCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCceEEecCCeEEecCc
Confidence 4677788888777789999999999874 3689999999999999 44444447776544
No 132
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=81.88 E-value=1.7 Score=31.70 Aligned_cols=43 Identities=14% Similarity=0.063 Sum_probs=34.0
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 75 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G 75 (90)
+-..|+..||- |..-+|.+|+.|++.|||.+....|=-+++..
T Consensus 35 sE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GTfV~~~~ 77 (241)
T PRK11402 35 TENELCTQYNV--------------SRITIRKAISDLVADGVLIRWQGKGTFVQSQK 77 (241)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEECCCc
Confidence 34567777775 45799999999999999998887777776654
No 133
>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=81.59 E-value=6.3 Score=23.80 Aligned_cols=52 Identities=19% Similarity=0.293 Sum_probs=38.0
Q ss_pred hhHHHHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC
Q 034587 3 ELVTSMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 68 (90)
Q Consensus 3 ~r~ASi~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G 68 (90)
...---|+-||. .+++....++...|-++ .-+=..|+.|++.|||+..+.+|
T Consensus 4 ~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~--------------~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 4 ESEEDYLKAIYELSEEGGPVRTKDIAERLGVSP--------------PTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp CHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEETTTE
T ss_pred cHHHHHHHHHHHHHcCCCCccHHHHHHHHCCCh--------------HHHHHHHHHHHHCCCEEecCCCC
Confidence 334445566665 36899999999887642 45778899999999999887654
No 134
>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=81.46 E-value=9.1 Score=22.89 Aligned_cols=53 Identities=11% Similarity=0.125 Sum_probs=38.6
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.|++.+- +++..+..|+..+|-. ..-|+..++.||+.|+....++.|..+.+.
T Consensus 4 ~il~~L~-~~~~~~~eLa~~l~vS--------------~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~ 56 (69)
T TIGR00122 4 RLLALLA-DNPFSGEKLGEALGMS--------------RTAVNKHIQTLREWGVDVLTVGKGYRLPPP 56 (69)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEecCCceEecCc
Confidence 3455544 6778899999988763 378999999999999964333567777543
No 135
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=81.25 E-value=2.1 Score=34.83 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=33.1
Q ss_pred HHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 48 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 48 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
....|++|++.|||+.+. +.=+||++|+-..|.|+..++
T Consensus 398 ~~~~l~~~~~~Gll~~~~-~~l~lT~~G~~~~~~i~~~~~ 436 (449)
T PRK09058 398 LAPLLAQWQQAGLVELSS-DCLRLTLAGRFWAVNLTQGLI 436 (449)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECCCcccHHHHHHHHHH
Confidence 445889999999999764 467899999999999998764
No 136
>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=79.99 E-value=3.8 Score=24.91 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=32.0
Q ss_pred HhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 12 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 12 lYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
|=-++.+.+..|++.|+- +-..++..|.+||..|.|++..
T Consensus 9 l~~~~~~S~~eLa~~~~~--------------s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 9 LRERGRVSLAELAREFGI--------------SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHS-SEEHHHHHHHTT----------------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEec
Confidence 445788999999998876 4479999999999999999765
No 137
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=79.54 E-value=2.7 Score=31.36 Aligned_cols=50 Identities=16% Similarity=0.283 Sum_probs=39.1
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHH-HHHhCCcccccCCCCeeeCcchHhhH
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDL 79 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~Lq-qLE~~glV~k~~~~GR~lT~~G~~~l 79 (90)
.+|+++..++...|-.. .-++.++. .|-+.++|++.. .||+.|++|...|
T Consensus 253 ~~~~~~~~ia~~lg~~~--------------~~~~~~~e~~Li~~~li~~~~-~g~~~~~~~~~~~ 303 (305)
T TIGR00635 253 GGPVGLKTLAAALGEDA--------------DTIEDVYEPYLLQIGFLQRTP-RGRIATELAYEHL 303 (305)
T ss_pred CCcccHHHHHHHhCCCc--------------chHHHhhhHHHHHcCCcccCC-chhhhhHHHHHHh
Confidence 34688888888877632 35667777 699999998664 7999999998876
No 138
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=78.95 E-value=4.3 Score=32.98 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=38.7
Q ss_pred hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 13 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 13 Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
|--||||+.+++-.-|-.+. .|-=.+===|-..|++++++ .||++|+++.+.|.
T Consensus 273 f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTp-RGR~aT~~ay~hl~ 326 (332)
T COG2255 273 FGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTP-RGRIATAKAYEHLG 326 (332)
T ss_pred hCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCC-CcceecHHHHHHhc
Confidence 44589999999998776431 12222223466789999998 59999999987663
No 139
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=78.92 E-value=2.8 Score=32.81 Aligned_cols=37 Identities=16% Similarity=0.098 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 48 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 48 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
.-..|++|++.|||+.+. +| ||++|.-+.|.|+..+.
T Consensus 313 ~~~~l~~l~~~gl~~~~~--~~-l~~~g~~~~d~i~~~~~ 349 (350)
T PRK08446 313 EEKKVKILIEENKLFIKN--NR-LYNKDFFLADEIALFLL 349 (350)
T ss_pred HHHHHHHHHHCCCEEeeC--CE-EcccchhhHHHHHHHhh
Confidence 345788999999998653 44 99999999999998754
No 140
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=78.58 E-value=3.4 Score=29.82 Aligned_cols=40 Identities=28% Similarity=0.413 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhCCcccccC----CCCeeeCcchHhhHHHHHHHh
Q 034587 47 IARHILQQLQNMNIIDIEP----KGGRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~----~~GR~lT~~G~~~lD~iA~~v 86 (90)
-+..+|.+|++.|+|.... +.=-.||++|...|+-+..+|
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~I 78 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRI 78 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhC
Confidence 4567899999999998642 235689999999998877665
No 141
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=78.54 E-value=2.4 Score=31.40 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
|.--+|++|++|++.|+|......|--+++.
T Consensus 44 SR~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 44 SRMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred cHHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence 5578999999999999999887778777765
No 142
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=78.18 E-value=8.2 Score=29.39 Aligned_cols=56 Identities=23% Similarity=0.274 Sum_probs=46.3
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
.+|-..|+..|--++.+.|..|+..||- |..-||.=|..||+.|++.+.. ||..+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~V--------------S~~TIRRDL~~Le~~G~l~r~~-GGa~~~ 71 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGV--------------STVTIRNDLAFLEKQGIAVRAY-GGALIC 71 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCC--------------CHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence 3567788888888899999999999965 3468999999999999999776 676654
No 143
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=77.63 E-value=3 Score=28.72 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=26.4
Q ss_pred HHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587 50 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 50 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
.++..+|-+|+|+... |-=.|||.|+++.+.
T Consensus 16 p~~eAaelLgf~~~~~-Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 16 PIVEAAELLGFAEVEE-GDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHcCCeeecC-CcEEeccchHHHHHC
Confidence 5788999999999774 778999999998863
No 144
>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=76.44 E-value=7.9 Score=27.58 Aligned_cols=44 Identities=14% Similarity=0.063 Sum_probs=37.1
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
+--|+..|..++.+..+.|+..-|-++ +.+|++|+.|.+.|||.
T Consensus 16 ~v~Vl~aL~~~~~~tdEeLa~~Lgi~~--------------~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 16 VGLVLFSLGIKGEFTDEEISLELGIKL--------------NEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCce
Confidence 344677777889999999999888765 58999999999999995
No 145
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=76.41 E-value=8.9 Score=28.79 Aligned_cols=49 Identities=14% Similarity=0.001 Sum_probs=42.4
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
+|-..|+..|--++.+.+..|+..||- |..-||.=|++||+.|+|++.-
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGI--------------SPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEec
Confidence 577788888888999999999999875 3467899999999999998875
No 146
>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=76.21 E-value=2.4 Score=29.02 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=27.4
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
-|.+..|+..|+- ++++.|.+|+.||+-|+|....
T Consensus 59 ~ITp~~lserlkI--------------~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 59 LITPSVLSERLKI--------------NGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp CECHHHHHHHHCC--------------SCHHHHHHHHHHHHCCSSEEEE
T ss_pred EeeHHHHHHhHhh--------------HHHHHHHHHHHHHHCCCEEEEe
Confidence 3666677776665 3689999999999999997554
No 147
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=75.87 E-value=7.3 Score=25.62 Aligned_cols=39 Identities=21% Similarity=0.310 Sum_probs=29.8
Q ss_pred cccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587 40 FCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 40 ~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
|..|+.+++ .+++.|-+-|||. +|+ |..||+.|.+.-+.
T Consensus 29 H~dA~p~~i-~a~~RLheKGLI~-~pd-GgyLT~~G~~~aEh 67 (77)
T TIGR02647 29 HSTASPAAV-AAAARLHEKGLTT-QPD-GGYLTSLGLEAAEH 67 (77)
T ss_pred cccCCHHHH-HHHHHHHHcCCcc-CCC-CCEecHHHHHHHHH
Confidence 466777666 6789999999996 444 45999999876553
No 148
>PF14178 YppF: YppF-like protein
Probab=75.82 E-value=6.1 Score=24.84 Aligned_cols=18 Identities=28% Similarity=0.778 Sum_probs=15.7
Q ss_pred HHHHHhhcCCCchhHHHH
Q 034587 8 MARKIYLRQGLGVGSFRR 25 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~ 25 (90)
.+|+.||.|.+.+...|.
T Consensus 27 Far~~Yi~gei~i~eYR~ 44 (60)
T PF14178_consen 27 FARKLYIQGEISINEYRN 44 (60)
T ss_pred HHHHHHHhCcccHHHHHH
Confidence 589999999999988766
No 149
>PF13730 HTH_36: Helix-turn-helix domain
Probab=75.39 E-value=3.1 Score=23.71 Aligned_cols=18 Identities=17% Similarity=0.368 Sum_probs=15.5
Q ss_pred chhHHHHHHHHHHhCCcc
Q 034587 44 SGAIARHILQQLQNMNII 61 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV 61 (90)
|..-|+++++.||+.|||
T Consensus 38 s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 38 SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHHHHHHCcCC
Confidence 446789999999999996
No 150
>PRK12423 LexA repressor; Provisional
Probab=75.09 E-value=3.5 Score=29.94 Aligned_cols=36 Identities=22% Similarity=0.445 Sum_probs=29.3
Q ss_pred CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
-.+..|+..+|=. |.+.+|..|+.||+.|+|+..+.
T Consensus 26 Ps~~eia~~~g~~-------------s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 26 PSLAEIAQAFGFA-------------SRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHhCCC-------------ChHHHHHHHHHHHHCCCEEecCC
Confidence 4888888877732 33688999999999999998874
No 151
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=75.03 E-value=2.8 Score=36.04 Aligned_cols=62 Identities=19% Similarity=0.355 Sum_probs=47.8
Q ss_pred HHHHHH---hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 7 SMARKI---YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 7 Si~Rkl---Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
++++++ ||+-+.=|+.+...||+-+ .=++.+|..||.-|+|+.-+++|=.||..||-.=--|
T Consensus 429 kvl~kiP~~~ikrg~liedi~~~~g~~e--------------eev~~sl~kleskgfveeL~n~gv~LTeaGe~~KtAi 493 (593)
T COG1542 429 KVLIKIPRKYIKRGELIEDIQGHVGGDE--------------EEVIKSLGKLESKGFVEELPNKGVKLTEAGELVKTAI 493 (593)
T ss_pred HHHHhccccccchhhHHHHHHhhcCccH--------------HHHHHHHHHHhhcchHHHhccCcEEeehhhHHHHHHH
Confidence 444444 5666667778888887643 4688999999999999999999999999998654333
No 152
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=74.61 E-value=5.5 Score=32.45 Aligned_cols=59 Identities=17% Similarity=0.242 Sum_probs=46.7
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
.-++-+..+...||- -. -..+...|+.+++.|+++.+. +.-+||+.|+-++|.|+....
T Consensus 352 ~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~-~~~~lt~~g~~~~~~i~~~f~ 410 (416)
T COG0635 352 NFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDG-DRLRLTEKGRLLLRSIAEAFD 410 (416)
T ss_pred hcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecC-CEEEECCcchhHHHHHHHHHH
Confidence 346777777777764 11 257889999999999999886 578999999999999988753
No 153
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=74.43 E-value=11 Score=28.48 Aligned_cols=55 Identities=13% Similarity=0.164 Sum_probs=46.2
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 71 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l 71 (90)
.+|-..|+..|--++.+.|..|+..||- |..-||.=|+.||+.|+|.+.- ||=++
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~V--------------S~~TIRRDL~~Le~~g~l~r~~-Gga~~ 58 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDT--------------TGTTIRKDLVILEHAGTVIRTY-GGVVL 58 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEE-CCEEc
Confidence 4678889999999999999999999986 3468999999999999998775 45444
No 154
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=73.92 E-value=3.2 Score=32.15 Aligned_cols=23 Identities=30% Similarity=0.521 Sum_probs=19.0
Q ss_pred hHHHHHHHHHHhCCcccccCCCC
Q 034587 46 AIARHILQQLQNMNIIDIEPKGG 68 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~G 68 (90)
.=+=.+|+.||++|+||+.+.|+
T Consensus 225 tTvsR~L~~LEk~GlIe~~K~G~ 247 (258)
T COG2512 225 TTVSRILRRLEKRGLIEKEKKGR 247 (258)
T ss_pred HHHHHHHHHHHhCCceEEEEeCC
Confidence 45667899999999999987644
No 155
>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=73.37 E-value=4.1 Score=25.62 Aligned_cols=60 Identities=27% Similarity=0.345 Sum_probs=38.9
Q ss_pred HHHHHHHHh---hc---CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC---CeeeCcch
Q 034587 5 VTSMARKIY---LR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSG 75 (90)
Q Consensus 5 ~ASi~RklY---l~---g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~~G 75 (90)
+-|++--|| +. +++-++.|-...+.- |+ +-.-+|.+|--|-+.||++....+ ...||++|
T Consensus 2 a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~~---Gv--------~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 2 ARSLIVTLLGDYLRPRGGWIWVASLIRLLAAF---GV--------SESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCCT---T----------HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred cceehHHHHHHHhccCCCceeHHHHHHHHHHc---CC--------ChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 446666666 43 356666666665431 22 236899999999999999988653 36788876
No 156
>PRK09213 pur operon repressor; Provisional
Probab=73.15 E-value=21 Score=27.86 Aligned_cols=79 Identities=15% Similarity=0.312 Sum_probs=57.1
Q ss_pred hhhHHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCc----
Q 034587 2 SELVTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITS---- 73 (90)
Q Consensus 2 ~~r~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~---- 73 (90)
|+|...+.+.|-=++ .+.+..|+..|+..|-- -.-.=.||+.+|++. .+|.|+..+ .||-+.+|
T Consensus 6 ~~r~~~~~~~l~~~p~~~~~l~~f~~~~~~aks~-------ised~~i~~~~~~~~-~~g~~~t~~ga~ggv~~~p~~~~ 77 (271)
T PRK09213 6 SERLVDMTKYLLENPNKLISLTFFAERYGAAKSS-------ISEDLVIIKETFEKQ-GIGTLETVPGAAGGVKYIPSISE 77 (271)
T ss_pred hhHHHHHHHHHHhCCCceEcHHHHHHHhccccch-------hhhhHHHHHHHHHhc-CCceEEEeCCCCCCeEEEcCCCH
Confidence 567777777666554 48999999999997621 112224899999874 688999887 36776665
Q ss_pred -chHhhHHHHHHHhhc
Q 034587 74 -SGQRDLDQVAGRIVV 88 (90)
Q Consensus 74 -~G~~~lD~iA~~v~~ 88 (90)
+.+++|+.++..+.+
T Consensus 78 ~~a~~~~~~L~~~L~~ 93 (271)
T PRK09213 78 EEAREFVEELCERLSE 93 (271)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 378889998887654
No 157
>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=72.51 E-value=3.9 Score=25.81 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHHhCCcccccC
Q 034587 45 GAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 45 g~iiR~~LqqLE~~glV~k~~ 65 (90)
.+||-++|..||.+|+|+.-.
T Consensus 18 RSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 18 RSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHhcCceeecc
Confidence 479999999999999998544
No 158
>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=71.40 E-value=18 Score=25.67 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=35.4
Q ss_pred HHHHHHHHh---hcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 5 VTSMARKIY---LRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 5 ~ASi~RklY---l~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
=.+||.-|. .++ |.++..|+..+|-+ |.+-++..|+.||+.|+|++.+.
