Query 043775
Match_columns 554
No_of_seqs 254 out of 1015
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:14:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043775hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 8.5E-98 2E-102 814.9 50.0 539 4-554 5-723 (725)
2 COG5647 Cullin, a subunit of E 100.0 4.6E-92 9.9E-97 737.9 47.2 535 5-554 16-769 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 2.2E-89 4.8E-94 702.1 37.8 472 66-551 66-656 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 8.4E-84 1.8E-88 634.1 36.6 518 3-549 5-720 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 2.1E-73 4.6E-78 565.4 42.5 534 7-554 11-773 (777)
6 PF00888 Cullin: Cullin family 100.0 3.4E-71 7.4E-76 615.7 44.5 453 13-491 1-588 (588)
7 smart00182 CULLIN Cullin. 99.9 3.4E-24 7.3E-29 194.0 13.6 110 298-412 1-142 (142)
8 KOG2165 Anaphase-promoting com 99.9 1.3E-18 2.7E-23 183.7 35.1 192 292-492 442-666 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.6 4.3E-16 9.3E-21 121.8 2.3 54 499-552 15-68 (68)
10 TIGR01610 phage_O_Nterm phage 94.5 0.13 2.9E-06 42.8 6.8 65 419-491 21-93 (95)
11 PF09339 HTH_IclR: IclR helix- 94.3 0.079 1.7E-06 38.7 4.4 46 426-473 6-52 (52)
12 PF02082 Rrf2: Transcriptional 93.7 0.24 5.1E-06 40.1 6.6 59 424-489 11-70 (83)
13 PF13412 HTH_24: Winged helix- 93.5 0.19 4.1E-06 35.9 5.0 46 422-469 2-47 (48)
14 PF12802 MarR_2: MarR family; 93.2 0.16 3.4E-06 38.3 4.6 51 421-473 3-55 (62)
15 PF08220 HTH_DeoR: DeoR-like h 92.2 0.29 6.2E-06 36.6 4.6 48 425-474 2-49 (57)
16 PF01047 MarR: MarR family; I 91.0 0.24 5.1E-06 37.0 3.1 51 421-473 1-51 (59)
17 PF13463 HTH_27: Winged helix 90.8 0.47 1E-05 36.4 4.7 51 421-473 1-52 (68)
18 PF12840 HTH_20: Helix-turn-he 90.8 0.45 9.7E-06 36.0 4.4 49 422-472 9-57 (61)
19 TIGR02337 HpaR homoprotocatech 90.1 0.68 1.5E-05 40.0 5.6 52 420-473 25-76 (118)
20 PF01022 HTH_5: Bacterial regu 88.7 1.3 2.8E-05 31.5 5.3 43 425-470 4-46 (47)
21 PRK11512 DNA-binding transcrip 88.5 1.1 2.3E-05 40.3 5.9 53 419-473 36-88 (144)
22 smart00550 Zalpha Z-DNA-bindin 88.2 1.1 2.4E-05 34.7 5.0 48 424-473 7-56 (68)
23 smart00346 HTH_ICLR helix_turn 86.4 1.9 4.2E-05 35.0 5.8 46 426-473 8-54 (91)
24 TIGR01889 Staph_reg_Sar staphy 85.4 2.4 5.3E-05 36.1 6.1 53 420-474 22-78 (109)
25 smart00347 HTH_MARR helix_turn 85.1 2 4.3E-05 35.3 5.3 54 418-473 5-58 (101)
26 smart00420 HTH_DEOR helix_turn 84.5 2.5 5.5E-05 30.1 5.0 45 426-472 3-47 (53)
27 PF08279 HTH_11: HTH domain; 84.4 2.3 4.9E-05 31.1 4.8 36 427-462 4-40 (55)
28 PF04492 Phage_rep_O: Bacterio 84.1 3.7 8E-05 34.5 6.4 61 420-490 29-97 (100)
29 PF01978 TrmB: Sugar-specific 83.7 1.3 2.8E-05 34.2 3.3 51 421-473 6-56 (68)
30 PRK10857 DNA-binding transcrip 83.4 3.9 8.4E-05 37.8 6.9 46 425-472 12-58 (164)
31 PF04703 FaeA: FaeA-like prote 83.1 3.6 7.8E-05 31.3 5.4 47 428-476 5-52 (62)
32 PRK11920 rirA iron-responsive 83.0 4 8.7E-05 37.2 6.8 45 426-472 13-57 (153)
33 PF13601 HTH_34: Winged helix 82.9 1.5 3.3E-05 35.2 3.5 45 425-471 2-46 (80)
34 PRK15090 DNA-binding transcrip 82.6 3.1 6.7E-05 41.3 6.4 47 425-473 16-62 (257)
35 PRK13777 transcriptional regul 81.6 3.6 7.9E-05 38.7 6.0 53 419-473 41-93 (185)
36 PRK03573 transcriptional regul 80.3 3.6 7.9E-05 36.7 5.5 53 419-473 27-80 (144)
37 TIGR02010 IscR iron-sulfur clu 80.1 5.4 0.00012 35.4 6.4 44 426-471 13-57 (135)
38 PF05584 Sulfolobus_pRN: Sulfo 79.2 5.5 0.00012 31.2 5.3 46 423-472 6-51 (72)
39 TIGR01884 cas_HTH CRISPR locus 78.8 3.7 8E-05 39.3 5.3 52 420-473 140-191 (203)
40 PF09012 FeoC: FeoC like trans 78.1 1.3 2.9E-05 34.3 1.6 43 499-549 7-49 (69)
41 TIGR03879 near_KaiC_dom probab 77.3 2.9 6.3E-05 32.9 3.3 41 428-470 23-63 (73)
42 COG3355 Predicted transcriptio 76.8 4.7 0.0001 35.3 4.8 38 433-472 38-75 (126)
43 PF13404 HTH_AsnC-type: AsnC-t 76.6 4.8 0.0001 28.0 3.9 35 427-461 7-41 (42)
44 smart00345 HTH_GNTR helix_turn 76.2 5.8 0.00013 29.0 4.7 40 432-473 14-54 (60)
45 COG1959 Predicted transcriptio 76.1 7.6 0.00016 35.2 6.2 46 425-472 12-58 (150)
46 PRK10870 transcriptional repre 75.8 7.6 0.00016 36.2 6.3 53 420-474 52-106 (176)
47 PF05732 RepL: Firmicute plasm 75.6 4.2 9.1E-05 37.6 4.5 49 437-494 75-123 (165)
48 cd00090 HTH_ARSR Arsenical Res 75.3 8.2 0.00018 29.3 5.6 48 422-472 6-53 (78)
49 PHA00738 putative HTH transcri 75.1 8.1 0.00018 32.7 5.6 67 418-490 7-73 (108)
50 smart00419 HTH_CRP helix_turn_ 74.7 8.2 0.00018 26.9 4.9 34 437-472 8-41 (48)
51 PF08280 HTH_Mga: M protein tr 73.2 5.7 0.00012 29.8 3.9 38 425-462 7-44 (59)
52 COG1414 IclR Transcriptional r 73.1 6.7 0.00015 38.7 5.5 47 426-474 7-54 (246)
53 PRK10163 DNA-binding transcrip 72.0 6.9 0.00015 39.2 5.4 47 425-473 27-74 (271)
54 PRK09834 DNA-binding transcrip 71.2 6.6 0.00014 39.1 5.0 47 426-474 14-61 (263)
55 PF08784 RPA_C: Replication pr 71.0 8.2 0.00018 32.3 4.9 44 420-463 44-91 (102)
56 PRK11569 transcriptional repre 70.7 8.1 0.00018 38.8 5.6 47 425-473 30-77 (274)
57 PF08539 HbrB: HbrB-like; Int 69.8 19 0.00042 32.9 7.3 48 7-58 3-50 (158)
58 TIGR02431 pcaR_pcaU beta-ketoa 69.7 11 0.00025 37.0 6.3 45 426-472 12-57 (248)
59 smart00344 HTH_ASNC helix_turn 69.6 9.6 0.00021 32.1 5.0 45 424-470 4-48 (108)
60 KOG2167 Cullins [Cell cycle co 69.2 1.7E+02 0.0037 32.5 15.0 46 108-155 270-324 (661)
61 TIGR00738 rrf2_super rrf2 fami 68.9 14 0.0003 32.4 6.1 46 425-472 12-58 (132)
62 PRK10141 DNA-binding transcrip 68.7 13 0.00028 32.2 5.6 57 426-488 19-75 (117)
63 TIGR02944 suf_reg_Xantho FeS a 68.1 14 0.0003 32.4 5.9 46 425-472 11-58 (130)
64 smart00418 HTH_ARSR helix_turn 68.0 12 0.00026 27.4 4.9 36 435-472 8-43 (66)
65 COG1846 MarR Transcriptional r 67.8 12 0.00027 31.6 5.5 51 421-473 20-70 (126)
66 PF04545 Sigma70_r4: Sigma-70, 64.1 18 0.00038 25.8 4.8 33 425-459 10-42 (50)
67 PF13730 HTH_36: Helix-turn-he 64.0 18 0.00038 26.3 4.9 24 439-462 27-50 (55)
68 PF01325 Fe_dep_repress: Iron 63.8 19 0.00041 27.1 5.0 45 427-473 12-56 (60)
69 PRK10434 srlR DNA-bindng trans 63.1 11 0.00024 37.4 4.7 50 424-475 6-55 (256)
70 TIGR00281 segregation and cond 62.6 27 0.00059 32.9 7.0 108 430-547 9-131 (186)
71 PF08221 HTH_9: RNA polymerase 61.8 14 0.0003 28.0 4.0 34 434-469 24-57 (62)
72 PRK11014 transcriptional repre 61.5 26 0.00057 31.2 6.5 40 432-473 20-59 (141)
73 cd00092 HTH_CRP helix_turn_hel 61.2 16 0.00034 27.5 4.3 36 436-473 24-59 (67)
74 PF01726 LexA_DNA_bind: LexA D 60.3 15 0.00033 28.2 4.0 25 527-551 39-63 (65)
75 COG2345 Predicted transcriptio 59.7 14 0.00029 35.7 4.4 44 426-471 14-57 (218)
76 TIGR02702 SufR_cyano iron-sulf 59.5 26 0.00055 33.4 6.4 60 427-488 5-65 (203)
77 PRK00135 scpB segregation and 59.4 44 0.00096 31.5 7.8 107 430-546 12-133 (188)
78 PF01047 MarR: MarR family; I 58.7 5 0.00011 29.7 1.1 32 520-551 23-56 (59)
79 COG1349 GlpR Transcriptional r 58.6 16 0.00035 36.2 5.0 51 425-477 7-57 (253)
80 PF02002 TFIIE_alpha: TFIIE al 58.4 10 0.00022 32.0 3.1 44 425-470 15-58 (105)
81 TIGR02698 CopY_TcrY copper tra 57.2 13 0.00028 32.8 3.7 38 514-551 22-59 (130)
82 PF08281 Sigma70_r4_2: Sigma-7 56.3 25 0.00054 25.3 4.5 24 436-459 25-48 (54)
83 PF01853 MOZ_SAS: MOZ/SAS fami 55.8 12 0.00027 35.1 3.4 27 436-462 149-175 (188)
84 PRK06266 transcription initiat 55.6 22 0.00048 33.2 5.1 44 425-470 24-67 (178)
85 PRK13509 transcriptional repre 54.9 23 0.0005 35.0 5.4 51 424-476 6-56 (251)
86 PF07393 Sec10: Exocyst comple 54.5 3.9E+02 0.0084 30.8 17.0 125 86-217 106-264 (710)
87 PF01726 LexA_DNA_bind: LexA D 53.5 22 0.00047 27.3 3.9 52 421-474 4-61 (65)
88 PF03965 Penicillinase_R: Peni 53.2 13 0.00029 31.8 3.0 38 513-550 20-57 (115)
89 COG4190 Predicted transcriptio 53.2 49 0.0011 29.1 6.3 65 425-491 66-133 (144)
90 cd07377 WHTH_GntR Winged helix 53.1 31 0.00068 25.5 4.8 39 433-473 20-59 (66)
91 smart00421 HTH_LUXR helix_turn 52.5 33 0.00071 24.4 4.7 39 422-462 5-43 (58)
92 PF10771 DUF2582: Protein of u 52.2 19 0.00042 27.6 3.3 38 426-463 11-48 (65)
93 cd06170 LuxR_C_like C-terminal 52.1 34 0.00073 24.4 4.7 38 422-461 2-39 (57)
94 PF14394 DUF4423: Domain of un 51.8 43 0.00094 31.1 6.3 57 416-474 17-76 (171)
95 PRK11169 leucine-responsive tr 50.8 27 0.00058 32.1 4.8 48 421-470 12-59 (164)
96 PRK00215 LexA repressor; Valid 50.5 39 0.00084 32.1 6.0 52 421-474 2-59 (205)
97 PRK10906 DNA-binding transcrip 49.9 28 0.00061 34.5 5.1 51 424-476 6-56 (252)
98 PRK11179 DNA-binding transcrip 49.5 34 0.00073 31.0 5.2 48 421-470 7-54 (153)
99 PF00325 Crp: Bacterial regula 49.0 24 0.00052 23.0 2.9 26 437-462 2-27 (32)
100 COG4189 Predicted transcriptio 48.5 31 0.00068 33.4 4.8 49 422-472 22-70 (308)
101 PRK09802 DNA-binding transcrip 48.4 29 0.00063 34.7 5.0 51 423-475 17-67 (269)
102 PF09012 FeoC: FeoC like trans 48.0 29 0.00063 26.7 3.9 34 429-462 6-39 (69)
103 TIGR00373 conserved hypothetic 46.8 40 0.00088 30.8 5.2 43 426-470 17-59 (158)
104 PF02796 HTH_7: Helix-turn-hel 46.6 36 0.00078 23.8 3.8 30 428-459 14-43 (45)
105 TIGR00498 lexA SOS regulatory 46.4 26 0.00057 33.1 4.2 51 421-473 4-60 (199)
106 PRK10411 DNA-binding transcrip 45.9 36 0.00078 33.4 5.1 48 424-473 5-52 (240)
107 PF12802 MarR_2: MarR family; 45.9 10 0.00022 28.2 1.0 27 523-549 30-56 (62)
108 COG1522 Lrp Transcriptional re 45.3 33 0.00072 30.7 4.5 49 421-471 6-54 (154)
109 KOG2747 Histone acetyltransfer 45.1 28 0.0006 36.6 4.2 83 366-462 262-354 (396)
110 PF13463 HTH_27: Winged helix 44.0 13 0.00028 28.2 1.3 28 520-547 24-51 (68)
111 PRK04172 pheS phenylalanyl-tRN 43.7 41 0.00089 36.8 5.6 51 420-472 3-53 (489)
112 TIGR02844 spore_III_D sporulat 43.4 42 0.00092 26.9 4.2 35 424-459 7-41 (80)
113 PF06784 UPF0240: Uncharacteri 43.0 39 0.00084 31.6 4.6 63 395-462 97-161 (179)
114 PRK06474 hypothetical protein; 41.8 82 0.0018 29.4 6.6 69 419-489 7-78 (178)
115 PF11994 DUF3489: Protein of u 41.6 63 0.0014 25.4 4.7 47 422-468 9-55 (72)
116 PLN03238 probable histone acet 41.4 43 0.00094 33.6 4.8 37 425-461 210-247 (290)
117 PRK04424 fatty acid biosynthes 41.1 29 0.00063 32.6 3.5 47 423-471 7-53 (185)
118 PF02270 TFIIF_beta: Transcrip 41.1 45 0.00097 33.5 5.0 57 424-490 217-273 (275)
119 PF01638 HxlR: HxlR-like helix 40.6 55 0.0012 26.6 4.7 44 426-472 8-52 (90)
120 cd06171 Sigma70_r4 Sigma70, re 39.8 65 0.0014 22.2 4.5 40 421-461 11-50 (55)
121 smart00345 HTH_GNTR helix_turn 39.2 22 0.00048 25.7 1.9 32 518-549 24-55 (60)
122 PF04967 HTH_10: HTH DNA bindi 39.0 46 0.001 24.4 3.5 31 431-461 17-47 (53)
123 PF00165 HTH_AraC: Bacterial r 38.7 45 0.00097 22.7 3.3 28 435-462 6-33 (42)
124 PF00196 GerE: Bacterial regul 38.7 54 0.0012 24.0 4.0 39 422-462 5-43 (58)
125 COG1318 Predicted transcriptio 38.3 47 0.001 30.6 4.1 50 391-461 36-85 (182)
126 PF09904 HTH_43: Winged helix- 37.5 71 0.0015 26.2 4.6 40 428-468 13-52 (90)
127 PRK11050 manganese transport r 37.3 85 0.0018 28.4 5.8 45 427-473 41-85 (152)
128 PF01978 TrmB: Sugar-specific 36.8 9.9 0.00022 29.1 -0.4 31 524-554 32-62 (68)
129 COG1654 BirA Biotin operon rep 36.7 1.1E+02 0.0024 24.5 5.6 42 430-471 12-53 (79)
130 PF12324 HTH_15: Helix-turn-he 36.7 95 0.0021 24.7 5.1 38 425-462 26-63 (77)
131 COG2996 Predicted RNA-bindinin 36.4 42 0.00092 33.3 3.8 38 432-473 243-280 (287)
132 COG5090 TFG2 Transcription ini 36.4 50 0.0011 31.8 4.1 36 427-462 199-234 (297)
133 PRK10681 DNA-binding transcrip 35.8 56 0.0012 32.3 4.7 39 424-462 8-46 (252)
134 KOG2905 Transcription initiati 35.7 52 0.0011 32.0 4.2 37 426-462 189-225 (254)
135 PF13384 HTH_23: Homeodomain-l 34.5 52 0.0011 23.1 3.2 32 428-461 10-41 (50)
136 PF13542 HTH_Tnp_ISL3: Helix-t 34.5 1E+02 0.0022 21.8 4.8 34 424-460 17-50 (52)
137 PF09860 DUF2087: Uncharacteri 33.9 48 0.001 26.0 3.1 14 537-550 52-65 (71)
138 PF09107 SelB-wing_3: Elongati 33.5 1.1E+02 0.0023 22.2 4.6 41 430-472 3-43 (50)
139 PLN00104 MYST -like histone ac 32.6 67 0.0014 34.5 4.8 35 427-461 363-398 (450)
140 PF01399 PCI: PCI domain; Int 32.3 92 0.002 25.4 4.9 40 424-463 47-86 (105)
141 TIGR01889 Staph_reg_Sar staphy 32.0 36 0.00079 28.8 2.3 29 523-551 52-82 (109)
142 PF03444 HrcA_DNA-bdg: Winged 32.0 1.7E+02 0.0036 23.4 5.8 48 424-473 10-57 (78)
143 PRK03902 manganese transport t 31.8 98 0.0021 27.5 5.2 44 427-472 12-55 (142)
144 COG3682 Predicted transcriptio 31.6 54 0.0012 28.6 3.3 47 501-551 15-61 (123)
145 smart00531 TFIIE Transcription 31.3 62 0.0014 29.1 3.9 30 434-463 12-41 (147)
146 PF00392 GntR: Bacterial regul 31.2 78 0.0017 23.7 3.9 38 434-473 20-58 (64)
147 PLN03239 histone acetyltransfe 31.1 74 0.0016 32.9 4.7 26 436-461 283-308 (351)
148 PF12108 SF3a60_bindingd: Spli 30.9 39 0.00085 21.4 1.7 14 299-312 3-16 (28)
149 smart00550 Zalpha Z-DNA-bindin 30.4 48 0.001 25.5 2.6 28 526-553 34-61 (68)
150 PRK09647 RNA polymerase sigma 30.4 74 0.0016 30.2 4.5 33 425-459 144-176 (203)
151 TIGR02989 Sig-70_gvs1 RNA poly 30.4 76 0.0017 28.3 4.4 37 421-459 112-149 (159)
152 TIGR00721 tfx DNA-binding prot 29.9 1E+02 0.0022 27.6 4.8 38 421-460 7-44 (137)
153 PF13545 HTH_Crp_2: Crp-like h 29.9 82 0.0018 24.2 3.9 34 437-472 28-61 (76)
154 PF10007 DUF2250: Uncharacteri 29.5 1.3E+02 0.0027 25.0 5.0 53 419-473 3-55 (92)
155 PF04182 B-block_TFIIIC: B-blo 29.4 1E+02 0.0022 24.2 4.3 49 423-473 2-52 (75)
156 TIGR02983 SigE-fam_strep RNA p 29.4 75 0.0016 28.5 4.2 40 421-461 111-150 (162)
157 PF05158 RNA_pol_Rpc34: RNA po 29.3 47 0.001 34.3 3.0 128 419-548 80-258 (327)
158 PRK10430 DNA-binding transcrip 29.2 1.4E+02 0.0031 28.7 6.4 49 421-471 159-210 (239)
159 PRK03573 transcriptional regul 29.1 40 0.00086 29.9 2.2 33 520-552 52-86 (144)
160 smart00753 PAM PCI/PINT associ 28.8 88 0.0019 24.9 4.1 30 433-462 20-49 (88)
161 smart00088 PINT motif in prote 28.8 88 0.0019 24.9 4.1 30 433-462 20-49 (88)
162 PF09681 Phage_rep_org_N: N-te 28.8 67 0.0014 28.0 3.4 51 420-472 26-86 (121)
163 PRK12529 RNA polymerase sigma 28.7 70 0.0015 29.5 3.9 38 421-459 128-165 (178)
164 PF00392 GntR: Bacterial regul 28.7 32 0.0007 25.9 1.3 32 518-549 28-59 (64)
165 PF13730 HTH_36: Helix-turn-he 28.6 38 0.00082 24.5 1.6 21 524-544 35-55 (55)
166 PF09114 MotA_activ: Transcrip 28.0 1.1E+02 0.0025 24.9 4.3 48 426-475 19-68 (96)
167 cd07377 WHTH_GntR Winged helix 27.7 46 0.001 24.5 2.1 31 519-549 30-60 (66)
168 PF04760 IF2_N: Translation in 27.5 44 0.00096 24.3 1.8 26 436-461 2-28 (54)
169 PRK08301 sporulation sigma fac 27.5 1E+02 0.0022 29.8 5.0 37 422-458 180-219 (234)
170 COG1321 TroR Mn-dependent tran 27.5 1.2E+02 0.0027 27.5 5.1 45 427-473 14-58 (154)
171 PHA02943 hypothetical protein; 27.1 1.1E+02 0.0024 27.7 4.5 54 428-488 16-69 (165)
172 COG4742 Predicted transcriptio 26.5 1.1E+02 0.0024 30.4 4.9 42 428-472 18-59 (260)
173 PRK12514 RNA polymerase sigma 26.4 84 0.0018 28.8 4.0 37 421-459 130-167 (179)
174 COG2512 Predicted membrane-ass 26.2 1E+02 0.0023 30.6 4.7 49 424-474 197-245 (258)
175 PRK00118 putative DNA-binding 26.2 1.1E+02 0.0025 25.8 4.3 25 436-460 32-56 (104)
