Query 006074
Match_columns 662
No_of_seqs 206 out of 1042
Neff 8.7
Searched_HMMs 46136
Date Thu Mar 28 17:58:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006074.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006074hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167 Cullins [Cell cycle co 100.0 5E-122 1E-126 951.4 47.9 655 4-662 1-661 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 5E-113 1E-117 948.5 61.1 647 3-660 62-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 2E-108 5E-113 869.1 55.4 652 1-662 78-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 2E-100 5E-105 756.2 47.3 622 2-662 55-728 (728)
5 PF00888 Cullin: Cullin family 100.0 2.2E-87 4.8E-92 763.5 56.8 541 1-564 36-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 7.4E-84 1.6E-88 644.3 51.5 655 3-662 57-777 (777)
7 smart00182 CULLIN Cullin. 100.0 1.1E-33 2.3E-38 259.9 17.4 141 344-485 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 8.3E-30 1.8E-34 270.0 44.0 491 129-652 223-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 2E-19 4.4E-24 141.7 3.6 66 591-656 1-68 (68)
10 TIGR01610 phage_O_Nterm phage 95.6 0.04 8.7E-07 46.5 6.5 66 491-564 20-93 (95)
11 PF09339 HTH_IclR: IclR helix- 94.6 0.047 1E-06 40.3 3.8 46 499-546 6-52 (52)
12 PF13412 HTH_24: Winged helix- 94.2 0.092 2E-06 38.0 4.6 46 495-542 2-47 (48)
13 PF02082 Rrf2: Transcriptional 94.0 0.15 3.4E-06 41.7 6.0 59 497-562 11-70 (83)
14 PF12802 MarR_2: MarR family; 93.8 0.076 1.6E-06 40.6 3.7 51 494-546 3-55 (62)
15 PF08220 HTH_DeoR: DeoR-like h 93.0 0.15 3.3E-06 38.5 4.0 47 498-546 2-48 (57)
16 PF13463 HTH_27: Winged helix 92.3 0.2 4.3E-06 39.1 4.1 51 494-546 1-52 (68)
17 PF01047 MarR: MarR family; I 92.1 0.11 2.4E-06 39.3 2.3 51 494-546 1-51 (59)
18 PF01022 HTH_5: Bacterial regu 91.6 0.43 9.3E-06 34.3 4.8 44 497-543 3-46 (47)
19 PF12840 HTH_20: Helix-turn-he 91.4 0.26 5.6E-06 37.7 3.7 49 495-545 9-57 (61)
20 TIGR02337 HpaR homoprotocatech 91.3 0.39 8.4E-06 42.2 5.3 52 493-546 25-76 (118)
21 PRK11512 DNA-binding transcrip 90.4 0.56 1.2E-05 42.9 5.6 54 492-547 36-89 (144)
22 smart00550 Zalpha Z-DNA-bindin 89.2 0.7 1.5E-05 36.2 4.5 48 497-546 7-56 (68)
23 TIGR01889 Staph_reg_Sar staphy 88.8 1.1 2.3E-05 38.8 5.9 54 492-547 21-78 (109)
24 smart00346 HTH_ICLR helix_turn 88.8 1.2 2.6E-05 36.9 6.0 46 499-546 8-54 (91)
25 PF08539 HbrB: HbrB-like; Int 88.6 3.9 8.6E-05 37.9 9.7 85 7-95 54-155 (158)
26 PF04492 Phage_rep_O: Bacterio 88.1 1.6 3.5E-05 37.0 6.2 62 493-564 29-98 (100)
27 PF01978 TrmB: Sugar-specific 87.1 0.47 1E-05 37.1 2.3 51 494-546 6-56 (68)
28 COG3682 Predicted transcriptio 87.0 1.1 2.3E-05 39.3 4.6 62 598-662 6-67 (123)
29 TIGR02698 CopY_TcrY copper tra 86.8 1.3 2.9E-05 39.7 5.3 60 600-662 6-65 (130)
30 smart00347 HTH_MARR helix_turn 86.4 1.3 2.9E-05 37.1 5.0 53 491-545 5-57 (101)
31 PHA00738 putative HTH transcri 86.3 1.6 3.5E-05 37.1 5.2 68 491-564 7-74 (108)
32 smart00420 HTH_DEOR helix_turn 86.2 1.5 3.2E-05 31.8 4.5 45 499-545 3-47 (53)
33 PRK11920 rirA iron-responsive 85.8 2.4 5.2E-05 39.2 6.7 57 499-562 13-69 (153)
34 PRK10857 DNA-binding transcrip 85.7 2.5 5.3E-05 39.6 6.7 57 499-562 13-70 (164)
35 PRK15090 DNA-binding transcrip 84.9 2 4.3E-05 43.5 6.3 143 499-652 17-197 (257)
36 PRK13777 transcriptional regul 84.2 2.2 4.7E-05 40.8 5.7 53 492-546 41-93 (185)
37 TIGR02010 IscR iron-sulfur clu 84.2 2.9 6.2E-05 37.8 6.3 45 499-545 13-58 (135)
38 PRK03573 transcriptional regul 83.2 2.3 5.1E-05 38.7 5.4 54 492-547 27-81 (144)
39 PF04703 FaeA: FaeA-like prote 82.9 2.5 5.4E-05 32.4 4.4 46 501-548 5-51 (62)
40 COG3355 Predicted transcriptio 82.8 3.1 6.7E-05 36.8 5.6 38 507-546 39-76 (126)
41 PF05584 Sulfolobus_pRN: Sulfo 82.2 3.4 7.4E-05 32.5 5.0 42 501-545 10-51 (72)
42 PF08279 HTH_11: HTH domain; 81.9 2.9 6.3E-05 30.9 4.5 36 500-535 4-40 (55)
43 PF05732 RepL: Firmicute plasm 81.8 2.7 5.7E-05 39.4 5.2 48 510-566 75-122 (165)
44 PF01978 TrmB: Sugar-specific 81.6 0.83 1.8E-05 35.7 1.5 56 600-661 10-65 (68)
45 PF03965 Penicillinase_R: Peni 81.0 0.76 1.6E-05 40.2 1.2 61 599-662 4-64 (115)
46 smart00419 HTH_CRP helix_turn_ 80.9 3.7 8E-05 29.1 4.7 34 510-545 8-41 (48)
47 COG1959 Predicted transcriptio 80.7 4.2 9.2E-05 37.4 6.0 59 497-562 11-70 (150)
48 cd00090 HTH_ARSR Arsenical Res 80.6 3.5 7.6E-05 32.1 5.0 48 495-545 6-53 (78)
49 PF13601 HTH_34: Winged helix 80.6 1.3 2.8E-05 36.0 2.3 44 499-544 3-46 (80)
50 KOG2167 Cullins [Cell cycle co 80.6 5.9 0.00013 43.7 7.9 201 32-248 191-416 (661)
51 TIGR00738 rrf2_super rrf2 fami 80.3 4.3 9.3E-05 36.3 5.9 46 498-545 12-58 (132)
52 PRK10870 transcriptional repre 80.0 4.3 9.3E-05 38.5 6.1 53 493-547 52-106 (176)
53 PRK10141 DNA-binding transcrip 79.6 3.6 7.9E-05 36.0 5.0 61 496-562 16-76 (117)
54 TIGR03879 near_KaiC_dom probab 79.4 2.4 5.1E-05 33.6 3.3 39 504-544 26-64 (73)
55 smart00345 HTH_GNTR helix_turn 79.3 3.6 7.8E-05 30.6 4.4 40 505-546 14-54 (60)
56 PF09012 FeoC: FeoC like trans 79.2 1.7 3.7E-05 34.1 2.6 45 603-653 5-49 (69)
57 TIGR01884 cas_HTH CRISPR locus 78.7 3.3 7.2E-05 40.2 5.0 52 493-546 140-191 (203)
58 COG1414 IclR Transcriptional r 78.7 4.5 9.8E-05 40.6 6.1 46 499-546 7-53 (246)
59 smart00418 HTH_ARSR helix_turn 78.1 4.4 9.6E-05 30.4 4.7 36 508-545 8-43 (66)
60 smart00550 Zalpha Z-DNA-bindin 77.1 6.1 0.00013 30.9 5.1 54 599-658 7-62 (68)
61 PRK11569 transcriptional repre 77.1 4.9 0.00011 41.1 5.9 46 499-546 31-77 (274)
62 PRK10163 DNA-binding transcrip 77.1 5.3 0.00011 40.8 6.1 56 499-562 28-84 (271)
63 TIGR02944 suf_reg_Xantho FeS a 76.8 6.1 0.00013 35.3 5.8 44 500-545 13-58 (130)
64 smart00344 HTH_ASNC helix_turn 75.9 4.8 0.0001 34.5 4.7 46 497-544 4-49 (108)
65 PF08784 RPA_C: Replication pr 75.5 4.3 9.3E-05 34.6 4.2 48 493-542 44-95 (102)
66 PRK09834 DNA-binding transcrip 75.3 5.6 0.00012 40.4 5.8 47 499-547 14-61 (263)
67 PF01325 Fe_dep_repress: Iron 74.0 6.4 0.00014 29.9 4.4 44 501-546 13-56 (60)
68 PF08221 HTH_9: RNA polymerase 73.8 4.3 9.4E-05 31.1 3.4 35 507-543 24-58 (62)
69 COG1846 MarR Transcriptional r 73.5 6.8 0.00015 34.0 5.2 51 494-546 20-70 (126)
70 TIGR02431 pcaR_pcaU beta-ketoa 73.3 7.6 0.00016 39.0 6.1 45 499-545 12-57 (248)
71 PRK11014 transcriptional repre 73.2 9.8 0.00021 34.5 6.2 50 505-561 20-69 (141)
72 PF13404 HTH_AsnC-type: AsnC-t 72.6 6.5 0.00014 27.5 3.8 36 499-534 6-41 (42)
73 PF08318 COG4: COG4 transport 72.4 1E+02 0.0022 32.4 14.6 159 202-367 8-213 (331)
74 PF01726 LexA_DNA_bind: LexA D 72.2 7.1 0.00015 30.3 4.3 55 595-654 7-62 (65)
75 PF13730 HTH_36: Helix-turn-he 71.6 9 0.0002 28.2 4.7 29 512-542 27-55 (55)