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~-------------s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLR-------------SPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC-------------ChHHHHHHHHHHHHCCCEecCCC
Confidence 344555444 433 46677999987763 34688999999999999998764
No 159
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=71.01 E-value=14 Score=23.52 Aligned_cols=70 Identities=11% Similarity=0.204 Sum_probs=48.9
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc-cC-----CCCee------eCcc
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI-EP-----KGGRR------ITSS 74 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k-~~-----~~GR~------lT~~ 74 (90)
.|++.+.-++++....|.+..|-. -.-++..++.|++.|+|.. .. .-|.. ++-.
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~~s--------------~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~ 72 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGLS--------------PSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLE 72 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEEC
Confidence 577888888889999999988653 3689999999999999983 21 12321 2222
Q ss_pred hHhhHHHHHHHhhcCC
Q 034587 75 GQRDLDQVAGRIVVAP 90 (90)
Q Consensus 75 G~~~lD~iA~~v~~~~ 90 (90)
.....|+++..+.+-|
T Consensus 73 ~~~~~~~v~~~l~~~p 88 (108)
T smart00344 73 SPDKLEEFLEKLEKLP 88 (108)
T ss_pred ChhHHHHHHHHHhCCc
Confidence 1346788888876543
No 160
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=70.87 E-value=6.2 Score=26.21 Aligned_cols=39 Identities=13% Similarity=0.067 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhCCcccccC---CCCeeeCcchHhhHHHHHHH
Q 034587 47 IARHILQQLQNMNIIDIEP---KGGRRITSSGQRDLDQVAGR 85 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~---~~GR~lT~~G~~~lD~iA~~ 85 (90)
=+=+++=.||..|+|.... ..--.+|++|...|++|-.+
T Consensus 43 elL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~~~~~ 84 (85)
T PF11313_consen 43 ELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLAEIKNE 84 (85)
T ss_pred HHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHHHHHhc
Confidence 3456778899999997443 22478999999999998643
No 161
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=69.77 E-value=7.4 Score=26.90 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=33.1
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
|.-.+.|+..+.-. -..++.+|+-|++.|+|+..+++--.|+.
T Consensus 53 py~~e~LA~~~~~~--------------~~~V~~AL~~f~k~glIe~~ed~~i~i~~ 95 (121)
T PF09681_consen 53 PYTAEMLALEFDRP--------------VDTVRLALAVFQKLGLIEIDEDGVIYIPN 95 (121)
T ss_pred CCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCeEEeec
Confidence 67777788777643 36899999999999999998765445543
No 162
>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=68.34 E-value=10 Score=24.94 Aligned_cols=34 Identities=24% Similarity=0.431 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHhC---CcccccC----CCCeeeCcchHhhH
Q 034587 46 AIARHILQQLQNM---NIIDIEP----KGGRRITSSGQRDL 79 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~----~~GR~lT~~G~~~l 79 (90)
+-+-..+++||+. .|++..+ .+|-.|||.|+..+
T Consensus 31 stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 31 KSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 4566678888875 5677764 24889999999986
No 163
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=68.16 E-value=6.5 Score=23.10 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHhC---CcccccCCCCeeeCcchH
Q 034587 45 GAIARHILQQLQNM---NIIDIEPKGGRRITSSGQ 76 (90)
Q Consensus 45 g~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~ 76 (90)
-+-+...+++||+. .|++... +|=.+|+.|+
T Consensus 27 ~~~vs~~i~~LE~~lg~~Lf~r~~-~~~~lT~~G~ 60 (60)
T PF00126_consen 27 QSAVSRQIKQLEEELGVPLFERSG-RGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHHHHHHTS-SEEECS-SSEEE-HHHH
T ss_pred chHHHHHHHHHHHHhCCeEEEECC-CCeeEChhhC
Confidence 35677888999974 6787765 5789999986
No 164
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=68.09 E-value=10 Score=27.43 Aligned_cols=48 Identities=13% Similarity=-0.053 Sum_probs=42.3
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~ 64 (90)
.|-..|+-.|--++.+.+..|...||- |..-||.=|++||+.|+|...
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~v--------------S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGV--------------SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCc--------------CHHHHHHHHHHHhcchHHHHH
Confidence 577788888889999999999999986 457899999999999999754
No 165
>TIGR01743 purR_Bsub pur operon repressor, Bacillus subtilis type. This model represents the puring operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.
Probab=67.23 E-value=32 Score=26.82 Aligned_cols=79 Identities=10% Similarity=0.207 Sum_probs=56.3
Q ss_pred hhhHHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcc---
Q 034587 2 SELVTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSS--- 74 (90)
Q Consensus 2 ~~r~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~--- 74 (90)
|+|...+.+.|-=++ .+.+..|+..|+..|-- -.-.=.||+.+|++. .+|.|+..+ .||-+.+|.
T Consensus 4 ~~r~~~~t~~l~~~p~~~~~l~~f~~~~~~aks~-------ised~~i~~~~~~~~-~~g~~~t~~ga~ggv~~~p~~~~ 75 (268)
T TIGR01743 4 SGRLVDLTNYLITNPNKLIPLNFFSERYESAKSS-------ISEDIVIIKETFEKF-GIGKLLTVPGAAGGVKYIPKMSQ 75 (268)
T ss_pred hHHHHHHHHHHHhCCCceEcHHHHHHHhccccch-------hhhhHHHHHHHHHhc-CCceEEEeCCCCCCeEEEeCCCH
Confidence 567777777666655 48999999999997621 111224899999874 688998887 367766653
Q ss_pred --hHhhHHHHHHHhhc
Q 034587 75 --GQRDLDQVAGRIVV 88 (90)
Q Consensus 75 --G~~~lD~iA~~v~~ 88 (90)
.+.+|++++..+.+
T Consensus 76 ~~~~~~~~~l~~~l~~ 91 (268)
T TIGR01743 76 AEAEEFVEELCQSLSE 91 (268)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 67778888877644
No 166
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=66.79 E-value=22 Score=26.80 Aligned_cols=56 Identities=14% Similarity=0.129 Sum_probs=45.5
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
.+|-..|+.-|--++.+.+..|+..|+- |-.-||.=|..||+.|++.+.- ||=.+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TiRRdL~~Le~~g~l~r~~-GGa~~~ 59 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSV--------------SPQTIRRDLNDLAEQNKILRHH-GGAALP 59 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEec-CCEEec
Confidence 4677788888888999999999999954 4468999999999999998774 554443
No 167
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=66.54 E-value=7.2 Score=30.65 Aligned_cols=41 Identities=12% Similarity=0.151 Sum_probs=33.0
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.+..|++.||- |.+-+|.++++||+.|||+..+..|-.+.+
T Consensus 31 s~r~la~~~~v--------------sr~tv~~a~~~L~~~g~i~~~~~~G~~v~~ 71 (431)
T PRK15481 31 PVRELASELGV--------------NRNTVAAAYKRLVTAGLAQSQGRNGTVIRG 71 (431)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCceEEcc
Confidence 56677777765 557999999999999999988877777754
No 168
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=64.70 E-value=9 Score=27.95 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++... +|-.||+.|+.+++.+-
T Consensus 33 avS~~I~~LE~~lg~~LF~R~~-~~~~lT~~G~~l~~~a~ 71 (300)
T TIGR02424 33 AVSKTLRELEEILGTPLFERDR-RGIRLTRYGELFLRHAG 71 (300)
T ss_pred HHHHHHHHHHHHhCCeEEEEcC-CCccccHhHHHHHHHHH
Confidence 566678888875 6677664 58899999998887643
No 169
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=64.46 E-value=28 Score=26.02 Aligned_cols=51 Identities=14% Similarity=0.055 Sum_probs=42.5
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
+.|--.|+..|.-++.+.+..|...+|- |-.-||.-|.+||+.|+|.....
T Consensus 3 ~~R~~~Il~~l~~~~~~~~~eLa~~l~V--------------S~~TiRRdL~~L~~~~~l~r~~G 53 (240)
T PRK10411 3 AARQQAIVDLLLNHTSLTTEALAEQLNV--------------SKETIRRDLNELQTQGKILRNHG 53 (240)
T ss_pred hHHHHHHHHHHHHcCCCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecC
Confidence 4566778888888899999999999963 44689999999999999987653
No 170
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=64.39 E-value=2.2 Score=29.72 Aligned_cols=33 Identities=21% Similarity=0.228 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 47 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
-+..-|..||.+|+|....+ =|..|+.||.+|.
T Consensus 8 ~~l~~l~~LE~~G~v~~~n~--------yQ~lln~IA~dI~ 40 (142)
T PF03836_consen 8 KILENLKELESLGIVSRSNN--------YQDLLNDIAKDIR 40 (142)
T ss_dssp -----------------------------------------
T ss_pred HHHHHHHHHHHCCCCCCccc--------HHHHHHHHHHHHh
Confidence 35566789999999976632 2458889998874
No 171
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=64.23 E-value=5.6 Score=26.46 Aligned_cols=28 Identities=29% Similarity=0.466 Sum_probs=20.4
Q ss_pred HHHhCCcc-cccCCC---CeeeCcchHhhHHH
Q 034587 54 QLQNMNII-DIEPKG---GRRITSSGQRDLDQ 81 (90)
Q Consensus 54 qLE~~glV-~k~~~~---GR~lT~~G~~~lD~ 81 (90)
+|..+||| ++.... --+||++|.+..|-
T Consensus 58 SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 58 SLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred hHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 58889999 444333 45799999988763
No 172
>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length. It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=63.95 E-value=5.6 Score=25.77 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=17.3
Q ss_pred HHHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587 50 HILQQLQNMNIIDIEPKGGRRITSSGQRD 78 (90)
Q Consensus 50 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 78 (90)
++++.|..+|.|+.+ + .||+-|+..
T Consensus 1 ~A~~~L~~Lgald~~--~--~lT~lG~~~ 25 (102)
T PF04408_consen 1 KALELLKSLGALDEN--G--NLTPLGRKM 25 (102)
T ss_dssp -HHHHHHHTTSB-TT--S---B-HHHHHH
T ss_pred CHHHHHHHCCCCCCC--C--CcCHHHHHH
Confidence 478999999999544 2 899999864
No 173
>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=62.03 E-value=35 Score=23.32 Aligned_cols=54 Identities=17% Similarity=0.196 Sum_probs=41.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
=..|+.-|+-.+|+.+..+....... ++. +-+-+..+|.-|++-|+|+... .||
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~--~~~--------~~tTv~T~L~rL~~KG~v~~~k-~gr 59 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEK--KDW--------SDSTIKTLLGRLVDKGCLTTEK-EGR 59 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhc--cCC--------cHHHHHHHHHHHHHCCceeeec-CCC
Confidence 35689999999999999988777543 221 2357899999999999998664 355
No 174
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=61.23 E-value=15 Score=26.99 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
+-+=+.+++||+. .|++..+ +|=.+|+.|+.+++.+..
T Consensus 34 ~avS~~i~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~~ 74 (302)
T PRK09791 34 PALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGESFYQHASL 74 (302)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceECccHHHHHHHHHH
Confidence 3566778889874 6677765 588999999998887654
No 175
>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=61.01 E-value=9.1 Score=29.74 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=22.8
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
|-.=++.+|+-|+++|+|+++.+|--+.|
T Consensus 152 s~~ev~~sL~~L~~~glikk~~~g~y~~t 180 (271)
T TIGR02147 152 SAEQVKESLDLLERLGLIKKNEDGFYKQT 180 (271)
T ss_pred CHHHHHHHHHHHHHCCCeeECCCCcEEee
Confidence 34568999999999999999876534544
No 176
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=60.66 E-value=11 Score=27.02 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=33.8
Q ss_pred chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587 19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 75 (90)
Q Consensus 19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G 75 (90)
.-..|+..||-. ...+|.+|+.|+..|+|......|-.+++..
T Consensus 27 sE~eLa~~~~Vs--------------r~Tvr~Al~~L~~eGli~~~~g~Gt~V~~~~ 69 (231)
T TIGR03337 27 SERDLGERFNTT--------------RVTIREALQQLEAEGLIYREDRRGWFVSPPR 69 (231)
T ss_pred CHHHHHHHHCCC--------------HHHHHHHHHHHHHCCeEEEeCCCEEEECCcc
Confidence 356677777763 5799999999999999998876777776543
No 177
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=60.54 E-value=30 Score=23.69 Aligned_cols=60 Identities=12% Similarity=0.062 Sum_probs=41.2
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCcchHhhHHH
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ 81 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~lD~ 81 (90)
.|++.|.-.++..|+.|...+|-.+ +-+=+=|+-|+++|||+.... || .|-+.....++.
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsq--------------stvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l~~~~~~~~~~ 83 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQ--------------PKISRHLALLRESGLLLDRKQ-GKWVHYRLSPHIPAWAAK 83 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCceEEEEE-cCEEEEEECchHHHHHHH
Confidence 4666665558899999999887642 345566899999999987765 54 455544333333
No 178
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=60.06 E-value=14 Score=29.61 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHhCCcccccCC--CC-eeeCcchHhhHHHHHHHhhcC
Q 034587 46 AIARHILQQLQNMNIIDIEPK--GG-RRITSSGQRDLDQVAGRIVVA 89 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~--~G-R~lT~~G~~~lD~iA~~v~~~ 89 (90)
..+|.+|.-|-++||+....+ ++ .+||++|...+-+-+..|...
T Consensus 43 ~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a~~riy~~ 89 (291)
T COG3327 43 TTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRAARRIYPR 89 (291)
T ss_pred HHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHHhhhhcCC
Confidence 478999999999999976552 12 568999999999988888653
No 179
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=59.98 E-value=8.7 Score=33.19 Aligned_cols=58 Identities=22% Similarity=0.304 Sum_probs=42.8
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe------eeCcchHhhHHHHHHHhhc
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR------RITSSGQRDLDQVAGRIVV 88 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR------~lT~~G~~~lD~iA~~v~~ 88 (90)
.+.+..|+-...+.. .-+|.+|+||++.||++-.+.-|| .+..++...+-..|++.++
T Consensus 23 ~~tl~eLA~~lfCS~--------------Rh~R~lL~q~q~~gWL~W~p~~GRGkrSrL~flr~~e~L~~q~a~~~le 86 (564)
T COG4533 23 ETTLNELADILFCSR--------------RHARTLLRQMQEAGWLTWQPQAGRGKRSRLTFLRTPEALLLQLAEKLLE 86 (564)
T ss_pred eeeHHHHHHHhccCH--------------HHHHHHHHHHHHcCCEEeccCCCCCcceeEEEecChHHHHHHHHHHHHh
Confidence 356677777666644 468999999999999999986665 2445677777777777654
No 180
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=59.47 E-value=12 Score=27.71 Aligned_cols=37 Identities=8% Similarity=0.143 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
.-+-..+++||+. .|++.+. .|=.||+.|+.+++.+-
T Consensus 40 pavS~~I~~LE~~lG~~Lf~R~~-r~~~lT~~G~~l~~~a~ 79 (303)
T PRK10082 40 PAFSRRIRALEQAIGVELFNRQV-TPLQLSEQGKIFHSQIR 79 (303)
T ss_pred HHHHHHHHHHHHHcCCEEEEecC-CCCccCHHHHHHHHHHH
Confidence 3567788999975 5566664 58899999999988743
No 181
>PHA02943 hypothetical protein; Provisional
Probab=58.95 E-value=35 Score=25.32 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=36.8
Q ss_pred hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
|.=-|++-| -.|...+..+++.-|-. -+=++++|..||+.|.|++.+.
T Consensus 12 R~~eILE~L-k~G~~TtseIAkaLGlS--------------~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 12 RMIKTLRLL-ADGCKTTSRIANKLGVS--------------HSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred HHHHHHHHH-hcCCccHHHHHHHHCCC--------------HHHHHHHHHHHHHcCceEEEee
Confidence 444566666 55667788888877753 3679999999999999999874
No 182
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=57.82 E-value=7.9 Score=26.98 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=19.7
Q ss_pred CchhHHHHHHHHHHhCCcccccC
Q 034587 43 SSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~ 65 (90)
=.|++.|.+|+.|++-|+|....