176 PHA02591 hypothetical protein; 25.9 83 0.0018 25.0 3.1 25 436-460 58-82 (83)
177 PRK13239 alkylmercury lyase; P 25.8 1.4E+02 0.0029 28.7 5.2 39 424-462 23-61 (206)
178 PF14947 HTH_45: Winged helix- 25.7 1.6E+02 0.0035 23.1 4.9 43 426-471 9-51 (77)
179 PF04539 Sigma70_r3: Sigma-70 25.7 74 0.0016 24.8 3.0 26 436-461 19-44 (78)
180 PRK00135 scpB segregation and 25.7 5.7E+02 0.012 24.1 9.9 111 374-491 34-153 (188)
181 PF00356 LacI: Bacterial regul 25.6 85 0.0018 22.2 2.9 21 439-459 1-21 (46)
182 TIGR00122 birA_repr_reg BirA b 25.5 2E+02 0.0043 21.8 5.3 32 431-463 8-39 (69)
183 PRK12522 RNA polymerase sigma 25.3 1.1E+02 0.0024 27.9 4.5 33 425-459 125-157 (173)
184 TIGR02835 spore_sigmaE RNA pol 25.0 1.2E+02 0.0026 29.4 5.0 35 425-459 184-220 (234)
185 PRK14165 winged helix-turn-hel 25.0 1.4E+02 0.003 28.9 5.2 46 426-473 10-55 (217)
186 PRK09642 RNA polymerase sigma 24.9 1.1E+02 0.0025 27.2 4.5 37 421-459 107-144 (160)
187 PRK09639 RNA polymerase sigma 24.8 1.3E+02 0.0028 27.0 4.8 32 425-459 118-149 (166)
188 TIGR02698 CopY_TcrY copper tra 24.5 2.2E+02 0.0048 25.0 6.0 50 421-472 2-55 (130)
189 PRK03975 tfx putative transcri 24.5 1.4E+02 0.0031 26.8 4.8 37 420-458 6-42 (141)
190 smart00418 HTH_ARSR helix_turn 24.4 44 0.00095 24.2 1.4 26 524-549 20-45 (66)
191 PRK12525 RNA polymerase sigma 24.4 98 0.0021 28.1 4.0 33 424-458 123-155 (168)
192 PRK08295 RNA polymerase factor 24.1 97 0.0021 29.1 4.1 37 422-460 157-193 (208)
193 cd07153 Fur_like Ferric uptake 24.0 1.9E+02 0.0041 24.3 5.5 57 427-488 5-67 (116)
194 PHA03103 double-strand RNA-bin 24.0 1.7E+02 0.0037 27.4 5.4 44 428-473 18-61 (183)
195 PRK12547 RNA polymerase sigma 23.9 1.3E+02 0.0028 27.1 4.7 40 421-461 113-152 (164)
196 TIGR02404 trehalos_R_Bsub treh 23.7 47 0.001 32.1 1.8 32 518-549 28-59 (233)
197 PF13936 HTH_38: Helix-turn-he 23.3 1.5E+02 0.0033 20.5 3.9 24 436-459 19-42 (44)
198 PRK12536 RNA polymerase sigma 23.1 1.1E+02 0.0024 28.2 4.1 38 422-460 131-168 (181)
199 PRK12527 RNA polymerase sigma 22.9 1.2E+02 0.0026 27.0 4.3 38 421-459 106-143 (159)
200 PRK11512 DNA-binding transcrip 22.9 61 0.0013 28.8 2.2 29 523-551 63-93 (144)
201 PF08220 HTH_DeoR: DeoR-like h 22.8 58 0.0013 24.0 1.7 40 501-548 9-48 (57)
202 COG2771 CsgD DNA-binding HTH d 22.4 2.4E+02 0.0052 20.5 5.2 41 420-462 4-44 (65)
203 PRK15431 ferrous iron transpor 22.4 74 0.0016 25.4 2.2 33 518-550 20-52 (78)
204 TIGR02999 Sig-70_X6 RNA polyme 21.9 1.4E+02 0.0031 27.2 4.6 37 422-459 136-172 (183)
205 TIGR02392 rpoH_proteo alternat 21.8 1.5E+02 0.0033 29.5 5.0 30 427-456 226-255 (270)
206 PRK04217 hypothetical protein; 21.8 1.1E+02 0.0023 26.3 3.3 39 421-460 43-81 (110)
207 PF08784 RPA_C: Replication pr 21.8 96 0.0021 25.7 3.1 22 525-546 76-97 (102)
208 PRK09047 RNA polymerase factor 21.8 1.5E+02 0.0032 26.4 4.6 24 436-459 121-144 (161)
209 PRK04214 rbn ribonuclease BN/u 21.6 2E+02 0.0044 30.7 6.2 39 432-472 305-343 (412)
210 PRK13719 conjugal transfer tra 21.6 1.7E+02 0.0037 28.3 5.0 41 420-462 143-183 (217)
211 PRK13919 putative RNA polymera 21.6 1.4E+02 0.0029 27.5 4.4 38 421-459 136-173 (186)
212 PRK12530 RNA polymerase sigma 21.6 1.2E+02 0.0027 28.1 4.2 37 422-459 136-172 (189)
213 PRK12533 RNA polymerase sigma 21.4 1.2E+02 0.0025 29.2 4.0 38 422-460 136-173 (216)
214 PF05043 Mga: Mga helix-turn-h 21.2 1.4E+02 0.0031 23.7 3.9 29 434-462 27-55 (87)
215 PF01418 HTH_6: Helix-turn-hel 21.2 98 0.0021 24.3 2.9 34 428-461 25-58 (77)
216 COG1386 scpB Chromosome segreg 21.1 5.3E+02 0.011 24.2 8.1 107 429-548 15-137 (184)
217 COG1733 Predicted transcriptio 21.1 3E+02 0.0065 23.8 6.1 57 426-486 26-83 (120)
218 TIGR02394 rpoS_proteo RNA poly 20.9 1.5E+02 0.0032 29.8 4.8 35 425-459 228-264 (285)
219 PF06163 DUF977: Bacterial pro 20.8 2E+02 0.0044 25.2 4.8 48 423-472 12-59 (127)
220 PF13314 DUF4083: Domain of un 20.8 2.1E+02 0.0045 21.4 4.1 33 264-296 23-55 (58)
221 COG1846 MarR Transcriptional r 20.8 65 0.0014 27.0 1.9 31 519-549 41-71 (126)
222 PF04801 Sin_N: Sin-like prote 20.7 1.1E+02 0.0024 32.7 4.1 37 427-463 341-377 (421)
223 PRK06704 RNA polymerase factor 20.6 1.4E+02 0.0029 29.2 4.3 38 421-459 117-154 (228)
224 PRK11402 DNA-binding transcrip 20.6 59 0.0013 31.7 1.8 31 519-549 38-68 (241)
225 TIGR01714 phage_rep_org_N phag 20.5 1.2E+02 0.0026 26.4 3.4 50 421-472 27-84 (119)
226 PRK07037 extracytoplasmic-func 20.5 1.5E+02 0.0032 26.5 4.3 35 422-458 111-146 (163)
227 PF07638 Sigma70_ECF: ECF sigm 20.4 1.1E+02 0.0025 28.4 3.6 26 436-461 150-175 (185)
228 PRK10079 phosphonate metabolis 20.4 63 0.0014 31.5 1.9 32 518-549 39-70 (241)
229 smart00529 HTH_DTXR Helix-turn 20.1 76 0.0017 25.7 2.1 31 519-549 4-34 (96)
230 PRK12545 RNA polymerase sigma 20.1 1.4E+02 0.003 28.1 4.2 37 422-459 141-177 (201)
231 PRK12543 RNA polymerase sigma 20.1 1.4E+02 0.003 27.4 4.1 37 421-458 118-154 (179)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=8.5e-98 Score=814.95 Aligned_cols=539 Identities=55% Similarity=0.920 Sum_probs=496.9
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhcCCCCCCchh---------------------
Q 043775 4 RRLIEFDEGWEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQNTPNNNSAS--------------------- 62 (554)
Q Consensus 4 ~~~~~~e~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~~~~~~y~~~--------------------- 62 (554)
+.+.+++.+|+.+++|++++.+..++-+...++..+|+.+|+++|++|+++++..+++.
T Consensus 5 ~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~ 84 (725)
T KOG2166|consen 5 PKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPAL 84 (725)
T ss_pred ccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988764444568888899999999999999988443211
Q ss_pred -------------------------------------hccC-CCCcHHHHH-HHHHHHHHHH-HHHHHHHHHHHH----H
Q 043775 63 -------------------------------------CKRR-NIPGFDEFG-LACFRDLVYD-ALKHKAKDAVID----E 98 (554)
Q Consensus 63 -------------------------------------v~~~-~~~~i~~l~-l~~fr~~v~~-~i~~~l~~~ll~----e 98 (554)
|+++ +..++++++ |.+||..++. ++++++++++|. +
T Consensus 85 ~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~e 164 (725)
T KOG2166|consen 85 REKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHKE 164 (725)
T ss_pred HhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHhh
Confidence 5544 666777777 8888888887 599999999999 9
Q ss_pred hcCCccCHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHchhc
Q 043775 99 REREQVDRALLANVLDIFVE---------------HMLQDTSSYYSRISTNWILKDPCPDYMRKAEECLKKERDRVSRYL 163 (554)
Q Consensus 99 R~g~~id~~~lk~~i~m~~~---------------~fL~~t~~yY~~~s~~~i~~~~~~~Yl~~ve~~l~eE~~r~~~yL 163 (554)
|.|++||+..|+++++|+.+ +|+++|+.||..++.+|+...++++|+.+|+.++.+|.+|+..||
T Consensus 165 R~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl 244 (725)
T KOG2166|consen 165 REGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYL 244 (725)
T ss_pred cccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999874 999999999999999999988999999999999999999999999
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHHHHHHHHHhhhhhh-----------------------
Q 043775 164 QSNGEEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDLSRMYRFYRTIRAG----------------------- 220 (554)
Q Consensus 164 ~~~t~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~----------------------- 220 (554)
+..+.+++...++.+++..|.+.++++.++||..|+.+++.+||.+||+|+++++.|
T Consensus 245 ~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~ 324 (725)
T KOG2166|consen 245 HSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARP 324 (725)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999876
Q ss_pred -----------------HHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHhhccCCCCCCHH
Q 043775 221 -----------------PHDNYMEYVTNCFMDHSLFQRALKEAFKIFCNKTVGGFSSSEQLATFCDNILKKSGNEKLSDE 283 (554)
Q Consensus 221 -----------------l~~~~~~l~~~~F~~~~~f~~~l~~af~~~iN~~~~~~~~~e~la~y~D~~lkk~~~~~~~~~ 283 (554)
++++|..++..||++|..|.++++.||..|+|.+.. .+||+||+|||.+||++ .++.+++
T Consensus 325 ~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~lkk~-~k~~~e~ 401 (725)
T KOG2166|consen 325 AETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDILKKG-SKKLSDE 401 (725)
T ss_pred hhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHhccc-ccCCchh
Confidence 799999999999999999999999999999999962 23699999999999995 4778899
Q ss_pred HHHHHHHHHhhHhccccChHHHHHHHHHHHHHHhcCCCCh-------------------------------hhHHHHHHH
Q 043775 284 AIEETLEKVVKVLVYISDKDLFAEFYRKKLARRLLFDRSR-------------------------------TLARKNQTG 332 (554)
Q Consensus 284 e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~-------------------------------~~s~dl~~~ 332 (554)
+++..+++++.+|+|+.|||+|+.+|+++||||||+++|. .+|+|+++.
T Consensus 402 ~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~ 481 (725)
T KOG2166|consen 402 AIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTA 481 (725)
T ss_pred HHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHH
Confidence 9999999999999999999999999999999999999996 457889999
Q ss_pred HHHHHhhccCCCCCCceeEEeeccCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCceeEEeecCceEEEEEEE
Q 043775 333 FEKYLRYNKNAHAGIDLSVTVLATGFWPSYKSSDLNPIFNLPSQMIKCVEVFKRFYETKTKHRKLSWIYSLGQCHINAKF 412 (554)
Q Consensus 333 f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~ 412 (554)
|+++ . ......+++|.|.|||+|+||.+++.++ .||++|..+++.|..||.++|+||+|+|+|++|.|+|.++|
T Consensus 482 F~~~-~-~~~~~~~~df~v~VLt~g~WP~~~~~~~----~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~ 555 (725)
T KOG2166|consen 482 FADY-A-NYSANLGIDFTVTVLTTGFWPSYKSTDI----NLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKF 555 (725)
T ss_pred HHhh-h-chhccCCCceeEEEeecCCcCCccCCCC----CCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEe
Confidence 9887 2 2223457999999999999999877666 99999999999999999999999999999999999999999
Q ss_pred cCceEEEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCCC
Q 043775 413 ELKNIELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFTD 492 (554)
Q Consensus 413 ~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~ 492 (554)
.+++|+|+|||+||||||+||+.+.+|+++|.++|+++.+++.++|+||++.|.+++.+ |.++. +|++.|.+|.+|++
T Consensus 556 ~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~s 633 (725)
T KOG2166|consen 556 DKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTS 633 (725)
T ss_pred cCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccC
Confidence 99999999999999999999999999999999999999999999999999989777766 77777 89999999999999
Q ss_pred cccccc-----------------------------ccccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcc
Q 043775 493 RMRGSR-----------------------------SLSHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDY 543 (554)
Q Consensus 493 ~~~ki~-----------------------------RiMK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIerey 543 (554)
+.+||+ ||||+||.|.|++|+.||++|+++||.|+|.+||+|||.||||||
T Consensus 634 k~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeY 713 (725)
T KOG2166|consen 634 KMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREY 713 (725)
T ss_pred cceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHH
Confidence 999988 999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCC
Q 043775 544 LERYPENPNTF 554 (554)
Q Consensus 544 l~Rd~~d~~~y 554 (554)
|+|| +|+++|
T Consensus 714 leR~-~~~~~Y 723 (725)
T KOG2166|consen 714 LERD-ENPNIY 723 (725)
T ss_pred Hhcc-CCCCcc
Confidence 9999 899987
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.6e-92 Score=737.90 Aligned_cols=535 Identities=28% Similarity=0.468 Sum_probs=469.9
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhcCCCCCCch----h------------------
Q 043775 5 RLIEFDEGWEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQNTPNNNSA----S------------------ 62 (554)
Q Consensus 5 ~~~~~e~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~~~~~~y~~----~------------------ 62 (554)
...||+++|..++.||++|..-+..+ ++...||+.|+.+||+|+.+.+..-++ +
T Consensus 16 ~~~df~~~W~~i~~~I~~I~~~l~~~----m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k 91 (773)
T COG5647 16 SEEDFESTWEFIERAIGQIFERLYDS----MAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAK 91 (773)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHhh----hhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHH
Confidence 45799999999999999997555432 444459999999999999886653111 0
Q ss_pred -----------------------------------------------hc-----cCCCCcHHHHHHHHHHHHHHHHHHHH
Q 043775 63 -----------------------------------------------CK-----RRNIPGFDEFGLACFRDLVYDALKHK 90 (554)
Q Consensus 63 -----------------------------------------------v~-----~~~~~~i~~l~l~~fr~~v~~~i~~~ 90 (554)
|+ .....++++++|..|+..+|.++++.
T Consensus 92 ~~i~~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~~ 171 (773)
T COG5647 92 NYIEEYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVDS 171 (773)
T ss_pred HHHHHhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhHH
Confidence 55 34567899999999999999999999
Q ss_pred HHHHHHH----HhcCCccCHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHhhcCChhHHH
Q 043775 91 AKDAVID----EREREQVDRALLANVLDIFVE---------------------HMLQDTSSYYSRISTNWILKDPCPDYM 145 (554)
Q Consensus 91 l~~~ll~----eR~g~~id~~~lk~~i~m~~~---------------------~fL~~t~~yY~~~s~~~i~~~~~~~Yl 145 (554)
+++.||. .|.|+.||+..+..++.|+.+ .||+.|.+||..++.+.+..+++.+||
T Consensus 172 lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL 251 (773)
T COG5647 172 LINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYL 251 (773)
T ss_pred HHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHH
Confidence 9999999 899999999999988887765 999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHchhcCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHHHHHHHHHhhhhhh-----
Q 043775 146 RKAEECLKKERDRVSRYLQSNGEEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDLSRMYRFYRTIRAG----- 220 (554)
Q Consensus 146 ~~ve~~l~eE~~r~~~yL~~~t~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~----- 220 (554)
++|+.++++|..++..|++.+|..++..+++++||+.|.+.|.+.. ||+..+++....+.|+.||+++++++.|
T Consensus 252 ~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~ 330 (773)
T COG5647 252 EKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPLQ 330 (773)
T ss_pred HHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHH
Confidence 9999999999999999999999999999999999999999997754 8999999999999999999999988664
Q ss_pred -----------------------------------------------HHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhcC
Q 043775 221 -----------------------------------------------PHDNYMEYVTNCFMDHSLFQRALKEAFKIFCNK 253 (554)
Q Consensus 221 -----------------------------------------------l~~~~~~l~~~~F~~~~~f~~~l~~af~~~iN~ 253 (554)
.++.+..++.++|.+|..+..++++||+.|+|.