76 COG2345 Predicted transcriptio 69.6 7.1 0.00015 38.1 4.6 44 499-544 14-57 (218)
77 PF09012 FeoC: FeoC like trans 69.4 6.1 0.00013 30.9 3.5 43 501-545 5-47 (69)
78 PF08280 HTH_Mga: M protein tr 67.6 7.4 0.00016 29.4 3.5 38 498-535 7-44 (59)
79 cd00092 HTH_CRP helix_turn_hel 66.8 9.4 0.0002 29.2 4.1 36 509-546 24-59 (67)
80 PRK10434 srlR DNA-bindng trans 65.6 7.9 0.00017 39.1 4.3 49 497-547 6-54 (256)
81 PF02002 TFIIE_alpha: TFIIE al 64.1 5 0.00011 34.3 2.2 44 498-543 15-58 (105)
82 PF13412 HTH_24: Winged helix- 63.8 13 0.00027 26.6 4.0 45 599-649 4-48 (48)
83 PF13463 HTH_27: Winged helix 63.3 13 0.00028 28.5 4.3 51 600-656 5-58 (68)
84 cd07377 WHTH_GntR Winged helix 62.1 15 0.00033 27.7 4.5 39 506-546 20-59 (66)
85 TIGR00373 conserved hypothetic 61.4 14 0.0003 34.4 4.7 43 499-543 17-59 (158)
86 PF01726 LexA_DNA_bind: LexA D 61.0 11 0.00024 29.2 3.4 52 494-547 4-61 (65)
87 PF10771 DUF2582: Protein of u 61.0 14 0.00031 28.6 3.9 37 499-535 11-47 (65)
88 PF14394 DUF4423: Domain of un 60.9 22 0.00047 33.5 6.0 55 490-546 18-75 (171)
89 COG1349 GlpR Transcriptional r 60.8 11 0.00024 38.0 4.4 49 498-548 7-55 (253)
90 PRK11179 DNA-binding transcrip 60.2 15 0.00032 33.9 4.8 50 493-544 6-55 (153)
91 COG4189 Predicted transcriptio 59.6 14 0.00031 35.9 4.5 50 495-546 22-71 (308)
92 PRK06266 transcription initiat 59.5 15 0.00033 34.8 4.7 44 498-543 24-67 (178)
93 PF00325 Crp: Bacterial regula 59.2 11 0.00025 24.6 2.6 30 510-541 2-31 (32)
94 PRK00215 LexA repressor; Valid 58.6 21 0.00045 34.6 5.7 52 494-547 2-59 (205)
95 TIGR02702 SufR_cyano iron-sulf 58.1 23 0.0005 34.3 5.9 44 500-545 5-48 (203)
96 PRK11169 leucine-responsive tr 58.1 16 0.00034 34.2 4.6 49 494-544 12-60 (164)
97 PRK13509 transcriptional repre 57.4 17 0.00036 36.7 4.9 50 497-548 6-55 (251)
98 PF04545 Sigma70_r4: Sigma-70, 54.6 31 0.00068 24.7 4.7 32 500-533 12-43 (50)
99 PRK10906 DNA-binding transcrip 54.4 17 0.00038 36.6 4.5 50 497-548 6-55 (252)
100 PRK04424 fatty acid biosynthes 54.1 14 0.0003 35.4 3.5 47 497-545 8-54 (185)
101 smart00418 HTH_ARSR helix_turn 53.4 27 0.00058 25.9 4.5 46 603-655 2-47 (66)
102 PRK09802 DNA-binding transcrip 53.0 18 0.0004 36.8 4.4 50 496-547 17-66 (269)
103 PF08220 HTH_DeoR: DeoR-like h 52.9 19 0.0004 27.0 3.4 47 601-653 3-49 (57)
104 PF01638 HxlR: HxlR-like helix 52.0 23 0.0005 29.3 4.1 45 498-545 7-52 (90)
105 COG1522 Lrp Transcriptional re 52.0 26 0.00055 32.0 4.9 49 494-544 6-54 (154)
106 PF08281 Sigma70_r4_2: Sigma-7 51.6 29 0.00062 25.3 4.2 24 509-532 25-48 (54)
107 TIGR00498 lexA SOS regulatory 51.5 31 0.00066 33.3 5.6 51 494-546 4-60 (199)
108 PF10007 DUF2250: Uncharacteri 51.1 30 0.00064 28.9 4.5 53 492-546 3-55 (92)
109 PF12395 DUF3658: Protein of u 51.0 34 0.00073 29.7 5.2 62 598-660 48-109 (111)
110 cd07153 Fur_like Ferric uptake 50.8 31 0.00067 29.8 5.0 58 602-660 5-63 (116)
111 PRK04172 pheS phenylalanyl-tRN 50.6 25 0.00055 39.2 5.5 51 493-545 3-53 (489)
112 PRK10411 DNA-binding transcrip 49.7 26 0.00056 35.0 4.8 46 498-545 6-51 (240)
113 smart00344 HTH_ASNC helix_turn 49.6 24 0.00051 30.1 4.0 46 599-650 4-49 (108)
114 PF11994 DUF3489: Protein of u 48.9 36 0.00078 26.9 4.4 47 495-541 9-55 (72)
115 PF12324 HTH_15: Helix-turn-he 48.0 47 0.001 26.6 4.9 38 498-535 26-63 (77)
116 PF02796 HTH_7: Helix-turn-hel 47.8 26 0.00056 24.7 3.3 31 500-532 13-43 (45)
117 PF04967 HTH_10: HTH DNA bindi 47.6 52 0.0011 24.4 4.9 30 505-534 18-47 (53)
118 PF09681 Phage_rep_org_N: N-te 47.2 29 0.00063 30.6 4.1 50 494-545 27-86 (121)
119 COG4742 Predicted transcriptio 47.2 30 0.00066 34.8 4.8 43 501-546 18-60 (260)
120 PF12802 MarR_2: MarR family; 46.9 21 0.00046 26.7 3.0 48 600-653 7-56 (62)
121 PF01853 MOZ_SAS: MOZ/SAS fami 46.7 20 0.00043 34.1 3.2 27 509-535 149-175 (188)
122 PF05158 RNA_pol_Rpc34: RNA po 46.6 18 0.0004 37.9 3.3 145 492-654 80-260 (327)
123 PF06784 UPF0240: Uncharacteri 46.5 33 0.00072 32.5 4.7 64 467-535 96-161 (179)
124 PHA02943 hypothetical protein; 46.1 37 0.0008 30.9 4.6 54 501-561 16-69 (165)
125 PF01047 MarR: MarR family; I 46.0 19 0.00042 26.8 2.6 47 600-652 5-51 (59)
126 PF02186 TFIIE_beta: TFIIE bet 45.9 18 0.00038 28.1 2.3 55 599-662 6-61 (65)
127 PF00392 GntR: Bacterial regul 45.3 24 0.00053 26.9 3.1 39 506-546 19-58 (64)
128 PF09339 HTH_IclR: IclR helix- 44.8 30 0.00066 25.1 3.4 44 603-652 8-52 (52)
129 PF04182 B-block_TFIIIC: B-blo 44.7 33 0.00071 27.3 3.8 50 495-546 1-52 (75)
130 PRK06474 hypothetical protein; 44.4 60 0.0013 30.8 6.2 52 493-546 8-61 (178)
131 cd06170 LuxR_C_like C-terminal 44.1 50 0.0011 23.8 4.6 39 495-535 2-40 (57)
132 smart00421 HTH_LUXR helix_turn 44.0 50 0.0011 23.7 4.6 39 495-535 5-43 (58)
133 COG1522 Lrp Transcriptional re 43.7 30 0.00066 31.5 4.0 50 597-652 7-56 (154)
134 PF09756 DDRGK: DDRGK domain; 43.7 21 0.00047 34.0 3.0 58 599-662 100-157 (188)
135 PF09763 Sec3_C: Exocyst compl 43.5 6E+02 0.013 29.8 21.5 112 157-284 570-701 (701)
136 PRK11050 manganese transport r 43.0 48 0.001 30.5 5.2 44 500-545 41-84 (152)
137 TIGR02844 spore_III_D sporulat 42.8 43 0.00092 27.2 4.1 35 497-532 7-41 (80)
138 TIGR01714 phage_rep_org_N phag 41.9 34 0.00074 30.1 3.7 49 495-545 28-84 (119)
139 smart00420 HTH_DEOR helix_turn 41.4 43 0.00094 23.8 3.8 45 603-653 5-49 (53)
140 PRK03902 manganese transport t 41.2 45 0.00097 30.2 4.7 43 500-544 12-54 (142)
141 PF03444 HrcA_DNA-bdg: Winged 41.2 89 0.0019 25.2 5.6 48 497-546 10-57 (78)
142 COG4190 Predicted transcriptio 41.0 97 0.0021 27.6 6.2 68 495-564 63-133 (144)
143 PF14947 HTH_45: Winged helix- 40.7 48 0.001 26.5 4.2 43 499-544 9-51 (77)
144 PRK11169 leucine-responsive tr 39.4 48 0.001 30.9 4.6 47 598-650 14-60 (164)
145 PF13384 HTH_23: Homeodomain-l 38.8 38 0.00082 24.2 3.1 33 501-535 10-42 (50)
146 PF09114 MotA_activ: Transcrip 37.3 47 0.001 27.3 3.5 47 499-547 19-67 (96)
147 PRK00135 scpB segregation and 36.9 94 0.002 29.8 6.2 111 447-564 34-153 (188)
148 PF06163 DUF977: Bacterial pro 36.7 83 0.0018 27.8 5.2 48 496-545 12-59 (127)
149 KOG2747 Histone acetyltransfer 36.2 45 0.00097 35.5 4.2 67 469-535 281-354 (396)
150 smart00753 PAM PCI/PINT associ 36.1 64 0.0014 26.2 4.4 36 506-543 20-55 (88)
151 smart00088 PINT motif in prote 36.1 64 0.0014 26.2 4.4 36 506-543 20-55 (88)
152 COG1321 TroR Mn-dependent tran 36.1 65 0.0014 29.7 4.9 45 500-546 14-58 (154)
153 PRK10681 DNA-binding transcrip 35.6 52 0.0011 33.1 4.6 39 497-535 8-46 (252)
154 PRK11179 DNA-binding transcrip 35.6 51 0.0011 30.3 4.1 47 598-650 9-55 (153)
155 PF00196 GerE: Bacterial regul 35.5 68 0.0015 23.8 4.1 40 494-535 4-43 (58)