T Consensus 72 IngsLAr~alr~L~~kG~Ik~Vs 94 (110)
T KOG1767|consen 72 INGSLARAALRELSNKGVIKQVS 94 (110)
T ss_pred hchHHHHHHHHHHHhcchHHHHh
Confidence 35789999999999999997544
No 183
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=56.88 E-value=16 Score=26.37 Aligned_cols=37 Identities=19% Similarity=0.251 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+-+=..+++||+. .|+.... .|=.||+.|+.+++.+-
T Consensus 30 savS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~~~ 69 (296)
T PRK11242 30 PTLSQQIRQLEESLGVQLFDRSG-RTVRLTDAGEVYLRYAR 69 (296)
T ss_pred hHHHHHHHHHHHHhCCeeEeEcC-CceeechhHHHHHHHHH
Confidence 3556678888875 6676664 68899999999887654
No 184
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=56.25 E-value=12 Score=27.40 Aligned_cols=36 Identities=17% Similarity=0.173 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++.+. .|-.||+.|+.++..+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~ 70 (301)
T PRK14997 32 KLSRRIAQLEERLGVRLIQRTT-RQFNVTEVGQTFYEHCK 70 (301)
T ss_pred HHHHHHHHHHHHhCCEeeeecc-CcceEcHhHHHHHHHHH
Confidence 445668899975 5566664 58999999998886643
No 185
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=55.78 E-value=19 Score=25.62 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
-+=..+++||+. .|++... .|=.||+.|+.++..
T Consensus 27 avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 27 TVTDQVRKLEERYGVELFHRNG-RRLELTDAGHRLLPI 63 (279)
T ss_pred HHHHHHHHHHHHhCCccEEEcC-CeEEEChhHHHHHHH
Confidence 455677888875 6666653 578888988888754
No 186
>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=55.77 E-value=35 Score=19.15 Aligned_cols=48 Identities=10% Similarity=0.119 Sum_probs=35.6
Q ss_pred hHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCC-cccccC
Q 034587 4 LVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMN-IIDIEP 65 (90)
Q Consensus 4 r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~g-lV~k~~ 65 (90)
|-..|+.-|+-. +++....|+..+|-. ..-|++-++.|++.+ .|+..+
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS--------------~rTi~~~i~~L~~~~~~I~~~~ 50 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVS--------------RRTIRRDIKELREWGIPIESKR 50 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS---------------HHHHHHHHHHHHHTT-EEEEET
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCeEEeeC
Confidence 345677777654 569999999988874 368999999999999 344443
No 187
>smart00847 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.
Probab=55.17 E-value=10 Score=23.46 Aligned_cols=24 Identities=29% Similarity=0.529 Sum_probs=19.5
Q ss_pred HHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587 51 ILQQLQNMNIIDIEPKGGRRITSSGQRD 78 (90)
Q Consensus 51 ~LqqLE~~glV~k~~~~GR~lT~~G~~~ 78 (90)
+++.|..+|.|+.+ | .||+-|+..
T Consensus 2 A~~~L~~LgAld~~---~-~lT~lG~~m 25 (92)
T smart00847 2 ALELLYELGALDDD---G-RLTPLGRKM 25 (92)
T ss_pred HHHHHHHCCCcCCC---C-CcCHHHHHH
Confidence 67899999999653 3 899999875
No 188
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=54.89 E-value=14 Score=30.20 Aligned_cols=34 Identities=29% Similarity=0.536 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
-++=.++..||+.|+|+.++ +|=.+|++|..+..
T Consensus 49 p~v~~i~~~l~~egiv~~~~-g~v~~TekG~E~~e 82 (354)
T COG1568 49 PLVASILEILEDEGIVKIEE-GGVELTEKGEELAE 82 (354)
T ss_pred hHHHHHHHHHHhcCcEEEec-CcEeehhhhHHHHH
Confidence 35667899999999999886 57999999998765
No 189
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=54.88 E-value=26 Score=25.93 Aligned_cols=37 Identities=16% Similarity=0.163 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=.-+++||+. .|++... .|=.||+.|+.+++.+..
T Consensus 38 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~~ 77 (302)
T TIGR02036 38 AISHRINQLEEELGIQLFVRSH-RKVELTHEGKRIYWALKS 77 (302)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceeECHhHHHHHHHHHH
Confidence 455678899874 6777775 689999999988876543
No 190
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=54.20 E-value=9.3 Score=30.16 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=33.2
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 63 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k 63 (90)
|+-|++|+..-|+.-. ++.+|... ++.+|..|++.|+|+.
T Consensus 231 P~kvetl~~lcGS~~~---~l~~FR~~----Lk~AL~eL~~~g~v~~ 270 (282)
T PF07042_consen 231 PIKVETLRELCGSESS---RLRKFRQQ----LKKALDELVAVGFVSS 270 (282)
T ss_pred CccHHHHHHHcCCCcc---CHHHHHHH----HHHHHHHHHhcCceeE
Confidence 8999999999888542 46677654 8999999999999974
No 191
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=54.10 E-value=51 Score=24.31 Aligned_cols=44 Identities=18% Similarity=0.121 Sum_probs=35.4
Q ss_pred hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587 3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 63 (90)
Q Consensus 3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k 63 (90)
.-+--+|--||.++|+.-..+.+..|-.. -.++++|.+.|||+.
T Consensus 90 ~aaLEtLaiIay~qPiTr~eI~~irGv~~-----------------~~ii~~L~~~gLI~e 133 (188)
T PRK00135 90 QAALEVLAIIAYKQPITRIEIDEIRGVNS-----------------DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCCCH-----------------HHHHHHHHHCCCeEE
Confidence 33445788899999999999999877642 567899999999974
No 192
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=54.08 E-value=21 Score=26.21 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
.-+-..+++||+. .|.+.+. .|=.||+.|+.+++..
T Consensus 30 pavS~~i~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a 68 (305)
T PRK11151 30 PTLSGQIRKLEDELGVMLLERTS-RKVLFTQAGLLLVDQA 68 (305)
T ss_pred hHHHHHHHHHHHHhCchheeeCC-CceeECccHHHHHHHH
Confidence 3566778888875 5666654 5889999999888764
No 193
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=53.92 E-value=21 Score=26.43 Aligned_cols=37 Identities=11% Similarity=0.088 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+-+-+.+++||+. .|++... .|=.+|+.|+.++....
T Consensus 30 ~avS~~I~~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~a~ 69 (305)
T PRK11233 30 PALSQQVATLEGELNQQLLIRTK-RGVTPTEAGKILYTHAR 69 (305)
T ss_pred hHHHHHHHHHHHHhCCceEEeCC-CCceECHhHHHHHHHHH
Confidence 3566778888874 6677665 58889999988776543
No 194
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=52.42 E-value=20 Score=25.76 Aligned_cols=39 Identities=13% Similarity=0.086 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
--+=.+|++|++.|+|+... +.|+=.=...|.++|..+.
T Consensus 184 etvsR~L~~L~~~G~I~~~~---~~i~I~d~~~L~~~~~~~~ 222 (226)
T PRK10402 184 RHLLYVLAQFIQDGYLKKSK---RGYLIKNRKQLSGLALELK 222 (226)
T ss_pred HHHHHHHHHHHHCCCEEeeC---CEEEEeCHHHHHHHHHHhc
Confidence 34555999999999998763 3455444556666676653
No 195
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=52.34 E-value=27 Score=24.55 Aligned_cols=37 Identities=11% Similarity=0.089 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++... .|=.||+.|+.+++.+..
T Consensus 7 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~~ 46 (269)
T PRK11716 7 TLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQQ 46 (269)
T ss_pred HHHHHHHHHHHHhCCeeEEecC-CceeECHhHHHHHHHHHH
Confidence 455677888874 6777764 588999999999887644
No 196
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=52.11 E-value=20 Score=26.16 Aligned_cols=37 Identities=24% Similarity=0.358 Sum_probs=27.3
Q ss_pred HHHHHHHHHHh---CCcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQN---MNIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~---~glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=+-+++||+ ..|++... .|=.||+.|+.+++.+..
T Consensus 31 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~~ 70 (275)
T PRK03601 31 AVSFRIRQLENQLGVNLFTRHR-NNIRLTAAGERLLPYAET 70 (275)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceEECHhHHHHHHHHHH
Confidence 44566888887 36777765 578899999998877654
No 197
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=51.10 E-value=44 Score=25.17 Aligned_cols=57 Identities=16% Similarity=0.231 Sum_probs=46.6
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
.+|=-.|+.-|=-+|-+-|..|...||-. ..-||.=|..||+.|++.+.- ||=.+++
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS--------------~~TIRRDL~~Le~~g~l~R~h-GGa~~~~ 60 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVS--------------EMTIRRDLNELEEQGLLLRVH-GGAVLPD 60 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCC--------------HHHHHHhHHHHHHCCcEEEEe-CCEecCC
Confidence 35667788888889999999999999864 478999999999999999875 4544433
No 198
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=50.80 E-value=22 Score=25.72 Aligned_cols=35 Identities=9% Similarity=0.112 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-+-..+++||+. .|++... +|=.+|+.|+.++..+
T Consensus 37 avS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 74 (294)
T PRK09986 37 PLSIHIKELEDQLGTPLFIRHS-RSVVLTHAGKILMEES 74 (294)
T ss_pred HHHHHHHHHHHHhCCeeEeeCC-CceeECHhHHHHHHHH
Confidence 456677888865 6666664 5788899998887654
No 199
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.79 E-value=17 Score=28.36 Aligned_cols=27 Identities=33% Similarity=0.412 Sum_probs=22.1
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeee
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRI 71 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~l 71 (90)
|..-+++.+..||+.|+|+++. .||.+
T Consensus 201 s~aTV~~~lk~l~~~Gii~~~~-~Gr~i 227 (240)
T COG3398 201 SVATVAYHLKKLEELGIIPEDR-EGRSI 227 (240)
T ss_pred cHHHHHHHHHHHHHcCCCcccc-cCceE
Confidence 5678999999999999999886 45543
No 200
>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=50.09 E-value=34 Score=22.45 Aligned_cols=51 Identities=8% Similarity=0.086 Sum_probs=41.3
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
..|++-|+=.|++.+..+.......+ +. +-+-++..|+-|++-|+|+....
T Consensus 6 ~~IM~~lW~~~~~t~~eI~~~l~~~~--~~--------~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 6 LEIMEILWESGEATVREIHEALPEER--SW--------AYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHCTTS--S----------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHhcc--cc--------chhHHHHHHHHHHhCCceeEeec
Confidence 46888889999999999999987762 21 33689999999999999997764
No 201
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=49.85 E-value=48 Score=25.32 Aligned_cols=56 Identities=20% Similarity=0.341 Sum_probs=42.8
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCe-----eeCcchHh
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGR-----RITSSGQR 77 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR-----~lT~~G~~ 77 (90)
|+.-+--.+|+.+..++..-|-.+ .-+|.=|+.||+.|+|+.... -|| .||.+|.+
T Consensus 16 il~lL~~~g~~sa~elA~~Lgis~--------------~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 16 ILELLKKSGPVSADELAEELGISP--------------MAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHhccCCccHHHHHHHhCCCH--------------HHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 444444479999999999888753 468999999999999985432 254 68999876
No 202
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=49.74 E-value=20 Score=27.10 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++....+-..||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~~a~ 71 (324)
T PRK12681 32 GISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAR 71 (324)
T ss_pred HHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHHHHH
Confidence 455678888874 6676665322369999999987653
No 203
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=49.69 E-value=24 Score=22.82 Aligned_cols=30 Identities=20% Similarity=0.220 Sum_probs=23.4
Q ss_pred chhHHHHHHHHHHhCCc-ccccCCCCeeeCc
Q 034587 44 SGAIARHILQQLQNMNI-IDIEPKGGRRITS 73 (90)
Q Consensus 44 sg~iiR~~LqqLE~~gl-V~k~~~~GR~lT~ 73 (90)
|..-|=+.+|+|++.|+ |+..+..|+.|.+
T Consensus 32 SRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~ 62 (79)
T COG1654 32 SRTAVWKHIQQLREEGVDIESVRGKGYLLPQ 62 (79)
T ss_pred cHHHHHHHHHHHHHhCCceEecCCCceeccC
Confidence 34677889999999998 5666666998865
No 204
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=49.43 E-value=25 Score=25.52 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|.+... .|-.||+.|+.+++.+.
T Consensus 31 avS~~Ik~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a~ 69 (291)
T TIGR03418 31 AVSQQVKRLEEELGTPLFERGH-RGIELTEDGQRLFEAVR 69 (291)
T ss_pred HHHHHHHHHHHHhCcHHhhcCC-CceeEcHhHHHHHHHHH
Confidence 455567888864 4555553 57888888888776544
No 205
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=49.37 E-value=23 Score=26.95 Aligned_cols=37 Identities=14% Similarity=0.144 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhC---CcccccCCCCe-eeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++.+. +|- .||+.|+.+++.+..
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~v~~LT~~G~~l~~~a~~ 72 (327)
T PRK12680 32 GLSKQLKQLEDELGFLLFVRKG-RSLESVTPAGVEVIERARA 72 (327)
T ss_pred HHHHHHHHHHHHhCCeEEEECC-CcCCccCccHHHHHHHHHH
Confidence 455678889874 5666665 344 399999999988654
No 206
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=48.71 E-value=20 Score=26.09 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=+.+++||+. .|++... .|=.+|+.|+..++.+-
T Consensus 31 avSr~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~ 69 (296)
T PRK09906 31 SLSQQIKDLENCVGVPLLVRDK-RKVALTAAGEVFLQDAR 69 (296)
T ss_pred HHHHHHHHHHHHhCCeeeeeCC-CcceEcHhHHHHHHHHH
Confidence 444567888864 6777664 68899999999887643
No 207
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=48.61 E-value=25 Score=25.85 Aligned_cols=37 Identities=11% Similarity=0.093 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++... .|=.||+.|+.++..+..
T Consensus 34 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~~ 73 (296)
T PRK11062 34 TITGQIKALEERLQGKLFKRKG-RGLEPTELGELVFRYADK 73 (296)
T ss_pred HHHHHHHHHHHHcCccceeecC-CceeECHhHHHHHHHHHH
Confidence 344567777764 5666654 578888888887766543
No 208
>PRK10632 transcriptional regulator; Provisional
Probab=48.46 E-value=31 Score=25.65 Aligned_cols=38 Identities=8% Similarity=0.165 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
.-+=..+++||+. .|++.+. .|-.||+.|+.+++.+..
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~i~lT~~G~~l~~~a~~ 71 (309)
T PRK10632 31 SSISQTVSKLEDELQVKLLNRST-RSIGLTEAGRIYYQGCRR 71 (309)
T ss_pred HHHHHHHHHHHHHhCCeeecccC-CCceechhHHHHHHHHHH
Confidence 3566778999974 6666665 589999999998776543
No 209
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=48.12 E-value=16 Score=22.37 Aligned_cols=45 Identities=16% Similarity=0.318 Sum_probs=29.7
Q ss_pred CCCchhHHHHHhcCC-CCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 16 QGLGVGSFRRIYGGS-KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~-krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.++-.+.+-..|-.- +..|..| -+-.-++.+|+.||..|+|+...
T Consensus 21 ~~~~~~~vy~~Y~~~c~~~~~~~-----l~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 21 EEATTGEVYEVYEELCEEIGVDP-----LTQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred CCccHHHHHHHHHHHHHHcCCCC-----CcHHHHHHHHHHHHHcCCeEEEE
Confidence 356666666666541 2234444 33356888999999999998554
No 210
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=47.75 E-value=27 Score=26.04 Aligned_cols=36 Identities=14% Similarity=0.130 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++... .|-.+|+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 70 (308)
T PRK10094 32 TISYRIKLLEENTGVALFFRTT-RSVTLTAAGEHLLSQAR 70 (308)
T ss_pred HHHHHHHHHHHHhCCEEEeeCC-CceeECHhHHHHHHHHH
Confidence 455678888875 5666664 58899999999877643
No 211
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=46.92 E-value=29 Score=25.02 Aligned_cols=35 Identities=11% Similarity=0.106 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-+=+.+++||+. .|++... .|=.||+.|+.+++.+
T Consensus 33 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 70 (290)
T PRK10837 33 AVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPRA 70 (290)
T ss_pred HHHHHHHHHHHHhCCccEeecC-CeEEECHhHHHHHHHH
Confidence 456677888874 6777665 5788999999888764
No 212
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=46.89 E-value=27 Score=25.40 Aligned_cols=36 Identities=19% Similarity=0.210 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++.. .|=.||+.|+.+++.+-.
T Consensus 31 avS~~I~~LE~~lg~~Lf~R~--r~~~lT~~G~~l~~~~~~ 69 (292)
T TIGR03298 31 AVSQRIKALEERLGQPLLVRT--QPCRATEAGQRLLRHARQ 69 (292)
T ss_pred HHHHHHHHHHHHhCchheecC--CCCcCCHhHHHHHHHHHH
Confidence 466778899875 677774 488999999999877543
No 213
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=46.03 E-value=27 Score=25.87 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+-+-..+++||+. .|++.+. +|=.||+.|+.+++.+.