T Consensus 331 ~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~ 410 (773)
T COG5647 331 EVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFING 410 (773)
T ss_pred HHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhcc
Confidence 667778899999999999999999999999999
Q ss_pred CCC-CCChhhHHHHHHHHHhhccCCCCCCHHHHHHHHHHHhhHhccccChHHHHHHHHHHHHHHhcCCCCh---------
Q 043775 254 TVG-GFSSSEQLATFCDNILKKSGNEKLSDEAIEETLEKVVKVLVYISDKDLFAEFYRKKLARRLLFDRSR--------- 323 (554)
Q Consensus 254 ~~~-~~~~~e~la~y~D~~lkk~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~--------- 323 (554)
+.+ ...+||+||+|+|.+||+++ +......++..+..++.||+|+.+||+|+++|+++||||||+++|+
T Consensus 411 ~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mi 489 (773)
T COG5647 411 NESADSGPSEYLAKYIDGLLKKDG-KQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMI 489 (773)
T ss_pred ccccccccHHHHHHHhHHHhhccc-cccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHH
Confidence 642 24699999999999999976 3333456888899999999999999999999999999999999995
Q ss_pred ----------------------hhHHHHHHHHHHHHhhccCCCCCCceeEEeeccCCCCCCCCCCCCCCCCCcHHHHHHH
Q 043775 324 ----------------------TLARKNQTGFEKYLRYNKNAHAGIDLSVTVLATGFWPSYKSSDLNPIFNLPSQMIKCV 381 (554)
Q Consensus 324 ----------------------~~s~dl~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~~~~~lP~~l~~~~ 381 (554)
.+|.+++..|+..- ......+|+.|.||++.+||..|+. ..|.||++|.+.+
T Consensus 490 s~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~---~s~~~~~Dl~v~VLt~a~WP~sp~~---~~~~lP~~l~p~l 563 (773)
T COG5647 490 SMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSP---QSYNKYLDLFVWVLTQAYWPLSPEE---VSIRLPKELVPIL 563 (773)
T ss_pred HHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCc---hhhccccchhHHHHHHhcCCCCccc---cccCCChHHHHHH
Confidence 23344444443322 1123568999999999999976552 2349999999999
Q ss_pred HHHHHHHHhcCCCceeEEeecCceEEEEEEEcCceEEEE---ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 382 EVFKRFYETKTKHRKLSWIYSLGQCHINAKFELKNIELI---ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 382 ~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~~~~~~~l~---vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
+.|++||.+||+||+|.|.|+||+|+|+++|+.+++.+. ++++|+.|+++||+++++|++||.+.|+|+..+++++|
T Consensus 564 e~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L 643 (773)
T COG5647 564 EGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVL 643 (773)
T ss_pred HHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHH
Confidence 999999999999999999999999999999998764444 66789999999999999999999999999999999999
Q ss_pred HHhhhccceeeeecCCCCCCCCCCeEEEcccCCCcccccc---------------------------------ccccccc
Q 043775 459 HSLSILYYKILIKEPDTKSISRSDYFELNSKFTDRMRGSR---------------------------------SLSHHRK 505 (554)
Q Consensus 459 ~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~~ki~---------------------------------RiMK~~k 505 (554)
+||+++|..++.+ +++.++|++.|.+|++|+++..||+ ||||+||
T Consensus 644 ~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk 721 (773)
T COG5647 644 QSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARK 721 (773)
T ss_pred HHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999776555544 4788999999999999999999999 9999999
Q ss_pred cCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCCCCC
Q 043775 506 VLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENPNTF 554 (554)
Q Consensus 506 ~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~~~y 554 (554)
+|+|++|++||+.|.++||.|+|.+||++||.|||||||+|.++| ..|
T Consensus 722 ~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY 769 (773)
T COG5647 722 KLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIY 769 (773)
T ss_pred cCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-cee
Confidence 999999999999999999999999999999999999999999888 444
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.2e-89 Score=702.13 Aligned_cols=472 Identities=31% Similarity=0.527 Sum_probs=442.8
Q ss_pred CCCCcHHHHHHHHHHHHHHH----HHHHHHHHHHHH----HhcCCccCHHHHHHHHHHHHH----------HHHHHHHHH
Q 043775 66 RNIPGFDEFGLACFRDLVYD----ALKHKAKDAVID----EREREQVDRALLANVLDIFVE----------HMLQDTSSY 127 (554)
Q Consensus 66 ~~~~~i~~l~l~~fr~~v~~----~i~~~l~~~ll~----eR~g~~id~~~lk~~i~m~~~----------~fL~~t~~y 127 (554)
..++|+|+||+.+||.+++. ++..++.++++. +|.|+++|+++|++++.|+.+ .|++.++++
T Consensus 66 p~v~siWem~l~LFR~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~l 145 (661)
T KOG2167|consen 66 PYVLSIWEMGLQLFRAHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFREL 145 (661)
T ss_pred CCcCCHHHhhHHHHHHHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence 45789999999999999998 577788888888 899999999999999999875 999999999
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHchhcCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHH
Q 043775 128 YSRISTNWILKDPCPDYMRKAEECLKKERDRVSRYLQSNGEEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDL 207 (554)
Q Consensus 128 Y~~~s~~~i~~~~~~~Yl~~ve~~l~eE~~r~~~yL~~~t~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L 207 (554)
|..++..+.++..+++||++|+.++.+|.+|+..|++.+|..++..+++++||..|++.++.+ |+..+++.++..++
T Consensus 146 Y~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~ 222 (661)
T KOG2167|consen 146 YAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDL 222 (661)
T ss_pred HHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccch
Confidence 999999999999999999999999999999999999999977799999999999999999875 79999999999999
Q ss_pred HHHHHHHhhhhhh-----------------------------------HHHHHHHHHHhhcCCc--HHHHHHHHHHHHHH
Q 043775 208 SRMYRFYRTIRAG-----------------------------------PHDNYMEYVTNCFMDH--SLFQRALKEAFKIF 250 (554)
Q Consensus 208 ~~ly~L~~~~~~~-----------------------------------l~~~~~~l~~~~F~~~--~~f~~~l~~af~~~ 250 (554)
.+||.|++++.+| ++++.+-++..||..+ ..|..++++||+.|
T Consensus 223 ~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~f 302 (661)
T KOG2167|consen 223 TRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETF 302 (661)
T ss_pred HhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 9999999998654 8888899999999988 89999999999999
Q ss_pred hcCCCCCCChhhHHHHHHHHHhhccCCCCCCHHHHHHHHHHHhhHhccccChHHHHHHHHHHHHHHhcCCCCh-------
Q 043775 251 CNKTVGGFSSSEQLATFCDNILKKSGNEKLSDEAIEETLEKVVKVLVYISDKDLFAEFYRKKLARRLLFDRSR------- 323 (554)
Q Consensus 251 iN~~~~~~~~~e~la~y~D~~lkk~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~------- 323 (554)
+|+.+ +++||+||+|.|.+|+.|. ++.++++++..+++++.+||||..|||||.||++.||+|||.++|+
T Consensus 303 ink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ 379 (661)
T KOG2167|consen 303 INKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKS 379 (661)
T ss_pred Hhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhH
Confidence 99875 6899999999999999865 5667888999999999999999999999999999999999999998
Q ss_pred ------------------------hhHHHHHHHHHHHHhhccCCCCCCceeEEeeccCCCCCCCCCCCCCCCCCcHHHHH
Q 043775 324 ------------------------TLARKNQTGFEKYLRYNKNAHAGIDLSVTVLATGFWPSYKSSDLNPIFNLPSQMIK 379 (554)
Q Consensus 324 ------------------------~~s~dl~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~~~~~lP~~l~~ 379 (554)
.+|++++..|+.+..++.....++ +.+.|||.|+||++++.++ .||++|..
T Consensus 380 ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev----~Lp~em~~ 454 (661)
T KOG2167|consen 380 MLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEV----LLPKEMRD 454 (661)
T ss_pred HHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhc----cCCHHHHH
Confidence 457888889988866544434455 9999999999999999888 99999999
Q ss_pred HHHHHHHHHHhcCCCceeEEeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 380 CVEVFKRFYETKTKHRKLSWIYSLGQCHINAKFELKNIELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 380 ~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+++.|+.||.++|+||+|.|++.+|+|.|++.|+.|+.+++||.+|++||++||+.+.+|++||.++|+|.+.+|.|+|+
T Consensus 455 ~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlq 534 (661)
T KOG2167|consen 455 CQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQ 534 (661)
T ss_pred HHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhccceeeeecCCCCCCCCCCeEEEcccCCCcccccc---------------------------------cccccccc
Q 043775 460 SLSILYYKILIKEPDTKSISRSDYFELNSKFTDRMRGSR---------------------------------SLSHHRKV 506 (554)
Q Consensus 460 sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~~ki~---------------------------------RiMK~~k~ 506 (554)
||+|+|.++|.++|+|+.+.++|.|.+|.+|+.|..||| ||||+||+
T Consensus 535 sl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~ 614 (661)
T KOG2167|consen 535 SLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKT 614 (661)
T ss_pred HHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999988 99999999
Q ss_pred CChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCC
Q 043775 507 LGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENP 551 (554)
Q Consensus 507 l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~ 551 (554)
|+|+.|++|+.+||+ ||..+ ++|+|||+||+||||+||++|.
T Consensus 615 l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd~n~~ 656 (661)
T KOG2167|consen 615 LSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERDDNNI 656 (661)
T ss_pred hchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccccccc
Confidence 999999999999997 99999 9999999999999999995543
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.4e-84 Score=634.07 Aligned_cols=518 Identities=24% Similarity=0.447 Sum_probs=455.2
Q ss_pred cccccCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhcCCCCC----Cchh----------------
Q 043775 3 QRRLIEFDEGWEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQNTPNN----NSAS---------------- 62 (554)
Q Consensus 3 ~~~~~~~e~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~~~~~~----y~~~---------------- 62 (554)
.|++++||++|..|.+.|-.+... +..+...|-.-++.||.+|..-+.+. |.+.
T Consensus 5 kp~vv~fd~~w~~l~~si~~ii~l------~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v 78 (728)
T KOG2284|consen 5 KPKVVEFDKVWVQLRPSIIDIINL------RPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIV 78 (728)
T ss_pred CceeeeHHHHHHHHHHHHHHHHhc------cchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhh
Confidence 688999999999999988776432 34666779999999999999876543 4221
Q ss_pred ------------------------------------hccC------------------CCCcHHHHHHHHHHHHHHHHHH
Q 043775 63 ------------------------------------CKRR------------------NIPGFDEFGLACFRDLVYDALK 88 (554)
Q Consensus 63 ------------------------------------v~~~------------------~~~~i~~l~l~~fr~~v~~~i~ 88 (554)
|+.+ .+.+|-.+||.+||+.++.++.
T Consensus 79 ~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~i~ 158 (728)
T KOG2284|consen 79 DVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKTIL 158 (728)
T ss_pred cCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHHHH
Confidence 2222 3457888999999999999999
Q ss_pred HHHHHHHHH----HhcCCccC-HHHHHHHHHHHHH--------------------------------HHHHHHHHHHHHH
Q 043775 89 HKAKDAVID----EREREQVD-RALLANVLDIFVE--------------------------------HMLQDTSSYYSRI 131 (554)
Q Consensus 89 ~~l~~~ll~----eR~g~~id-~~~lk~~i~m~~~--------------------------------~fL~~t~~yY~~~ 131 (554)
..|+..+|. +|.|+..+ ...+.+++++|+. |||.+|..||+.+
T Consensus 159 ~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~ 238 (728)
T KOG2284|consen 159 PQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSAL 238 (728)
T ss_pred HHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHH
Confidence 999999888 99999766 5678888887763 9999999999999
Q ss_pred HHHHhhcCChhHHHHHHHHHHHHHHHHHchhcCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHHHHHH
Q 043775 132 STNWILKDPCPDYMRKAEECLKKERDRVSRYLQSNGEEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDLSRMY 211 (554)
Q Consensus 132 s~~~i~~~~~~~Yl~~ve~~l~eE~~r~~~yL~~~t~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly 211 (554)
|+..+.+.+|++||++|..++++|+-||..|||+++..+++..|++.+|..|.+.| +..|..++.+++..|++.||
T Consensus 239 a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~~nmy 314 (728)
T KOG2284|consen 239 AQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDLRNMY 314 (728)
T ss_pred HHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999887 45799999999999999999
Q ss_pred HHHhhhhhh--------------------------------------HHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhcC
Q 043775 212 RFYRTIRAG--------------------------------------PHDNYMEYVTNCFMDHSLFQRALKEAFKIFCNK 253 (554)
Q Consensus 212 ~L~~~~~~~--------------------------------------l~~~~~~l~~~~F~~~~~f~~~l~~af~~~iN~ 253 (554)
.|+..+..| +|.+|..++...|.+|..|..+++.|+..++|.
T Consensus 315 ~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~ 394 (728)
T KOG2284|consen 315 RLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNS 394 (728)
T ss_pred HHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhcc
Confidence 999877554 899999999999999999999999999999998
Q ss_pred CCC---CCChhhHHHHHHHHHhhccCCCCCCHHHHHHHHHHHhhHhccccChHHHHHHHHHHHHHHhcCCCChhhH-HHH
Q 043775 254 TVG---GFSSSEQLATFCDNILKKSGNEKLSDEAIEETLEKVVKVLVYISDKDLFAEFYRKKLARRLLFDRSRTLA-RKN 329 (554)
Q Consensus 254 ~~~---~~~~~e~la~y~D~~lkk~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~~s-~dl 329 (554)
..+ ..+.||.||+|||.+|||+. +++++.++|..|+..+.+|+|++|||+|++||.++||+||+.+.|.+|- .++
T Consensus 395 ~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~ 473 (728)
T KOG2284|consen 395 KEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEEL 473 (728)
T ss_pred CCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHH
Confidence 764 35799999999999999986 7899999999999999999999999999999999999999999987553 232
Q ss_pred -HHHHHHHHhhccCCCCCCceeEEeeccCCCCCCCC---CCC-------CCCCCCcHHHHHHHHHHHHHHHhcCCCceeE
Q 043775 330 -QTGFEKYLRYNKNAHAGIDLSVTVLATGFWPSYKS---SDL-------NPIFNLPSQMIKCVEVFKRFYETKTKHRKLS 398 (554)
Q Consensus 330 -~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~---~~~-------~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~ 398 (554)
.+..++.+ +.+| ++.||...+ .++ -.+|.+|.+|+..++.|+.||.++|+||+|+
T Consensus 474 minklkqac--------gyef------ts~~~~td~~~s~~lnn~f~~~i~nf~~pq~l~~~iq~fe~fyt~~~~grklt 539 (728)
T KOG2284|consen 474 MINKLKQAC--------GYEF------TSSWPLTDPQLSTNLNNQFAQDIANFHLPQILQPVIQEFEKFYTGKHNGRKLT 539 (728)
T ss_pred HHHHHHHHh--------Ccee------cccCCCCChhhccccchhHHHHHHhccchHHHHHHHHHHHHHhccccCCceeh
Confidence 23343333 3444 356885322 111 2468999999999999999999999999999
Q ss_pred EeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCC
Q 043775 399 WIYSLGQCHINAKFELKNIELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSI 478 (554)
Q Consensus 399 W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~ 478 (554)
|++.+++++|+.+|-++.|.-.|.+|||++||+||..+.+++.||.+.+|++.++|.+++.++. ..++|... +..+
T Consensus 540 wl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~til--dv~~~~~d--~~~~ 615 (728)
T KOG2284|consen 540 WLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCD--DQNL 615 (728)
T ss_pred hhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHH--hceeeccc--cccc
Confidence 9999999999999999999999999999999999999999999999999999999999999996 56677654 3467
Q ss_pred CCCCeEEEcccCCCcccccc----------------------------------ccccccccCChHHHHHHHHHHhccCC
Q 043775 479 SRSDYFELNSKFTDRMRGSR----------------------------------SLSHHRKVLGHQQLVSECIELLGRMF 524 (554)
Q Consensus 479 ~~~d~f~~N~~F~~~~~ki~----------------------------------RiMK~~k~l~~~~L~~ev~~~l~~~F 524 (554)
..+..|++|.+|+++..|.+ ||||+||.+.|+.|++||++|.+.||
T Consensus 616 ~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf 695 (728)
T KOG2284|consen 616 TADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRF 695 (728)
T ss_pred ChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccC
Confidence 77889999999999998877 99999999999999999999999999
Q ss_pred CCChHHHHHHHHhhhhhcccccCCC
Q 043775 525 KPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 525 ~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.|++++||+|||.||++.||+|.+.
T Consensus 696 ~p~v~~ikk~ie~li~k~yi~rt~~ 720 (728)
T KOG2284|consen 696 SPDVPFIKKSIEDLIEKMYIQRTDQ 720 (728)
T ss_pred CCCchHHHHHHHHHHHHHHHhhccc
Confidence 9999999999999999999999754
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-73 Score=565.39 Aligned_cols=534 Identities=26% Similarity=0.472 Sum_probs=472.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhc--CCCCC-C----------chh-----------
Q 043775 7 IEFDEGWEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQ--NTPNN-N----------SAS----------- 62 (554)
Q Consensus 7 ~~~e~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~--~~~~~-y----------~~~----------- 62 (554)
.-||+.|....+.+-++.+ +..+|+..|.+|+-.||..|.. ++|.. | ..+
T Consensus 11 ~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d 84 (777)
T KOG2285|consen 11 DQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTD 84 (777)
T ss_pred hhhhhhccccchHHHHHHh------hccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 4799999999999988754 2469999999999999999974 44431 1 000
Q ss_pred --------------------------------------hccC--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH----H
Q 043775 63 --------------------------------------CKRR--NIPGFDEFGLACFRDLVYDALKHKAKDAVID----E 98 (554)
Q Consensus 63 --------------------------------------v~~~--~~~~i~~l~l~~fr~~v~~~i~~~l~~~ll~----e 98 (554)
++.. .-.+|..+.|.-|.+++|..|+.+|...-+. |
T Consensus 85 ~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklVhaE 164 (777)
T KOG2285|consen 85 GALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLVHAE 164 (777)
T ss_pred cHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2222 2348999999999999999999999988777 9
Q ss_pred hcCCccCHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHc
Q 043775 99 REREQVDRALLANVLDIFVE------------------HMLQDTSSYYSRISTNWILKDPCPDYMRKAEECLKKERDRVS 160 (554)
Q Consensus 99 R~g~~id~~~lk~~i~m~~~------------------~fL~~t~~yY~~~s~~~i~~~~~~~Yl~~ve~~l~eE~~r~~ 160 (554)
|+|+.+|..++-++-++|+. .||++|.+||+..+.+++++.++.+||+.|..-+++|+.|+.
T Consensus 165 R~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAk 244 (777)
T KOG2285|consen 165 RDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAK 244 (777)
T ss_pred hccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHH
Confidence 99999999999888877764 999999999999999999999999999999999999999999
Q ss_pred hhcCc--ccHHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHHHHHHHHHhhhhhh------------------
Q 043775 161 RYLQS--NGEEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDLSRMYRFYRTIRAG------------------ 220 (554)
Q Consensus 161 ~yL~~--~t~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~------------------ 220 (554)
+||.+ .|..+++.++..+||.+|.+.|+. .|..|+...+.+.|++||+|..+++.|
T Consensus 245 RYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLa 320 (777)
T KOG2285|consen 245 RYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLA 320 (777)
T ss_pred HhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHH
Confidence 99977 678899999999999999999985 599999999999999999999999887
Q ss_pred ----------------------HHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhcCCC------------------CCCCh
Q 043775 221 ----------------------PHDNYMEYVTNCFMDHSLFQRALKEAFKIFCNKTV------------------GGFSS 260 (554)
Q Consensus 221 ----------------------l~~~~~~l~~~~F~~~~~f~~~l~~af~~~iN~~~------------------~~~~~ 260 (554)
++++|..+|.++|.+|+.|..|-+.||..++|... +..++
T Consensus 321 DM~~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKC 400 (777)
T KOG2285|consen 321 DMRNAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKC 400 (777)
T ss_pred HHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCccccc
Confidence 89999999999999999999999999999999864 12579
Q ss_pred hhHHHHHHHHHhhccC-CCCCCHHHHHHHHHHHhhHhccccChHHHHHHHHHHHHHHhcCCCCh----------------
Q 043775 261 SEQLATFCDNILKKSG-NEKLSDEAIEETLEKVVKVLVYISDKDLFAEFYRKKLARRLLFDRSR---------------- 323 (554)
Q Consensus 261 ~e~la~y~D~~lkk~~-~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~---------------- 323 (554)
||+||.|||.+||+.. +++++.+++++.|.+++-+++|+++||+|..|++.||.+||+.+.|+
T Consensus 401 pELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLREvG 480 (777)
T KOG2285|consen 401 PELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLREVG 480 (777)
T ss_pred HHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHcC
Confidence 9999999999999964 46788999999999999999999999999999999999999999987
Q ss_pred ----------------hhHHHHHHHHHHHHhhccCCCCCCceeEEeeccCCCCCCCC-CCCCCCCCCcHHHHHHHHHHHH
Q 043775 324 ----------------TLARKNQTGFEKYLRYNKNAHAGIDLSVTVLATGFWPSYKS-SDLNPIFNLPSQMIKCVEVFKR 386 (554)
Q Consensus 324 ----------------~~s~dl~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~~~~~lP~~l~~~~~~F~~ 386 (554)
.+|+|++.+|+..+......+..-.+++.||..|.|...+. ..+ .||.+|+..+-.-+.
T Consensus 481 MPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~v----SLP~ELED~iPdveE 556 (777)
T KOG2285|consen 481 MPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRV----SLPRELEDFIPDVEE 556 (777)
T ss_pred CcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEE----eCchhHHHhCccHHH
Confidence 45789999999988765544455678999999999987644 344 999999999999999
Q ss_pred HHHhcCCCceeEEeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhC--CCccCHHHHHHHhCCCHHHHHHHHHHhhh-
Q 043775 387 FYETKTKHRKLSWIYSLGQCHINAKFELKNIELIISTYHAAILDLFNA--SNRLSYSQVITQLNLTHDDLVRLLHSLSI- 463 (554)
Q Consensus 387 fY~~k~~~RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~- 463 (554)
||.++|+||+|.|.|+++.+.|.+.-+-|.|++.|+|+||+||.+||+ ++.+|++.+.-+|.+|+.+|.|+|.||+.
T Consensus 557 fykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAf 636 (777)
T KOG2285|consen 557 FYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAF 636 (777)
T ss_pred HHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhh
Confidence 999999999999999999999988766689999999999999999997 57999999999999999999999999985
Q ss_pred --ccceeeeecCC----CCCCCCCCeEEEcccCCC-------cccccc--------------------------------
Q 043775 464 --LYYKILIKEPD----TKSISRSDYFELNSKFTD-------RMRGSR-------------------------------- 498 (554)
Q Consensus 464 --~k~kiL~~~~~----~~~~~~~d~f~~N~~F~~-------~~~ki~-------------------------------- 498 (554)
.|..||..+|+ .+++.+++.|.+|.+|.- +.-||+
T Consensus 637 PK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaI 716 (777)
T KOG2285|consen 637 PKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAI 716 (777)
T ss_pred hhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHH
Confidence 25788888774 256777899999999962 122333
Q ss_pred -ccccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCCCCC
Q 043775 499 -SLSHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENPNTF 554 (554)
Q Consensus 499 -RiMK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~~~y 554 (554)
+|||.||+++..+|-.|.++.|+..|-|+..+||..||-|||..|++||++|.++|
T Consensus 717 ikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtF 773 (777)
T KOG2285|consen 717 IKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTF 773 (777)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccce
Confidence 89999999999999999999999999999999999999999999999999998875
No 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=3.4e-71 Score=615.75 Aligned_cols=453 Identities=36% Similarity=0.644 Sum_probs=380.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhcCCCC-CCchh-----------------------------
Q 043775 13 WEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQNTPN-NNSAS----------------------------- 62 (554)
Q Consensus 13 W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~~~~~-~y~~~----------------------------- 62 (554)
|+.|++||+.|. . ..++..+||++|++||++|.++.+. .|...