156 PF01399 PCI: PCI domain; Int 34.9 57 0.0012 27.1 4.1 45 497-543 47-91 (105)
157 COG3355 Predicted transcriptio 34.7 60 0.0013 28.8 4.1 41 606-652 36-76 (126)
158 PF08461 HTH_12: Ribonuclease 34.4 65 0.0014 25.0 3.9 50 602-652 2-52 (66)
159 PLN03238 probable histone acet 34.4 64 0.0014 32.8 4.8 39 497-535 209-248 (290)
160 PF08784 RPA_C: Replication pr 34.3 40 0.00086 28.5 2.9 45 598-648 47-95 (102)
161 PF13545 HTH_Crp_2: Crp-like h 33.8 52 0.0011 25.8 3.4 34 510-545 28-61 (76)
162 PRK09334 30S ribosomal protein 33.3 44 0.00095 27.5 2.8 36 627-662 50-85 (86)
163 cd06171 Sigma70_r4 Sigma70, re 33.3 93 0.002 21.7 4.5 40 494-534 11-50 (55)
164 TIGR02698 CopY_TcrY copper tra 33.0 1.1E+02 0.0024 27.3 5.7 50 494-545 2-55 (130)
165 PF09904 HTH_43: Winged helix- 32.6 1E+02 0.0022 25.5 4.7 40 501-543 13-52 (90)
166 PRK04214 rbn ribonuclease BN/u 32.6 1.1E+02 0.0024 33.3 6.8 39 505-545 305-343 (412)
167 smart00347 HTH_MARR helix_turn 32.0 83 0.0018 25.8 4.6 48 599-652 11-58 (101)
168 smart00531 TFIIE Transcription 31.9 55 0.0012 29.9 3.7 29 507-535 12-40 (147)
169 PF00165 HTH_AraC: Bacterial r 31.2 67 0.0015 22.0 3.2 28 508-535 6-33 (42)
170 COG1654 BirA Biotin operon rep 31.2 96 0.0021 25.1 4.4 34 502-535 11-44 (79)
171 PF00538 Linker_histone: linke 31.1 1.2E+02 0.0026 24.1 5.1 54 598-652 8-65 (77)
172 PF13542 HTH_Tnp_ISL3: Helix-t 30.9 1.2E+02 0.0026 21.7 4.7 35 497-533 16-50 (52)
173 PRK14165 winged helix-turn-hel 30.9 89 0.0019 30.7 5.1 45 499-545 10-54 (217)
174 PRK13239 alkylmercury lyase; P 30.7 89 0.0019 30.3 4.9 39 497-535 23-61 (206)
175 cd07977 TFIIE_beta_winged_heli 30.5 61 0.0013 25.9 3.2 58 597-662 8-70 (75)
176 PHA03103 double-strand RNA-bin 30.4 1.1E+02 0.0024 29.1 5.4 44 501-546 18-61 (183)
177 PF09107 SelB-wing_3: Elongati 30.3 1E+02 0.0022 22.5 4.1 42 502-545 2-43 (50)
178 PF02270 TFIIF_beta: Transcrip 29.9 74 0.0016 32.5 4.6 58 496-563 216-273 (275)
179 smart00526 H15 Domain in histo 29.5 1.7E+02 0.0037 22.4 5.5 53 598-651 10-64 (66)
180 cd07153 Fur_like Ferric uptake 29.2 1.2E+02 0.0026 26.1 5.2 57 500-561 5-67 (116)
181 PRK10430 DNA-binding transcrip 29.2 85 0.0018 31.0 4.9 49 494-544 159-210 (239)
182 TIGR01889 Staph_reg_Sar staphy 29.2 1.1E+02 0.0024 26.2 4.9 41 609-655 40-82 (109)
183 COG2512 Predicted membrane-ass 28.8 71 0.0015 32.3 4.1 49 497-547 197-245 (258)
184 TIGR00122 birA_repr_reg BirA b 28.7 1.8E+02 0.0038 22.4 5.6 39 501-542 5-43 (69)
185 smart00762 Cog4 COG4 transport 28.4 3.7E+02 0.008 28.2 9.6 54 201-254 7-64 (324)
186 TIGR01610 phage_O_Nterm phage 28.4 95 0.0021 25.9 4.2 38 609-652 44-81 (95)
187 KOG2905 Transcription initiati 27.4 82 0.0018 31.0 4.0 57 498-564 188-244 (254)
188 PF06163 DUF977: Bacterial pro 27.1 1.3E+02 0.0028 26.6 4.8 52 596-653 10-61 (127)
189 smart00346 HTH_ICLR helix_turn 26.7 1.1E+02 0.0025 24.7 4.5 45 603-653 10-55 (91)
190 TIGR02989 Sig-70_gvs1 RNA poly 26.5 1.1E+02 0.0023 27.8 4.7 38 493-532 111-149 (159)
191 COG1510 Predicted transcriptio 26.2 77 0.0017 29.6 3.5 57 502-564 34-91 (177)
192 COG0735 Fur Fe2+/Zn2+ uptake r 26.1 97 0.0021 28.2 4.2 52 492-545 17-74 (145)
193 PF01638 HxlR: HxlR-like helix 26.1 82 0.0018 25.9 3.4 54 601-660 8-63 (90)
194 PRK12423 LexA repressor; Provi 25.8 1.1E+02 0.0023 29.7 4.7 52 494-547 4-61 (202)
195 PLN03239 histone acetyltransfe 25.6 99 0.0021 32.5 4.5 39 497-535 267-309 (351)
196 PHA02591 hypothetical protein; 25.6 86 0.0019 25.1 3.1 25 509-533 58-82 (83)
197 TIGR02787 codY_Gpos GTP-sensin 25.3 1.4E+02 0.003 29.7 5.2 44 501-546 188-232 (251)
198 KOG3054 Uncharacterized conser 25.1 88 0.0019 30.8 3.8 56 601-662 203-258 (299)
199 TIGR02147 Fsuc_second hypothet 24.9 1.7E+02 0.0037 29.8 6.1 35 510-546 137-173 (271)
200 PRK11512 DNA-binding transcrip 24.9 1.2E+02 0.0026 27.3 4.6 45 602-652 44-88 (144)
201 PF07106 TBPIP: Tat binding pr 24.7 1.3E+02 0.0029 28.0 5.0 59 498-562 3-64 (169)
202 COG1378 Predicted transcriptio 24.3 1E+02 0.0022 30.9 4.4 52 492-545 12-63 (247)
203 COG2771 CsgD DNA-binding HTH d 24.0 1.9E+02 0.0042 21.4 5.0 41 493-535 4-44 (65)
204 TIGR00721 tfx DNA-binding prot 23.7 1.5E+02 0.0032 26.8 4.8 40 493-534 6-45 (137)
205 smart00529 HTH_DTXR Helix-turn 23.5 97 0.0021 25.5 3.5 32 513-546 2-33 (96)
206 PF04760 IF2_N: Translation in 23.0 53 0.0011 24.1 1.5 22 510-531 3-24 (54)
207 PRK09462 fur ferric uptake reg 22.7 1.6E+02 0.0036 26.7 5.1 51 601-652 20-72 (148)
208 PF04157 EAP30: EAP30/Vps36 fa 22.7 2.4E+02 0.0052 27.7 6.6 81 444-543 132-221 (223)
209 PRK10046 dpiA two-component re 22.7 1.2E+02 0.0026 29.6 4.5 43 500-544 166-209 (225)
210 PF03428 RP-C: Replication pro 22.5 1.1E+02 0.0024 28.9 4.0 32 512-545 72-104 (177)
211 PRK13713 conjugal transfer pro 22.0 5.4E+02 0.012 22.5 10.2 39 93-131 3-44 (118)
212 COG1733 Predicted transcriptio 21.8 1.6E+02 0.0035 25.9 4.6 44 499-545 26-70 (120)
213 PRK00118 putative DNA-binding 21.5 1.5E+02 0.0033 25.3 4.2 39 495-534 19-57 (104)
214 PLN00104 MYST -like histone ac 21.3 1.4E+02 0.003 32.7 4.7 38 498-535 361-399 (450)
215 PF00356 LacI: Bacterial regul 21.1 1.2E+02 0.0026 21.6 3.0 21 512-532 1-21 (46)
216 PHA02701 ORF020 dsRNA-binding 21.1 2.2E+02 0.0047 27.0 5.5 45 500-546 8-53 (183)
217 TIGR02337 HpaR homoprotocatech 21.0 1.6E+02 0.0034 25.4 4.5 47 600-652 30-76 (118)
218 PRK09333 30S ribosomal protein 20.9 1.1E+02 0.0023 28.1 3.3 50 497-548 54-117 (150)
219 TIGR03338 phnR_burk phosphonat 20.9 1.2E+02 0.0025 29.3 4.0 42 504-547 28-69 (212)
220 PRK12529 RNA polymerase sigma 20.8 1.2E+02 0.0025 28.5 3.8 38 494-532 128-165 (178)
221 PRK09642 RNA polymerase sigma 20.8 1.4E+02 0.003 27.2 4.3 37 494-532 107-144 (160)
222 PRK12525 RNA polymerase sigma 20.6 1.5E+02 0.0032 27.4 4.5 33 498-532 124-156 (168)
223 PF13601 HTH_34: Winged helix 20.5 61 0.0013 26.2 1.5 45 601-651 3-47 (80)
224 TIGR02983 SigE-fam_strep RNA p 20.3 1.4E+02 0.003 27.3 4.2 40 494-534 111-150 (162)
225 PF13936 HTH_38: Helix-turn-he 20.2 1.7E+02 0.0037 20.4 3.6 24 509-532 19-42 (44)
226 PRK10906 DNA-binding transcrip 20.2 83 0.0018 31.7 2.8 46 600-651 7-52 (252)
227 PRK03975 tfx putative transcri 20.2 1.9E+02 0.0041 26.3 4.7 38 493-532 6-43 (141)
228 TIGR02716 C20_methyl_CrtF C-20 20.0 1.3E+02 0.0028 31.1 4.3 35 509-545 22-56 (306)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.5e-122 Score=951.39 Aligned_cols=655 Identities=65% Similarity=1.007 Sum_probs=632.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcc-CCCcccHHHHHHHHHH
Q 006074 4 NLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ-TPNVRSLWDMGLQLFR 82 (662)
Q Consensus 4 ~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~-~~~~~~i~~l~l~~f~ 82 (662)