T Consensus 33 savS~~Ik~LE~~lg~~Lf~R~~-~~v~LT~~G~~l~~~a~ 72 (309)
T PRK11013 33 PTVSRELARFEKVIGLKLFERVR-GRLHPTVQGLRLFEEVQ 72 (309)
T ss_pred HHHHHHHHHHHHHhCceeeeecC-CCcccCHHHHHHHHHHH
Confidence 4677888999975 6777665 57889999999888653
No 214
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=45.87 E-value=27 Score=26.06 Aligned_cols=38 Identities=21% Similarity=0.191 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++.+.++...||+.|+.+++.+..
T Consensus 32 avS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~ 72 (313)
T PRK12684 32 GVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVER 72 (313)
T ss_pred HHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHHH
Confidence 344567888864 56665543224689999988876543
No 215
>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=45.69 E-value=28 Score=22.47 Aligned_cols=35 Identities=23% Similarity=0.307 Sum_probs=25.8
Q ss_pred hhHHHHHHHHHHhCCcccccCC--CCeeeCcchHhhH
Q 034587 45 GAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDL 79 (90)
Q Consensus 45 g~iiR~~LqqLE~~glV~k~~~--~GR~lT~~G~~~l 79 (90)
.+-+.++|++|-+.++|..... .|-+||-.|-..|
T Consensus 38 ~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~L 74 (82)
T PF09202_consen 38 EGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYL 74 (82)
T ss_dssp HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHH
T ss_pred HHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHH
Confidence 4567789999999999987542 5999999996543
No 216
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=45.32 E-value=20 Score=26.65 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-+=..+++||+. .|++.+. .|=.||+.|+.+++.+
T Consensus 44 avS~~I~~LE~~lG~~LF~R~~-r~~~LT~~G~~l~~~a 81 (311)
T PRK10086 44 AVSHRINQLEEELGIKLFVRSH-RKVELTEEGKRVFWAL 81 (311)
T ss_pred HHHHHHHHHHHHhCCeeEEEcC-CCcccCHhHHHHHHHH
Confidence 344567888874 5666664 5889999999988763
No 217
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=44.87 E-value=33 Score=25.34 Aligned_cols=38 Identities=16% Similarity=0.116 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhC---CcccccCCCCe-eeCcchHhhHHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVAGR 85 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~lD~iA~~ 85 (90)
-+=..+++||+. .|++... .|- .||+.|+.+++.+..-
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~~~~~ 73 (309)
T PRK12682 32 GVSKAIIELEEELGIEIFIRHG-KRLKGLTEPGKAVLDVIERI 73 (309)
T ss_pred HHHHHHHHHHHHhCCeeEEECC-CCcCccCHhHHHHHHHHHHH
Confidence 556678888874 5666554 353 6999999998876543
No 218
>PRK09954 putative kinase; Provisional
Probab=44.07 E-value=99 Score=23.77 Aligned_cols=56 Identities=13% Similarity=0.027 Sum_probs=44.3
Q ss_pred ChhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587 1 MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 73 (90)
Q Consensus 1 ~~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~ 73 (90)
|..+=..|++-|.-++++....|++..|- |.+-++..|++|++.|+|+ ..|-.|.+
T Consensus 1 ~~~~~~~il~~l~~~~~~s~~~la~~l~~--------------s~~~v~~~i~~L~~~g~i~---~~~~~l~~ 56 (362)
T PRK09954 1 MNNREKEILAILRRNPLIQQNEIADILQI--------------SRSRVAAHIMDLMRKGRIK---GKGYILTE 56 (362)
T ss_pred CChHHHHHHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCcC---CcEEEEcC
Confidence 45566678998998999999999998885 3468999999999999994 23555543
No 219
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=43.76 E-value=28 Score=30.43 Aligned_cols=32 Identities=25% Similarity=0.309 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587 47 IARHILQQLQNMNIIDIEPKGGRRITSSGQRD 78 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 78 (90)
=++++|..||.-|+|+--++++=++|+.|+..
T Consensus 466 ~i~~AL~kLEArGfI~~Lp~g~iilTeaG~~i 497 (591)
T PF04458_consen 466 EIIEALEKLEARGFIEILPNGMIILTEAGELI 497 (591)
T ss_pred HHHHHHHHHHhcchHHHcCCCcEEEehhhHHH
Confidence 35679999999999999999999999999753
No 220
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=43.49 E-value=25 Score=25.87 Aligned_cols=32 Identities=16% Similarity=0.327 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587 49 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 49 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
=.|...++.+|+|+-.. |.=.||++|+..++.
T Consensus 46 ~piv~ta~~Lglv~~e~-GDiilT~~Gk~~v~~ 77 (157)
T COG4754 46 MPIVETASLLGLVTAES-GDIILTDEGKEYVES 77 (157)
T ss_pred HHHHHHHHhcCceeccC-CCEEEehhhHHHHhC
Confidence 35678889999997664 778999999999874
No 221
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=43.46 E-value=35 Score=25.56 Aligned_cols=49 Identities=27% Similarity=0.375 Sum_probs=37.7
Q ss_pred HHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCee
Q 034587 8 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRR 70 (90)
Q Consensus 8 i~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~ 70 (90)
|.=-+|+ +.|+.++.++..-|-.| +-+=..+..||..++|++... |-|+
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sk--------------s~vS~~lkkL~~~~lV~~~~~~G~Rk 81 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSK--------------SNVSMGLKKLQDWNLVKKVFEKGDRK 81 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCc--------------chHHHHHHHHHhcchHHhhhccCcch
Confidence 4445789 88999999999999865 235578999999999986653 4443
No 222
>PRK06474 hypothetical protein; Provisional
Probab=43.38 E-value=89 Score=22.46 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=34.2
Q ss_pred HHHHHHhhcCC-CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 7 SMARKIYLRQG-LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 7 Si~RklYl~g~-vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.|+.-|.-.++ ..+..|....+ .-+.+-+=+-|+.|++.|+|+..+
T Consensus 15 ~Il~~L~~~~~~~ta~el~~~l~-------------~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKEGLTPLELVKILK-------------DVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 35666666554 89999988764 245566778899999999999765
No 223
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=43.34 E-value=32 Score=25.97 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=24.0
Q ss_pred HHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 48 ARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 48 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+=.-+++||+. .|++.+. .|-.||+.|+.+++.+.
T Consensus 42 vS~~I~~LE~~lG~~LF~R~~-~~~~LT~~G~~l~~~a~ 79 (310)
T PRK15092 42 VSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYAR 79 (310)
T ss_pred HHHHHHHHHHHhCcceEEECC-CCceECHhHHHHHHHHH
Confidence 33456777764 6666664 47889999988876644
No 224
>PF14502 HTH_41: Helix-turn-helix domain
Probab=43.28 E-value=27 Score=20.96 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=20.5
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCe
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
|...|-++|+-||+.|-|.-.+. |+
T Consensus 19 s~GtiQ~Alk~Le~~gaI~Le~r-Gh 43 (48)
T PF14502_consen 19 SRGTIQNALKFLEENGAIKLESR-GH 43 (48)
T ss_pred chhHHHHHHHHHHHCCcEEeeec-Cc
Confidence 45789999999999999986653 44
No 225
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=43.26 E-value=38 Score=24.72 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
+-+=..+++||+. .|++... .|=.||+.|+.++..+.
T Consensus 35 ~avS~~i~~LE~~lg~~Lf~R~~-r~l~lT~~G~~l~~~~~ 74 (297)
T PRK11139 35 AAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDIR 74 (297)
T ss_pred HHHHHHHHHHHHHhCchheEecC-CceeECHhHHHHHHHHH
Confidence 3566778889876 6676664 58899999999887753
No 226
>PF02980 FokI_C: Restriction endonuclease FokI, catalytic domain; InterPro: IPR004233 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition (IPR004234 from INTERPRO) and cleavage functions, respectively. The catalytic domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. The catalytic domain is sequestered in a 'piggyback' fashion by the recognition domain [].; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=43.16 E-value=24 Score=25.58 Aligned_cols=44 Identities=23% Similarity=0.339 Sum_probs=30.7
Q ss_pred ccccCchhHHHHHHHHHHhCCcccccCC----------------CCeeeCcchHhhHHHH
Q 034587 39 HFCKSSGAIARHILQQLQNMNIIDIEPK----------------GGRRITSSGQRDLDQV 82 (90)
Q Consensus 39 h~~~asg~iiR~~LqqLE~~glV~k~~~----------------~GR~lT~~G~~~lD~i 82 (90)
-+.-.|.+-+|.|..=|.++|||++.++ ...+||-+|...|.+.
T Consensus 76 d~EgTSDKYaR~I~~wL~k~glv~~~~k~vt~~~~~~~~~~~i~~~YkIT~~Gl~aL~~~ 135 (142)
T PF02980_consen 76 DWEGTSDKYARMICGWLKKVGLVEQKTKKVTRTIGGRKYKETIGQSYKITGKGLTALKRA 135 (142)
T ss_dssp H---HHHHHHHHHHHHHHHTTSEEE--EEEE-BTTBTT-EEEESSEEEE-HHHHHHHHHH
T ss_pred ccccchHHHHHHHHHHHHHhchheecceEEEeeccCccccccccceEEEeccHHHHHHHh
Confidence 3445678899999999999999985541 1457888888888764
No 227
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=43.08 E-value=37 Score=25.05 Aligned_cols=36 Identities=14% Similarity=0.152 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..|++||+. .|++... .|=.+|+.|+.+++...
T Consensus 35 avS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 73 (305)
T CHL00180 35 AVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYGN 73 (305)
T ss_pred HHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHHH
Confidence 566778888875 5666654 58899999999976643
No 228
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=43.04 E-value=34 Score=25.73 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-+=..+++||+. .|++... .|=.||+.|+.+++.+
T Consensus 32 aVS~~Ik~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~a 69 (317)
T PRK15421 32 ALSHQFSDLEQRLGFRLFVRKS-QPLRFTPQGEILLQLA 69 (317)
T ss_pred HHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHH
Confidence 445566777764 4555553 4667777777776553
No 229
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=43.03 E-value=23 Score=30.93 Aligned_cols=40 Identities=20% Similarity=0.212 Sum_probs=32.3
Q ss_pred CchhHHHHHHHHHHhCCcccccCCC----CeeeCcchHhhHHHH
Q 034587 43 SSGAIARHILQQLQNMNIIDIEPKG----GRRITSSGQRDLDQV 82 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~~~----GR~lT~~G~~~lD~i 82 (90)
..-.+++.+|..||.-+||+...++ -..||+-|++.++..
T Consensus 327 ~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 327 KNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred cchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 3445789999999999999866633 378999999999855
No 230
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=43.00 E-value=27 Score=26.93 Aligned_cols=37 Identities=24% Similarity=0.187 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCcccccC-CCC--eeeCcchHhhHHHHHHH
Q 034587 49 RHILQQLQNMNIIDIEP-KGG--RRITSSGQRDLDQVAGR 85 (90)
Q Consensus 49 R~~LqqLE~~glV~k~~-~~G--R~lT~~G~~~lD~iA~~ 85 (90)
=.+|++||+.|+|+... +.| =.+|++|...|-..-.+
T Consensus 37 ~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d 76 (214)
T COG1339 37 ARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYED 76 (214)
T ss_pred HHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHHH
Confidence 34689999999998554 334 36899999988765444
No 231
>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=42.85 E-value=23 Score=21.99 Aligned_cols=44 Identities=20% Similarity=0.279 Sum_probs=25.3
Q ss_pred CCchhHHHHHhcCC-CCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 17 GLGVGSFRRIYGGS-KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~-krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
++-.+.+-..|-.- ...|..|- +-.=++..|.+||.+|+|+...
T Consensus 15 ~~~~~~vy~~Y~~lc~~~~~~pl-----s~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 15 EVTTGEVYEVYEELCESLGVDPL-----SYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp SEEHHHHHHHHHHHHHHTTS---------HHHHHHHHHHHHHTTSEEEEE
T ss_pred ceeHHHHHHHHHHHHHHcCCCCC-----CHHHHHHHHHHHHhCCCeEEEe
Confidence 45555555555431 12333332 2245788999999999998655
No 232
>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=42.68 E-value=27 Score=21.81 Aligned_cols=38 Identities=16% Similarity=0.200 Sum_probs=24.8
Q ss_pred hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
-.+.+.++.|.+.|.---+| .=.++.+||+.|+|.-..
T Consensus 17 ~~~~~S~S~lQR~~rIGynr--------------Aariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 17 EEGKASISLLQRKFRIGYNR--------------AARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp HCTCECHHHHHHHHT--HHH--------------HHHHHHHHHHCTSBE---
T ss_pred HcCCccHHHHHHHhCCCHHH--------------HHHHHHHHHHCCCCCCCC
Confidence 36778888888877653222 336899999999997544
No 233
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=42.16 E-value=38 Score=24.61 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. .|++.. +|-.+|+.|+.+++.+-.
T Consensus 32 avS~~i~~LE~~lg~~Lf~R~--r~i~lT~~G~~l~~~a~~ 70 (294)
T PRK13348 32 AVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLRQ 70 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccChhHHHHHHHHHH
Confidence 455677888875 566664 478999999888876553
No 234
>PHA00738 putative HTH transcription regulator
Probab=41.74 E-value=80 Score=21.83 Aligned_cols=48 Identities=17% Similarity=0.047 Sum_probs=33.6
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCee
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR 70 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~ 70 (90)
|+..|.-.++..|..|...++-. ..-+=+=|+.|+++|||+..+ .||.