T Consensus 1 W~~l~~~i~~i~---~----~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~ 73 (588)
T PF00888_consen 1 WEILEEAIDQIF---K----KSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQ 73 (588)
T ss_dssp HHHHHHHHHHHH---T----T-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHH
T ss_pred ChHHHHHHHHHH---c----CCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHH
Confidence 999999999974 2 2467777999999999998877654 23221
Q ss_pred ------------------hccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH----HhcCCccCHHHHHHHHHHHHH--
Q 043775 63 ------------------CKRRNIPGFDEFGLACFRDLVYDALKHKAKDAVID----EREREQVDRALLANVLDIFVE-- 118 (554)
Q Consensus 63 ------------------v~~~~~~~i~~l~l~~fr~~v~~~i~~~l~~~ll~----eR~g~~id~~~lk~~i~m~~~-- 118 (554)
..++-+.. .+||+.|+.+++++++.+++. +|.|+.+|+.+++++++|+.+
T Consensus 74 ~w~~~~~~~~~i~~if~yLdr~yv~~------~~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~ 147 (588)
T PF00888_consen 74 EWEKYKKAIKYISDIFSYLDRNYVKR------NLFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELG 147 (588)
T ss_dssp HHHHHHHHHHHHHHHTHHHHHTSTTT------THHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHhHhhhhh------hhHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccc
Confidence 00000000 089999999999999999988 999999999999999999962
Q ss_pred -----------HHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHchhcCcccHHHHHHHHHHHHHHHHHHHH
Q 043775 119 -----------HMLQDTSSYYSRISTNWILKDPCPDYMRKAEECLKKERDRVSRYLQSNGEEKLVEKVQHELLVVYATQL 187 (554)
Q Consensus 119 -----------~fL~~t~~yY~~~s~~~i~~~~~~~Yl~~ve~~l~eE~~r~~~yL~~~t~~kl~~~~~~~Li~~~~~~l 187 (554)
+|+++|.+||+.++ ++..++.+||.+|+.++.+|.+|+..||+++|..++.++++++||..|.+.|
T Consensus 148 ~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l 224 (588)
T PF00888_consen 148 SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL 224 (588)
T ss_dssp HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH
T ss_pred hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999 6677999999999999999999999999999999999999999999999988
Q ss_pred HHhhhhhHhhhhccCChHHHHHHHHHHhhhhhh--------------------------------------HHHHHHHHH
Q 043775 188 LEKEQSGCGALFRGNKVDDLSRMYRFYRTIRAG--------------------------------------PHDNYMEYV 229 (554)
Q Consensus 188 l~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~--------------------------------------l~~~~~~l~ 229 (554)
.+|+..|+++++.++|++||+|++++++| ++++|+.++
T Consensus 225 ----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 225 ----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp ----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred ----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999998665 788999999
Q ss_pred HhhcCCcHHHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHhhccCCCCCCHHHHHHHHHHHhhHhccccChHHHHHHH
Q 043775 230 TNCFMDHSLFQRALKEAFKIFCNKTVGGFSSSEQLATFCDNILKKSGNEKLSDEAIEETLEKVVKVLVYISDKDLFAEFY 309 (554)
Q Consensus 230 ~~~F~~~~~f~~~l~~af~~~iN~~~~~~~~~e~la~y~D~~lkk~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y 309 (554)
..||++++.|..++++||+.++|.+. ..+|++||+|||.+|++++ ++.++++++..++.++.+|+|+++||+|+.+|
T Consensus 301 ~~~F~~~~~f~~~l~~af~~~~n~~~--~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y 377 (588)
T PF00888_consen 301 QECFDNDSEFKKALDEAFEEFLNKNN--NKIPELLAKYCDSLLRKSN-KKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYY 377 (588)
T ss_dssp HHTTTT-HHHHHHHHHHHHHHHHCST--SHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHH
T ss_pred HHhccccHHHHHHHHHhHHHHHHcCC--cchHHHHHHHhhHhhhhcc-cccchHHHHHHhhhhEEEeeecchhHHHHHHH
Confidence 99999999999999999999999983 6899999999999999976 56778899999999999999999999999999
Q ss_pred HHHHHHHhcCCCCh-------------------------------hhHHHHHHHHHHHHhhccCCC-CCCceeEEeeccC
Q 043775 310 RKKLARRLLFDRSR-------------------------------TLARKNQTGFEKYLRYNKNAH-AGIDLSVTVLATG 357 (554)
Q Consensus 310 ~~~LakRLL~~~s~-------------------------------~~s~dl~~~f~~~~~~~~~~~-~~~~~~~~VLt~~ 357 (554)
+++||+|||.+++. ..|+++++.|++.....+... .+++|++.||++|
T Consensus 378 ~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~ 457 (588)
T PF00888_consen 378 KKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKG 457 (588)
T ss_dssp HHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETT
T ss_pred HHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCC
Confidence 99999999998876 335666777877766543221 2789999999999
Q ss_pred CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCceeEEeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhCCCc
Q 043775 358 FWPSYKSSDLNPIFNLPSQMIKCVEVFKRFYETKTKHRKLSWIYSLGQCHINAKFELKNIELIISTYHAAILDLFNASNR 437 (554)
Q Consensus 358 ~WP~~~~~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~~~~ 437 (554)
+||..+... ++.||++|+.+++.|++||.++|+||+|+|+|++|+|+|++++++++++++||++||+||++||+.++
T Consensus 458 ~Wp~~~~~~---~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~ 534 (588)
T PF00888_consen 458 YWPKYPSEN---NIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDS 534 (588)
T ss_dssp TS-S-S-SS--------HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSE
T ss_pred CCCCCCCCc---cccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCC
Confidence 999987654 24999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCC
Q 043775 438 LSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFT 491 (554)
Q Consensus 438 lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~ 491 (554)
+|++||++.||+++++++++|.+|+..+..++.+.|++++++++|.|++|.+|+
T Consensus 535 ~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 535 LTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 999999999999999999999999754433333778889999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=99.91 E-value=3.4e-24 Score=194.02 Aligned_cols=110 Identities=40% Similarity=0.812 Sum_probs=96.4
Q ss_pred cccChHHHHHHHHHHHHHHhcCCCCh-------------------------------hhHHHHHHHHHHHHhhccCCCCC
Q 043775 298 YISDKDLFAEFYRKKLARRLLFDRSR-------------------------------TLARKNQTGFEKYLRYNKNAHAG 346 (554)
Q Consensus 298 ~l~~KD~F~~~Y~~~LakRLL~~~s~-------------------------------~~s~dl~~~f~~~~~~~~~~~~~ 346 (554)
|+++||+|+.+|+++||+|||..++. ..|+++++.|++++..+. ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 78999999999999999999999885 346777888887766432 2346
Q ss_pred CceeEEeeccCCCCCCCC-CCCCCCCCCcHHHHHHHHHHHHHHHhcCCCceeEEeecCceEEEEEEE
Q 043775 347 IDLSVTVLATGFWPSYKS-SDLNPIFNLPSQMIKCVEVFKRFYETKTKHRKLSWIYSLGQCHINAKF 412 (554)
Q Consensus 347 ~~~~~~VLt~~~WP~~~~-~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~ 412 (554)
++|+|.|||.++||..+. .. +.||++|+.+++.|++||..+|+||+|+|+|++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~----~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVE----INLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCc----eECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999876 44 499999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.86 E-value=1.3e-18 Score=183.71 Aligned_cols=192 Identities=25% Similarity=0.394 Sum_probs=161.9
Q ss_pred HhhHhccccChHHHHHHHHHHHHHHhcCCCCh-------------------------hh------HHHHHHHHHHHH-hh
Q 043775 292 VVKVLVYISDKDLFAEFYRKKLARRLLFDRSR-------------------------TL------ARKNQTGFEKYL-RY 339 (554)
Q Consensus 292 i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~-------------------------~~------s~dl~~~f~~~~-~~ 339 (554)
+-.+...+.+|+.|.+.||.+||.||+..... .| |+++.+.+++.. ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 34556667799999999999999999998876 12 445555665531 11
Q ss_pred cc-CCCCCCceeEEeeccCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCceeEEeecCceEEEEEEEcCceEE
Q 043775 340 NK-NAHAGIDLSVTVLATGFWPSYKSSDLNPIFNLPSQMIKCVEVFKRFYETKTKHRKLSWIYSLGQCHINAKFELKNIE 418 (554)
Q Consensus 340 ~~-~~~~~~~~~~~VLt~~~WP~~~~~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~~~~~~~~ 418 (554)
.+ ...+.+.+++.||++.+||......+ .||.+++..++.|.+-|.+-..+|+|.|.+++|.|+|.+.|.+.+.+
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~----~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~ 597 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAF----HLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLV 597 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccc----cCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEE
Confidence 11 12346788999999999998766555 99999999999999999999999999999999999999999999999
Q ss_pred EEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCCC
Q 043775 419 LIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFTD 492 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~ 492 (554)
++||+.||+|+++|.+.++||++|+++.+|||...+.|.|.-|. +.++|..+|. ++++.+|++++.=.+
T Consensus 598 ~tVsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d 666 (765)
T KOG2165|consen 598 LTVSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMD 666 (765)
T ss_pred EeeCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeecccccc
Confidence 99999999999999999999999999999999999999999996 6799988764 266788888885443
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.59 E-value=4.3e-16 Score=121.81 Aligned_cols=54 Identities=43% Similarity=0.746 Sum_probs=50.0
Q ss_pred ccccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCCC
Q 043775 499 SLSHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENPN 552 (554)
Q Consensus 499 RiMK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~~ 552 (554)
||||++|+++|++|+.+|.++++++|+|++.+||++||.||+||||+||++|+|
T Consensus 15 rimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 15 RIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred hhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 999999999999999999999999999999999999999999999999999986
No 10
>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=94.52 E-value=0.13 Score=42.81 Aligned_cols=65 Identities=12% Similarity=0.170 Sum_probs=52.8
Q ss_pred EEecHHHHHHHHHhh--------CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccC
Q 043775 419 LIISTYHAAILDLFN--------ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKF 490 (554)
Q Consensus 419 l~vs~~Q~~ILllFN--------~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F 490 (554)
..++.-|+.+|+..- ..+.+|-.||++.+|++.+.+.++|..|. +.++|.+..+ ...|++|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~~------~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQGM------MGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeecC------CceeecCCCc
Confidence 457888998888654 46789999999999999999999999995 6788876532 3678999876
Q ss_pred C
Q 043775 491 T 491 (554)
Q Consensus 491 ~ 491 (554)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 4
No 11
>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=94.30 E-value=0.079 Score=38.74 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=37.8
Q ss_pred HHHHHHhhCCC-ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 426 AAILDLFNASN-RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 426 ~~ILllFN~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+.||..|.+.+ .+|+.||++.+|+|...+.+.|..|. ..+.+.++|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecCc
Confidence 46888888765 48999999999999999999999996 567777653
No 12
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=93.73 E-value=0.24 Score=40.12 Aligned_cols=59 Identities=12% Similarity=0.197 Sum_probs=41.8
Q ss_pred HHHHHHHHhhCCCc-cCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEccc
Q 043775 424 YHAAILDLFNASNR-LSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSK 489 (554)
Q Consensus 424 ~Q~~ILllFN~~~~-lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~ 489 (554)
.++.+.+..+..+. +|.+||++.+++|+..+.+.++.|. +.+++...++ ++..|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~G-----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSRG-----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEETS-----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecCC-----CCCceeecCC
Confidence 34555555554443 9999999999999999999999995 6788875532 3456666543
No 13
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=93.49 E-value=0.19 Score=35.94 Aligned_cols=46 Identities=15% Similarity=0.330 Sum_probs=37.0
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceee
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKIL 469 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL 469 (554)
+..+..||....+++.+|..||++.+|++...+.++|..|. +.+++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~--~~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE--EKGLI 47 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCcCc
Confidence 45677888888888999999999999999999999999996 44544
No 14
>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=93.25 E-value=0.16 Score=38.31 Aligned_cols=51 Identities=14% Similarity=0.258 Sum_probs=43.1
Q ss_pred ecHHHHHHHHHhhCCCc--cCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFNASNR--LSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~--lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+|+.|+.||......+. +|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 47789999988877766 9999999999999999999999996 567887764
No 15
>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=92.24 E-value=0.29 Score=36.59 Aligned_cols=48 Identities=15% Similarity=0.301 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
|..|+...++++.+|++||++.+|+++..+.+-|..|. +.+++.+.-+
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEcC
Confidence 45678888899999999999999999999999999996 5567766543
No 16
>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=91.04 E-value=0.24 Score=37.00 Aligned_cols=51 Identities=14% Similarity=0.332 Sum_probs=43.6
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+|..|+.||....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 367899999988888889999999999999999999999996 567887653
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=90.78 E-value=0.47 Score=36.35 Aligned_cols=51 Identities=14% Similarity=0.280 Sum_probs=39.4
Q ss_pred ecHHHHHHHHHhh-CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFN-ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN-~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+|..|..||.... ....++..+|++.++++...+.+.|..|. ..+++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~--~~glv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLE--EKGLVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEecC
Confidence 3677899999888 78899999999999999999999999996 457886653
No 18
>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=90.77 E-value=0.45 Score=35.96 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=40.8
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
++.-..||.++...+.+|+.||++.+|++...+.++|..|. +.+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 45566788888778899999999999999999999999995 57787654
No 19
>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=90.13 E-value=0.68 Score=40.03 Aligned_cols=52 Identities=13% Similarity=0.217 Sum_probs=46.4
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.++..|..||.....++.+|..+|++.++++...+-+.+..|. +.+++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 4588899999988888899999999999999999999999996 678888765
No 20
>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=88.75 E-value=1.3 Score=31.52 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=34.1
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
..-||.+.-+ ...++.||++.+|++...+.++|..|. +.+++.
T Consensus 4 R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 4556666666 679999999999999999999999995 556654
No 21
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=88.50 E-value=1.1 Score=40.29 Aligned_cols=53 Identities=17% Similarity=0.187 Sum_probs=46.3
Q ss_pred EEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 419 LIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..++..|+.||......+.+|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 35678899999877777889999999999999999999999995 778888775
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.21 E-value=1.1 Score=34.74 Aligned_cols=48 Identities=23% Similarity=0.282 Sum_probs=39.3
Q ss_pred HHHHHHHHhhCCCc--cCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 424 YHAAILDLFNASNR--LSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 424 ~Q~~ILllFN~~~~--lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..-.||.++.+... +|..||++.+|++...+.++|..|. +.+.+.+.+
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 44567777777765 9999999999999999999999995 567776643
No 23
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.43 E-value=1.9 Score=35.03 Aligned_cols=46 Identities=20% Similarity=0.316 Sum_probs=38.7
Q ss_pred HHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 426 AAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 426 ~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..||..+... +.+|+.||++.+|++...+.+.|..|. +.++|.+.+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 4567777766 689999999999999999999999996 568887654
No 24
>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=85.45 E-value=2.4 Score=36.09 Aligned_cols=53 Identities=23% Similarity=0.330 Sum_probs=44.6
Q ss_pred EecHHHHHHHHHhh----CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 420 IISTYHAAILDLFN----ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 420 ~vs~~Q~~ILllFN----~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
.+|..|..||.... ..+.+|..+|++.++++...+.+.+..|. +.+.+.+.+.
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~~ 78 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKERS 78 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccCC
Confidence 46888888887655 55789999999999999999999999996 6788887653
No 25
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=85.15 E-value=2 Score=35.32 Aligned_cols=54 Identities=19% Similarity=0.309 Sum_probs=46.6
Q ss_pred EEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 418 ELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 418 ~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
++.++..+..||......+.+|..+|++.++++...+.++|..|. +.+++.+..
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~~ 58 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRLP 58 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEecC
Confidence 356788899999988888889999999999999999999999996 567887653
No 26
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=84.46 E-value=2.5 Score=30.08 Aligned_cols=45 Identities=20% Similarity=0.304 Sum_probs=36.1
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
-.|+..+.....+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~--~~g~i~~~ 47 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLE--EQGLLTRV 47 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 3466666666789999999999999999999999996 44666554
No 27
>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=84.45 E-value=2.3 Score=31.13 Aligned_cols=36 Identities=17% Similarity=0.370 Sum_probs=29.0
Q ss_pred HHHHHh-hCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 427 AILDLF-NASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 427 ~ILllF-N~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
-||.++ +..+.+|.++|++.+|++...+.+.|..|.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344444 666679999999999999999999999995
No 28
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=84.13 E-value=3.7 Score=34.53 Aligned_cols=61 Identities=23% Similarity=0.321 Sum_probs=45.8
Q ss_pred EecHHHHHHHHH-------hhC-CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccC
Q 043775 420 IISTYHAAILDL-------FNA-SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKF 490 (554)
Q Consensus 420 ~vs~~Q~~ILll-------FN~-~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F 490 (554)
.+|.-|.-|++. ||. .+.+|..++++.||++...+.+++..|. +.++|...+ ..+.+|.+.
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~g--------~~~G~N~~i 97 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRDG--------KRIGVNKNI 97 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC--------cEEeeeccc
Confidence 345556666654 554 4689999999999999999999999996 778997652 455566554
No 29
>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=83.70 E-value=1.3 Score=34.16 Aligned_cols=51 Identities=16% Similarity=0.221 Sum_probs=41.0
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.|-.++-|+...-..+..|..||++.+|++...+.+.|..|. +.+++.+.+
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~--~~GlV~~~~ 56 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE--EKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 345566666655577889999999999999999999999996 567777654
No 30
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=83.38 E-value=3.9 Score=37.77 Aligned_cols=46 Identities=11% Similarity=0.132 Sum_probs=37.4
Q ss_pred HHHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 425 HAAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 425 Q~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+++.+.|+.. ..+|.++|++.+++|...+.+.|+.|. +.+++...
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~ 58 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSV 58 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC
Confidence 34455567654 579999999999999999999999995 67888753
No 31
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=83.06 E-value=3.6 Score=31.31 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=36.1
Q ss_pred HHHHhhC-CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCC
Q 043775 428 ILDLFNA-SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTK 476 (554)
Q Consensus 428 ILllFN~-~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~ 476 (554)
||-.++. +..+|..||++.+|++.....+.|..|. +.+.+.+.|.++
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~r 52 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRR 52 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SS
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCC
Confidence 4555666 7789999999999999999999999996 667777766544
No 32
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=83.03 E-value=4 Score=37.18 Aligned_cols=45 Identities=9% Similarity=0.042 Sum_probs=36.4
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+++.|..+..+.+|..+|++..++|...|.+.|+.|. +.+++...
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~ 57 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETV 57 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEee
Confidence 3344555655678999999999999999999999995 77888754
No 33
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=82.89 E-value=1.5 Score=35.24 Aligned_cols=45 Identities=27% Similarity=0.344 Sum_probs=34.8
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
...||...+..+.+++.+|.+.+|+++..+-++|..|. +.+.+..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le--~~GyV~~ 46 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLE--EAGYVEV 46 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEE
Confidence 34566666778899999999999999999999999996 4555553
No 34
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=82.59 E-value=3.1 Score=41.29 Aligned_cols=47 Identities=11% Similarity=0.265 Sum_probs=41.0
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
-+.||.+|.....+|+.||++.+|+|...+.+.|..|. ..+.|.+.+
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~ 62 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEG 62 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 35688899887889999999999999999999999996 567887764
No 35
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=81.60 E-value=3.6 Score=38.74 Aligned_cols=53 Identities=11% Similarity=-0.052 Sum_probs=46.7
Q ss_pred EEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 419 LIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+.++..|..||.....++.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEecC
Confidence 45678899999999988999999999999999999999999995 668888764
No 36
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=80.31 E-value=3.6 Score=36.75 Aligned_cols=53 Identities=19% Similarity=0.228 Sum_probs=45.0
Q ss_pred EEecHHHHHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 419 LIISTYHAAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+.++..|..||...... +.+|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeec
Confidence 45788899888877654 578999999999999999999999995 678888765
No 37
>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=80.10 E-value=5.4 Score=35.38 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=35.5
Q ss_pred HHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 426 AAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 426 ~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
+++.|.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3444555543 479999999999999999999999995 6788864
No 38
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=79.24 E-value=5.5 Score=31.15 Aligned_cols=46 Identities=11% Similarity=0.185 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 423 TYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 423 ~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+|.+ |+..... .+|++||.+.||++...|...|.-|+ +.+++.+.
T Consensus 6 ~~~~I-L~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQKI-LIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred HHHHH-HHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 34443 3333333 89999999999999999999999996 67787754
No 39
>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=78.82 E-value=3.7 Score=39.25 Aligned_cols=52 Identities=15% Similarity=0.204 Sum_probs=46.1
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.++..|..||..+.+++.++..||++.+|++...+.++|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 4678899999999888889999999999999999999999996 568888764
No 40
>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=78.09 E-value=1.3 Score=34.31 Aligned_cols=43 Identities=21% Similarity=0.309 Sum_probs=31.2
Q ss_pred ccccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 499 SLSHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 499 RiMK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.+|+.++.++.+||- .+|..+++.+..-++.|+.+|||++.+.
T Consensus 7 ~~l~~~~~~S~~eLa--------~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 7 DYLRERGRVSLAELA--------REFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHS-SEEHHHHH--------HHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHcCCcCHHHHH--------HHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 445666666665554 4589999999999999999999998654
No 41
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=77.31 E-value=2.9 Score=32.89 Aligned_cols=41 Identities=15% Similarity=0.073 Sum_probs=30.9
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
++.++...+.+|+.||++.+|++...++..+..+. +.++|.
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 33333444688999999999999999999988764 445554
No 42
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=76.80 E-value=4.7 Score=35.30 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=34.0
Q ss_pred hCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 433 NASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 433 N~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+.++.+|+++|++.++.+...+.++|+.|. ..+++.++
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Re 75 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVERE 75 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeee
Confidence 367899999999999999999999999996 57888875
No 43
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=76.62 E-value=4.8 Score=28.01 Aligned_cols=35 Identities=29% Similarity=0.506 Sum_probs=26.9
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
.||-........++.+|++.+|++...+.+-+.-|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46667777789999999999999999998877655
No 44
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=76.19 E-value=5.8 Score=28.98 Aligned_cols=40 Identities=18% Similarity=0.332 Sum_probs=33.3
Q ss_pred hhCCCcc-CHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 432 FNASNRL-SYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 432 FN~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 4455667 999999999999999999999996 567877654
No 45
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=76.06 E-value=7.6 Score=35.24 Aligned_cols=46 Identities=11% Similarity=0.129 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCC-ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 425 HAAILDLFNASN-RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 425 Q~~ILllFN~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++...