.||+.+++.+++|+++.+..+-..+.+...+|..+.++|..|...+.+++++|.||||.|+.. ++..+|+|++++.+||
T Consensus 1 ~ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR 80 (661)
T KOG2167|consen 1 VLYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFR 80 (661)
T ss_pred ChHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHH
Confidence 389999999999999888777666666678999999999999999999999999999999999 7789999999999999
Q ss_pred HHhcC--CcchHHHHHHHHHHHHHHHhCCCcCChHHHHHHHHHHhhhhccHHhhhHHHHHHHHHHHHHHHHHHhhcCChh
Q 006074 83 KYLSS--YSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVP 160 (662)
Q Consensus 83 ~~v~~--~~~~~~~l~~~ll~~I~~~R~g~~i~~~~ik~~i~ml~~l~~Y~~~fE~~~l~~t~~yY~~~s~~~~~~~~~~ 160 (662)
.+++. .+.+..++.++++..++++|.|+++|+..|++++.|+.++++|.+.|+..|++.+.++|..+..+..++..++
T Consensus 81 ~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~ 160 (661)
T KOG2167|consen 81 AHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVP 160 (661)
T ss_pred HHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccH
Confidence 99998 6788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCHHHHHHHHHHhccc-chHHHHH
Q 006074 161 DYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLR 239 (662)
Q Consensus 161 ~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~il~~gl~~ll~~~~~~~L~~ly~l~~~~-~~l~~l~ 239 (662)
+||++++.++.+|.+++..+++.++...+..++++.|+..|++.|+..|+..+++..++.++.+||.|++++ ++...++
T Consensus 161 eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~ 240 (661)
T KOG2167|consen 161 EYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLL 240 (661)
T ss_pred HHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHH
Confidence 999999999999999999999988877799999999999999999999999999999999999999999999 8999999
Q ss_pred HHHHHHHHHHhchhccCccchHHHHHHHHHHHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHH
Q 006074 240 QALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDE 317 (662)
Q Consensus 240 ~~~~~~i~~~g~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~--~~~~~~~~~af~~~ln~~~~~~~e~La~y~d~ 317 (662)
..|++|++..|.+++.+...++++|+.++.++++.+-++..||..+ ..|..++++||+.|+|..++++||+||+|.|.
T Consensus 241 qq~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAelIak~~dt 320 (661)
T KOG2167|consen 241 QQWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAELIAKYVDT 320 (661)
T ss_pred HHHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999988 99999999999999999999999999999999
Q ss_pred HhhcCCCCCCHHHHHhhhhccceeeEeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhccchhHhHHHHH
Q 006074 318 KLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMF 397 (662)
Q Consensus 318 ~lk~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml 397 (662)
.|+.|+++.++++++..+++++.||||+..||+|+.+|++.||+|||.++|+|.|+|+.|+++||.+||..||+||++|+
T Consensus 321 ~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMf 400 (661)
T KOG2167|consen 321 KLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMF 400 (661)
T ss_pred HHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCc
Q 006074 398 KDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLG 477 (662)
Q Consensus 398 ~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~ 477 (662)
+|+..|++++..|+.+...++..+.++ +.|.|+|.|+||.+++.++.||++|.++++.|..||..+|.||+|.|.+++|
T Consensus 401 kdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg 479 (661)
T KOG2167|consen 401 KDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLG 479 (661)
T ss_pred hhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCc
Confidence 999999999999999865534444455 9999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEecCceEEEEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeE
Q 006074 478 HCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSF 557 (662)
Q Consensus 478 ~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~ 557 (662)
+|.+++.|+.|++++.||++|++||++||+++.+|++||.+.|+|.+.+|+++|+||.||+.++|.++|+|+.+.+++.|
T Consensus 480 ~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f 559 (661)
T KOG2167|consen 480 HCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKF 559 (661)
T ss_pred chhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCCCcceEEecccccccchhhhhhhhHHHHHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHH
Q 006074 558 VFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKK 637 (662)
Q Consensus 558 ~~N~~f~~~~~~i~i~~~~~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~ 637 (662)
.+|..|+++..||+|++|..|++.+|++.|.++|.+||++.||||||||||+||+|+|+.|+.++.++++||+.+ ++|+
T Consensus 560 ~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlkfpv~~-d~kk 638 (661)
T KOG2167|consen 560 IVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLKFPVKP-DLKK 638 (661)
T ss_pred EechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcCCCCCh-hHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999988 9999
Q ss_pred HHHhhhhhccccccCCCCCceeecC
Q 006074 638 RIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 638 ~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
|||+||+|||++|| +| +.|.|||
T Consensus 639 riesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 639 RIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHHhHHHhccc-cc-ccccccC
Confidence 99999999999999 44 8999998
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.6e-113 Score=948.45 Aligned_cols=647 Identities=39% Similarity=0.670 Sum_probs=604.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCcccHHHHH-HHHH
Q 006074 3 GNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMG-LQLF 81 (662)
Q Consensus 3 e~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~~i~~l~-l~~f 81 (662)
++||+++++++.+|+.+.+.+....+++ +.+|..+...|.+|+.++.+++++|+||||+||.++.+..++++++ +.+|
T Consensus 62 ~~lY~~l~~~~~~yl~~~~~~~~~~~~~-~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~ 140 (725)
T KOG2166|consen 62 QQLYDKYREVIEEYLIQTVLPALREKHD-EYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCF 140 (725)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEe
Confidence 8999999999999999999888877765 7999999999999999999999999999999999773366777766 9999
Q ss_pred HHHhcCCcchHHHHHHHHHHHHHHHhCCCcCChHHHHHHHHHHhhhh-----ccHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 006074 82 RKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALG-----IYSESFEKPFLECTSEFYAAEGMKYMQQ 156 (662)
Q Consensus 82 ~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~~~~ik~~i~ml~~l~-----~Y~~~fE~~~l~~t~~yY~~~s~~~~~~ 156 (662)
+..+... ++.+.++++++.+|..+|.|++||+..|+++++|+..+| +|..+||++|++.|+.||..+++.|+..