T Consensus 17 IL~lL~~~e~~~V~eLae~l~lS--------------QptVS~HLKvLreAGLV~srK-~Gr~ 64 (108)
T PHA00738 17 ILELIAENYILSASLISHTLLLS--------------YTTVLRHLKILNEQGYIELYK-EGRT 64 (108)
T ss_pred HHHHHHHcCCccHHHHHHhhCCC--------------HHHHHHHHHHHHHCCceEEEE-ECCE
Confidence 44445434578899999888643 234556689999999998776 4654
No 235
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=41.62 E-value=41 Score=24.96 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
-+-..+++||+. .|++... .|=.||+.|+.+++.+
T Consensus 37 avS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a 74 (312)
T PRK10341 37 AVSKIINDIEDYFGVELIVRKN-TGVTLTPAGQVLLSRS 74 (312)
T ss_pred HHHHHHHHHHHHhCCeEEEEcC-CCceEChhHHHHHHHH
Confidence 566778899875 5666665 5889999999998753
No 236
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=41.12 E-value=62 Score=25.95 Aligned_cols=48 Identities=15% Similarity=0.201 Sum_probs=36.6
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 69 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR 69 (90)
|+-.|-.++|.-|..++..-|=.+ +.+-.-+|.||++|+++.....+|
T Consensus 28 Il~lL~~k~plNvneiAe~lgLpq--------------st~s~~ik~Le~aGlirT~t~kar 75 (308)
T COG4189 28 ILQLLHRKGPLNVNEIAEALGLPQ--------------STMSANIKVLEKAGLIRTETVKAR 75 (308)
T ss_pred HHHHHHHhCCCCHHHHHHHhCCch--------------hhhhhhHHHHHhcCceeeeeeccc
Confidence 555666789999999999888632 566777999999999986653333
No 237
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=39.67 E-value=39 Score=21.27 Aligned_cols=42 Identities=19% Similarity=0.438 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHhCCc--ccccCCCCeeeCcc--h------HhhHHHHHHHhhcCC
Q 034587 45 GAIARHILQQLQNMNI--IDIEPKGGRRITSS--G------QRDLDQVAGRIVVAP 90 (90)
Q Consensus 45 g~iiR~~LqqLE~~gl--V~k~~~~GR~lT~~--G------~~~lD~iA~~v~~~~ 90 (90)
|.-++..|+.| |+ |+.. .-|+.++=. | ...++.+|.+++.+|
T Consensus 18 G~ai~~~l~~l---g~~~v~~V-r~~k~~~l~~~~~~~~~a~~~v~~i~~~lL~Np 69 (80)
T PRK05974 18 GQAIKGALGSL---GYDGVEDV-RQGKYFELELEGESEEKAEADLKEMCEKLLANP 69 (80)
T ss_pred HHHHHHHHHHc---CCCCcceE-EEEEEEEEEEcCCchhhhHHHHHHHHHHhcCCc
Confidence 44445555554 55 2322 235555443 3 677899999988766
No 238
>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=39.37 E-value=28 Score=26.24 Aligned_cols=51 Identities=18% Similarity=0.289 Sum_probs=41.0
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
.+|..+..|+..-|-. | .-++..|..|..+|++++.. +...+|+.+...|+
T Consensus 21 ~gp~t~~eLA~~~~~~------~--------~~~~~lL~~L~~lgll~~~~-~~y~~t~~~~~~l~ 71 (306)
T TIGR02716 21 EGPKDLATLAADTGSV------P--------PRLEMLLETLRQMRVINLED-GKWSLTEFADYMFS 71 (306)
T ss_pred cCCCCHHHHHHHcCCC------h--------HHHHHHHHHHHhCCCeEecC-CcEecchhHHhhcc
Confidence 4788999998755432 2 47899999999999999874 78999999977665
No 239
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=39.04 E-value=12 Score=26.23 Aligned_cols=58 Identities=17% Similarity=0.200 Sum_probs=38.4
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL 79 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l 79 (90)
|-.++..|...||.-...|++.=|..+ ..+|++. --=||.|..++|=..||++|+..|
T Consensus 61 Al~~A~~L~~~Gp~~~~~l~~~~~~~~------------A~~IL~~-----N~YGWFeRv~rGvY~LT~~G~~al 118 (118)
T PF09929_consen 61 ALRCAAALAEHGPSRPADLRKATGVPK------------ATSILRD-----NHYGWFERVERGVYALTPAGRAAL 118 (118)
T ss_pred HHHHHHHHHHcCCCCHHHHHHhcCCCh------------HHHHHHh-----CcccceeeeccceEecCcchhhcC
Confidence 334455566688888888877544321 1223221 234999999998899999999764
No 240
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=38.60 E-value=60 Score=24.06 Aligned_cols=37 Identities=19% Similarity=0.275 Sum_probs=15.5
Q ss_pred hhHHHHHhcC----CCCCCCCCCccccCchhHHHHHHHHHH
Q 034587 20 VGSFRRIYGG----SKRNGSRPPHFCKSSGAIARHILQQLQ 56 (90)
Q Consensus 20 V~~Lr~~YGg----~krrG~~P~h~~~asg~iiR~~LqqLE 56 (90)
+..|...+|. +..+|+.|......--..++.++++++
T Consensus 57 I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~~~~~l~~~~ 97 (314)
T PRK09508 57 VARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQ 97 (314)
T ss_pred HHHHHHhhCCCcEEEcCCCCcCcHHHHHHHHHHHHHHHHHH
Confidence 3444444444 344444444433332233344444444
No 241
>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=38.25 E-value=40 Score=19.88 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHhCCcccccC
Q 034587 44 SGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~ 65 (90)
|..-+=.+|+.|++.|||+...
T Consensus 41 sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 41 SRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp CHHHHHHHHHHHHHTTSEEEET
T ss_pred CHHHHHHHHHHHHHCCCEEEcC
Confidence 4456778999999999999664
No 242
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=38.02 E-value=33 Score=22.02 Aligned_cols=36 Identities=28% Similarity=0.278 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHhCCccc--------c-cCCCCeeeCcchHhhHHH
Q 034587 46 AIARHILQQLQNMNIID--------I-EPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~--------k-~~~~GR~lT~~G~~~lD~ 81 (90)
.-.-.+|++|.+.|+|+ . .....=.||++|...|.+
T Consensus 25 ~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 55668999999999995 1 112345799999998864
No 243
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=38.01 E-value=23 Score=27.42 Aligned_cols=38 Identities=26% Similarity=0.462 Sum_probs=28.8
Q ss_pred Cchh-HHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587 43 SSGA-IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 80 (90)
Q Consensus 43 asg~-iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD 80 (90)
|-|+ .+..+--=|...|+++.+.++++.+|+-|+..+|
T Consensus 39 GvGkNMV~siryWl~a~gli~~~~~~~~~~T~lG~~i~~ 77 (286)
T PF13182_consen 39 GVGKNMVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIFD 77 (286)
T ss_pred CCCHhHHHHHHHHHHHcCCcccCCCCCcccCHHHHHHHh
Confidence 3444 3444555688999999888777799999999993
No 244
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=37.72 E-value=43 Score=24.98 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhC---CcccccCCCC-eeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGG-RRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~G-R~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++... .| ..+|+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lg~~Lf~R~~-r~~~~lT~~G~~l~~~a~ 71 (309)
T PRK12683 32 GVSKQIKDLEDELGVEIFIRRG-KRLTGLTEPGKELLQIVE 71 (309)
T ss_pred HHHHHHHHHHHHhCCeeEeeCC-CCcCCcCHHHHHHHHHHH
Confidence 566778888875 5565553 34 258999999887654
No 245
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=37.29 E-value=45 Score=26.39 Aligned_cols=35 Identities=23% Similarity=0.283 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHH
Q 034587 49 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 49 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-.=+.+|-+.|+|+++..+-..||.+|-+.|-+-+
T Consensus 43 sehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~ 77 (260)
T COG1497 43 SEHIKELVKEGLIEKEGRGEYEITKKGAEWLLEQL 77 (260)
T ss_pred HHHHHHHHhccceeecCCeeEEEehhHHHHHHHHH
Confidence 34578999999999854334579999987665433
No 246
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=35.51 E-value=53 Score=26.35 Aligned_cols=47 Identities=19% Similarity=0.384 Sum_probs=28.3
Q ss_pred HHHHhhcCCCchhH---HHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCC
Q 034587 9 ARKIYLRQGLGVGS---FRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMN 59 (90)
Q Consensus 9 ~RklYl~g~vGV~~---Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~g 59 (90)
-+-|||.||||.|. +--.|..-.-..-+.-||+. .+..+-+.|-+..
T Consensus 62 ~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~----Fm~~vh~~l~~~~ 111 (362)
T PF03969_consen 62 PKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHE----FMLDVHSRLHQLR 111 (362)
T ss_pred CceEEEECCCCCchhHHHHHHHHhCCccccccccccH----HHHHHHHHHHHHh
Confidence 45689999999985 33445543332334456663 5566666665554
No 247
>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=35.22 E-value=58 Score=20.94 Aligned_cols=44 Identities=14% Similarity=0.165 Sum_probs=28.5
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
++-|++-|.-+|.+-=+.|++.-|-. -+.+|++|+.|.+.|+|.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~--------------~~~vRkiL~~L~~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLK--------------PKEVRKILYKLYEDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S---------------HHHHHHHHHHHHHHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCeE
Confidence 45566666666666667777654442 379999999999999995
No 248
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=34.76 E-value=65 Score=23.65 Aligned_cols=37 Identities=11% Similarity=0.196 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
.-+-..+++||+. -|++.+. .|=.||+.|+.++..+-
T Consensus 31 pavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~~~ 70 (300)
T PRK11074 31 SAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEAR 70 (300)
T ss_pred HHHHHHHHHHHHHhCCeeEEeCC-CCceECccHHHHHHHHH
Confidence 3566778888874 5666654 57889999988876543
No 249
>TIGR02802 Pal_lipo peptidoglycan-associated lipoprotein. Members of this protein are Pal (also called OprL), the Peptidoglycan-Associated Lipoprotein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly conserved low-complexity region, together comprising about 65 amino acids, and a well-conserved C-terminal domain. The seed alignment for this model includes only the conserved C-terminal domain.
Probab=34.73 E-value=42 Score=21.25 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=18.7
Q ss_pred CCeeeCcchHhhHHHHHHHhhcCC
Q 034587 67 GGRRITSSGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 67 ~GR~lT~~G~~~lD~iA~~v~~~~ 90 (90)
+.-.||++++..||++|..+...|
T Consensus 7 ~s~~l~~~~~~~L~~~a~~l~~~~ 30 (104)
T TIGR02802 7 DSSDLKSEAQAILDAHAAYLKKNP 30 (104)
T ss_pred CccccCHHHHHHHHHHHHHHHHCC
Confidence 345799999999999988776543
No 250
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=34.24 E-value=44 Score=24.50 Aligned_cols=35 Identities=20% Similarity=0.196 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|.+.. .|-.+|+.|+.++..+-
T Consensus 32 avS~~I~~LE~~lg~~LF~R~--~~~~lT~~G~~l~~~a~ 69 (294)
T PRK03635 32 AVSQRIKALEERVGQVLLVRT--QPCRPTEAGQRLLRHAR 69 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccCHHHHHHHHHHH
Confidence 344567888874 556664 48999999999876654
No 251
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=34.11 E-value=1e+02 Score=20.12 Aligned_cols=41 Identities=17% Similarity=0.181 Sum_probs=34.6
Q ss_pred HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 11 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 11 klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.|-++|-+....|+..|+.. -..|+..|..|+.+|-|++.+
T Consensus 10 ~l~~~gr~s~~~Ls~~~~~p--------------~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 10 LLALRGRMEAAQISQTLNTP--------------QPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHcCcccHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEeec
Confidence 45668889999999888763 369999999999999999876
No 252
>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=34.05 E-value=31 Score=21.35 Aligned_cols=20 Identities=15% Similarity=0.092 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHhCCcccccC
Q 034587 46 AIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~ 65 (90)
.-+-+.++.||+.|||.+.+
T Consensus 33 r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 33 RSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHHHHHHHCCCEEEEE
Confidence 46778999999999998765
No 253
>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=34.01 E-value=52 Score=22.83 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=30.2
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
|--++.|+..++-. =..+|.+|+-|++.|+|+...++--.|+
T Consensus 51 py~~e~LA~~~~~~--------------~~~V~~Al~~f~k~glIe~~d~g~i~i~ 92 (119)
T TIGR01714 51 PYNAEMLATMFNRN--------------VGDIRITLQTLESLGLIEKKNNGDIFLE 92 (119)
T ss_pred CCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCcEEeh
Confidence 55666666666532 3589999999999999998865544444
No 254
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=33.88 E-value=57 Score=24.37 Aligned_cols=36 Identities=14% Similarity=0.070 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhC---CcccccCCCCe-eeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. .|++... .|. .||+.|+.+++.+.
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~a~ 71 (316)
T PRK12679 32 GVSRHIRELEDELGIEIFIRRG-KRLLGMTEPGKALLVIAE 71 (316)
T ss_pred HHHHHHHHHHHHhCCEEEEECC-CcccccCHhHHHHHHHHH
Confidence 455678888875 4455443 232 69999998876543
No 255
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.85 E-value=31 Score=25.69 Aligned_cols=19 Identities=21% Similarity=0.382 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhCCcccccC
Q 034587 47 IARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~ 65 (90)
-||.+|..|+++|+++...
T Consensus 47 ~i~e~l~dL~elGLier~t 65 (175)
T COG4344 47 RIREYLKDLKELGLIERYT 65 (175)
T ss_pred HHHHHHHHHHHcCCeeecc
Confidence 5899999999999998654
No 256
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=33.27 E-value=33 Score=27.03 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHHhCCcccccC
Q 034587 45 GAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 45 g~iiR~~LqqLE~~glV~k~~ 65 (90)
.+||-++|..||.+|+||...
T Consensus 218 RSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 218 RSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred HHHHHHHHHHhhhcCceeecc
Confidence 589999999999999998654
No 257
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=33.03 E-value=50 Score=26.56 Aligned_cols=29 Identities=10% Similarity=0.168 Sum_probs=22.3
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT 72 (90)
+-.+++.+|.+|+++|||...++++-.++
T Consensus 323 ~~~~v~~iL~~L~~agLI~~~~~g~~~l~ 351 (412)
T PRK04214 323 GYDELGELLCELARIGLLRRGERGQWVLA 351 (412)
T ss_pred CHHHHHHHHHHHHhCCCeEecCCCceEec
Confidence 44699999999999999987655444443
No 258
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=32.59 E-value=86 Score=23.48 Aligned_cols=45 Identities=18% Similarity=0.222 Sum_probs=34.5
Q ss_pred CchhHHHHHHHHHHhCCcccccCC------CCeeeCcchHhhHHHHHHHhh
Q 034587 43 SSGAIARHILQQLQNMNIIDIEPK------GGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~~------~GR~lT~~G~~~lD~iA~~v~ 87 (90)
.|-.++=.++.-|+..|+|+-... -=-.||+.||..|+..-.+=+
T Consensus 44 ps~~Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT~~Gr~~l~~Llt~~v 94 (175)
T PF14557_consen 44 PSLDLLGTSIELLREEGLVEAVDGEGMEDNALLAITDAGRRELQTLLTAPV 94 (175)
T ss_pred CchhhhhhHHHHHHhcCCcccccccCCCccceeeeCcchHHHHHHHHhCcC
Confidence 345678889999999999996621 234799999999998766543
No 259
>PF10396 TrmE_N: GTP-binding protein TrmE N-terminus; InterPro: IPR018948 This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein []. ; PDB: 1XZQ_B 1XZP_A 3GEE_A 3GEI_B 3GEH_A.
Probab=32.52 E-value=41 Score=23.20 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=21.1
Q ss_pred CccccCchhHHHHHHHHHHhCCcccccC
Q 034587 38 PHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 38 ~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
+-|+.++-.|++.+|+.|.++|.=.-.|
T Consensus 75 Ei~~HGg~~v~~~il~~l~~~G~R~A~p 102 (114)
T PF10396_consen 75 EIHCHGGPAVVRRILEALLKAGARLAEP 102 (114)
T ss_dssp EEEEESSHHHHHHHHHHHHHTT-EE--T
T ss_pred EEEcCCCHHHHHHHHHHHHHcCceEcCC
Confidence 3577899999999999999998654444
No 260
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=32.35 E-value=68 Score=22.58 Aligned_cols=37 Identities=16% Similarity=0.323 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhC-C--cccccCCCCeeeCcchHhhHHHHHH
Q 034587 47 IARHILQQLQNM-N--IIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 47 iiR~~LqqLE~~-g--lV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
-+=..+++||+. | |++... +|=.||+.|+.+++.+-.
T Consensus 31 avS~~I~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~ 70 (297)
T COG0583 31 AVSRQIKRLEEELGVPLFERTT-RRVRLTEAGERLLERARR 70 (297)
T ss_pred HHHHHHHHHHHHhCchheeecC-CceeeCHhHHHHHHHHHH
Confidence 356678888883 3 343332 345799999988876543
No 261
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=32.17 E-value=80 Score=23.73 Aligned_cols=34 Identities=12% Similarity=0.055 Sum_probs=17.5
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQ 81 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~ 81 (90)
-+-+.+++||+. .|++... .|=.+|+.|+.++..
T Consensus 59 avS~~I~~LE~~lG~~LF~R~~-r~v~lT~~G~~l~~~ 95 (317)
T PRK11482 59 AISQSIQKLRVIFPDPLFIRKG-QGVTPTAYATHLHEY 95 (317)
T ss_pred HHHHHHHHHHHHhCCcceEecC-CCccCCHHHHHHHHH
Confidence 344555666652 3444432 355666666655544
No 262
>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=32.12 E-value=44 Score=20.87 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=25.9
Q ss_pred cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587 15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64 (90)
Q Consensus 15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~ 64 (90)
.+.+.++.|.+.|.---|| .-.++.+||+.|+|.-.
T Consensus 17 ~~~~S~S~lQR~~~IGynr--------------Aariid~lE~~GiV~p~ 52 (63)
T smart00843 17 TQKASTSLLQRRLRIGYNR--------------AARLIDQLEEEGIVGPA 52 (63)
T ss_pred hCCCChHHHHHHHhcchhH--------------HHHHHHHHHHCcCCCCC
Confidence 5667788888766553332 44689999999999744
No 263
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=31.86 E-value=74 Score=24.35 Aligned_cols=37 Identities=14% Similarity=0.074 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
.-+=..+++||+. .|++... .|=.||+.|+.+++..-
T Consensus 33 pavS~~Ik~LE~eLG~~LF~R~~-r~~~LT~aG~~ll~~a~ 72 (297)
T PRK15243 33 TPLSRVISDLERELKQRLFIRKN-GTLIPTEFAQTIYRKVK 72 (297)
T ss_pred HHHHHHHHHHHHHhCCccEEeCC-CCeeECHHHHHHHHHHH
Confidence 3566778899975 5666554 58899999999887643
No 264
>PF02923 BamHI: Restriction endonuclease BamHI; InterPro: IPR004194 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents BamHI restriction endonucleases, which recognises the DNA sequence GGATCC and cleaves after G-1 [, ].; PDB: 1ESG_A 3BAM_B 1BHM_B 2BAM_A 1BAM_A.