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~ 58 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSV 58 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEee
Confidence 444555555554 58899999999999999999999995 78888765
No 46
>PRK10870 transcriptional repressor MprA; Provisional
Probab=75.76 E-value=7.6 Score=36.21 Aligned_cols=53 Identities=11% Similarity=0.087 Sum_probs=43.8
Q ss_pred EecHHHHHHHHHhhC--CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 420 IISTYHAAILDLFNA--SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
.+|..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+.
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~~ 106 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRES 106 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecCC
Confidence 356778888877654 4579999999999999999999999996 6788887653
No 47
>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=75.63 E-value=4.2 Score=37.56 Aligned_cols=49 Identities=14% Similarity=0.221 Sum_probs=40.9
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCCCcc
Q 043775 437 RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFTDRM 494 (554)
Q Consensus 437 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~ 494 (554)
.+|..+|++.+|++...+.+++..|. +.++|.+.. ...|.+|++|.-+-
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG 123 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKG 123 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeC
Confidence 47899999999999999999999996 568888763 45899999976443
No 48
>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=75.25 E-value=8.2 Score=29.33 Aligned_cols=48 Identities=21% Similarity=0.272 Sum_probs=39.0
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|. ..+++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLE--EAGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEEE
Confidence 345777887777766 9999999999999999999999995 45666654
No 49
>PHA00738 putative HTH transcription regulator
Probab=75.12 E-value=8.1 Score=32.74 Aligned_cols=67 Identities=19% Similarity=0.186 Sum_probs=49.2
Q ss_pred EEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccC
Q 043775 418 ELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKF 490 (554)
Q Consensus 418 ~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F 490 (554)
++...+.=-.||.+..+.+.+++.+|++.++|+...+-++|.-|- ..+|+.....|+. -.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~----vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRT----LYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCE----EEEEECCCc
Confidence 344555555667666677789999999999999999999999995 5788886654432 345666554
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.66 E-value=8.2 Score=26.85 Aligned_cols=34 Identities=24% Similarity=0.359 Sum_probs=29.7
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 437 RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 437 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 47899999999999999999999996 56788654
No 51
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=73.21 E-value=5.7 Score=29.76 Aligned_cols=38 Identities=13% Similarity=0.345 Sum_probs=30.0
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
|.-+|-++-+.+.+|++||++.+|++...++.-+.-|-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566555448899999999999999999999888773
No 52
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=73.06 E-value=6.7 Score=38.72 Aligned_cols=47 Identities=30% Similarity=0.472 Sum_probs=40.6
Q ss_pred HHHHHHhhCCCc-cCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 426 AAILDLFNASNR-LSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 426 ~~ILllFN~~~~-lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
+.||.+|...+. +++.||++.+|+|...+.+.|..|. ..+.+.+.+.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~~ 54 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDPE 54 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcCC
Confidence 468889987654 7899999999999999999999996 6788988764
No 53
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=72.03 E-value=6.9 Score=39.19 Aligned_cols=47 Identities=26% Similarity=0.312 Sum_probs=39.9
Q ss_pred HHHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 425 HAAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 425 Q~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
-..||.+|... ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 35688899865 579999999999999999999999996 567887754
No 54
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=71.16 E-value=6.6 Score=39.13 Aligned_cols=47 Identities=15% Similarity=0.166 Sum_probs=39.5
Q ss_pred HHHHHHhhCCC-ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 426 AAILDLFNASN-RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 426 ~~ILllFN~~~-~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
+.||.+|.+.+ .+|..||++.+|++...+.+.|..|. ..+.|.+.+.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~~ 61 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSAS 61 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecC
Confidence 45788887654 59999999999999999999999996 5688877653
No 55
>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=71.04 E-value=8.2 Score=32.33 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=37.4
Q ss_pred EecHHHHHHHHHhhC----CCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 420 IISTYHAAILDLFNA----SNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~----~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
.++..|-.||-.+.+ .+.+++++|++.++++..+++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 678899999998887 46799999999999999999999999974
No 56
>PRK11569 transcriptional repressor IclR; Provisional
Probab=70.74 E-value=8.1 Score=38.77 Aligned_cols=47 Identities=15% Similarity=0.223 Sum_probs=39.9
Q ss_pred HHHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 425 HAAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 425 Q~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
-..||.+|.+. ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 45688899874 579999999999999999999999996 567887754
No 57
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=69.81 E-value=19 Score=32.91 Aligned_cols=48 Identities=21% Similarity=0.362 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhcCCCCC
Q 043775 7 IEFDEGWEYIQKGIGKLKRILEGLREPPFSSEEYMALHITIYNMCSQNTPNN 58 (554)
Q Consensus 7 ~~~e~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vY~~c~~~~~~~ 58 (554)
...++.|..+..++-.+ ++|+.-. .+-++.-++-+.--..|+++.+..
T Consensus 3 ~~~~~~W~~~~~~vl~l---F~g~~l~-~~iEdlN~lv~~~i~~~~~~~~~~ 50 (158)
T PF08539_consen 3 MSSDDAWNSLCAKVLPL---FQGERLR-LPIEDLNELVRFHIKLCIQSFPPS 50 (158)
T ss_pred CchhhhHHHHHHHHHHH---HcCCCCC-cCHHHHHHHHHHHHHHhhcccchH
Confidence 46789999999998886 4555433 666666666666667788876543
No 58
>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=69.67 E-value=11 Score=37.00 Aligned_cols=45 Identities=24% Similarity=0.352 Sum_probs=38.2
Q ss_pred HHHHHHhhC-CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 426 AAILDLFNA-SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 426 ~~ILllFN~-~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+.||.+|.. ...+|+.||++.+|+|...+.+.|.+|. ..+.|.+.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~--~~G~l~~~ 57 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV--ELGYVTSD 57 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC
Confidence 468889986 5679999999999999999999999996 45677653
No 59
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=69.62 E-value=9.6 Score=32.07 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=38.2
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
..-.||..+.....+|+.+|++.+|++...+.+.+..|. +.+++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCee
Confidence 345678888888899999999999999999999999996 456665
No 60
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=69.18 E-value=1.7e+02 Score=32.49 Aligned_cols=46 Identities=13% Similarity=0.200 Sum_probs=34.2
Q ss_pred HHHHHHHHHHH---------HHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 043775 108 LLANVLDIFVE---------HMLQDTSSYYSRISTNWILKDPCPDYMRKAEECLKKE 155 (554)
Q Consensus 108 ~lk~~i~m~~~---------~fL~~t~~yY~~~s~~~i~~~~~~~Yl~~ve~~l~eE 155 (554)
..|+-++|..+ +|+..++++|..+++ .+...+.+|+.+....+-.+
T Consensus 270 ~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 270 DFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred HHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 35555665543 899999999999888 45667889999987755444
No 61
>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=68.94 E-value=14 Score=32.39 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=35.2
Q ss_pred HHHHHHHhhCC-CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 425 HAAILDLFNAS-NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 425 Q~~ILllFN~~-~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
++++.+.-++. ..+|.++|++.+++|...+.+.|..|. +.++|...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 34444443433 379999999999999999999999996 56777653
No 62
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=68.70 E-value=13 Score=32.22 Aligned_cols=57 Identities=21% Similarity=0.257 Sum_probs=42.6
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcc
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNS 488 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~ 488 (554)
..||.+.-+.++.++.||++.++++...+-+||.-|. ..+++.....|+ .-.|.+|.
T Consensus 19 l~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 19 LGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 3455444445679999999999999999999999995 578888765443 23567765
No 63
>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=68.08 E-value=14 Score=32.39 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=36.1
Q ss_pred HHHHHHHhh--CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 425 HAAILDLFN--ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 425 Q~~ILllFN--~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
-..+|..+. ..+.+|+.||++.+|+|...+.+.|..|. +.+++...
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 334555554 34579999999999999999999999996 67888653
No 64
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=67.99 E-value=12 Score=27.37 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=31.1
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 435 SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 435 ~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+..|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 5678999999999999999999999996 45777654
No 65
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=67.79 E-value=12 Score=31.56 Aligned_cols=51 Identities=14% Similarity=0.230 Sum_probs=44.3
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+++.|..||......+..+..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 788899999888877776669999999999999999999996 678887764
No 66
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=64.08 E-value=18 Score=25.78 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=24.7
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+|-+.| .+.+|++||++.+|++...+.+...
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34455666 5678999999999999998877554
No 67
>PF13730 HTH_36: Helix-turn-helix domain
Probab=63.97 E-value=18 Score=26.26 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=22.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 439 SYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 439 t~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
|.+.|++.+|++...+.+++..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999995
No 68
>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=63.77 E-value=19 Score=27.12 Aligned_cols=45 Identities=18% Similarity=0.305 Sum_probs=35.9
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+|..+-.+...++..+|++.+|+++..+...+.-|. +.+++...|
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 344455577899999999999999999999999996 567777654
No 69
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=63.12 E-value=11 Score=37.44 Aligned_cols=50 Identities=18% Similarity=0.186 Sum_probs=43.4
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDT 475 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~ 475 (554)
-|..||-+.+.++.+++.||++.+|++...++|-|..|. +.++|.+..+|
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~Gg 55 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTYGG 55 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEECC
Confidence 467889999999999999999999999999999999995 66777776544
No 70
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=62.64 E-value=27 Score=32.88 Aligned_cols=108 Identities=14% Similarity=0.187 Sum_probs=62.8
Q ss_pred HHhhCCCc-cCHHHHHHHhCCC-HHHHHHHHHHhhhc----cceeeeecCCCCCCCCCCeEEEcccCCCccccccccccc
Q 043775 430 DLFNASNR-LSYSQVITQLNLT-HDDLVRLLHSLSIL----YYKILIKEPDTKSISRSDYFELNSKFTDRMRGSRSLSHH 503 (554)
Q Consensus 430 llFN~~~~-lt~~ei~~~t~i~-~~~l~~~L~sL~~~----k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~~ki~RiMK~ 503 (554)
++|-..+. +|.++|++.++++ .+.+...+.-|..- ..++-... +..+=.|..+..|.+-.. +.+..
T Consensus 9 lLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~-----~~~~y~l~tk~e~~~~i~---~~~~~ 80 (186)
T TIGR00281 9 LLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIK-----FGQSYSLVTKPAFADYIH---RFLPA 80 (186)
T ss_pred HHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEE-----ECCEEEEEEhHHHHHHHH---HHhcc
Confidence 56777787 9999999999998 45666666666321 01122111 111233444555554333 33332
Q ss_pred -cccCChHHHHHHHHHHhccCCCCChHHHH--------HHHHhhhhhcccccC
Q 043775 504 -RKVLGHQQLVSECIELLGRMFKPAVKAFK--------KRIEGLISQDYLERY 547 (554)
Q Consensus 504 -~k~l~~~~L~~ev~~~l~~~F~~~~~~iK--------~~Ie~LIereyl~Rd 547 (554)
+++|+...| ||...+.=+=|.+...|. ..|..|++||.|+..
T Consensus 81 ~~~~LS~aaL--EtLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~ergLI~~~ 131 (186)
T TIGR00281 81 KLKNLNSASL--EVLAIIAYKQPITRARINEIRGVKSYQIVDDLVEKGLVVEL 131 (186)
T ss_pred ccccCCHHHH--HHHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHHCCCeEec
Confidence 233777777 444444323455555554 569999999999865
No 71
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=61.81 E-value=14 Score=28.02 Aligned_cols=34 Identities=15% Similarity=0.312 Sum_probs=26.6
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceee
Q 043775 434 ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKIL 469 (554)
Q Consensus 434 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL 469 (554)
....+|+.+|...|++|...++..|..|. +.+++
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v 57 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLV 57 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCe
Confidence 35689999999999999999999999996 55555
No 72
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=61.48 E-value=26 Score=31.19 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=33.7
Q ss_pred hhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 432 FNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 432 FN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+.....+|..+|++..|+|...+.++|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 4445578999999999999999999999995 678887654
No 73
>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=61.15 E-value=16 Score=27.52 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=31.5
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..+|..+|++.+|++...+.+.|..|. +.+++...+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 469999999999999999999999996 567887654
No 74
>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=60.26 E-value=15 Score=28.19 Aligned_cols=25 Identities=16% Similarity=0.464 Sum_probs=20.3
Q ss_pred ChHHHHHHHHhhhhhcccccCCCCC
Q 043775 527 AVKAFKKRIEGLISQDYLERYPENP 551 (554)
Q Consensus 527 ~~~~iK~~Ie~LIereyl~Rd~~d~ 551 (554)
++.-+..-++.|.++|||+|+++-+
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 3556678899999999999998644
No 75
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.65 E-value=14 Score=35.74 Aligned_cols=44 Identities=20% Similarity=0.267 Sum_probs=36.5
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
..||.+.+..+..|.+||++.+||+...+++||..|. .-+++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le--~~Glv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLE--AEGLVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHH--hCcceee
Confidence 3467777788899999999999999999999999996 3455543
No 76
>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=59.48 E-value=26 Score=33.41 Aligned_cols=60 Identities=13% Similarity=0.128 Sum_probs=41.7
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC-CCCCCCCCeEEEcc
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD-TKSISRSDYFELNS 488 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~-~~~~~~~d~f~~N~ 488 (554)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.+. ...-.+.-.|.+.+
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~~~~~~~gRp~~~y~LT~ 65 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYEAVVQGMGRPQYHYQLSR 65 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEeecccCCCCCceEEEECc
Confidence 455544455679999999999999999999999996 5678876532 11112344455543
No 77
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=59.37 E-value=44 Score=31.54 Aligned_cols=107 Identities=16% Similarity=0.212 Sum_probs=66.2
Q ss_pred HHhhCCCc-cCHHHHHHHhCCCHHHHHHHHHHhhhc----cceeeeecCCCCCCCCCCeEEEcccCCCcccccccccc--
Q 043775 430 DLFNASNR-LSYSQVITQLNLTHDDLVRLLHSLSIL----YYKILIKEPDTKSISRSDYFELNSKFTDRMRGSRSLSH-- 502 (554)
Q Consensus 430 llFN~~~~-lt~~ei~~~t~i~~~~l~~~L~sL~~~----k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~~ki~RiMK-- 502 (554)
++|-..+. +|+++|++.++++..++...|..|... ..++-... +..+=.|..+.+|..-.. +...
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~-----~~~~y~l~tk~e~~~~v~---~~~~~~ 83 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIE-----FNDVYKLVTKEENADYLQ---KLVKTP 83 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEE-----ECCEEEEEEcHHHHHHHH---HHhccc
Confidence 56777776 999999999999999999999998531 11222211 111223344555543222 2222
Q ss_pred ccccCChHHHHHHHHHHhccCCCCChHHHH--------HHHHhhhhhccccc
Q 043775 503 HRKVLGHQQLVSECIELLGRMFKPAVKAFK--------KRIEGLISQDYLER 546 (554)
Q Consensus 503 ~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK--------~~Ie~LIereyl~R 546 (554)
.++.|+...| ||+..+.-+=+.+...|- ..|..|+++|+|+.
T Consensus 84 ~~~~LS~aaL--EtLaiIay~qPiTr~eI~~irGv~~~~ii~~L~~~gLI~e 133 (188)
T PRK00135 84 IKQSLSQAAL--EVLAIIAYKQPITRIEIDEIRGVNSDGALQTLLAKGLIKE 133 (188)
T ss_pred ccCCCCHHHH--HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHCCCeEE
Confidence 3446776665 566665544455555554 45899999999974
No 78
>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=58.68 E-value=5 Score=29.66 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=24.5
Q ss_pred hccCCCCChHHHHHHHHhhhhhcccccC--CCCC
Q 043775 520 LGRMFKPAVKAFKKRIEGLISQDYLERY--PENP 551 (554)
Q Consensus 520 l~~~F~~~~~~iK~~Ie~LIereyl~Rd--~~d~ 551 (554)
+...+..+...+-+.|..|.++|||+|. ++|.
T Consensus 23 la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 23 LAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 3445667889999999999999999984 4454
No 79
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=58.59 E-value=16 Score=36.21 Aligned_cols=51 Identities=18% Similarity=0.301 Sum_probs=43.9
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCC
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKS 477 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~ 477 (554)
|-.||-+.++++.++++||++.+|+++..++|=|..|. +.++|.+..+|..
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGGa~ 57 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGGAV 57 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCCEe
Confidence 56788899999999999999999999999999999995 6678887655543
No 80
>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=58.39 E-value=10 Score=31.98 Aligned_cols=44 Identities=18% Similarity=0.244 Sum_probs=30.9
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
.+.|+..+..+..++-++|++.+|++..++.+.|..|. ..+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~--~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLY--EDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHH--HHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeE
Confidence 45666666666789999999999999999999999996 345554
No 81
>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=57.23 E-value=13 Score=32.79 Aligned_cols=38 Identities=16% Similarity=0.164 Sum_probs=30.0
Q ss_pred HHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCC
Q 043775 514 SECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENP 551 (554)
Q Consensus 514 ~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~ 551 (554)
.+|.+.+..+..+....|...|..|.+||||+|..+.+
T Consensus 22 ~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr 59 (130)
T TIGR02698 22 RDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR 59 (130)
T ss_pred HHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCC
Confidence 45555665567788999999999999999999875443
No 82
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=56.34 E-value=25 Score=25.34 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=17.5
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+|++||++.+|++...++..+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999887764
No 83
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=55.82 E-value=12 Score=35.06 Aligned_cols=27 Identities=15% Similarity=0.385 Sum_probs=22.9
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
..+|+++|++.|||..+++..+|+.|-
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 379999999999999999999999983
No 84
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.57 E-value=22 Score=33.24 Aligned_cols=44 Identities=9% Similarity=0.129 Sum_probs=36.3
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
...||.+.-.+..+|-++|++.+||+...+.++|..|. ..+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~--e~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLY--DARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeE
Confidence 45566666676789999999999999999999999996 456665
No 85
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=54.86 E-value=23 Score=35.04 Aligned_cols=51 Identities=20% Similarity=0.228 Sum_probs=43.3
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTK 476 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~ 476 (554)
-|..|+-.++++..+++.||++.+|++...+.|-|..|. +.+++.+..+|.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gga 56 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCCc
Confidence 466788899999999999999999999999999999995 557777765544
No 86
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=54.51 E-value=3.9e+02 Score=30.76 Aligned_cols=125 Identities=13% Similarity=0.254 Sum_probs=76.2
Q ss_pred HHHHHHHHHHHH--HhcCCccCHHHHHHHHHHHHH---------HHHHHHHHHHHHHH----------HHHh--h-----
Q 043775 86 ALKHKAKDAVID--EREREQVDRALLANVLDIFVE---------HMLQDTSSYYSRIS----------TNWI--L----- 137 (554)
Q Consensus 86 ~i~~~l~~~ll~--eR~g~~id~~~lk~~i~m~~~---------~fL~~t~~yY~~~s----------~~~i--~----- 137 (554)
...+.+-+++|. ++.-..-|...++.+...+.. .|++...-|+.... ..|- .
T Consensus 106 ~~~e~fE~~LL~eFe~ay~~~d~~~M~~~A~vL~~fngg~~~i~~fi~k~~~f~~~~~~~~~~~~~~~~~~~~l~d~~~~ 185 (710)
T PF07393_consen 106 KYCEIFENALLREFEIAYREGDYERMKEFAKVLLEFNGGSSCIDFFINKHEFFIDEDQLDESNGFEDEEIWEKLSDPDSH 185 (710)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcHHHHHHHHhChhhhhhhhhccccccchhHHHHhccCcccc
Confidence 555667777777 555555567788888777655 67766655552111 1111 0
Q ss_pred ----cCChhHHHHHHHHHHHHHHHHHchhcCccc--HHHHHHHHHHHHHHHHHHHHHHhhhhhHhhhhccCChHHHHHHH
Q 043775 138 ----KDPCPDYMRKAEECLKKERDRVSRYLQSNG--EEKLVEKVQHELLVVYATQLLEKEQSGCGALFRGNKVDDLSRMY 211 (554)
Q Consensus 138 ----~~~~~~Yl~~ve~~l~eE~~r~~~yL~~~t--~~kl~~~~~~~Li~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly 211 (554)
..++.+++..+...+++|...+..-+++.. ..++++.+-..-|..++..+++.. ...+...-|+.++
T Consensus 186 ~~~~~~~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~~a-------~~~s~~~YLr~l~ 258 (710)
T PF07393_consen 186 PPINEESLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLEEA-------SSISTLAYLRTLH 258 (710)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhh-------ccCCHHHHHHHHH
Confidence 123668999999999999999998775432 234445555555666666665432 1123344577777
Q ss_pred HHHhhh
Q 043775 212 RFYRTI 217 (554)
Q Consensus 212 ~L~~~~ 217 (554)
.++..+
T Consensus 259 ~~y~~t 264 (710)
T PF07393_consen 259 GLYSQT 264 (710)
T ss_pred HHHHHH
Confidence 777665
No 87
>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=53.50 E-value=22 Score=27.29 Aligned_cols=52 Identities=13% Similarity=0.293 Sum_probs=36.0
Q ss_pred ecHHHHHHHHHhhC-----CCccCHHHHHHHhCCC-HHHHHHHHHHhhhccceeeeecCC
Q 043775 421 ISTYHAAILDLFNA-----SNRLSYSQVITQLNLT-HDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 421 vs~~Q~~ILllFN~-----~~~lt~~ei~~~t~i~-~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
++.-|.-||...-+ .-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.|.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~~ 61 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDPG 61 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGCC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCCC
Confidence 34557767654432 2356999999999997 899999999996 5678887653
No 88
>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=53.23 E-value=13 Score=31.80 Aligned_cols=38 Identities=21% Similarity=0.176 Sum_probs=29.8
Q ss_pred HHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCC
Q 043775 513 VSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPEN 550 (554)
Q Consensus 513 ~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d 550 (554)
+.+|.+.+.....+....|+..+..|.+||||+|....