T Consensus 141 r~~v~~~-~~~~~~~~all~lI~~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~ 219 (725)
T KOG2166|consen 141 RDLVYKF-EMQSEAIDALLALIHKEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEE 219 (725)
T ss_pred ehHHHHH-HHHHHHHHHHHHHHHhhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhh
Confidence 9988765 699999999999999999999999999999999999986 9999999999999999999999999998
Q ss_pred CChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHH---HhHHHHhhccCCHHHHHHHHHHhccc-
Q 006074 157 SDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAIL---DKGFTMLMDGHRTEDLQRMYSLFSRV- 232 (662)
Q Consensus 157 ~~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~il---~~gl~~ll~~~~~~~L~~ly~l~~~~- 232 (662)
.++.+|+.+++.++.+|..|+..|++..+.+++...+...++..+++.++ .+|+..|+.+++.++|.+||++++++
T Consensus 220 ~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~ 299 (725)
T KOG2166|consen 220 NSCLDYLKKIEECLKEERERVTHYLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRIL 299 (725)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhccc
Confidence 89999999999999999999999988877777888888888877777666 58999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHhchhccCc-----cchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcCCCCc
Q 006074 233 NALESLRQALAMYIRRTGHGIVMDE-----EKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRP 307 (662)
Q Consensus 233 ~~l~~l~~~~~~~i~~~g~~~~~~~-----~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~~~~~~~~af~~~ln~~~~~~ 307 (662)
+|++.+.+.+..|++.+|..++... .+++.+++.+++++++|..++..||+++..|.++++.||..|+|.+...+
T Consensus 300 ~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~ 379 (725)
T KOG2166|consen 300 PGLEPLASVFKQHVREEGNALVARPAETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATS 379 (725)
T ss_pred ccchhHHHHHHHHHHhhHHHHhhhhhhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCc
Confidence 9999999999999999998777432 45789999999999999999999999999999999999999999998544
Q ss_pred HHHHHHHHHHHhhcCCCCCCHHHHHhhhhccceeeEeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhcc
Q 006074 308 AELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGS 387 (662)
Q Consensus 308 ~e~La~y~d~~lk~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~ 387 (662)
+|+||+|||..+|++.++.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|++.|+.||.+|+++||.
T Consensus 380 ~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~ 459 (725)
T KOG2166|consen 380 AELLATYCDDILKKGSKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGE 459 (725)
T ss_pred HHHHHHHhHHHhcccccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHh
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHhHHHHHhhHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCC
Q 006074 388 QFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSG 467 (662)
Q Consensus 388 ~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~ 467 (662)
+||+||++|++|+..|++++..|.++ .+ .....+++|.|.|||+|+||.+++.++.||++|.++++.|..||..+|+|
T Consensus 460 ~~T~kL~~Mf~D~~~s~~l~~~F~~~-~~-~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~g 537 (725)
T KOG2166|consen 460 QFTSKLEGMFTDLTLSRELQTAFADY-AN-YSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNG 537 (725)
T ss_pred HHHHHHHhhcccHHHHHHHHHHHHhh-hc-hhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCC
Confidence 99999999999999999999999976 21 22335799999999999999988888999999999999999999999999
Q ss_pred eeeEeccCCceEEEEEEecCceEEEEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 468 RRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 468 R~L~w~~~l~~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
|+|+|+|++|+|+|.++|.+++++++||++||+||++||+.+.+|+++|.+.|+++.+++.+.|+||++.|.+++.. |.
T Consensus 538 R~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~ 616 (725)
T KOG2166|consen 538 RRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PM 616 (725)
T ss_pred CeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-cc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998767666666 77
Q ss_pred CCCCCCCCeEEEecCCCCCcceEEecccccccchhhhhhhhHHHHHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhc-
Q 006074 548 GRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL- 626 (662)
Q Consensus 548 ~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l- 626 (662)
++. ++++.|.+|.+|+++.+|++++.++.+ |.+.+.+.+++||+..|+||||||||+||.+.|++|+.||.+|+
T Consensus 617 s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~ 691 (725)
T KOG2166|consen 617 SRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLS 691 (725)
T ss_pred ccC-CCCcEEEeeccccCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence 766 889999999999999999999977654 66778889999999999999999999999999999999999999
Q ss_pred -CCCCChhhHHHHHHhhhhhccccccCCCCCceee
Q 006074 627 -KFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 660 (662)
Q Consensus 627 -~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 660 (662)
||.|++.+||+|||.|||||||+|| +|+++|.|
T Consensus 692 ~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 692 ERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred hhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 7999999999999999999999999 89999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-108 Score=869.08 Aligned_cols=652 Identities=36% Similarity=0.578 Sum_probs=592.7
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCC----CcccHHHH
Q 006074 1 MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP----NVRSLWDM 76 (662)
Q Consensus 1 ~ge~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~----~~~~i~~l 76 (662)
+|+.||+++....+.++.....+.. ..+.++||..++..|++|..++.+++++|.||||+|++..+ .+..++++
T Consensus 78 ~~s~li~~L~~~~k~~i~~~~~~~s--~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~sl 155 (773)
T COG5647 78 LGSRLIQKLVDYAKNYIEEYNRGRS--QENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSL 155 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccc--chhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehh
Confidence 4788999999999999988765421 12347999999999999999999999999999999999221 25677788
Q ss_pred HHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCcCChHHHHHHHHHHhhh-----------hccHHhhhHHHHHHHHHH
Q 006074 77 GLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTAL-----------GIYSESFEKPFLECTSEF 145 (662)
Q Consensus 77 ~l~~f~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~~~~ik~~i~ml~~l-----------~~Y~~~fE~~~l~~t~~y 145 (662)
++..|+-.+|. .+.+.+++.+|..+.+.|.|+.+|+..+..++.|+..+ .+|.+.||+.||+.|.+|
T Consensus 156 cl~~~~~~~f~--~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~f 233 (773)
T COG5647 156 CLVKEKIESFR--LIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEF 233 (773)
T ss_pred hhhHHHHHHHH--hhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHH
Confidence 99999998886 79999999999999999999999999999999999998 589999999999999999
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHH--hHHHHhhccCCHHHHH
Q 006074 146 YAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILD--KGFTMLMDGHRTEDLQ 223 (662)
Q Consensus 146 Y~~~s~~~~~~~~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~il~--~gl~~ll~~~~~~~L~ 223 (662)
|..++++.+..+++.+||.+|..++++|..++..|++.++..++..+++++||.+|.+.+.. +|+..+++..+.+.|.
T Consensus 234 Y~~ess~~i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~ 313 (773)
T COG5647 234 YEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQ 313 (773)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999885 3899999999999999
Q ss_pred HHHHHhccc-chHHHHHHHHHHHHHHHhc--h-----hcc----------CccchHHHHHHHHHHHHHHHHHHHHhcCCC
Q 006074 224 RMYSLFSRV-NALESLRQALAMYIRRTGH--G-----IVM----------DEEKDKDMVSSLLEFKASLDTIWEQSFSKN 285 (662)
Q Consensus 224 ~ly~l~~~~-~~l~~l~~~~~~~i~~~g~--~-----~~~----------~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~ 285 (662)
.+|++++++ .++..|.+.|.+||++.|. . ++. .+..+..+++.++++++.+..++.+.|.+|
T Consensus 314 ~lY~l~se~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D 393 (773)
T COG5647 314 VLYRLLSETKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGD 393 (773)
T ss_pred HHHHHhhhhhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCc
Confidence 999999999 7899999999999999991 1 110 123367999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCC---CcHHHHHHHHHHHhhcCCCCCCHHHHHhhhhccceeeEeccChhHHHHHHHHHHHHH
Q 006074 286 EAFCNTIKDAFEYLINLRQN---RPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKR 362 (662)
Q Consensus 286 ~~~~~~~~~af~~~ln~~~~---~~~e~La~y~d~~lk~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~R 362 (662)
..+..++++||+.|+|.+.. .++|+||+|+|.++|++.+......++..+.+++.||+|+.+||+|+++|+++||||
T Consensus 394 ~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKR 473 (773)
T COG5647 394 GSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKR 473 (773)
T ss_pred chHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 99999999999999998542 589999999999999987654456688888999999999999999999999999999
Q ss_pred hcCCCCCChHHHHHHHHHHHHHhccchhHhHHHHHhhHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCC-
Q 006074 363 LLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP- 441 (662)
Q Consensus 363 LL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~- 441 (662)
||+++|.|.+.|..||++||+.||.+||+|+++||+|+..|.++...|+....+ ..+.+++.|.||++.+||..+.
T Consensus 474 LL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~ 550 (773)
T COG5647 474 LLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEE 550 (773)
T ss_pred HhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccc
Confidence 999999999999999999999999999999999999999999999999874422 2256899999999999997665
Q ss_pred CCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEE---ecHHHHHHHHHhcCCCCCCHHHHHH
Q 006074 442 MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELA---VSLFQTVVLMLFNDAQKLSFQDIKD 518 (662)
Q Consensus 442 ~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~---vs~~Q~~iLl~Fn~~~~~t~~ei~~ 518 (662)
..+.||++|.+.++.|++||.++|+||+|.|.++||+|+|+++|+.|++.+. ++++|+.|+++||+++++|+++|.+
T Consensus 551 ~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e 630 (773)
T COG5647 551 VSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILE 630 (773)
T ss_pred cccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHh
Confidence 6899999999999999999999999999999999999999999998854443 6689999999999999999999999
Q ss_pred HhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCCCcceEEecccccccchhhhhhhhHHHHHhhHhh
Q 006074 519 ATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQ 598 (662)
Q Consensus 519 ~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~~~~~e~~~~~~~~~~~r~~~ 598 (662)
.|+++.++++++|+||+ +.+++...++++.+++++.|.+|++|+++..||+++.+..++..+++..+.+.+++||+..