Probab=31.84 E-value=20 Score=26.41 Aligned_cols=29 Identities=24% Similarity=0.305 Sum_probs=20.9
Q ss_pred HHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 25 RIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 25 ~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
..|.++|.+||+| |==.|.+.|++-||.-
T Consensus 43 ~InPt~K~NGVKP---------IKe~cm~~L~~~gW~l 71 (158)
T PF02923_consen 43 TINPTRKGNGVKP---------IKEACMAHLEKHGWYL 71 (158)
T ss_dssp EEE-SSTTB-SHH---------HHHHHHHHHHTT--EE
T ss_pred EECCccccCCCcc---------hHHHHHHHHHhcCceE
Confidence 3588999999999 7778999999889864
No 265
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=31.78 E-value=37 Score=24.45 Aligned_cols=42 Identities=19% Similarity=0.418 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHH
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQL 55 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqL 55 (90)
|=.+++.+|-.++.+...|...||. ......|.|-|..|-++
T Consensus 30 aD~i~~~l~~~~~~~~~~l~~~FG~---------~il~~~g~idR~~L~~~ 71 (180)
T PF01121_consen 30 ADEIAHELYEPGSEGYKALKERFGE---------EILDEDGEIDRKKLAEI 71 (180)
T ss_dssp HHHHHHHCTSCTCHHHHHHHHHHGG---------GGBETTSSB-HHHHHHH
T ss_pred ccHHHHHHhhcCHHHHHHHHHHcCc---------cccCCCCCChHHHHHHH
Confidence 3468899999999999999999995 33444567777776654
No 266
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=31.38 E-value=89 Score=23.68 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHhCCcccccCCC---CeeeCcchHhhHHHHH
Q 034587 46 AIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA 83 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~---GR~lT~~G~~~lD~iA 83 (90)
.+|-+.|..|++.|||+....+ --.+|+.|.+.--+.|
T Consensus 114 h~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~acarYa 154 (199)
T COG5631 114 HNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRACARYA 154 (199)
T ss_pred hhHHHHHHHHHhccceecCCCCceEEEEEecchHHHHHHHH
Confidence 4788999999999999876521 2367899987665544
No 267
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=31.19 E-value=47 Score=21.50 Aligned_cols=18 Identities=39% Similarity=0.591 Sum_probs=15.3
Q ss_pred CchhHHHHHHHHHHhCCc
Q 034587 43 SSGAIARHILQQLQNMNI 60 (90)
Q Consensus 43 asg~iiR~~LqqLE~~gl 60 (90)
.-..++|.+++.|-.||+
T Consensus 68 ~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 68 KLAGILRNIMDSLANMGI 85 (85)
T ss_pred cHHHHHHHHHHHHHHCCC
Confidence 345699999999999996
No 268
>PF09661 DUF2398: Protein of unknown function (DUF2398); InterPro: IPR013494 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=30.46 E-value=1.2e+02 Score=24.47 Aligned_cols=51 Identities=16% Similarity=0.309 Sum_probs=36.7
Q ss_pred hhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 20 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 20 V~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
|..++..||..=++ .....+...+.+.++..|++.|+++..+++|=.|.|.
T Consensus 308 l~~l~~~~~~~W~k----~~~~~~~~~L~~~vl~~L~~~~L~~~~~~~~v~l~Pa 358 (368)
T PF09661_consen 308 LAELRERYGSGWSK----EYREMDPEELAEEVLELLEEWGLARVDGDGGVVLLPA 358 (368)
T ss_pred HHHHHHHhhccccc----ccccCCHHHHHHHHHHHHHHCCCceECCCCeEEEccc
Confidence 34566777764333 3455666789999999999999999887655566654
No 269
>PRK09801 transcriptional activator TtdR; Provisional
Probab=30.30 E-value=47 Score=24.83 Aligned_cols=36 Identities=25% Similarity=0.393 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhC---CcccccCCCCeeeCcchHhhHHHHH
Q 034587 47 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 83 (90)
Q Consensus 47 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~lD~iA 83 (90)
-+=..+++||+. -|++... .|=.||+.|+.+++.+-
T Consensus 36 avS~~I~~LE~~LG~~Lf~R~~-r~~~lT~~G~~l~~~a~ 74 (310)
T PRK09801 36 FVTKRIQILENTLATTLLNRSA-RGVALTESGQRCYEHAL 74 (310)
T ss_pred HHHHHHHHHHHHhCCEeeeecC-CCCcccHhHHHHHHHHH
Confidence 455678889875 4566664 58899999998877643
No 270
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=30.12 E-value=56 Score=23.27 Aligned_cols=36 Identities=8% Similarity=0.058 Sum_probs=26.1
Q ss_pred ccCchhHHHHHHHHHHhCCcccc-cCCCCeeeCcchH
Q 034587 41 CKSSGAIARHILQQLQNMNIIDI-EPKGGRRITSSGQ 76 (90)
Q Consensus 41 ~~asg~iiR~~LqqLE~~glV~k-~~~~GR~lT~~G~ 76 (90)
..-+..+++++++.|.++|+|.- ....+..++...+
T Consensus 149 ~~~~k~v~~~a~E~L~~l~Ll~~~~~~~~~~~~~e~r 185 (203)
T PF14629_consen 149 KVWSKPVALKAWEHLLSLELLKPNYDGSSNNVQKEFR 185 (203)
T ss_pred ccCCHHHHHHHHHHHHHCCCceecccCCCCccCccce
Confidence 45567899999999999999976 2234555555553
No 271
>PRK04158 transcriptional repressor CodY; Validated
Probab=30.08 E-value=29 Score=27.26 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHhCCcccccC
Q 034587 45 GAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 45 g~iiR~~LqqLE~~glV~k~~ 65 (90)
.|||=++|..||.+|+||.-.
T Consensus 215 RSVIVNALRK~ESAGvIESrS 235 (256)
T PRK04158 215 RSVIVNALRKLESAGVIESRS 235 (256)
T ss_pred hhhhhhhhhhhhcccceeecc
Confidence 489999999999999999654
No 272
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=29.95 E-value=60 Score=23.40 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhCCccccc
Q 034587 47 IARHILQQLQNMNIIDIE 64 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~ 64 (90)
-+=.+|++|++.|+|+..
T Consensus 195 tlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 195 TVSRALSQLQDRGLIGLS 212 (230)
T ss_pred HHHHHHHHHHHCCcEEec
Confidence 444579999999999765
No 273
>TIGR03350 type_VI_ompA type VI secretion system OmpA/MotB family protein. The flagellar motor protein MotB and the Gram-negative bacterial outer membrane protein OmpA share a region of sequence homology. This model describes a domain found fused to type VI secretion system homologs of the type IV system protein DotU (see model TIGR03349), with OmpA/MotB homology.
Probab=29.87 E-value=45 Score=22.41 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=18.8
Q ss_pred CeeeCcchHhhHHHHHHHhhcCC
Q 034587 68 GRRITSSGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 68 GR~lT~~G~~~lD~iA~~v~~~~ 90 (90)
.-.|+|.++..||++|..+...|
T Consensus 38 s~~L~~~~~~~L~~ia~~l~~~~ 60 (137)
T TIGR03350 38 SAEVRADFEPLLDRIAKALAAVP 60 (137)
T ss_pred ccccCHHHHHHHHHHHHHHHhCC
Confidence 44799999999999998876543
No 274
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=29.69 E-value=41 Score=25.50 Aligned_cols=23 Identities=26% Similarity=0.329 Sum_probs=15.8
Q ss_pred HHHHHHHhCCcccccCCCCeeeC
Q 034587 50 HILQQLQNMNIIDIEPKGGRRIT 72 (90)
Q Consensus 50 ~~LqqLE~~glV~k~~~~GR~lT 72 (90)
.+|.-||++|||+-.++.|-..|
T Consensus 111 RaL~lLq~aGLI~Lk~~~~~~~t 133 (237)
T PF03180_consen 111 RALKLLQEAGLITLKDGVGLTAT 133 (237)
T ss_dssp HHHHHHHHTTSEEE-TT-GCC-S
T ss_pred HHHHHHHhCCeEEEcCCCCCccC
Confidence 57999999999997765454444
No 275
>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=28.61 E-value=48 Score=24.31 Aligned_cols=21 Identities=24% Similarity=0.199 Sum_probs=17.9
Q ss_pred chhHHHHHHHHHHhCCccccc
Q 034587 44 SGAIARHILQQLQNMNIIDIE 64 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~ 64 (90)
|.+-+|..|-.|.++|||...
T Consensus 84 s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 84 SERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred CHHHHHHHHHHHHHCCCeeec
Confidence 456899999999999999743
No 276
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=28.43 E-value=50 Score=19.28 Aligned_cols=50 Identities=12% Similarity=0.129 Sum_probs=25.0
Q ss_pred HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587 5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 62 (90)
Q Consensus 5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~ 62 (90)
++.|...+ .|+..+..+....-..- ++-|. .+ -.=+...|++|.+.|||+
T Consensus 19 a~~Iw~~~--~g~~t~~ei~~~l~~~y--~~~~~---~~-~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 19 AAFIWELL--DGPRTVEEIVDALAEEY--DVDPE---EA-EEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHHHHH----SSS-HHHHHHHHHHHT--T--HH---HH-HHHHHHHHHHHHHTT---
T ss_pred HHHHHHHc--cCCCCHHHHHHHHHHHc--CCCHH---HH-HHHHHHHHHHHHHCcCcC
Confidence 34445544 77888776655544432 22222 11 345677899999999985
No 277
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=28.22 E-value=2.2e+02 Score=20.93 Aligned_cols=56 Identities=18% Similarity=0.225 Sum_probs=38.3
Q ss_pred HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCCeee-CcchHhhHHH
Q 034587 9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGRRI-TSSGQRDLDQ 81 (90)
Q Consensus 9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~GR~l-T~~G~~~lD~ 81 (90)
|==|..+.|+.=+.+..++|.. +-+ +++.|++.|||.... ..||-. =.....|+|.
T Consensus 98 LAiIAY~QPiTR~eI~~iRGv~----------------~~~-~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~Fl~~ 157 (184)
T COG1386 98 LAIIAYKQPVTRSEIEEIRGVA----------------VSQ-VISTLLERGLIREVGRRDTPGRPYLYGTTEKFLDY 157 (184)
T ss_pred HHHHHHcCCccHHHHHHHhCcc----------------HHH-HHHHHHHCCCeEecCCCCCCCCceeeeccHHHHHH
Confidence 3345668899999999988874 445 889999999998765 245432 2334455554
No 278
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=28.20 E-value=64 Score=22.42 Aligned_cols=26 Identities=19% Similarity=0.123 Sum_probs=20.2
Q ss_pred CchhHHHHHHHHHHhCCcccccCCCC
Q 034587 43 SSGAIARHILQQLQNMNIIDIEPKGG 68 (90)
Q Consensus 43 asg~iiR~~LqqLE~~glV~k~~~~G 68 (90)
.|-.-+=..|++|+++|+|.+....|
T Consensus 53 islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 53 ISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 44556778999999999998776433
No 279
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.00 E-value=1.6e+02 Score=23.17 Aligned_cols=49 Identities=18% Similarity=0.179 Sum_probs=34.6
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCee
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR 70 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~ 70 (90)
|.-.||-+|+..+..+++.-+- + .+-.|+-|.+||+.++|+....+|+.
T Consensus 106 Iy~~i~~nPG~~lsEl~~nl~i--~------------R~TlRyhlriLe~~~li~a~~~~g~~ 154 (240)
T COG3398 106 IYNYIKPNPGFSLSELRANLYI--N------------RSTLRYHLRILESNPLIEAGRVGGAL 154 (240)
T ss_pred HHHHhccCCCccHHHHHHhcCC--C------------hHHHHHHHHHHHhCcchhhhccCCce
Confidence 4445566677777777664332 2 36899999999999999977766554
No 280
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.64 E-value=1.3e+02 Score=24.32 Aligned_cols=45 Identities=16% Similarity=0.231 Sum_probs=35.4
Q ss_pred HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
|+|=||+.+|+-...+..+.-.. +-.-...+++.|.++.++...+
T Consensus 36 VmrLL~~~~pv~~~~l~~Wv~~~-------------~~~~~~~al~~L~~L~Ii~~~~ 80 (366)
T PF03849_consen 36 VMRLLFVEQPVPQADLESWVKPE-------------SKKEHDEALKRLRSLHIIQESE 80 (366)
T ss_pred HHHHHhcCCCcCHHHHHHHhCcc-------------chHHHHHHHHHHhhCeeEeecc
Confidence 67888999999999998765332 2456789999999999997554
No 281
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=27.28 E-value=1.1e+02 Score=25.89 Aligned_cols=74 Identities=18% Similarity=0.220 Sum_probs=49.6
Q ss_pred HHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCcccc---------CchhHHHHHHHHHHhCCcccccCC--CCeeeCcc
Q 034587 7 SMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCK---------SSGAIARHILQQLQNMNIIDIEPK--GGRRITSS 74 (90)
Q Consensus 7 Si~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~---------asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~~ 74 (90)
.++.-+|- .+..|.+.+...+-|.++.-++-..+.+ -+..-++.+++||...|+++.... ..=.||++
T Consensus 418 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~ 497 (607)
T PRK11057 418 KALSCIYRVNQRFGMGYVVEVLRGANNQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQHSALQLTEA 497 (607)
T ss_pred HHHHHHHHhcCCCCcceeeeeeeccCcchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceeccCccceEEECHH
Confidence 34444442 5678888888888777666554432222 234588999999999999976542 24578888
Q ss_pred hHhhHH
Q 034587 75 GQRDLD 80 (90)
Q Consensus 75 G~~~lD 80 (90)
|+..|.
T Consensus 498 ~~~~l~ 503 (607)
T PRK11057 498 ARPVLR 503 (607)
T ss_pred HHHHhc
Confidence 887765
No 282
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.23 E-value=68 Score=23.98 Aligned_cols=27 Identities=19% Similarity=0.233 Sum_probs=22.0
Q ss_pred cccCchhHHHHHHHHHHhCCcccccCC
Q 034587 40 FCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 40 ~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
+++=|-.+|+.||++||+.|+.+-..+
T Consensus 63 ~R~Ls~~~i~~Il~~l~k~g~~e~~Dk 89 (174)
T KOG4068|consen 63 QRRLSQEFIDEILEELEKKGLAEPTDK 89 (174)
T ss_pred hccCCHHHHHHHHHHHHHccCCccccc
Confidence 445677899999999999999986543
No 283
>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=26.92 E-value=82 Score=22.63 Aligned_cols=31 Identities=23% Similarity=0.308 Sum_probs=24.0
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
|-.-+..+++.||+.+++.+...|=-.|-|.
T Consensus 88 S~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~ 118 (165)
T PF05732_consen 88 SKPTVSRAIKELEEKNIIKKIRNGAYMINPN 118 (165)
T ss_pred CHHHHHHHHHHHHhCCcEEEccCCeEEECcH
Confidence 4457888999999999999876554666664
No 284
>PF06399 GFRP: GTP cyclohydrolase I feedback regulatory protein (GFRP); InterPro: IPR009112 GTP cyclohydrolase I feedback regulatory protein (GFRP) in mammals helps regulate the biosynthesis of tetrahydrobiopterin through the feedback inhibition of the rate-limiting enzyme GTP cyclohydrolase I (GTPCHI). Tetrahydrobiopterin is the cofactor required for the hydroxylation of aromatic amino acids. The crystal structure of GFRP reveals that the protein forms a homopentamer []. In the presence of phenylalanine, the stimulatory complex consists of a GTPCHI decamer sandwiched by two GFRP pentamers, which is thought to enhance GTPCHI activity by locking the enzyme in the active state []. The structure of GFRP consists of two alpha/beta layers arranged beta(2)-alpha-beta(2)-alpha-beta(2), with antiparallel beta-sheets in the order 342165.; GO: 0009890 negative regulation of biosynthetic process; PDB: 1IS7_N 1IS8_Q 1WPL_T 1JG5_C.