T Consensus 20 ~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g 57 (115)
T PF03965_consen 20 VREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG 57 (115)
T ss_dssp HHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC
Confidence 35666777777788999999999999999999997643
No 89
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=53.16 E-value=49 Score=29.14 Aligned_cols=65 Identities=15% Similarity=0.236 Sum_probs=51.8
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCC---CeEEEcccCC
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRS---DYFELNSKFT 491 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~---d~f~~N~~F~ 491 (554)
-..+|-+..+.+..|+.|+++.+|=+.+.+.+.|..|. .++|+..+.+|+...|. +.|.++-.|.
T Consensus 66 nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 66 NLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 34456677788899999999999999999999999995 78898877666655543 5667777775
No 90
>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=53.14 E-value=31 Score=25.51 Aligned_cols=39 Identities=18% Similarity=0.334 Sum_probs=30.8
Q ss_pred hCCCcc-CHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 433 NASNRL-SYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 433 N~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.....+ |..+|++.+|++...+.++|..|. +.++|...+
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~~ 59 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELE--AEGLVERRP 59 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 333444 499999999999999999999996 567776553
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=52.48 E-value=33 Score=24.36 Aligned_cols=39 Identities=13% Similarity=0.303 Sum_probs=29.5
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
|.-+.-|+.++- ..+|..+|++.+|++...+.+.+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555555553 457999999999999999998887663
No 92
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=52.19 E-value=19 Score=27.65 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=32.6
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
..|--+.++...+|+.+|++.|++++.++..+|--|+.
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 34666788889999999999999999999999999973
No 93
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=52.09 E-value=34 Score=24.39 Aligned_cols=38 Identities=11% Similarity=0.248 Sum_probs=28.1
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
+..|.-|+.++- +.+|..+|++.+|++...+...+..+
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344455554442 46799999999999999988887765
No 94
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=51.81 E-value=43 Score=31.06 Aligned_cols=57 Identities=21% Similarity=0.264 Sum_probs=44.6
Q ss_pred eEEEEecHHHHHHHHHhhCCCcc-CHHHHHHHh--CCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 416 NIELIISTYHAAILDLFNASNRL-SYSQVITQL--NLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 416 ~~~l~vs~~Q~~ILllFN~~~~l-t~~ei~~~t--~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
.+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++..|..|. +.++|.+..+
T Consensus 17 ~~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~~ 76 (171)
T PF14394_consen 17 EFEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDGD 76 (171)
T ss_pred HHHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECCC
Confidence 34455566677777766654443 899999999 999999999999995 7899998754
No 95
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=50.84 E-value=27 Score=32.05 Aligned_cols=48 Identities=13% Similarity=0.218 Sum_probs=41.0
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
+.-.-..||-....+..+|+.+|++.+|++...+.+-++.|. +.+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeE
Confidence 344566788888899999999999999999999999999996 566665
No 96
>PRK00215 LexA repressor; Validated
Probab=50.48 E-value=39 Score=32.12 Aligned_cols=52 Identities=17% Similarity=0.301 Sum_probs=40.6
Q ss_pred ecHHHHHHHHHhh-----CCCccCHHHHHHHhCC-CHHHHHHHHHHhhhccceeeeecCC
Q 043775 421 ISTYHAAILDLFN-----ASNRLSYSQVITQLNL-THDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 421 vs~~Q~~ILllFN-----~~~~lt~~ei~~~t~i-~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
++.-|..||.... .....|+.||++.+|+ +...+.+.|..|. +.+.+.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCC
Confidence 3566888886554 2446899999999999 9999999999996 5577776643
No 97
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=49.90 E-value=28 Score=34.48 Aligned_cols=51 Identities=16% Similarity=0.316 Sum_probs=43.0
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTK 476 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~ 476 (554)
-|..|+-+.+++..+++.||++.++++...+.|-|..|. +.++|.+.-+|.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~GGa 56 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHGGA 56 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCE
Confidence 456788888999999999999999999999999999996 567777765544
No 98
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=49.50 E-value=34 Score=30.97 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=40.8
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
+...--.||.++..+...|+.+|++.+|+++..+.+-+..|. ..+++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~--~~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK--QAGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCee
Confidence 455667788888888999999999999999999999999996 456664
No 99
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=49.03 E-value=24 Score=23.04 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=20.9
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 437 RLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 437 ~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.+|-+||++.+|++.+.+-|.|.-|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999999884
No 100
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=48.45 E-value=31 Score=33.36 Aligned_cols=49 Identities=20% Similarity=0.303 Sum_probs=42.0
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
|..-..||-+......+.+.||++.+|+|...+..+++.|. +.+++..+
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeee
Confidence 44555788888888999999999999999999999999995 77888754
No 101
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=48.44 E-value=29 Score=34.73 Aligned_cols=51 Identities=8% Similarity=0.068 Sum_probs=43.4
Q ss_pred HHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCC
Q 043775 423 TYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDT 475 (554)
Q Consensus 423 ~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~ 475 (554)
--|..|+.+.+.+..+++.||++.+|++...++|-|..|. ..+++.+..+|
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~GG 67 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEeCC
Confidence 4578899999999999999999999999999999999995 45677766544
No 102
>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=47.99 E-value=29 Score=26.73 Aligned_cols=34 Identities=15% Similarity=0.353 Sum_probs=26.9
Q ss_pred HHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 429 LDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 429 LllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.-...+...+|+.||+..++++++.+...|..|.
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~ 39 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLI 39 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3344567889999999999999999999999997
No 103
>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=46.79 E-value=40 Score=30.81 Aligned_cols=43 Identities=9% Similarity=0.118 Sum_probs=34.4
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeee
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILI 470 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 470 (554)
..|+...=.+..+|-+||++.+||+..++.+.|..|. ..+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~--e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALY--DAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCce
Confidence 4455544455689999999999999999999999996 456664
No 104
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=46.64 E-value=36 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.483 Sum_probs=21.1
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999988764
No 105
>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=46.36 E-value=26 Score=33.09 Aligned_cols=51 Identities=18% Similarity=0.277 Sum_probs=40.9
Q ss_pred ecHHHHHHHHHhhC-----CCccCHHHHHHHhCCC-HHHHHHHHHHhhhccceeeeecC
Q 043775 421 ISTYHAAILDLFNA-----SNRLSYSQVITQLNLT-HDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 421 vs~~Q~~ILllFN~-----~~~lt~~ei~~~t~i~-~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 46778888876653 2348899999999998 999999999996 667887754
No 106
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=45.86 E-value=36 Score=33.44 Aligned_cols=48 Identities=23% Similarity=0.350 Sum_probs=39.3
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
-|..|+..++++..++++||++.+|+++..++|-|.-|.. .+.|.+..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r~~ 52 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT--QGKILRNH 52 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEec
Confidence 3567888888889999999999999999999999999953 34555543
No 107
>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=45.85 E-value=10 Score=28.15 Aligned_cols=27 Identities=11% Similarity=0.159 Sum_probs=21.3
Q ss_pred CCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 523 MFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 523 ~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.+..+.+.+.+.|..|.++|||+|..+
T Consensus 30 ~l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 30 RLGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 344678889999999999999999643
No 108
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=45.27 E-value=33 Score=30.68 Aligned_cols=49 Identities=16% Similarity=0.319 Sum_probs=40.9
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
+.-.-.-||-........++.+|++.+|++...+.+.+.-|. +.+|+..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 344556788888888889999999999999999999999995 5677764
No 109
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=45.11 E-value=28 Score=36.56 Aligned_cols=83 Identities=22% Similarity=0.340 Sum_probs=48.9
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHhcCCCc-eeEEeecCceEEEEEEEcCceEEEEe-------cHHHHHHHHHh-hCCC
Q 043775 366 DLNPIFNLPSQMIKCVEVFKRFYETKTKHR-KLSWIYSLGQCHINAKFELKNIELII-------STYHAAILDLF-NASN 436 (554)
Q Consensus 366 ~~~~~~~lP~~l~~~~~~F~~fY~~k~~~R-kL~W~~~lg~~~l~~~~~~~~~~l~v-------s~~Q~~ILllF-N~~~ 436 (554)
++.+-..||+. +.+-=|| =+.+.|.||..|=++--+.+. |.= +-.-..||-++ ...+
T Consensus 262 NlaCILtLPpy------------QRkGYGklLIdFSYeLSr~E~~~GsPEKP--LSDLGllsYrsYW~~~ll~~L~~~~~ 327 (396)
T KOG2747|consen 262 NLACILTLPPY------------QRKGYGKLLIDFSYELSRREGKIGSPEKP--LSDLGLLSYRSYWRCVLLELLRKHRG 327 (396)
T ss_pred ceeeeeecChh------------hhcccchhhhhhhhhhhcccCcCCCCCCC--cchhhHHHHHHHHHHHHHHHHHhcCC
Confidence 34455688983 3332233 445667777766443222221 211 22233344333 3222
Q ss_pred -ccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 437 -RLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 437 -~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.+|+++|++.|||..+++..+|++|-
T Consensus 328 ~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 328 EHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred CcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 39999999999999999999999994
No 110
>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=43.95 E-value=13 Score=28.18 Aligned_cols=28 Identities=14% Similarity=0.177 Sum_probs=21.0
Q ss_pred hccCCCCChHHHHHHHHhhhhhcccccC
Q 043775 520 LGRMFKPAVKAFKKRIEGLISQDYLERY 547 (554)
Q Consensus 520 l~~~F~~~~~~iK~~Ie~LIereyl~Rd 547 (554)
+...+..+.+.+-+.|+.|+++|||++.
T Consensus 24 l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 24 LAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 3334667788899999999999999774
No 111
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=43.71 E-value=41 Score=36.85 Aligned_cols=51 Identities=12% Similarity=0.174 Sum_probs=44.2
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.++..|..||......+.+|..+|++.+|++...+.+.+.+|. +.+++...
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le--~kGlV~~~ 53 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLE--EKGLVKVE 53 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHH--hCCCEEEE
Confidence 4688999999999988899999999999999999999999996 34666543
No 112
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=43.43 E-value=42 Score=26.94 Aligned_cols=35 Identities=3% Similarity=0.025 Sum_probs=30.9
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
-++.|+-.... ...|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 999999999999999999998775
No 113
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=43.02 E-value=39 Score=31.64 Aligned_cols=63 Identities=11% Similarity=0.091 Sum_probs=48.5
Q ss_pred ceeEEeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhCC--CccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 395 RKLSWIYSLGQCHINAKFELKNIELIISTYHAAILDLFNAS--NRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 395 RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~~--~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
|.-.|.+.+|..+++- .+.|+ ||..||.-|+.-... ..||.+.|++..+|+.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~~-vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPEK-VPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCccc-CCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3445778888877753 33343 678999888765443 479999999999999999999999884
No 114
>PRK06474 hypothetical protein; Provisional
Probab=41.82 E-value=82 Score=29.38 Aligned_cols=69 Identities=16% Similarity=0.285 Sum_probs=46.7
Q ss_pred EEecHHHHHHHHHhhCCC-ccCHHHHHHHh-CCCHHHHHHHHHHhhhccceeeeecCCCCCC-CCCCeEEEccc
Q 043775 419 LIISTYHAAILDLFNASN-RLSYSQVITQL-NLTHDDLVRLLHSLSILYYKILIKEPDTKSI-SRSDYFELNSK 489 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~~-~lt~~ei~~~t-~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~-~~~d~f~~N~~ 489 (554)
+-.++.-..||-.+-..+ .+|..+|.+.+ +++...+-++|..|. +.+++...+..+.- ...-.|.+|..
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~~~~~~~~~ek~y~~~~~ 78 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVKEKKVRSVSEKYYAINEE 78 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEeecccccCceeEEEEeccc
Confidence 334566677776555444 49999999999 799999999999996 67888765432100 01234666654
No 115
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=41.61 E-value=63 Score=25.37 Aligned_cols=47 Identities=9% Similarity=0.110 Sum_probs=39.2
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhcccee
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKI 468 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~ki 468 (554)
.+=|+.++-++...+.-|+++|++.||-....+.-.|..+...|.++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl 55 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGL 55 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCc
Confidence 45689999999888999999999999999999999998885334343
No 116
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=41.37 E-value=43 Score=33.58 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=30.2
Q ss_pred HHHHHHHh-hCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 425 HAAILDLF-NASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 425 Q~~ILllF-N~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
...|+-.+ +....+|+++|++.|||..+++..+|++|
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 34555443 34578999999999999999999999988
No 117
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=41.09 E-value=29 Score=32.59 Aligned_cols=47 Identities=6% Similarity=0.086 Sum_probs=39.8
Q ss_pred HHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 423 TYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 423 ~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
.-+..|+.+.+.+..+++++|++.+|++...+.|=|..|. +.+++.+
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~--~~g~~~r 53 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG--IPELRER 53 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh--cchHHHH
Confidence 3577889999999999999999999999999999999996 3444443
No 118
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=41.08 E-value=45 Score=33.53 Aligned_cols=57 Identities=16% Similarity=0.304 Sum_probs=32.3
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKF 490 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F 490 (554)
+--.|+-+|..+.-||+.+|.+.|+-|+..|+.+|..++ ++.+.++ -...|.+-..|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 344677899999999999999999999999999999886 5555431 12456665554
No 119
>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=40.65 E-value=55 Score=26.61 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=36.1
Q ss_pred HHHHHHhhCCCccCHHHHHHHh-CCCHHHHHHHHHHhhhccceeeeec
Q 043775 426 AAILDLFNASNRLSYSQVITQL-NLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t-~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+.||..... +...+.||.+.+ |+++..|.+.|..|. ..+++.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 566766655 689999999999 999999999999996 56888775
No 120
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=39.81 E-value=65 Score=22.20 Aligned_cols=40 Identities=18% Similarity=0.291 Sum_probs=28.6
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
++..+..++.++- .+.+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444555554432 256899999999999999998877654
No 121
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=39.17 E-value=22 Score=25.74 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=26.7
Q ss_pred HHhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 518 ELLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 518 ~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.++..+|..+.+.+.+.+..|.+.|+|.+.++
T Consensus 24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 24 RELAAQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34555678899999999999999999988764
No 122
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=39.04 E-value=46 Score=24.44 Aligned_cols=31 Identities=13% Similarity=0.386 Sum_probs=25.5
Q ss_pred HhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 431 LFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 431 lFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
.|+.--..|.+||++.+||+...+..+|..-
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4666668999999999999999888877643
No 123
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=38.71 E-value=45 Score=22.68 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=20.6
Q ss_pred CCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 435 SNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 435 ~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
...+|+++|++..|++...+.+..+...
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4679999999999999999998877653
No 124
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=38.68 E-value=54 Score=24.04 Aligned_cols=39 Identities=10% Similarity=0.229 Sum_probs=30.7
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
|.-+..||.++-. ..+..||++..|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 4556677776655 46899999999999999999998886
No 125
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=38.27 E-value=47 Score=30.61 Aligned_cols=50 Identities=22% Similarity=0.322 Sum_probs=37.9
Q ss_pred cCCCceeEEeecCceEEEEEEEcCceEEEEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 391 KTKHRKLSWIYSLGQCHINAKFELKNIELIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 391 k~~~RkL~W~~~lg~~~l~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
+++.++|+|.++|-. -|.++-. +.-..|+++|++..|.++.+++++|+.=
T Consensus 36 ~~~~~~lTWvdSLav-------------------AAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLAV-------------------AAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHHH-------------------HHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 468899999986632 2223333 4457899999999999999999998854
No 126
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=37.50 E-value=71 Score=26.21 Aligned_cols=40 Identities=10% Similarity=0.208 Sum_probs=25.8
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhcccee
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKI 468 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~ki 468 (554)
+..+..+.+. ++..|.+.||||.-.++.+|.+|......+
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT-EE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCCeEE
Confidence 3344555556 999999999999999999999996433333
No 127
>PRK11050 manganese transport regulator MntR; Provisional
Probab=37.33 E-value=85 Score=28.39 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=37.0
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.|+.++...+.++..+|++.++++...+.+.|..|. +.+++.+.+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le--~~GlI~r~~ 85 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLA--RDGLVEMRP 85 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 455566777889999999999999999999999996 457776654
No 128
>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=36.76 E-value=9.9 Score=29.11 Aligned_cols=31 Identities=13% Similarity=0.277 Sum_probs=25.4
Q ss_pred CCCChHHHHHHHHhhhhhcccccCCCCCCCC
Q 043775 524 FKPAVKAFKKRIEGLISQDYLERYPENPNTF 554 (554)
Q Consensus 524 F~~~~~~iK~~Ie~LIereyl~Rd~~d~~~y 554 (554)
...+...+-+.++.|.++|+++|.+.++..|
T Consensus 32 l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 32 LGISRSTVYRALKSLEEKGLVEREEGRPKVY 62 (68)
T ss_dssp HTSSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence 3457788999999999999999988766554
No 129
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=36.71 E-value=1.1e+02 Score=24.48 Aligned_cols=42 Identities=14% Similarity=0.078 Sum_probs=33.1
Q ss_pred HHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 430 DLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 430 llFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
+.-++.+.+|=++|++.+|++...+-++++.|-...+.|...
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~ 53 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESV 53 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEec
Confidence 444566689999999999999999999999996434555543
No 130
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=36.69 E-value=95 Score=24.74 Aligned_cols=38 Identities=13% Similarity=0.256 Sum_probs=27.9
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.-.+|-+.-....+|..+|+..+|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 34466677788899999999999999999999998884
No 131
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=36.37 E-value=42 Score=33.31 Aligned_cols=38 Identities=13% Similarity=0.200 Sum_probs=31.3
Q ss_pred hhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 432 FNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 432 FN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
||+. =|.++|.+..||+...++++|-.|. |.+.+..++
T Consensus 243 f~DK--SsPEdIk~~FgiSKg~FKrAiGgL~--K~g~I~q~g 280 (287)
T COG2996 243 FNDK--SSPEDIKATFGISKGQFKRAIGGLM--KAGKIKQDG 280 (287)
T ss_pred cCCC--CCHHHHHHHhCcCHHHHHHHHHHHH--hCCeEEEcC
Confidence 4544 3889999999999999999999996 777776653
No 132
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=36.35 E-value=50 Score=31.85 Aligned_cols=36 Identities=8% Similarity=0.111 Sum_probs=32.8
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.++-+|.+.+.||+..|++.+|-|+..|+.+|.+.+
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia 234 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA 234 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH
Confidence 456689999999999999999999999999999886
No 133
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=35.85 E-value=56 Score=32.28 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=36.3
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
-|..|+.+.+.+..+++.||++.+|+++..++|=|..|.
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 478899999999999999999999999999999999885
No 134
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=35.71 E-value=52 Score=32.03 Aligned_cols=37 Identities=8% Similarity=0.177 Sum_probs=33.4
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
..++-+|..++.||+.+|.+.|+-|...|+..|..++
T Consensus 189 d~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic 225 (254)
T KOG2905|consen 189 DMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC 225 (254)
T ss_pred HHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH
Confidence 3456688899999999999999999999999999986
No 135
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.51 E-value=52 Score=23.13 Aligned_cols=32 Identities=16% Similarity=0.363 Sum_probs=21.6
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
|+.++.+ .+|..+|++.+|++...+.+-+.-+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444444 7899999999999999998877655
No 136
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=34.49 E-value=1e+02 Score=21.82 Aligned_cols=34 Identities=15% Similarity=0.218 Sum_probs=25.4
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
-|+++-++.+. .|+.+|+..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRES---RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34444444333 69999999999999999998764
No 137
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=33.89 E-value=48 Score=25.96 Aligned_cols=14 Identities=29% Similarity=0.349 Sum_probs=12.3
Q ss_pred hhhhhcccccCCCC
Q 043775 537 GLISQDYLERYPEN 550 (554)
Q Consensus 537 ~LIereyl~Rd~~d 550 (554)
.||+-+||+|++++
T Consensus 52 ~LVd~g~L~R~~dg 65 (71)
T PF09860_consen 52 YLVDYGLLERTRDG 65 (71)
T ss_pred HHHHcCCeeecCCC
Confidence 68999999999865
No 138
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=33.55 E-value=1.1e+02 Score=22.23 Aligned_cols=41 Identities=17% Similarity=0.197 Sum_probs=33.8
Q ss_pred HHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 430 DLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 430 llFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
-+|++++.+|+.+..+.+|++=+.....|.-| .+.++..+.
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~l--D~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYL--DREGITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHH--HHTTSEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHH--hccCCEEEe
Confidence 46778899999999999999999999999888 466776665
No 139
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=32.61 E-value=67 Score=34.49 Aligned_cols=35 Identities=23% Similarity=0.384 Sum_probs=29.1
Q ss_pred HHHH-HhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 427 AILD-LFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 427 ~ILl-lFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
.||- +.+....+|+++|++.|+|..+++..+|+.|
T Consensus 363 ~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 363 VLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 4443 3445568999999999999999999999999
No 140
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=32.34 E-value=92 Score=25.36 Aligned_cols=40 Identities=18% Similarity=0.269 Sum_probs=32.2
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
...++.-++....++++++|++.++++.+++...+..++.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 3445555666788999999999999999999999988863
No 141
>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=32.02 E-value=36 Score=28.76 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=23.4
Q ss_pred CCCCChHHHHHHHHhhhhhccccc--CCCCC
Q 043775 523 MFKPAVKAFKKRIEGLISQDYLER--YPENP 551 (554)
Q Consensus 523 ~F~~~~~~iK~~Ie~LIereyl~R--d~~d~ 551 (554)
....+.+.+-+.|..|.++|||.| |++|.