T Consensus 631 ~T~l~~~dl~~~L~sl~--~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~ 708 (773)
T COG5647 631 LTKLSTDDLKRVLQSLS--CAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAE 708 (773)
T ss_pred hcCCChhhHHHHHHHHH--hhheeeeccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHH
Confidence 99999999999999999 6666666566888999999999999999999999998776655566777778999999999
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhc--CCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
+|||||||||++|+|.|++|+++|+.+. ||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 709 lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 709 LQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 9999999999999999999999999999 7999999999999999999999998888 7899997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-100 Score=756.24 Aligned_cols=622 Identities=27% Similarity=0.490 Sum_probs=576.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCC-------------
Q 006074 2 GGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP------------- 68 (662)
Q Consensus 2 ge~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~------------- 68 (662)
||.||..++.++.+|+...+......+ ++..|..|.+.|+.|..+..++..+|.|||..|+++++
T Consensus 55 ~erly~e~k~~i~~hvrq~~~~~v~~~--p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~ 132 (728)
T KOG2284|consen 55 SERLYNEVKACIQEHVRQKRQDIVDVD--PDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAF 132 (728)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhhhcCC--HHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcch
Confidence 899999999999999998776655433 35799999999999999999999999999999999864
Q ss_pred ----CcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCcCC-hHHHHHHHHHHhhhh---------------
Q 006074 69 ----NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVD-RTLLNHLLKMFTALG--------------- 128 (662)
Q Consensus 69 ----~~~~i~~l~l~~f~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~-~~~ik~~i~ml~~l~--------------- 128 (662)
++..|..+|+.+|++.++. ++...|+.-++..|.++|.|+.++ ...+.+++..|+.+.
T Consensus 133 ~~~~~~~eig~lal~~w~~~~v~--~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryk 210 (728)
T KOG2284|consen 133 LQIPDVKEIGCLALEIWKEDLVK--TILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYK 210 (728)
T ss_pred hcCCcHHHHhHHHHHHHHHHHHH--HHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchh
Confidence 2446778899999999985 799999999999999999999888 577888888887652
Q ss_pred -------ccHHhhhHHHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHH
Q 006074 129 -------IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERH 201 (662)
Q Consensus 129 -------~Y~~~fE~~~l~~t~~yY~~~s~~~~~~~~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~ 201 (662)
+|++.||.|||.+|.+||+.+++..+++.+|++|+.+|..++++|+-||..|||+++..++...|++.+|..|
T Consensus 211 a~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h 290 (728)
T KOG2284|consen 211 ARESTTAFYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAH 290 (728)
T ss_pred hccccHHHHHHHhccccccchHHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHHHHhhccCCHHHHHHHHHHhccc-chHHHHHHHHHHHHHHHhchhccCc---cchHHHHHHHHHHHHHHHHH
Q 006074 202 ISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTI 277 (662)
Q Consensus 202 ~~~il~~gl~~ll~~~~~~~L~~ly~l~~~~-~~l~~l~~~~~~~i~~~g~~~~~~~---~~~~~~i~~ll~l~~~~~~l 277 (662)
.+.+ .-.+..++.+.+..|++.||.|+..+ -|+..+...|.+||.+.|...++.. .-+..||+.++.+|.+|..+
T Consensus 291 ~~~l-ha~ch~~i~~e~~~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~ 369 (728)
T KOG2284|consen 291 KDKL-HAVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDM 369 (728)
T ss_pred HHHH-HHHHHHHHhhhhhhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHH
Confidence 9865 67899999999999999999999999 8999999999999999999887653 34679999999999999999
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHhhcCC-----CCcHHHHHHHHHHHhhcCCCCCCHHHHHhhhhccceeeEeccChhHHH
Q 006074 278 WEQSFSKNEAFCNTIKDAFEYLINLRQ-----NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFE 352 (662)
Q Consensus 278 ~~~~F~~~~~~~~~~~~af~~~ln~~~-----~~~~e~La~y~d~~lk~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~ 352 (662)
+...|.+|..|..+++.|+..++|... .+.+|.||+|||.+|+++.+|+++.++|.+|+..+.+|+|+.|||+|.
T Consensus 370 ~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifq 449 (728)
T KOG2284|consen 370 KTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQ 449 (728)
T ss_pred HHHHhcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHH
Confidence 999999999999999999999999754 268999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhccchhHhHHHHHhhHHHHHHHHHHHHHHhhhccCCCCCccEEEEEee
Q 006074 353 AFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLT 432 (662)
Q Consensus 353 ~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt 432 (662)
++|.++||+||+.+.|.|.|.|..||++||+.||++||+++- +.|+..|.+++++|.+.+.+
T Consensus 450 kfys~mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~n---------------- 511 (728)
T KOG2284|consen 450 KFYSKMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIAN---------------- 511 (728)
T ss_pred HHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHHh----------------
Confidence 999999999999999999999999999999999999999998 99999999999999875432
Q ss_pred cCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEecHHHHHHHHHhcCCCCCC
Q 006074 433 TGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLS 512 (662)
Q Consensus 433 ~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~~~~t 512 (662)
+.+|.+|+..++.|+.||..+|+||+|+|++.++++++++++-++.|.-.++++||++||+||..+.++
T Consensus 512 -----------f~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~ 580 (728)
T KOG2284|consen 512 -----------FHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAIL 580 (728)
T ss_pred -----------ccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccch
Confidence 679999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCCCcceEEecccc-cccchhhhhhhhHHH
Q 006074 513 FQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQ-MKETVEENTSTTERV 591 (662)
Q Consensus 513 ~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~-~~~~~~e~~~~~~~~ 591 (662)
+.+|.+.+|++.+.|.+.+.++. ..++|..... .+..+..|++|.+|++++.+.++.+++ .|.++.|.+.+...+
T Consensus 581 ~k~i~~~~~~~~~~l~kti~til--dv~~~~~d~~--~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v 656 (728)
T KOG2284|consen 581 VKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCDDQ--NLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTV 656 (728)
T ss_pred HHhhhhhhCccHHHHHHHHHHHH--hceeeccccc--ccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhh
Confidence 99999999999999999999999 8888887543 567788999999999999999987644 345677888888899
Q ss_pred HHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhc--CCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 592 FQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 592 ~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
.+||++.++||||||||+||.+.|+.|+.+|+.|. ||.|++++||++||.||++.||+|.+.+ +.|.|+|
T Consensus 657 ~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 657 SQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 99999999999999999999999999999999999 6999999999999999999999999865 7899997
No 5
>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=2.2e-87 Score=763.47 Aligned_cols=541 Identities=43% Similarity=0.725 Sum_probs=491.5
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCcccHHHHHHHH
Q 006074 1 MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQL 80 (662)
Q Consensus 1 ~ge~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~~i~~l~l~~ 80 (662)
+|+.||+++++.+.+|+..++.++.+..+ .++|..|.++|.+|+.++.+|+++|+||||+|+.++ +
T Consensus 36 ~~~~LY~~l~~~i~~~~~~~~~~l~~~~~--~~~l~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~------------~ 101 (588)
T PF00888_consen 36 YGEQLYDKLKEFISEYLKNIIESLLSSSD--EDLLEEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN------------L 101 (588)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHCTTTT--CHHHHHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT------------H
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhcCh--hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh------------h
Confidence 69999999999999999999888776533 699999999999999999999999999999999774 9
Q ss_pred HHHHhcCCcchHHHHHHHHHHHHHHHhCCCcCChHHHHHHHHHHhhhh---ccHHhhhHHHHHHHHHHHHHHHHHHhhcC
Q 006074 81 FRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALG---IYSESFEKPFLECTSEFYAAEGMKYMQQS 157 (662)
Q Consensus 81 f~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~~~~ik~~i~ml~~l~---~Y~~~fE~~~l~~t~~yY~~~s~~~~~~~ 157 (662)
|++.|+. ++.+.++++++++|.++|.|+.+|+..++.+++|++++| +|.+.||++|++.|.+||+.++ +.+.