Probab=26.78 E-value=47 Score=22.14 Aligned_cols=14 Identities=29% Similarity=0.494 Sum_probs=12.1
Q ss_pred HHHHHHHHHhCCcc
Q 034587 48 ARHILQQLQNMNII 61 (90)
Q Consensus 48 iR~~LqqLE~~glV 61 (90)
=|.+|..||.+||=
T Consensus 52 Pr~VLnKLE~~G~k 65 (83)
T PF06399_consen 52 PRVVLNKLEKMGYK 65 (83)
T ss_dssp HHHHHHHHHHTTEE
T ss_pred hHHHHHHHHhcCeE
Confidence 48899999999983
No 285
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.78 E-value=58 Score=27.44 Aligned_cols=31 Identities=29% Similarity=0.380 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCcccccCCCC-eeeCcchHhhH
Q 034587 49 RHILQQLQNMNIIDIEPKGG-RRITSSGQRDL 79 (90)
Q Consensus 49 R~~LqqLE~~glV~k~~~~G-R~lT~~G~~~l 79 (90)
..+++=|...|+++...+++ ..||++|-++|
T Consensus 156 ~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFL 187 (448)
T TIGR00625 156 EDVLQLLKQAGLMKSTEPGEPPCITSAGFQFL 187 (448)
T ss_pred hHHHHHHHhCCCCcccCCCCCccCchhhHHHH
Confidence 55677788899998743344 78999999886
No 286
>TIGR03703 plsB glycerol-3-phosphate O-acyltransferase. Members of this protein family are PlsB, glycerol-3-phosphate O-acyltransferase, present in E. coli and numerous related species. In many bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system.
Probab=26.65 E-value=1.6e+02 Score=26.54 Aligned_cols=49 Identities=16% Similarity=0.281 Sum_probs=38.4
Q ss_pred CCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587 35 SRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 87 (90)
Q Consensus 35 ~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~ 87 (90)
..|+.|. ..+.+.++|.|.+.|+|+++. .|-...++-...++..|..++
T Consensus 743 ~~pef~d---k~lf~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l 791 (799)
T TIGR03703 743 NAPEFFD---KAVFSTFIATLREQGYLDDDG-DGKLIFDEKLEELADQLKALL 791 (799)
T ss_pred CCccccc---HHHHHHHHHHHHHCCCCCccc-ccchhhHHHHHHHHHHHHHhc
Confidence 3577776 568999999999999997654 577777888888887776664
No 287
>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=26.59 E-value=45 Score=21.34 Aligned_cols=49 Identities=12% Similarity=0.034 Sum_probs=31.8
Q ss_pred HHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 8 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 8 i~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
|+.-|.- .+++.+..+-..-... + ..-|-.-+=..|+.|++.|+|.+..
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~---~------~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKK---G------PSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhc---C------CCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 4455544 4577887776655321 1 1234456777899999999998765
No 288
>PRK13239 alkylmercury lyase; Provisional
Probab=26.45 E-value=1.9e+02 Score=21.85 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=31.3
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 71 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l 71 (90)
+|+|.+---.|+.+..|.+..|... .-++.+|++ +..++-+++ |+.+
T Consensus 26 ~llr~la~G~pvt~~~lA~~~~~~~--------------~~v~~~L~~---l~~~~~d~~-g~iv 72 (206)
T PRK13239 26 PLLRLLAKGRPVSVTTLAAALGWPV--------------EEVEAVLEA---MPDTEYDED-GRII 72 (206)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCH--------------HHHHHHHHh---CCCeEECCC-CCEE
Confidence 5777766456999999999887643 445555555 456666664 5554
No 289
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=26.36 E-value=55 Score=23.79 Aligned_cols=31 Identities=13% Similarity=0.083 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587 46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQ 76 (90)
Q Consensus 46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 76 (90)
+=+=.+|++|.+.||+.+..+|--.|+|..-
T Consensus 167 ~eae~lL~~lv~~gWl~~s~~G~y~L~~Ral 197 (200)
T PF07574_consen 167 SEAESLLDRLVEDGWLYRSREGFYSLGPRAL 197 (200)
T ss_dssp HHHHHHHHHHHHTTSE-EEETTEEEE-HHHH
T ss_pred HHHHHHHHHHHHCCCceeCCCCEEEEChHHH
Confidence 4577899999999999888776666666543
No 290
>PF00727 IL4: Interleukin 4 This family is a subset of the SCOP family; InterPro: IPR002354 Cytokines are protein messengers that carry information from cell to cell []. Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE []; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4) has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds []. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []. The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet [].; GO: 0005136 interleukin-4 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 1HIK_A 1HZI_A 1ITI_A 2INT_A 1RCB_A 1CYL_A 3QB7_A 1BBN_A 2B8Z_A 1ITM_A ....
Probab=26.21 E-value=43 Score=23.45 Aligned_cols=12 Identities=17% Similarity=0.387 Sum_probs=11.0
Q ss_pred hHHHHHHHHhhc
Q 034587 4 LVTSMARKIYLR 15 (90)
Q Consensus 4 r~ASi~RklYl~ 15 (90)
|||.++|++|..
T Consensus 47 rAatvLr~~y~~ 58 (117)
T PF00727_consen 47 RAATVLRQFYSH 58 (117)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHhc
Confidence 899999999985
No 291
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=25.79 E-value=67 Score=20.53 Aligned_cols=16 Identities=13% Similarity=0.310 Sum_probs=13.2
Q ss_pred HHHHHHHHHhCCcccc
Q 034587 48 ARHILQQLQNMNIIDI 63 (90)
Q Consensus 48 iR~~LqqLE~~glV~k 63 (90)
.+.++..||+.||...
T Consensus 9 ~ke~ik~Le~~Gf~~v 24 (66)
T COG1724 9 AKEVIKALEKDGFQLV 24 (66)
T ss_pred HHHHHHHHHhCCcEEE
Confidence 3678899999999873
No 292
>PF08183 SpoV: Stage V sporulation protein family; InterPro: IPR012609 This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic alpha-helix and is recruited to the polar septum shortly after the sporangium undergoes asymmetric division. The function of SpoVM depends on proper subcellular localisation [].
Probab=25.76 E-value=42 Score=17.85 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=13.6
Q ss_pred ccCchhHHHHHHHHHHh
Q 034587 41 CKSSGAIARHILQQLQN 57 (90)
Q Consensus 41 ~~asg~iiR~~LqqLE~ 57 (90)
.++-|.++|.+|..|++
T Consensus 9 pkf~Gg~v~~~L~sf~k 25 (26)
T PF08183_consen 9 PKFLGGVVRALLFSFKK 25 (26)
T ss_pred hHHHhHHHHHHHHHHhc
Confidence 35678899999998875
No 293
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.62 E-value=41 Score=27.09 Aligned_cols=30 Identities=30% Similarity=0.389 Sum_probs=23.3
Q ss_pred HHHHHHHhCCcccc-cCCCCeeeCcchHhhH
Q 034587 50 HILQQLQNMNIIDI-EPKGGRRITSSGQRDL 79 (90)
Q Consensus 50 ~~LqqLE~~glV~k-~~~~GR~lT~~G~~~l 79 (90)
.+++=|...||++. ..+++..||++|-++|
T Consensus 157 ~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFL 187 (366)
T PF03849_consen 157 DVKQLLKRSGLMKRSESGGSLKITSKGFQFL 187 (366)
T ss_pred HHHHHHHHcCCCcCcCCCCCCcEehhheeee
Confidence 55666778999987 3357889999998875
No 294
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=25.54 E-value=1.6e+02 Score=22.30 Aligned_cols=44 Identities=16% Similarity=0.336 Sum_probs=29.5
Q ss_pred CCCchhHHHHHhcCC-CCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587 16 QGLGVGSFRRIYGGS-KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~-krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~ 64 (90)
+++..+.+-..|-.- ..-|..|-. -.-++.+|+.||.+|||+..
T Consensus 306 ~~~~~~~~~~~y~~~~~~~~~~~~~-----~~~~~~~l~~l~~~gli~~~ 350 (365)
T TIGR02928 306 DPFRTGEVYEVYKEVCEDIGVDPLT-----QRRISDLLNELDMLGLVEAE 350 (365)
T ss_pred CCccHHHHHHHHHHHHHhcCCCCCc-----HHHHHHHHHHHHhcCCeEEE
Confidence 456667666655431 223445533 37889999999999999854
No 295
>COG1485 Predicted ATPase [General function prediction only]
Probab=25.51 E-value=80 Score=26.11 Aligned_cols=49 Identities=24% Similarity=0.441 Sum_probs=33.7
Q ss_pred HHHHHHhhcCCCchhH---HHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCC
Q 034587 7 SMARKIYLRQGLGVGS---FRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMN 59 (90)
Q Consensus 7 Si~RklYl~g~vGV~~---Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~g 59 (90)
...|=||+.||||.|. +-..|.+-.-..-+.-||+ ..++.+-|.|.++.
T Consensus 63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh----~FM~~vH~~l~~l~ 114 (367)
T COG1485 63 GPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFH----RFMARVHQRLHTLQ 114 (367)
T ss_pred CCCceEEEECCCCccHHHHHHHHHhhCCccccccccHH----HHHHHHHHHHHHHc
Confidence 3456699999999985 4566666443333344665 38888888888876
No 296
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=25.46 E-value=63 Score=25.49 Aligned_cols=20 Identities=30% Similarity=0.378 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhCCcccccCC
Q 034587 47 IARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~ 66 (90)
=||.-||.|.+.|+||....
T Consensus 229 KIRQqLQ~LRD~g~IeFl~r 248 (254)
T PF06044_consen 229 KIRQQLQILRDKGIIEFLGR 248 (254)
T ss_dssp HHHHHHHHHHHTTSEEE-ST
T ss_pred HHHHHHHHHhhCCceEEecC
Confidence 49999999999999998763
No 297
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=24.50 E-value=1.1e+02 Score=19.98 Aligned_cols=53 Identities=17% Similarity=0.066 Sum_probs=36.0
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 74 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~ 74 (90)
.++.+++|+..-...- | +-..-|-.+++.+|.+|-+.+-|=....|=..+||+
T Consensus 28 ~~at~E~l~~~L~~~y-----p-~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivtP~ 80 (80)
T PF10264_consen 28 QPATQETLREHLRKHY-----P-GIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVTPQ 80 (80)
T ss_pred CcchHHHHHHHHHHhC-----C-CCCCCCHHHHHHHHHHHHHcCceeeCCCceEeeCCC
Confidence 4566666555443322 2 223446689999999999999998776666777774
No 298
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=24.33 E-value=1.5e+02 Score=22.42 Aligned_cols=37 Identities=14% Similarity=0.215 Sum_probs=30.5
Q ss_pred HHHHHHHhCCccccc-CCCCeeeCcchHhhHHHHHHHh
Q 034587 50 HILQQLQNMNIIDIE-PKGGRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 50 ~~LqqLE~~glV~k~-~~~GR~lT~~G~~~lD~iA~~v 86 (90)
+.-|=|.++|+|+.. ++|-..+.|.|...+++|-..+
T Consensus 5 ~~~~~l~~ag~~~~~~~~G~~~~lP~g~~i~~~I~~~i 42 (264)
T cd00772 5 KSLEHIGKAELADQGPGRGIINFLPLAKAILDKIENVL 42 (264)
T ss_pred HHHHHHHhcCCccccCCCCEEEECCcHHHHHHHHHHHH
Confidence 345678999999987 5788999999999999886654
No 299
>PF12052 VGCC_beta4Aa_N: Voltage gated calcium channel subunit beta domain 4Aa N terminal; InterPro: IPR000584 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. Co-expression of beta subunit mRNA with alpha-1 subunit mRNA in xenopus oocytes produces increased calcium currents, which are accompanied by a shift in the voltage-dependence of activation to more negative membrane potentials. Conversely, microinjection of antisense oligonucleotides to beta subunit mRNA produces decreased calcium currents and shifts voltage-dependent activation to more positive membrane potentials. There are four distinct beta subunits: beta-1, beta-2, beta-3 and beta-4; and the magnitude of the shift in the voltage-dependence of activation of change to membrane potentials varies with the particular subtype []. This entry represents the beta subunits found in L-type voltage-gated calcium channels.; GO: 0005245 voltage-gated calcium channel activity, 0006816 calcium ion transport, 0051925 regulation of calcium ion transport via voltage-gated calcium channel activity; PDB: 1T0J_A 1T0H_A 2D46_A 1T3S_A 1T3L_A 4DEY_A 4DEX_A 1VYT_B 1VYU_A.
Probab=23.75 E-value=48 Score=19.47 Aligned_cols=13 Identities=31% Similarity=0.447 Sum_probs=10.3
Q ss_pred HHHHHHHHHHhCC
Q 034587 47 IARHILQQLQNMN 59 (90)
Q Consensus 47 iiR~~LqqLE~~g 59 (90)
.-|.++.|||+++
T Consensus 28 ~erqA~~QLekAk 40 (42)
T PF12052_consen 28 AERQALAQLEKAK 40 (42)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhh
Confidence 4467999999875
No 300
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.53 E-value=1.4e+02 Score=16.14 Aligned_cols=39 Identities=21% Similarity=0.366 Sum_probs=29.0
Q ss_pred HhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587 12 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 12 lYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~ 65 (90)
.|+.|. ++..+++.||-. -+-++..+++.++-|+-...+
T Consensus 8 ~~~~g~-s~~~~a~~~gis--------------~~tv~~w~~~y~~~G~~~l~~ 46 (52)
T PF13518_consen 8 LYLEGE-SVREIAREFGIS--------------RSTVYRWIKRYREGGIEGLKP 46 (52)
T ss_pred HHHcCC-CHHHHHHHHCCC--------------HhHHHHHHHHHHhcCHHHhcc
Confidence 366765 999999999873 246788999999988654333
No 301
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=23.46 E-value=1.7e+02 Score=20.31 Aligned_cols=57 Identities=7% Similarity=-0.035 Sum_probs=39.1
Q ss_pred HHHHHHHhhcCC---------CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587 6 TSMARKIYLRQG---------LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66 (90)
Q Consensus 6 ASi~RklYl~g~---------vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~ 66 (90)
.-+||.+|.... +.++.+.-.|..-... .+-....-.-++.+|..|++.|+|+....
T Consensus 80 LL~LR~~y~e~~~~~~~~~~~v~~~ei~e~~~~~~~~----~~d~~~~~~~~~~~l~~l~~~~ll~~~~~ 145 (166)
T PF13835_consen 80 LLVLRLLYEEKESLSGSERVVVTREEIVEKLESFLPE----SRDEAPFKKRLDAALRRLKRYGLLRRLDG 145 (166)
T ss_pred HHHHHHHHHHHhccCCCCcEEEeHHHHHHHHHHHccc----cccccchHHHHHHHHHHHHHCCCeeccCC
Confidence 457899998753 5667777666652221 12334455678999999999999987763
No 302
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=23.02 E-value=1.3e+02 Score=22.96 Aligned_cols=34 Identities=18% Similarity=0.350 Sum_probs=24.0
Q ss_pred HHHHHHHHHHh-C--CcccccC----CCCeeeCcchHhhHH
Q 034587 47 IARHILQQLQN-M--NIIDIEP----KGGRRITSSGQRDLD 80 (90)
Q Consensus 47 iiR~~LqqLE~-~--glV~k~~----~~GR~lT~~G~~~lD 80 (90)
-+=..+++||+ + -|++... .+|=.||+.|+.++.
T Consensus 47 a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~lT~~G~~l~~ 87 (263)
T PRK10676 47 SAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGERLIQ 87 (263)
T ss_pred HHHHHHHHHHHHhCCCeEEEecCCCCCCCcEECHHHHHHHH
Confidence 45567888887 3 4566652 246689999999984
No 303
>PF08604 Nup153: Nucleoporin Nup153-like; InterPro: IPR013913 This entry contains both the nucleoporin Nup153 from human and Nup153 from fission yeast. These have been demonstrated to be functionally equivalent [].
Probab=22.59 E-value=51 Score=28.42 Aligned_cols=13 Identities=54% Similarity=0.767 Sum_probs=11.6
Q ss_pred hHHHHHHHHHHhC
Q 034587 46 AIARHILQQLQNM 58 (90)
Q Consensus 46 ~iiR~~LqqLE~~ 58 (90)
+-.|+|||.||+|
T Consensus 197 sTArRILqsLEkM 209 (519)
T PF08604_consen 197 STARRILQSLEKM 209 (519)
T ss_pred HHHHHHHHHHHHh
Confidence 4579999999999
No 304
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=22.59 E-value=54 Score=23.10 Aligned_cols=30 Identities=20% Similarity=0.383 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHHh-CCcccccCCCCeeeCcc
Q 034587 45 GAIARHILQQLQN-MNIIDIEPKGGRRITSS 74 (90)
Q Consensus 45 g~iiR~~LqqLE~-~glV~k~~~~GR~lT~~ 74 (90)
=+.+|++|+.--+ ..||.+.|+.|.+++..