T Consensus 52 ~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 52 EILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 345677889999999999999997 55554
No 142
>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=31.97 E-value=1.7e+02 Score=23.44 Aligned_cols=48 Identities=8% Similarity=0.142 Sum_probs=38.3
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+++.|=+.-.....+.-.+|++.++.++..++..+..|- ..++|.+.|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 445555555667889999999999999999999999995 578887654
No 143
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=31.82 E-value=98 Score=27.46 Aligned_cols=44 Identities=18% Similarity=0.254 Sum_probs=35.8
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.|..+.+..+..++.+|++.++++...+.+.|..|. +.+++...
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~~ 55 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIYE 55 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEEe
Confidence 345555677788999999999999999999999996 55777644
No 144
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=31.64 E-value=54 Score=28.63 Aligned_cols=47 Identities=13% Similarity=0.109 Sum_probs=36.0
Q ss_pred ccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCCCCC
Q 043775 501 SHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYPENP 551 (554)
Q Consensus 501 MK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d~ 551 (554)
|=.++..+.+|++.++ ...+.++...|+--|..|..||.|.|.-+++
T Consensus 15 lW~~~~~t~~eI~~~l----~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr 61 (123)
T COG3682 15 LWSRGPATVREIIEEL----PADREWSYSTVKTLLNRLVKKGLLTRKKDGR 61 (123)
T ss_pred HHHcCCccHHHHHHHH----hhcccccHHHHHHHHHHHHhccchhhhhcCC
Confidence 3346666666666554 4458899999999999999999999986554
No 145
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.34 E-value=62 Score=29.11 Aligned_cols=30 Identities=13% Similarity=0.168 Sum_probs=27.1
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 434 ASNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 434 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
.++.+|-++|++.+||+...+.+.|..|..
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 345899999999999999999999999974
No 146
>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=31.22 E-value=78 Score=23.73 Aligned_cols=38 Identities=16% Similarity=0.304 Sum_probs=31.0
Q ss_pred CCCcc-CHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 434 ASNRL-SYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 434 ~~~~l-t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..+.+ |..+|++..|++-..+.++|.-|. ..+++...|
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~--~~g~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLE--AEGLIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHH--HCCcEEEEC
Confidence 45688 999999999999999999999996 567887665
No 147
>PLN03239 histone acetyltransferase; Provisional
Probab=31.14 E-value=74 Score=32.91 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=24.6
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
..+|+++|+..|||..+++..+|+.|
T Consensus 283 ~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 283 SSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 47999999999999999999999998
No 148
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=30.87 E-value=39 Score=21.35 Aligned_cols=14 Identities=50% Similarity=0.835 Sum_probs=8.6
Q ss_pred ccChHHHHHHHHHH
Q 043775 299 ISDKDLFAEFYRKK 312 (554)
Q Consensus 299 l~~KD~F~~~Y~~~ 312 (554)
++..|.|.+||.++
T Consensus 3 is~~d~f~eFY~rl 16 (28)
T PF12108_consen 3 ISGGDPFSEFYERL 16 (28)
T ss_dssp --S--HHHHHHHHH
T ss_pred CCCCChHHHHHHHH
Confidence 45779999999875
No 149
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=30.45 E-value=48 Score=25.49 Aligned_cols=28 Identities=11% Similarity=0.071 Sum_probs=23.4
Q ss_pred CChHHHHHHHHhhhhhcccccCCCCCCC
Q 043775 526 PAVKAFKKRIEGLISQDYLERYPENPNT 553 (554)
Q Consensus 526 ~~~~~iK~~Ie~LIereyl~Rd~~d~~~ 553 (554)
.+...+.+.+..|.++||+.++++.+..
T Consensus 34 l~~~~v~r~L~~L~~~G~V~~~~~~~~~ 61 (68)
T smart00550 34 LPKKEVNRVLYSLEKKGKVCKQGGTPPL 61 (68)
T ss_pred CCHHHHHHHHHHHHHCCCEEecCCCCCc
Confidence 5667899999999999999998876544
No 150
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=30.43 E-value=74 Score=30.20 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=24.0
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+++|.| .+.++++||++.+|++...++..|.
T Consensus 144 r~v~~L~~--~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 144 RAAVVLCD--IEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44444544 4568999999999999987766544
No 151
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=30.41 E-value=76 Score=28.25 Aligned_cols=37 Identities=19% Similarity=0.341 Sum_probs=28.4
Q ss_pred ecHHHHHHHHH-hhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAILDL-FNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~ILll-FN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+|+-|..|+.+ | -+.++++||++.+|++...+...+.
T Consensus 112 L~~~~r~v~~l~~--~~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRY--QRGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHH--hcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 46666666655 4 3578999999999999988877654
No 152
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=29.89 E-value=1e+02 Score=27.55 Aligned_cols=38 Identities=16% Similarity=0.287 Sum_probs=30.4
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
+|.-|..|+.++ ...+|.+||++.+|++...+...+..
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 567788888886 46899999999999999887754443
No 153
>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=29.88 E-value=82 Score=24.23 Aligned_cols=34 Identities=18% Similarity=0.304 Sum_probs=29.6
Q ss_pred ccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 437 RLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 437 ~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+|-++|++.+|++...+.+.|.-|. +.+++...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEc
Confidence 47899999999999999999999995 56777654
No 154
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=29.46 E-value=1.3e+02 Score=24.95 Aligned_cols=53 Identities=15% Similarity=0.224 Sum_probs=43.9
Q ss_pred EEecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 419 LIISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+..+....-||..+...+.=...-|+..+++|.+++...|..|. ..++|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 44566778899888877766788899999999999999999996 578888764
No 155
>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=29.43 E-value=1e+02 Score=24.20 Aligned_cols=49 Identities=14% Similarity=0.234 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhC--CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 423 TYHAAILDLFNA--SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 423 ~~Q~~ILllFN~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
..|.++|...-. ...++-.+|...+|++...+-..+..|. +.+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 457778877764 4578999999999999999999999996 567777754
No 156
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=29.39 E-value=75 Score=28.50 Aligned_cols=40 Identities=20% Similarity=0.182 Sum_probs=28.1
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
++.-|-.|+.++- .+.+|++||++.+|++...++..+.--
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3455555554432 457899999999999998887765543
No 157
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=29.31 E-value=47 Score=34.28 Aligned_cols=128 Identities=13% Similarity=0.216 Sum_probs=38.1
Q ss_pred EEecHHHHHHHHHhhC--CCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec-----C-----------CCCCCCC
Q 043775 419 LIISTYHAAILDLFNA--SNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE-----P-----------DTKSISR 480 (554)
Q Consensus 419 l~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~-----~-----------~~~~~~~ 480 (554)
-.++..+..|.-+..+ ...+-..+|...|||+...+.++|.+|.. | ++++.. | ++.++..
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~-k-~lIK~vksv~~~~rK~Yml~~l~Ps~eiTG 157 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES-K-KLIKSVKSVKNPNRKVYMLYDLEPSEEITG 157 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH-T-TSEEEE--SS-SS--EEEESSS--------
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh-C-CCEEEecCcCCCCeEEEEEccCCcCcccCC
Confidence 4567788888877765 56788999999999999999999999974 2 454432 1 1233443
Q ss_pred CCeE---EEcccCCCcccccc-cccccccc-----------------------------CChHHHHHHHHHHhccCCCCC
Q 043775 481 SDYF---ELNSKFTDRMRGSR-SLSHHRKV-----------------------------LGHQQLVSECIELLGRMFKPA 527 (554)
Q Consensus 481 ~d~f---~~N~~F~~~~~ki~-RiMK~~k~-----------------------------l~~~~L~~ev~~~l~~~F~~~ 527 (554)
+.-| .++..|-+..+.+- +.+.++.. .+.+++..-+.+.=-..-..+
T Consensus 158 G~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~sgIs~v~Ls 237 (327)
T PF05158_consen 158 GPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINKSGISNVELS 237 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHHHHHcCCCceecC
Confidence 3333 34555554443333 44444333 233343333332211134568
Q ss_pred hHHHHHHHHhhhhhcccccCC
Q 043775 528 VKAFKKRIEGLISQDYLERYP 548 (554)
Q Consensus 528 ~~~iK~~Ie~LIereyl~Rd~ 548 (554)
+++|...++.|+=-|-|++-.
T Consensus 238 ~eDI~~LL~tLVyDgkIE~v~ 258 (327)
T PF05158_consen 238 EEDIESLLDTLVYDGKIEEVR 258 (327)
T ss_dssp ---------------------
T ss_pred HHHHHHHHHHHhhCceeEEEe
Confidence 888999999888777777643
No 158
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.20 E-value=1.4e+02 Score=28.66 Aligned_cols=49 Identities=14% Similarity=0.137 Sum_probs=36.5
Q ss_pred ecHHHHHHHHH---hhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 421 ISTYHAAILDL---FNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 421 vs~~Q~~ILll---FN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
.+.-+.-+++. -+....+|.++|++.+++++..++.++..|+ .++++..
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~--~~~~~~~ 210 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLV--NCHILFT 210 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHH--hCCEEEE
Confidence 34555444432 2345789999999999999999999999996 5677743
No 159
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=29.09 E-value=40 Score=29.92 Aligned_cols=33 Identities=9% Similarity=0.215 Sum_probs=25.3
Q ss_pred hccCCCCChHHHHHHHHhhhhhcccccCC--CCCC
Q 043775 520 LGRMFKPAVKAFKKRIEGLISQDYLERYP--ENPN 552 (554)
Q Consensus 520 l~~~F~~~~~~iK~~Ie~LIereyl~Rd~--~d~~ 552 (554)
+..++..+.+.+.+.|+.|.++|||+|.. +|+.
T Consensus 52 La~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR 86 (144)
T PRK03573 52 LAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRR 86 (144)
T ss_pred HHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcC
Confidence 33345677788999999999999999964 4543
No 160
>smart00753 PAM PCI/PINT associated module.
Probab=28.84 E-value=88 Score=24.94 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=26.7
Q ss_pred hCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 433 NASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 433 N~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
....++++++|++.++++.+++...+..++
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i 49 (88)
T smart00753 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI 49 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH
Confidence 346789999999999999999999888886
No 161
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=28.84 E-value=88 Score=24.94 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=26.7
Q ss_pred hCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 433 NASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 433 N~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
....++++++|++.++++.+++...+..++
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i 49 (88)
T smart00088 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI 49 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH
Confidence 346789999999999999999999888886
No 162
>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=28.76 E-value=67 Score=28.02 Aligned_cols=51 Identities=8% Similarity=0.053 Sum_probs=39.8
Q ss_pred EecHHHHHHHHH--hh--------CCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 420 IISTYHAAILDL--FN--------ASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 420 ~vs~~Q~~ILll--FN--------~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+-.+.-..++. -| ..-..|.++|+..++-+.+.++.+|..|. +.+++...
T Consensus 26 ~~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 26 YTVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred eHHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344556666666 34 44579999999999999999999999995 78888764
No 163
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.70 E-value=70 Score=29.46 Aligned_cols=38 Identities=5% Similarity=0.165 Sum_probs=26.9
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
++.-|-.|+.+. ..+.+|++||++.+|++...++..|.
T Consensus 128 Lp~~~R~v~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMA-TLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 455555555442 12578999999999999988876554
No 164
>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=28.65 E-value=32 Score=25.89 Aligned_cols=32 Identities=16% Similarity=0.300 Sum_probs=26.2
Q ss_pred HHhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 518 ELLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 518 ~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.++.++|..+...+.+++..|.+.|+|++.++
T Consensus 28 ~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 34555788999999999999999999998764
No 165
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.57 E-value=38 Score=24.46 Aligned_cols=21 Identities=10% Similarity=0.248 Sum_probs=18.1
Q ss_pred CCCChHHHHHHHHhhhhhccc
Q 043775 524 FKPAVKAFKKRIEGLISQDYL 544 (554)
Q Consensus 524 F~~~~~~iK~~Ie~LIereyl 544 (554)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 456788899999999999987
No 166
>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=28.05 E-value=1.1e+02 Score=24.95 Aligned_cols=48 Identities=21% Similarity=0.158 Sum_probs=35.6
Q ss_pred HHHHHHhhCCCccCHHHHHHHh--CCCHHHHHHHHHHhhhccceeeeecCCC
Q 043775 426 AAILDLFNASNRLSYSQVITQL--NLTHDDLVRLLHSLSILYYKILIKEPDT 475 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t--~i~~~~l~~~L~sL~~~k~kiL~~~~~~ 475 (554)
+.||-..-.++-+|..++.+.+ .++...+.+++.-|. |.+++.++++|
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSGDG 68 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSGDG 68 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEETTE
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccCCc
Confidence 4455555677789999999976 888999999999995 77888887543
No 167
>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=27.67 E-value=46 Score=24.54 Aligned_cols=31 Identities=16% Similarity=0.261 Sum_probs=25.5
Q ss_pred HhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 519 LLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 519 ~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
++..+|..+.+.+.+.+..|.++|||.+.++
T Consensus 30 ~la~~~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 30 ELAEELGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 4445577888999999999999999998753
No 168
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=27.55 E-value=44 Score=24.26 Aligned_cols=26 Identities=15% Similarity=0.468 Sum_probs=20.7
Q ss_pred CccCHHHHHHHhCCCHHHHHHHH-HHh
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLL-HSL 461 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L-~sL 461 (554)
+.+++.||++.+|++..++.+.| ..+
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l~~~~ 28 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKLFKEL 28 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH-HHH
T ss_pred CceEHHHHHHHHCcCHHHHHHHHHHhC
Confidence 35789999999999999999888 435
No 169
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=27.53 E-value=1e+02 Score=29.77 Aligned_cols=37 Identities=22% Similarity=0.223 Sum_probs=26.5
Q ss_pred cHHHHHH-HHHh--hCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 422 STYHAAI-LDLF--NASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 422 s~~Q~~I-LllF--N~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
|.-|-.| .|.| +..+.+|++||++.+|++...++..+
T Consensus 180 p~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~ 219 (234)
T PRK08301 180 SDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3444444 4444 34678999999999999998886654
No 170
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=27.46 E-value=1.2e+02 Score=27.50 Aligned_cols=45 Identities=16% Similarity=0.308 Sum_probs=37.4
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
+|..++.+.......+|++.+++++..+...++-|. +.+++...|
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 455566677889999999999999999999999995 567877765
No 171
>PHA02943 hypothetical protein; Provisional
Probab=27.15 E-value=1.1e+02 Score=27.70 Aligned_cols=54 Identities=20% Similarity=0.241 Sum_probs=39.5
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcc
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNS 488 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~ 488 (554)
||-.+ ..+.-|..||++.+|++-....-+|.-|. |-+.+.+..-| .-..+.+|+
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~~G----~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVEIG----RAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEeec----ceEEEEECh
Confidence 44444 56678899999999999999999999885 66666665422 235566666
No 172
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=26.51 E-value=1.1e+02 Score=30.38 Aligned_cols=42 Identities=14% Similarity=0.323 Sum_probs=34.4
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
||++.-+ +.-|++||...++++...+..+|.-|. +.+++.++
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 4444444 688999999999999999999999995 56787765
No 173
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.41 E-value=84 Score=28.77 Aligned_cols=37 Identities=16% Similarity=0.301 Sum_probs=25.7
Q ss_pred ecHHHHH-HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAA-ILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~-ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
++.-|-. +++.| -+.+|++||++.+|++...++..|.
T Consensus 130 L~~~~r~i~~l~~--~~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 130 LEKDRAAAVRRAY--LEGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CCHHHHHHHHHHH--HcCCCHHHHHHHHCCChHHHHHHHH
Confidence 3444443 44444 3568999999999999988776554
No 174
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=26.22 E-value=1e+02 Score=30.62 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=41.0
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecCC
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEPD 474 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 474 (554)
-|.++-+.-+....++-+||..++|+|...+-|+|..|- |.+++.+...
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~K~ 245 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKEKK 245 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEEEe
Confidence 466666677778889999999999999999999999995 7788876543
No 175
>PRK00118 putative DNA-binding protein; Validated
Probab=26.15 E-value=1.1e+02 Score=25.82 Aligned_cols=25 Identities=8% Similarity=0.282 Sum_probs=21.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
+..|+.||++.+|++...+.+.+..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3689999999999999888776654
No 176
>PHA02591 hypothetical protein; Provisional
Probab=25.94 E-value=83 Score=25.04 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=22.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
..+|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 4789999999999999999888765
No 177
>PRK13239 alkylmercury lyase; Provisional
Probab=25.77 E-value=1.4e+02 Score=28.72 Aligned_cols=39 Identities=13% Similarity=0.283 Sum_probs=34.4
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
+...||-++-+....|+++|++.+|.+.+.+.+.|..|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 455677777788999999999999999999999999984
No 178
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=25.74 E-value=1.6e+02 Score=23.13 Aligned_cols=43 Identities=19% Similarity=0.284 Sum_probs=30.6
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeee
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIK 471 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 471 (554)
+-||.... .+..+..+|+..+|++...+.+.|..|. +.+++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~--~~gLI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELE--EKGLIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCcCeeC
Confidence 44666665 6678999999999999999999999996 5677744
No 179
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=25.68 E-value=74 Score=24.78 Aligned_cols=26 Identities=12% Similarity=0.302 Sum_probs=20.6
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
-.-|.+||++.+||+.+.+...+...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 45799999999999999999988754
No 180
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=25.65 E-value=5.7e+02 Score=24.08 Aligned_cols=111 Identities=14% Similarity=0.147 Sum_probs=59.2
Q ss_pred cHHHHHHHHHHHHHHHhcCCCceeEEeecCceEEEEEE--E-------cCceEEEEecHHHHHHHHHhhCCCccCHHHHH
Q 043775 374 PSQMIKCVEVFKRFYETKTKHRKLSWIYSLGQCHINAK--F-------ELKNIELIISTYHAAILDLFNASNRLSYSQVI 444 (554)
Q Consensus 374 P~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~--~-------~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~ 444 (554)
|.++..+++....-|.....| +.-...=|.-.+..+ | ......-..|..++-+|-..--+..+|-.||.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~~g--i~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDDRG--LKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCCCC--EEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 467999999999999876433 333222222222211 0 00111123444444455444444689999999
Q ss_pred HHhCCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCC
Q 043775 445 TQLNLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFT 491 (554)
Q Consensus 445 ~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~ 491 (554)
+.+|++.. .++..|. ..+++...+..........|.++..|-
T Consensus 112 ~irGv~~~---~ii~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNSD---GALQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCHH---HHHHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 99999974 4455553 345665432111112335566666663
No 181
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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 groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=25.62 E-value=85 Score=22.22 Aligned_cols=21 Identities=10% Similarity=0.346 Sum_probs=18.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 043775 439 SYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 439 t~~ei~~~t~i~~~~l~~~L~ 459 (554)
|+.||++..|++...+-+.|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999988876
No 182
>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=25.47 E-value=2e+02 Score=21.78 Aligned_cols=32 Identities=13% Similarity=0.213 Sum_probs=26.6
Q ss_pred HhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 431 LFNASNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 431 lFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
.+.+. ..+..+|++.+|++...+.+.+..|..
T Consensus 8 ~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 8 LLADN-PFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34443 478999999999999999999999953
No 183
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=1.1e+02 Score=27.88 Aligned_cols=33 Identities=15% Similarity=0.279 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+++|.+- +.+|++||++.+|++...++..|.
T Consensus 125 r~i~~l~~~--~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 125 KTVLVLYYY--EQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 334444443 357999999999999988776654
No 184
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=25.00 E-value=1.2e+02 Score=29.36 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=25.9
Q ss_pred HHHHHHHh--hCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLF--NASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllF--N~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+|.+.| ++.+.+|++||++.+|++...++..+.
T Consensus 184 R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 184 KKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred HHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44444544 345789999999999999998876653
No 185
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=24.96 E-value=1.4e+02 Score=28.93 Aligned_cols=46 Identities=17% Similarity=0.222 Sum_probs=36.8
Q ss_pred HHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 426 AAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
.+.+-.-++...+|..||++.++++...+.+.|..|. +.+++.+..
T Consensus 10 iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~~ 55 (217)
T PRK14165 10 LALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRTI 55 (217)
T ss_pred HHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEE
Confidence 3344455566689999999999999999999999995 668887653
No 186
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.94 E-value=1.1e+02 Score=27.25 Aligned_cols=37 Identities=11% Similarity=0.140 Sum_probs=25.4
Q ss_pred ecHHHHHHH-HHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAIL-DLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~IL-llFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+|.-|-.|+ |.+- +.+|++||++.+|++...++..|.
T Consensus 107 Lp~~~r~v~~l~~~--~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 107 LPENYRDVVLAHYL--EEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CCHHHHHHHHHHHH--hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 444433333 4442 467999999999999998866554
No 187
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.79 E-value=1.3e+02 Score=27.04 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=24.2
Q ss_pred HHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.++.+.+ ..+|++||++.+|++...++..+.
T Consensus 118 r~il~l~~---~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 118 RTVLLLRF---SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred HHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44444555 578999999999999988776553
No 188
>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=24.50 E-value=2.2e+02 Score=24.97 Aligned_cols=50 Identities=18% Similarity=0.177 Sum_probs=38.6
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHh----CCCHHHHHHHHHHhhhccceeeeec
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQL----NLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t----~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+|.-+..|+..+=+.+..|+.||.+.+ +++...+...|.-|. +-+++...