T Consensus 102 f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~ 176 (588)
T PF00888_consen 102 FREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELGSLEVYEEEFEKPFLEETKEYYKSES---IQEN 176 (588)
T ss_dssp HHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTTHTHHHHHHTHHHHHHHHHHHHHHHH---HHHS
T ss_pred HHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccchHHhhHHHHHHHHHHHHHHHHHHHH---HHhc
Confidence 9999986 599999999999999999999999999999999999765 8999999999999999999999 5777
Q ss_pred ChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCHHHHHHHHHHhccc-chHH
Q 006074 158 DVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALE 236 (662)
Q Consensus 158 ~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~il~~gl~~ll~~~~~~~L~~ly~l~~~~-~~l~ 236 (662)
++.+|+++|+.++.+|.+|+..|++++|.+++.+++.++||.+|.+.+ .+|+..|+++++.++|+++|++++++ ++++
T Consensus 177 ~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l-~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~ 255 (588)
T PF00888_consen 177 SVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL-SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLE 255 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH-HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHH
T ss_pred CchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHHHHHHHHHhhcccCCCc
Confidence 999999999999999999999999999999999999999999999987 78999999999999999999999999 9999
Q ss_pred HHHHHHHHHHHHHhchhccC---ccchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcCCCCcHHHHHH
Q 006074 237 SLRQALAMYIRRTGHGIVMD---EEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAK 313 (662)
Q Consensus 237 ~l~~~~~~~i~~~g~~~~~~---~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~~~~~~~~af~~~ln~~~~~~~e~La~ 313 (662)
.+++.|++||...|.+++.. ...+..+|+.+++++++++.++.+||++++.|..++++||+.++|.+..+++++||+
T Consensus 256 ~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~e~La~ 335 (588)
T PF00888_consen 256 SLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKNNNKIPELLAK 335 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCSTSHHHHHHHH
T ss_pred hHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcCCcchHHHHHH
Confidence 99999999999999999865 356789999999999999999999999999999999999999999996689999999
Q ss_pred HHHHHhhcCCCCCCHHHHHhhhhccceeeEeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhccchhHhH
Q 006074 314 FLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKL 393 (662)
Q Consensus 314 y~d~~lk~~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl 393 (662)
|||.+++++.++.++++++..++.++.+|+|+++||+|+.+|+++||+|||.+++.+.+.|..+|++|+.+||.+++++|
T Consensus 336 y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl 415 (588)
T PF00888_consen 336 YCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKL 415 (588)
T ss_dssp HHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHH
T ss_pred HhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHH
Confidence 99999999987788889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhHHHHHHHHHHHHHHhhhccCCCC--CccEEEEEeecCCCCCCCCCC-ccCChhHHHHHHHHHHHHhhcCCCeee
Q 006074 394 EGMFKDIELSKEINESFKQSSQARTKLPS--GIEMSVHVLTTGYWPTYPPMD-VRLPHELNVYQDIFKEFYLSKYSGRRL 470 (662)
Q Consensus 394 ~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~--~~~~~~~VLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L 470 (662)
++|++|+..|++++++|++...+ .+... +++|+|.||++++||..+..+ +.+|++|+.+++.|++||+++|+||+|
T Consensus 416 ~~M~~D~~~S~~~~~~f~~~~~~-~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L 494 (588)
T PF00888_consen 416 EVMLKDIKNSKELNEEFKQKQSQ-NNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKL 494 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHT-TT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEE
T ss_pred HHHHHHHhhcHHHHHHHHHHhhh-ccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEE
Confidence 99999999999999999998765 22222 799999999999999998876 999999999999999999999999999
Q ss_pred EeccCCceEEEEEEecCceEEEEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee--cCCCC
Q 006074 471 MWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ--KLPKG 548 (662)
Q Consensus 471 ~w~~~l~~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~--~~~~~ 548 (662)
+|.|.+|+|+|++++++|+++++||++||+||++||+++++|+++|++.||+++++++++|.+|+ +.+++. +.+++
T Consensus 495 ~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~--~~~~l~~~~~~~~ 572 (588)
T PF00888_consen 495 TWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLV--KSKILILLKEPNS 572 (588)
T ss_dssp EEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCC--TTTTCSEEETTTS
T ss_pred EEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHH--hCCcceeecCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999 777766 67888
Q ss_pred CCCCCCCeEEEecCCC
Q 006074 549 RDVEDDDSFVFNEGFT 564 (662)
Q Consensus 549 ~~~~~~~~~~~N~~f~ 564 (662)
+++++++.|.+|.+|+
T Consensus 573 ~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 573 KSFSDNDEFSVNENFT 588 (588)
T ss_dssp SS--TT-EEEE-TT--
T ss_pred CCCCCCCEEEeCCCCC
Confidence 9999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.4e-84 Score=644.29 Aligned_cols=655 Identities=28% Similarity=0.453 Sum_probs=583.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCC-------CcccHHH
Q 006074 3 GNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-------NVRSLWD 75 (662)
Q Consensus 3 e~LY~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~-------~~~~i~~ 75 (662)
.++|+-+++.+.+++.+...++.+..++ ..+|..|..+|.+|....+++.-.|.-|+..-....+ +-.+|..
T Consensus 57 aKI~d~L~~dI~efi~qAq~rv~s~q~d-~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRk 135 (777)
T KOG2285|consen 57 AKIRDILTRDINEFIHQAQKRVRSLQTD-GALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRK 135 (777)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccc-cHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHH
Confidence 3688999999999999877777655544 6899999999999999999999999999987544332 2358999
Q ss_pred HHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCcCChHHHHHHHHHHhhhh--------ccHHhhhHHHHHHHHHHHH
Q 006074 76 MGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALG--------IYSESFEKPFLECTSEFYA 147 (662)
Q Consensus 76 l~l~~f~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~i~~~~ik~~i~ml~~l~--------~Y~~~fE~~~l~~t~~yY~ 147 (662)
+.+..|.+++|. .++.+|+.+.+.++..+|.|+.+|.+.+-++-+.++.|. +|++.||..||+.|.+||+
T Consensus 136 lMLd~WNe~IF~--nIk~rLq~sAmklVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr 213 (777)
T KOG2285|consen 136 LMLDKWNEIIFM--NIKERLQVSAMKLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYR 213 (777)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999997 699999999999999999999999999989999998874 9999999999999999999
Q ss_pred HHHHHHhhcCChhHHHHHHHHHHHHHHHHHhhhcCC--CcHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCHHHHHHH
Q 006074 148 AEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRM 225 (662)
Q Consensus 148 ~~s~~~~~~~~~~~Yl~~v~~~i~eE~~r~~~~l~~--~t~~~l~~~l~~~LI~~~~~~il~~gl~~ll~~~~~~~L~~l 225 (662)
..+..++++.++-+|++++...++||+.|+.+||.+ .+..++++++.++|+.++.+.|+ -.+..|+...+++-|.+|
T Consensus 214 ~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIl-AEC~~lI~~~etErL~lm 292 (777)
T KOG2285|consen 214 KICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTIL-AECSKLIASKETERLQLM 292 (777)
T ss_pred HHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhhhHHHHHHH
Confidence 999999999999999999999999999999999965 78899999999999999999998 468999999999999999
Q ss_pred HHHhccc-chHHHHHHHHHHHHHHHhchhccC-----ccchHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 006074 226 YSLFSRV-NALESLRQALAMYIRRTGHGIVMD-----EEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYL 299 (662)
Q Consensus 226 y~l~~~~-~~l~~l~~~~~~~i~~~g~~~~~~-----~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~~~~~~~~af~~~ 299 (662)
|+|+.++ .|++.+...+..||+..|.+-+.. ..++..+|+.|+.++++|..++.+.|..|+.|..|.+.||+.+
T Consensus 293 frLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaV 372 (777)
T KOG2285|consen 293 FRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAV 372 (777)
T ss_pred HHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHh
Confidence 9999999 999999999999999999876532 2345699999999999999999999999999999999999999
Q ss_pred hhcCC--------------------CCcHHHHHHHHHHHhhcCC--CCCCHHHHHhhhhccceeeEeccChhHHHHHHHH
Q 006074 300 INLRQ--------------------NRPAELIAKFLDEKLRAGN--KGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKK 357 (662)
Q Consensus 300 ln~~~--------------------~~~~e~La~y~d~~lk~~~--~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~ 357 (662)
+|... +++||+||.|||.++|+.. |.++.+|++.+|.+++-+++|+.+||+|..|++.
T Consensus 373 VNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHka 452 (777)
T KOG2285|consen 373 VNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKA 452 (777)
T ss_pred hcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHH
Confidence 99631 3689999999999999964 5678899999999999999999999999999999
Q ss_pred HHHHHhcCCCCCChHHHHHHHHHHHHHhc--cchhHhHHHHHhhHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCC
Q 006074 358 DLAKRLLLGKSASIDAEKSMISKLKTECG--SQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGY 435 (662)
Q Consensus 358 ~La~RLL~~~s~s~~~E~~~i~~Lk~~~G--~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~ 435 (662)
+|++||+.+.|++.+.|..|++.|+ +|| .+|++|+..||+|++.|+++++.|++.+...+.....-.+++.||+.|.