T Consensus 75 I~~LRr~L~d~~~~~~~I~TvPrrGyk~~~~ 105 (148)
T COG3710 75 ISALRRALRDIGDGHRLIATVPRRGYKFTAD 105 (148)
T ss_pred HHHHHHHHhccCCcceEEEEeCCcceEEecc
Confidence 3578888888776 78899999999988753
No 305
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.44 E-value=48 Score=23.84 Aligned_cols=27 Identities=30% Similarity=0.417 Sum_probs=19.6
Q ss_pred CCCCCCCCCccccCchhHHHHHHHHHHhCCc
Q 034587 30 SKRNGSRPPHFCKSSGAIARHILQQLQNMNI 60 (90)
Q Consensus 30 ~krrG~~P~h~~~asg~iiR~~LqqLE~~gl 60 (90)
-|.=|+-|+.+-+.|.+|+| +||.+|+
T Consensus 52 vK~Ig~P~s~y~k~skkvlk----aleq~gI 78 (139)
T COG1710 52 VKVIGCPPSLYPKVSKKVLK----ALEQMGI 78 (139)
T ss_pred cceecCCchhhhHHHHHHHH----HHHhCCc
Confidence 46668888888877766666 7777775
No 306
>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=22.31 E-value=76 Score=20.24 Aligned_cols=33 Identities=27% Similarity=0.231 Sum_probs=23.9
Q ss_pred CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587 17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 63 (90)
Q Consensus 17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k 63 (90)
++.|..+....+- +-.=+|.+|+.|...|+|=.
T Consensus 65 Gv~v~~I~~~l~~--------------~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 65 GVHVDEIAQQLGM--------------SENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp TEEHHHHHHHSTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred cccHHHHHHHhCc--------------CHHHHHHHHHHHHhCCeEec
Confidence 4667777775522 34679999999999999843
No 307
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=22.19 E-value=73 Score=22.59 Aligned_cols=23 Identities=9% Similarity=0.326 Sum_probs=19.4
Q ss_pred CCeeeCcchHhhHHHHHHHhhcC
Q 034587 67 GGRRITSSGQRDLDQVAGRIVVA 89 (90)
Q Consensus 67 ~GR~lT~~G~~~lD~iA~~v~~~ 89 (90)
+.-.|+++++..||++|..+.+.
T Consensus 59 ~sa~L~~~~~~~L~~ia~~l~~~ 81 (160)
T PRK09967 59 NDYKLLPESQQQIQTMAAKLAST 81 (160)
T ss_pred CccccCHHHHHHHHHHHHHHHhC
Confidence 45689999999999999987654
No 308
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=22.11 E-value=1e+02 Score=22.15 Aligned_cols=31 Identities=26% Similarity=0.208 Sum_probs=23.2
Q ss_pred CcccccCCCCeeeCcchHhhHHHHHHHhhcCC
Q 034587 59 NIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 59 glV~k~~~~GR~lT~~G~~~lD~iA~~v~~~~ 90 (90)
+.|-.+. +.-.|||+++..||.+|..+...|
T Consensus 69 ~~v~F~~-d~~~l~~~~~~~L~~~a~~L~~~p 99 (173)
T PRK10802 69 NIVYFDL-DKYDIRSDFAQMLDAHANFLRSNP 99 (173)
T ss_pred CeEEecC-CCccCCHHHHHHHHHHHHHHHhCC
Confidence 3454454 356899999999999998876544
No 309
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=22.08 E-value=1.1e+02 Score=21.00 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=23.8
Q ss_pred chhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587 44 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG 84 (90)
Q Consensus 44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~ 84 (90)
+..-+=.+|.+|++.|+|+.. ++.|+=.=...|.++|.
T Consensus 162 tretvsR~l~~l~~~g~I~~~---~~~i~I~d~~~L~~~~~ 199 (202)
T PRK13918 162 VRETVTKVIGELSREGYIRSG---YGKIQLLDLKGLEELAE 199 (202)
T ss_pred cHHHHHHHHHHHHHCCCEEcC---CCEEEEECHHHHHHHHh
Confidence 344566789999999999854 23454333444445544
No 310
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.07 E-value=76 Score=20.34 Aligned_cols=21 Identities=24% Similarity=0.374 Sum_probs=16.5
Q ss_pred hhHHHHHHHHHHhCCcc-cccC
Q 034587 45 GAIARHILQQLQNMNII-DIEP 65 (90)
Q Consensus 45 g~iiR~~LqqLE~~glV-~k~~ 65 (90)
-+.+|++||-||+.++- |--|
T Consensus 15 vGF~rk~L~I~E~~~is~Eh~P 36 (76)
T cd04911 15 VGFGRKLLSILEDNGISYEHMP 36 (76)
T ss_pred hcHHHHHHHHHHHcCCCEeeec
Confidence 35899999999999985 4444
No 311
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=21.87 E-value=76 Score=22.37 Aligned_cols=23 Identities=22% Similarity=0.329 Sum_probs=19.7
Q ss_pred CeeeCcchHhhHHHHHHHhhcCC
Q 034587 68 GRRITSSGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 68 GR~lT~~G~~~lD~iA~~v~~~~ 90 (90)
--.|.|+.+..||.+|..+.+.|
T Consensus 91 s~~l~p~~~~~L~~~a~~L~~~p 113 (190)
T COG2885 91 SSVLKPKAQATLDELAKYLKKNP 113 (190)
T ss_pred ccccCHhHHHHHHHHHHHHHhCC
Confidence 55899999999999999887654
No 312
>TIGR00302 phosphoribosylformylglycinamidine synthase, purS protein. In species such as Bacillus subtilis in which FGAM synthetase is split into two ORFs purL and purQ, this small protein, previously called yexA, is required for FGAM synthetase activity. Although the article does not make it clear whether this is a subunit or an accessory protein, it is encoded as part of the operon, which suggests stochiometric amounts, = subunit.
Probab=21.79 E-value=1e+02 Score=19.32 Aligned_cols=15 Identities=13% Similarity=0.696 Sum_probs=11.8
Q ss_pred HhhHHHHHHHhhcCC
Q 034587 76 QRDLDQVAGRIVVAP 90 (90)
Q Consensus 76 ~~~lD~iA~~v~~~~ 90 (90)
...++.+|.+++.+|
T Consensus 55 ~~~v~~i~~~lL~Np 69 (80)
T TIGR00302 55 EREVEEMCEKLLANP 69 (80)
T ss_pred HHHHHHHHHHhcCCc
Confidence 366899999888776
No 313
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=21.76 E-value=64 Score=21.06 Aligned_cols=34 Identities=9% Similarity=0.096 Sum_probs=24.6
Q ss_pred CCCCCCCcccc---CchhHHHHHHHHHHhCCcccccC
Q 034587 32 RNGSRPPHFCK---SSGAIARHILQQLQNMNIIDIEP 65 (90)
Q Consensus 32 rrG~~P~h~~~---asg~iiR~~LqqLE~~glV~k~~ 65 (90)
-+|+.|-.... ....++..+++.|.+.|+++...
T Consensus 58 ~~GV~p~~~~~~~~~~~~~~~~a~~~~~~~g~~~~gd 94 (117)
T PF02887_consen 58 YWGVYPVLIEEFDKDTEELIAEALEYAKERGLLKPGD 94 (117)
T ss_dssp STTEEEEECSSHSHSHHHHHHHHHHHHHHTTSS-TTS
T ss_pred ccceEEEEeccccccHHHHHHHHHHHHHHcCCCCCCC
Confidence 46777743333 35789999999999999987543
No 314
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen
Probab=21.68 E-value=1e+02 Score=22.54 Aligned_cols=33 Identities=12% Similarity=0.220 Sum_probs=25.6
Q ss_pred hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCC
Q 034587 2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSR 36 (90)
Q Consensus 2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~ 36 (90)
++-||||+=|++-+-- +..|...||-..+.|+-
T Consensus 142 ~VaAASIlAKv~Rd~~--m~~l~~~yg~~~~~G~g 174 (208)
T cd06590 142 AVAAASILARYAFLEK--MEKLSKQYGMKLPKGAS 174 (208)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHhCCCCCCCCC
Confidence 5679999999988755 47888999877666643
No 315
>smart00351 PAX Paired Box domain.
Probab=21.56 E-value=2.6e+02 Score=18.72 Aligned_cols=39 Identities=21% Similarity=0.200 Sum_probs=26.4
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC
Q 034587 16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 68 (90)
Q Consensus 16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G 68 (90)
.+.....+++.||-.. +.+.+++++..+-|.++--+.+|
T Consensus 32 ~G~s~~~iA~~~gvs~--------------~tV~kwi~r~~~~G~~~pk~~gg 70 (125)
T smart00351 32 NGVRPCDISRQLCVSH--------------GCVSKILGRYYETGSIRPGAIGG 70 (125)
T ss_pred cCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHcCCcCCcCCCC
Confidence 5566777777777643 57777788888888876544333
No 316
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=21.05 E-value=2.6e+02 Score=19.36 Aligned_cols=70 Identities=9% Similarity=0.066 Sum_probs=48.3
Q ss_pred HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc-----cC-CCCeeeC--------
Q 034587 7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI-----EP-KGGRRIT-------- 72 (90)
Q Consensus 7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k-----~~-~~GR~lT-------- 72 (90)
.|++.|--++.+....|++.-|= |.+-++.=++.||+.|+|+. ++ +-|..++
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lgl--------------S~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~ 83 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGL--------------SPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLN 83 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEc
Confidence 46777777888888888887665 44678889999999999984 22 2243222
Q ss_pred cchHhhHHHHHHHhhcCC
Q 034587 73 SSGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 73 ~~G~~~lD~iA~~v~~~~ 90 (90)
+.....+|+++..+...|
T Consensus 84 ~~~~~~~~~~~~~l~~~p 101 (164)
T PRK11169 84 RGAPDVFEQFNAAVQKLE 101 (164)
T ss_pred CCChHHHHHHHHHHhcCc
Confidence 233556788877765543
No 317
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=21.01 E-value=1.6e+02 Score=19.37 Aligned_cols=49 Identities=10% Similarity=0.128 Sum_probs=28.7
Q ss_pred HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHh
Q 034587 6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQN 57 (90)
Q Consensus 6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~ 57 (90)
..+.++++-....++..|.+.||.....- .|.+..--...-.+++.|.+
T Consensus 117 ~~~~~~~~~~~~~~L~~l~~~~~~~~~~~---~H~A~~Da~~t~~l~~~~~~ 165 (169)
T smart00479 117 LKLARALNPGRKYSLKKLAERLGLEVIGR---AHRALDDARATAKLFKKLVE 165 (169)
T ss_pred HHHHHHHCCCCCCCHHHHHHHCCCCCCCC---CcCcHHHHHHHHHHHHHHHH
Confidence 34555555444789999999999875431 24444443444455554443
No 318
>PF03004 Transposase_24: Plant transposase (Ptta/En/Spm family); InterPro: IPR004252 Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.92 E-value=1.6e+02 Score=19.55 Aligned_cols=59 Identities=10% Similarity=0.165 Sum_probs=39.2
Q ss_pred CCCCC-CCCCCccccCchhHHHHHHHHHHhC-Cc--------ccccC-CCCeeeCcchHhhHHHHHHHhhc
Q 034587 29 GSKRN-GSRPPHFCKSSGAIARHILQQLQNM-NI--------IDIEP-KGGRRITSSGQRDLDQVAGRIVV 88 (90)
Q Consensus 29 g~krr-G~~P~h~~~asg~iiR~~LqqLE~~-gl--------V~k~~-~~GR~lT~~G~~~lD~iA~~v~~ 88 (90)
.+.|| +-.+.+|.-||.++.+..=+ |++. |- .+.+. +.|.-+++..+..+|.+...+.+
T Consensus 24 nk~nR~~~~~~~H~~Gs~s~~~~~~~-m~~~~g~~p~~~el~~~th~kkdG~~v~~~a~~~~~~~~~~~~e 93 (141)
T PF03004_consen 24 NKANRSAKGKHPHTTGSKSFAAHREE-MEKKKGREPSRIELFKETHTKKDGTYVDERAEEIIEEMEERLEE 93 (141)
T ss_pred HHHhhhcCCCcccCcCCchHHHHHHH-HhccccCCCCHHHHHHHHHhcCcCcccCHHHHHHHHHHHHHHhc
Confidence 35566 77889999999998876654 4433 21 11111 35778888888888888776643
No 319
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.51 E-value=1.5e+02 Score=22.86 Aligned_cols=33 Identities=30% Similarity=0.538 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587 47 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 82 (90)
Q Consensus 47 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i 82 (90)
+-|+||.-|...|+|...|+ .+|++=--....|
T Consensus 149 lDrHIlr~l~r~g~i~e~~k---t~t~K~YLe~E~i 181 (210)
T COG1059 149 LDRHILRWLVRYGLIDENPK---TLTRKLYLEIEEI 181 (210)
T ss_pred HHHHHHHHHHHhcccccCcc---cccHHHHHHHHHH
Confidence 77999999999999999886 6787754444433
No 320
>PF05427 FIBP: Acidic fibroblast growth factor binding (FIBP) ; InterPro: IPR008614 Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF [].; GO: 0017134 fibroblast growth factor binding
Probab=20.46 E-value=45 Score=27.44 Aligned_cols=19 Identities=32% Similarity=0.742 Sum_probs=17.5
Q ss_pred CeeeCcchHhhHHHHHHHh
Q 034587 68 GRRITSSGQRDLDQVAGRI 86 (90)
Q Consensus 68 GR~lT~~G~~~lD~iA~~v 86 (90)
|+.||+.=++|||+|++..
T Consensus 108 GkKLs~~~rKdLdevsekt 126 (361)
T PF05427_consen 108 GKKLSSRTRKDLDEVSEKT 126 (361)
T ss_pred hhhhcccccccHHHHHHHh
Confidence 9999999999999999863
No 321
>smart00190 IL4_13 Interleukins 4 and 13. Interleukins-4 and -13 are cytokines involved in inflammatory and immune responses. IL-4 stimulates B and T cells.
Probab=20.31 E-value=2.9e+02 Score=19.85 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=23.7
Q ss_pred hHHHHHHHHhhcCCCch-hHHHHHhcC---CCCCCCCCCccccCc
Q 034587 4 LVTSMARKIYLRQGLGV-GSFRRIYGG---SKRNGSRPPHFCKSS 44 (90)
Q Consensus 4 r~ASi~RklYl~g~vGV-~~Lr~~YGg---~krrG~~P~h~~~as 44 (90)
|||-++|++|.+..-+| ..++..++. .-+-+..|....+-+
T Consensus 72 rA~~vLr~~y~~~~s~i~k~lr~L~r~l~~l~~~~~c~v~e~~~t 116 (138)
T smart00190 72 RALKVLRNFYFHNCSAILKTLRKLDRNCSGLASQTSCTVNEAKDT 116 (138)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHhhhhcccCCCcCCcccCccc
Confidence 79999999998744444 344544443 333443444444433
No 322
>COG3177 Fic family protein [Function unknown]
Probab=20.21 E-value=1.1e+02 Score=24.08 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=23.3
Q ss_pred cCchhHHHHHHHHHHhCCcccccCCCCee
Q 034587 42 KSSGAIARHILQQLQNMNIIDIEPKGGRR 70 (90)
Q Consensus 42 ~asg~iiR~~LqqLE~~glV~k~~~~GR~ 70 (90)
+.|-.-+++-|+.|.+.|++++.+.+||.
T Consensus 315 ~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~ 343 (348)
T COG3177 315 GVSKATATRDLKELLELGILEEVKGRGRS 343 (348)
T ss_pred CccHHHHHHHHHHHHhCCCeeecCCCCCc
Confidence 34556899999999999999998865553
No 323
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=20.02 E-value=1.1e+02 Score=18.81 Aligned_cols=23 Identities=22% Similarity=0.494 Sum_probs=15.1
Q ss_pred CeeeCc--chHhhHHHHHHHhhcCC
Q 034587 68 GRRITS--SGQRDLDQVAGRIVVAP 90 (90)
Q Consensus 68 GR~lT~--~G~~~lD~iA~~v~~~~ 90 (90)
|+.++= .....++.+|.+++.+|
T Consensus 39 ~k~~~l~~~~~~~~~~i~~~lL~Np 63 (73)
T PRK06423 39 SKVYYFDADSYNEVDEIAGKILTNP 63 (73)
T ss_pred EEEEEEecCCHHHHHHHHHHhcCCc
Confidence 444443 33566888998888776
Done!