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceeee
Confidence 466778888777667789999977765 788899999999996 55777654
No 189
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=24.46 E-value=1.4e+02 Score=26.75 Aligned_cols=37 Identities=11% Similarity=0.224 Sum_probs=29.2
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
..|.-|..||.++ ...+|.+||++.+|++...+....
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie 42 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIE 42 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4577788888776 467999999999999997655544
No 190
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.42 E-value=44 Score=24.22 Aligned_cols=26 Identities=12% Similarity=0.143 Sum_probs=21.8
Q ss_pred CCCChHHHHHHHHhhhhhcccccCCC
Q 043775 524 FKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 524 F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
+..+.+.+.+.|+.|.+++++.+..+
T Consensus 20 l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 20 LGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 34677889999999999999997654
No 191
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=24.36 E-value=98 Score=28.08 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=23.9
Q ss_pred HHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 424 YHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 424 ~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
.+.++.|.+ .+.+|++||++.+|++...++..|
T Consensus 123 ~r~v~~L~~--~eg~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 123 ARAAFLMSQ--LEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344444444 346899999999999998877654
No 192
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.14 E-value=97 Score=29.08 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=26.6
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
+..+..|+.++- +.+|++||++.+|++...++..|.-
T Consensus 157 ~~~~r~vl~l~~--e~~s~~EIA~~lgis~~tV~~~l~r 193 (208)
T PRK08295 157 SELEKEVLELYL--DGKSYQEIAEELNRHVKSIDNALQR 193 (208)
T ss_pred CHHHHHHHHHHH--ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 444555554443 4789999999999999888765543
No 193
>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=23.98 E-value=1.9e+02 Score=24.33 Aligned_cols=57 Identities=19% Similarity=0.274 Sum_probs=40.0
Q ss_pred HHHHHhhC-CCccCHHHHHHHh-----CCCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcc
Q 043775 427 AILDLFNA-SNRLSYSQVITQL-----NLTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNS 488 (554)
Q Consensus 427 ~ILllFN~-~~~lt~~ei~~~t-----~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~ 488 (554)
.||-.+.. ...+|.+||.+.+ +++...+-|+|..|. ..+++.+...+. ....|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~--~~Gli~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLE--EAGLVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH--hCCCEEEEEeCC---CceEEEeCC
Confidence 45555544 5579999999988 689999999999996 567887653211 124566653
No 194
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=23.95 E-value=1.7e+02 Score=27.45 Aligned_cols=44 Identities=9% Similarity=0.153 Sum_probs=36.3
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeecC
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKEP 473 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 473 (554)
++.-.+.++..|..+|+..+||+..++.|+|-.|. +.+-+...|
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~~ 61 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMSD 61 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecCC
Confidence 55566778899999999999999999999999996 556665553
No 195
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.91 E-value=1.3e+02 Score=27.14 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=27.3
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
+|.-|-.|+.+.-- +.+|++||++.+|++...++..|.--
T Consensus 113 L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 113 LSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35545554444322 56899999999999998877665533
No 196
>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=23.72 E-value=47 Score=32.14 Aligned_cols=32 Identities=13% Similarity=0.246 Sum_probs=27.6
Q ss_pred HHhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 518 ELLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 518 ~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.+|..+|..+...+.++|+.|++.|+|.|..+
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 35556799999999999999999999999653
No 197
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.28 E-value=1.5e+02 Score=20.49 Aligned_cols=24 Identities=17% Similarity=0.300 Sum_probs=16.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
..+|+.+|++.+|.+...+.+.|.
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 468999999999999988877653
No 198
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.11 E-value=1.1e+02 Score=28.18 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=26.7
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
|.-|-.|+.++ ..+.+|++||++.+|++...++..|..
T Consensus 131 ~~~~r~v~~l~-~~~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 131 PDRQRLPIVHV-KLEGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred CHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44455544332 134679999999999999988876654
No 199
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.92 E-value=1.2e+02 Score=27.05 Aligned_cols=38 Identities=13% Similarity=0.098 Sum_probs=26.6
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
++.-+.-|+.+. ..+.+|++||++.+|++...++..|.
T Consensus 106 L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 106 LPPACRDSFLLR-KLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 455555555443 24578999999999999987765443
No 200
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.86 E-value=61 Score=28.77 Aligned_cols=29 Identities=17% Similarity=0.523 Sum_probs=23.8
Q ss_pred CCCCChHHHHHHHHhhhhhcccccCC--CCC
Q 043775 523 MFKPAVKAFKKRIEGLISQDYLERYP--ENP 551 (554)
Q Consensus 523 ~F~~~~~~iK~~Ie~LIereyl~Rd~--~d~ 551 (554)
++..+.+.+-+.|+.|.++|||+|.+ +|+
T Consensus 63 ~l~i~~~tvsr~l~~Le~~GlI~R~~~~~Dr 93 (144)
T PRK11512 63 VLSVDLGALTRMLDRLVCKGWVERLPNPNDK 93 (144)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEeccCcccC
Confidence 35578888999999999999999954 454
No 201
>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=22.85 E-value=58 Score=24.03 Aligned_cols=40 Identities=13% Similarity=0.217 Sum_probs=30.4
Q ss_pred ccccccCChHHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccCC
Q 043775 501 SHHRKVLGHQQLVSECIELLGRMFKPAVKAFKKRIEGLISQDYLERYP 548 (554)
Q Consensus 501 MK~~k~l~~~~L~~ev~~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~ 548 (554)
++.++.++..+|. ..|..+...|.+=+..|-+++.|.|.-
T Consensus 9 l~~~~~~s~~ela--------~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 9 LKEKGKVSVKELA--------EEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHcCCEEHHHHH--------HHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4445555555444 358899999999999999999999853
No 202
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=22.40 E-value=2.4e+02 Score=20.48 Aligned_cols=41 Identities=15% Similarity=0.223 Sum_probs=35.1
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.++.-+.-++.++-.. .+..||+...+++...+..++..+.
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577788888888775 7999999999999999999888775
No 203
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=22.37 E-value=74 Score=25.43 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=28.6
Q ss_pred HHhccCCCCChHHHHHHHHhhhhhcccccCCCC
Q 043775 518 ELLGRMFKPAVKAFKKRIEGLISQDYLERYPEN 550 (554)
Q Consensus 518 ~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~d 550 (554)
.+|+.+|..+++.|..-+|.|+.+|=++|-+.+
T Consensus 20 ~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~~~ 52 (78)
T PRK15431 20 AQISQTLNTPQPMINAMLQQLESMGKAVRIQEE 52 (78)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeEeeccC
Confidence 356667999999999999999999999998643
No 204
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=21.89 E-value=1.4e+02 Score=27.25 Aligned_cols=37 Identities=14% Similarity=0.150 Sum_probs=25.3
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.-|-.|+.+.- .+.+|++||++.+|++...++..|.
T Consensus 136 p~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 136 DPRQAEVVELRF-FAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred CHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 444444443322 2468999999999999988876654
No 205
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=21.84 E-value=1.5e+02 Score=29.49 Aligned_cols=30 Identities=7% Similarity=0.245 Sum_probs=23.1
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHH
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVR 456 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~ 456 (554)
+|.+.|-..+.+|+.||++.+|++...+.+
T Consensus 226 vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q 255 (270)
T TIGR02392 226 IIEARWLDDDKLTLQELAAEYGVSAERIRQ 255 (270)
T ss_pred HHHHHhcCCCCcCHHHHHHHHCCCHHHHHH
Confidence 344455444589999999999999988774
No 206
>PRK04217 hypothetical protein; Provisional
Probab=21.82 E-value=1.1e+02 Score=26.27 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=26.5
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
++.-|..++.+. ..+.+|++||++.+|++...+.+.|..
T Consensus 43 Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 43 MTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444444332 234679999999999999888776653
No 207
>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=21.81 E-value=96 Score=25.74 Aligned_cols=22 Identities=9% Similarity=0.075 Sum_probs=17.8
Q ss_pred CCChHHHHHHHHhhhhhccccc
Q 043775 525 KPAVKAFKKRIEGLISQDYLER 546 (554)
Q Consensus 525 ~~~~~~iK~~Ie~LIereyl~R 546 (554)
..+...|+++|+.|++.|+|=-
T Consensus 76 ~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 76 GMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEE
T ss_pred CcCHHHHHHHHHHHHhCCeEec
Confidence 3478899999999999998743
No 208
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.76 E-value=1.5e+02 Score=26.38 Aligned_cols=24 Identities=0% Similarity=0.081 Sum_probs=19.9
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHH
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+|++||++.+|++...++..+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999988775543
No 209
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=21.64 E-value=2e+02 Score=30.67 Aligned_cols=39 Identities=18% Similarity=0.181 Sum_probs=34.1
Q ss_pred hhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 432 FNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 432 FN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+...+.+|.++|++.+++|...+.+.|..|. +.+++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEec
Confidence 5667799999999999999999999999995 67888754
No 210
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.60 E-value=1.7e+02 Score=28.26 Aligned_cols=41 Identities=15% Similarity=0.244 Sum_probs=36.1
Q ss_pred EecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 420 IISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 420 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
.+|+-+..||.+.-. .+|.+||++.+++++..++.++..+.
T Consensus 143 ~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 143 KVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 578889999988766 57999999999999999999998886
No 211
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.57 E-value=1.4e+02 Score=27.54 Aligned_cols=38 Identities=11% Similarity=0.133 Sum_probs=26.9
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+|.-|-.|+.+.- .+.+|++||++.+|++...++..|.
T Consensus 136 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 136 LSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4555555555432 3468999999999999988775443
No 212
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.56 E-value=1.2e+02 Score=28.10 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=25.1
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.-|-.|+.+.- .+.+|++||++.+|++...++..|.
T Consensus 136 p~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 136 PAQQARVFMMRE-YLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred CHHHHHHHhHHH-HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 444444444432 2378999999999999988776543
No 213
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=1.2e+02 Score=29.21 Aligned_cols=38 Identities=13% Similarity=0.174 Sum_probs=25.9
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHS 460 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~s 460 (554)
+.-|-.|+.++- .+.+|++||++.+|++...++..|.-
T Consensus 136 p~~~R~v~~L~y-~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 136 PVEYREVLVLRE-LEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred CHHHHhHhhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 333444444421 24789999999999999888776553
No 214
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=21.18 E-value=1.4e+02 Score=23.72 Aligned_cols=29 Identities=14% Similarity=0.275 Sum_probs=22.5
Q ss_pred CCCccCHHHHHHHhCCCHHHHHHHHHHhh
Q 043775 434 ASNRLSYSQVITQLNLTHDDLVRLLHSLS 462 (554)
Q Consensus 434 ~~~~lt~~ei~~~t~i~~~~l~~~L~sL~ 462 (554)
..+..|++++++.++++...+.+.+..+-
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678999999999999999998887774
No 215
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.17 E-value=98 Score=24.32 Aligned_cols=34 Identities=21% Similarity=0.290 Sum_probs=24.0
Q ss_pred HHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 428 ILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 428 ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
||....+-..+|+.||++.+|+++..+.|-.+.|
T Consensus 25 il~~~~~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 25 ILENPDEIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp HHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 3444445568999999999999999999887766
No 216
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=21.11 E-value=5.3e+02 Score=24.24 Aligned_cols=107 Identities=16% Similarity=0.266 Sum_probs=62.6
Q ss_pred HHHhhCCCccCHHHHHHHhCC-CHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEEcccCCCcccc-----cccccc
Q 043775 429 LDLFNASNRLSYSQVITQLNL-THDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFELNSKFTDRMRG-----SRSLSH 502 (554)
Q Consensus 429 LllFN~~~~lt~~ei~~~t~i-~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~N~~F~~~~~k-----i~RiMK 502 (554)
.++|-..+.+|.++|++.+++ +...+...|.-|... + . +. +-+...+...|.-..+. +.+.+.
T Consensus 15 all~a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~-y----~---~r---g~~L~~~~~~~r~~t~~~~~~~~~~l~~ 83 (184)
T COG1386 15 ALLFAGGEPLSLKELAEILGIVSADAIIDALAELKEE-Y----E---DR---GLELVEVAEGWRLQTKQEYAEYLEKLQE 83 (184)
T ss_pred HHHHhcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHh-h----c---CC---CeeEEEEcCceeEEehHHHHHHHHHHhc
Confidence 467788889999999999999 667788888777531 1 0 00 01122222222211111 114444
Q ss_pred cc--ccCChHHHHHHHHHHhccCCCCChHHHH--------HHHHhhhhhcccccCC
Q 043775 503 HR--KVLGHQQLVSECIELLGRMFKPAVKAFK--------KRIEGLISQDYLERYP 548 (554)
Q Consensus 503 ~~--k~l~~~~L~~ev~~~l~~~F~~~~~~iK--------~~Ie~LIereyl~Rd~ 548 (554)
.+ +.++-..| ||...+.=+=|.+..+|. +.|..|.++|.|+-.+
T Consensus 84 ~~~~~~LSraal--EtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~glI~~~g 137 (184)
T COG1386 84 QRPKRELSRAAL--ETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERGLIREVG 137 (184)
T ss_pred ccccccccHHHH--HHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCCCeEecC
Confidence 43 34777776 444444422344555554 5699999999998653
No 217
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=21.07 E-value=3e+02 Score=23.85 Aligned_cols=57 Identities=12% Similarity=0.085 Sum_probs=40.3
Q ss_pred HHHHHHhhCCCccCHHHHHHHhC-CCHHHHHHHHHHhhhccceeeeecCCCCCCCCCCeEEE
Q 043775 426 AAILDLFNASNRLSYSQVITQLN-LTHDDLVRLLHSLSILYYKILIKEPDTKSISRSDYFEL 486 (554)
Q Consensus 426 ~~ILllFN~~~~lt~~ei~~~t~-i~~~~l~~~L~sL~~~k~kiL~~~~~~~~~~~~d~f~~ 486 (554)
+.||....+ ...-|+||...++ |+..-|.+.|..|. ..+++.+..- ..+++.-.|++
T Consensus 26 ~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le--~~Glv~R~~~-~~~PprveY~L 83 (120)
T COG1733 26 LLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELE--EDGLVERVVY-PEEPPRVEYRL 83 (120)
T ss_pred HHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHH--HCCCEEeeec-CCCCceeEEEE
Confidence 345544434 7889999999998 99999999999996 6788887531 22334444544
No 218
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=20.92 E-value=1.5e+02 Score=29.84 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=25.8
Q ss_pred HHHHHHHh--hCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 425 HAAILDLF--NASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 425 Q~~ILllF--N~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.+|.+.| ...+.+|+.||++.+|+|...++..+.
T Consensus 228 R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 228 REVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred HHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 44455544 456789999999999999988766443
No 219
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.85 E-value=2e+02 Score=25.17 Aligned_cols=48 Identities=19% Similarity=0.329 Sum_probs=39.2
Q ss_pred HHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 423 TYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 423 ~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
.+.+-|+-+--++..+|+.++...||++-..+++++.-|+. .+-|..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeC
Confidence 35667777888899999999999999999999999999973 3444444
No 220
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=20.82 E-value=2.1e+02 Score=21.43 Aligned_cols=33 Identities=24% Similarity=0.515 Sum_probs=22.6
Q ss_pred HHHHHHHHhhccCCCCCCHHHHHHHHHHHhhHh
Q 043775 264 LATFCDNILKKSGNEKLSDEAIEETLEKVVKVL 296 (554)
Q Consensus 264 la~y~D~~lkk~~~~~~~~~e~~~~l~~i~~lf 296 (554)
++.++-.++.++..++.+..+++++||+|+.++
T Consensus 23 Ftl~IRri~~~s~~kkq~~~~~eqKLDrIIeLL 55 (58)
T PF13314_consen 23 FTLFIRRILINSNAKKQDVDSMEQKLDRIIELL 55 (58)
T ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHH
Confidence 445566666655434445568999999999885
No 221
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.80 E-value=65 Score=26.98 Aligned_cols=31 Identities=13% Similarity=0.189 Sum_probs=24.9
Q ss_pred HhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 519 LLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 519 ~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
++..+...+.+.+.+.|+.|.++|||+|..+
T Consensus 41 ~la~~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 41 ELAERLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 3444556788999999999999999999653
No 222
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=20.66 E-value=1.1e+02 Score=32.66 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=34.3
Q ss_pred HHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHHHhhh
Q 043775 427 AILDLFNASNRLSYSQVITQLNLTHDDLVRLLHSLSI 463 (554)
Q Consensus 427 ~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~sL~~ 463 (554)
.||++|.....++-.+|...++++.++++..|..++.
T Consensus 341 ~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~ 377 (421)
T PF04801_consen 341 YILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAV 377 (421)
T ss_pred HHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhh
Confidence 3889999999999999999999999999999999963
No 223
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=20.59 E-value=1.4e+02 Score=29.16 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=26.1
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
++.-|-.|+++.- .+.+|++||++.+|+|...++..|.
T Consensus 117 Lp~~~R~v~lL~~-~eg~S~~EIAe~LgiS~~tVksrL~ 154 (228)
T PRK06704 117 LNVQQSAILLLKD-VFQYSIADIAKVCSVSEGAVKASLF 154 (228)
T ss_pred CCHHHhhHhhhHH-hhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3454555554432 2368999999999999987766543
No 224
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=20.56 E-value=59 Score=31.69 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=26.9
Q ss_pred HhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 519 LLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 519 ~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
+|..+|..+...+.++|+.|++.|+|.|..+
T Consensus 38 eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 68 (241)
T PRK11402 38 ELCTQYNVSRITIRKAISDLVADGVLIRWQG 68 (241)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4555699999999999999999999999753
No 225
>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=20.54 E-value=1.2e+02 Score=26.37 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=39.1
Q ss_pred ecHHHHHHHHHhhCC--------CccCHHHHHHHhCCCHHHHHHHHHHhhhccceeeeec
Q 043775 421 ISTYHAAILDLFNAS--------NRLSYSQVITQLNLTHDDLVRLLHSLSILYYKILIKE 472 (554)
Q Consensus 421 vs~~Q~~ILllFN~~--------~~lt~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 472 (554)
+..+.-..|+..|.. -..+.++|+..++-+.+.++.+|..|. +++++...
T Consensus 27 ~~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 27 TIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344555666665543 478999999999999999999999995 78888754
No 226
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.50 E-value=1.5e+02 Score=26.54 Aligned_cols=35 Identities=3% Similarity=-0.048 Sum_probs=24.3
Q ss_pred cHHHHHHH-HHhhCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 422 STYHAAIL-DLFNASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 422 s~~Q~~IL-llFN~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
+.-+-.|+ +.|- +.+|++||++.+|++...++..+
T Consensus 111 ~~~~r~v~~l~~~--~~~s~~EIA~~lgis~~tV~~~l 146 (163)
T PRK07037 111 PARTRYAFEMYRL--HGETQKDIARELGVSPTLVNFMI 146 (163)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHH
Confidence 44444444 3332 36799999999999998877654
No 227
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.43 E-value=1.1e+02 Score=28.40 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=23.1
Q ss_pred CccCHHHHHHHhCCCHHHHHHHHHHh
Q 043775 436 NRLSYSQVITQLNLTHDDLVRLLHSL 461 (554)
Q Consensus 436 ~~lt~~ei~~~t~i~~~~l~~~L~sL 461 (554)
+.+|.+||++.+|+++..+.+.|...
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999988755
No 228
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=20.37 E-value=63 Score=31.51 Aligned_cols=32 Identities=13% Similarity=0.383 Sum_probs=27.4
Q ss_pred HHhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 518 ELLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 518 ~~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
.+|..+|..+...+.++|+.|++.|||.|..+
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34555799999999999999999999998653
No 229
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=20.14 E-value=76 Score=25.73 Aligned_cols=31 Identities=10% Similarity=0.116 Sum_probs=26.0
Q ss_pred HhccCCCCChHHHHHHHHhhhhhcccccCCC
Q 043775 519 LLGRMFKPAVKAFKKRIEGLISQDYLERYPE 549 (554)
Q Consensus 519 ~l~~~F~~~~~~iK~~Ie~LIereyl~Rd~~ 549 (554)
++...+..+.+.+-+.+..|.++|||.|.++
T Consensus 4 ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 4 EIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 3444567888999999999999999999874
No 230
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.13 E-value=1.4e+02 Score=28.12 Aligned_cols=37 Identities=16% Similarity=0.138 Sum_probs=24.9
Q ss_pred cHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHHH
Q 043775 422 STYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLLH 459 (554)
Q Consensus 422 s~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L~ 459 (554)
+.-|-.|+.+. ..+.+|++||++.+|++...++..|.
T Consensus 141 p~~~r~v~~L~-~~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 141 PEQIGRVFMMR-EFLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred CHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44344444332 13467999999999999988775443
No 231
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.10 E-value=1.4e+02 Score=27.43 Aligned_cols=37 Identities=8% Similarity=0.048 Sum_probs=24.7
Q ss_pred ecHHHHHHHHHhhCCCccCHHHHHHHhCCCHHHHHHHH
Q 043775 421 ISTYHAAILDLFNASNRLSYSQVITQLNLTHDDLVRLL 458 (554)
Q Consensus 421 vs~~Q~~ILllFN~~~~lt~~ei~~~t~i~~~~l~~~L 458 (554)
+|.-|-.|+.+. ..+.+|++||++.+|+|...++..|
T Consensus 118 Lp~~~r~i~~l~-~~e~~s~~EIA~~lgis~~tV~~~l 154 (179)
T PRK12543 118 LPYKLRQVIILR-YLHDYSQEEIAQLLQIPIGTVKSRI 154 (179)
T ss_pred CCHHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHH
Confidence 345555444442 1246799999999999998765543
Done!