T Consensus 453 HLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGA 531 (777)
T KOG2285|consen 453 HLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGA 531 (777)
T ss_pred HHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccc
Confidence 9999999999999999999999998 577 5799999999999999999999999977542222334567889999999
Q ss_pred CCCCCC-CCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEEEecHHHHHHHHHhcCC--CCCC
Q 006074 436 WPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLS 512 (662)
Q Consensus 436 WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~--~~~t 512 (662)
|...+. ..+.||.+|++.+-..++||+++|+||+|+|.|+++.++|++.-+-|.|++.|+++||+||.+||+. +.+|
T Consensus 532 W~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS 611 (777)
T KOG2285|consen 532 WGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKIS 611 (777)
T ss_pred cccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccc
Confidence 987754 5799999999999999999999999999999999999999977666899999999999999999985 6999
Q ss_pred HHHHHHHhCCCHHHHHHHhhHhhc-CC--ccceecCCCC----CCCCCCCeEEEecCCCC-----CcceEEecccccc--
Q 006074 513 FQDIKDATGIEDKELRRTLQSLAC-GK--VRVLQKLPKG----RDVEDDDSFVFNEGFTA-----PLYRIKVNAIQMK-- 578 (662)
Q Consensus 513 ~~ei~~~t~i~~~~l~~~L~~L~~-~k--~~iL~~~~~~----~~~~~~~~~~~N~~f~~-----~~~~i~i~~~~~~-- 578 (662)
++.+.-.|.+|+.+|+++|-||+. || ..||..+|+. +++.++..|.+|.+|.- ..+|.+++.|..-
T Consensus 612 ~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQL 691 (777)
T KOG2285|consen 612 LENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQL 691 (777)
T ss_pred hHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeee
Confidence 999999999999999999999997 65 6788887753 67888999999999962 2346677655321
Q ss_pred cchhhhhhhhHHHHHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhcC--CCCChhhHHHHHHhhhhhccccccCCCCC
Q 006074 579 ETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLK--FPIKPADLKKRIESLIDREYLERDKNNPQ 656 (662)
Q Consensus 579 ~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~--F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 656 (662)
.+....++..+.+.+-|-...+-+|++|||.||+++..+|..+..+-++ |.|...+||+.||.|||..|++||++|-+
T Consensus 692 stEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDIN 771 (777)
T KOG2285|consen 692 STERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDIN 771 (777)
T ss_pred hhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhcc
Confidence 1222223334678899999999999999999999999999999999995 99999999999999999999999999999
Q ss_pred ceeecC
Q 006074 657 IYNYLA 662 (662)
Q Consensus 657 ~y~Yia 662 (662)
+|+|+|
T Consensus 772 tFiYia 777 (777)
T KOG2285|consen 772 TFIYIA 777 (777)
T ss_pred ceeeeC
Confidence 999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=1.1e-33 Score=259.89 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=132.5
Q ss_pred eccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhccchhHhHHHHHhhHHHHHHHHHHHHHHhhhccCCCCC
Q 006074 344 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 423 (662)
Q Consensus 344 ~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 423 (662)
|++|||+|+.+|+++||+|||..++++.+.|..+|++||.+||.++|++|++|++|++.|++++++|++...+ .+...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~-~~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLEN-NSNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999987754 223357
Q ss_pred ccEEEEEeecCCCCCCCC-CCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEe
Q 006074 424 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 485 (662)
Q Consensus 424 ~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~ 485 (662)
++|+|.|||+++||..+. .++.+|++|+.+++.|++||..+|+||+|+|+|++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999888 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.3e-30 Score=270.03 Aligned_cols=491 Identities=20% Similarity=0.259 Sum_probs=325.6
Q ss_pred ccHHhhhHHHHHHHHHHHHHHHHHHhhcCC-------hhH--HHHHHHHHHHHHHHHHhhhcCC-CcHHHHHHHHHHHHH
Q 006074 129 IYSESFEKPFLECTSEFYAAEGMKYMQQSD-------VPD--YLKHVEIRLHEEHERCLLYLDV-STRKPLIATAERQLL 198 (662)
Q Consensus 129 ~Y~~~fE~~~l~~t~~yY~~~s~~~~~~~~-------~~~--Yl~~v~~~i~eE~~r~~~~l~~-~t~~~l~~~l~~~LI 198 (662)
.|...+-..+.+-..++..+++..-....+ +.. |=..+.-++++=.+.+..|.++ .+...+..+++..=-
T Consensus 223 ~~~~s~l~s~~~wI~~~~~~wl~~V~~~e~~~~~~~~l~~~~~~~fa~lr~~~~f~Iv~dyPdS~~aiedLK~cle~t~q 302 (765)
T KOG2165|consen 223 VWDRSVLESFNKWINTVWGQWLKLVFSQESDHAFKLTLDYFFYEIFARLRINEIFDIVLDYPDSKPAIEDLKYCLERTDQ 302 (765)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcccccceeeeeHHHHHHHHHHHHHhhHHHHHHhCCccchhHHHHHHHHHHhcc
Confidence 455555555555555555555444222211 112 2233444666666777888765 455555555554332
Q ss_pred HHHHHHHHHhHHHH-hh-ccCCHHHHHHHHHHhcc-------c-chHHHHHHHHHHHHHHHhchhccCccchHHHHHHHH
Q 006074 199 ERHISAILDKGFTM-LM-DGHRTEDLQRMYSLFSR-------V-NALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLL 268 (662)
Q Consensus 199 ~~~~~~il~~gl~~-ll-~~~~~~~L~~ly~l~~~-------~-~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~i~~ll 268 (662)
..++-.-+-+.+.. +| ...++.|+-..|--.-+ . -.++..+..++.|++.+-.++ +..|..|.
T Consensus 303 r~~ltesfi~~l~~riL~asv~T~DIL~~YVstIkalr~lDptgV~Le~v~~pIR~YLr~R~DtV-------k~iVs~lt 375 (765)
T KOG2165|consen 303 RVYLTESFISDLKTRILTASVDTVDILLRYVSTIKALRVLDPTGVILEKVTEPIRDYLRERKDTV-------KQIVSGLT 375 (765)
T ss_pred hHHHHHHHHHHHHhhhcCCCCcHHHHHHHHHHHHHHHHhhCCcceehHHhhHhHHHHHhhCccHH-------HHHHHHHh
Confidence 22221111123333 22 45578888777754322 2 257899999999999874432 11122211
Q ss_pred HH------------HHHHHHHHHH--hcCCCHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHhhcCCCCCCHHHHHhh
Q 006074 269 EF------------KASLDTIWEQ--SFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGT 334 (662)
Q Consensus 269 ~l------------~~~~~~l~~~--~F~~~~~~~~~~~~af~~~ln~~~~~~~e~La~y~d~~lk~~~~~~~~~e~~~~ 334 (662)
+. -.+.+..-++ -++.|..-.. ...++ +.|..|+ | +|.---+|+++...
T Consensus 376 ~~~k~~~~~Dl~~els~~d~~~~e~i~~n~D~~td~--~~~~e-~~~W~Pd-P-------iDA~pg~~s~k~r~------ 438 (765)
T KOG2165|consen 376 DLPKSEGEKDLSAELSKVDTLHDEDIGENDDSPTDD--FMNYE-ILNWMPD-P-------IDADPGKGSSKYRK------ 438 (765)
T ss_pred cCCccCCcccHHHHHhccCccchhhcccCcCCCcch--hhhhh-hhhccCC-C-------ccCCCCCCCccccc------
Confidence 11 1111100000 1111111111 11233 3355443 2 34433333332211
Q ss_pred hhccceeeEeccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhccchhHhHHHHHhhHHHHHHHHHHHHHHh
Q 006074 335 LDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSS 414 (662)
Q Consensus 335 l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~ 414 (662)
.|-+..+...+.+|+.|++.||++||.|||....++.+.|..-++.||-++|....+.|++|++|+..|+++++.+++..
T Consensus 439 ~Di~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~ 518 (765)
T KOG2165|consen 439 VDIFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNES 518 (765)
T ss_pred ccHHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhh
Confidence 22334556667999999999999999999999999999999999999999999999999999999999999999998842
Q ss_pred --hhccCCCCCccEEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEEecCceEEE
Q 006074 415 --QARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKEL 492 (662)
Q Consensus 415 --~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l 492 (662)
..+....+.+.+++.+||+.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|.|+++++|.+++.++
T Consensus 519 ~~~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~ 598 (765)
T KOG2165|consen 519 ELSRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVL 598 (765)
T ss_pred hhhcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEE
Confidence 211112235788999999999999988899999999999999999999999999999999999999999999999999
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCCCcceEEe
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKV 572 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i 572 (662)
+||+.||+|+.+|.+.++||++++++.+|||.+.+++.|..|+ +.|+|..+|.. ++..+|+++++=.+..+- .
T Consensus 599 tVsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~~---s~tgt~T~iEse~d~~q~--~ 671 (765)
T KOG2165|consen 599 TVSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPII---SDTGTLTVIESEMDFDQA--E 671 (765)
T ss_pred eeCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCCC---CCCceeeecccccccccc--C
Confidence 9999999999999999999999999999999999999999999 99999998753 677899999854332111 1
Q ss_pred cccccccchhhhhh--hhHHHHHhh--HhhhhhhhhhhhcCCCCCChHHHHHHHHHhc-----CCCCChhhHHHHHHhhh
Q 006074 573 NAIQMKETVEENTS--TTERVFQDR--QYQVDAAIVRIMKTRKVLSHTLLITELFQQL-----KFPIKPADLKKRIESLI 643 (662)
Q Consensus 573 ~~~~~~~~~~e~~~--~~~~~~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l-----~F~~~~~~ik~~Ie~Li 643 (662)
.++.. +..++..+ ....+.+-+ -..-...||..+-.-+.|..+.+.+. .+.. ...++-++++.-+..++
T Consensus 672 ~~~~~-e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnm-LkmF~~~~~~~~~TlqeL~~fLq~kV 749 (765)
T KOG2165|consen 672 GTVLL-EAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNM-LKMFVPPDGSAEITLQELQGFLQRKV 749 (765)
T ss_pred CCccc-ccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHH-HeeeecCCCCCcccHHHHHHHHHHHh
Confidence 11111 11111111 111222211 22344588887777799998876533 3322 13456688888888888
Q ss_pred hhccccccC
Q 006074 644 DREYLERDK 652 (662)
Q Consensus 644 ereyi~r~~ 652 (662)
..|-|+-.+
T Consensus 750 ~e~kL~f~~ 758 (765)
T KOG2165|consen 750 REGKLEFIA 758 (765)
T ss_pred hccceEEec
Confidence 888777664
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=99.76 E-value=2e-19 Score=141.69 Aligned_cols=66 Identities=59% Similarity=0.959 Sum_probs=60.1
Q ss_pred HHHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhc--CCCCChhhHHHHHHhhhhhccccccCCCCC
Q 006074 591 VFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 656 (662)
Q Consensus 591 ~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l--~F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 656 (662)
++++|...|+|+||||||++|+++|++|+.+|.+++ +|+|+..+||++||+||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 357899999999999999999999999999999999 699999999999999999999999999875
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=95.55 E-value=0.04 Score=46.50 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=55.4
Q ss_pred EEEecHHHHHHHHHhc--------CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 491 ELAVSLFQTVVLMLFN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 491 ~l~vs~~Q~~iLl~Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
...+++-|+.+|+... ....+|-.||++.+|++.+.+.++|..|. +.+++.+.. ....|++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3567888999888665 45789999999999999999999999999 999998653 2478999988
Q ss_pred CC
Q 006074 563 FT 564 (662)
Q Consensus 563 f~ 564 (662)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
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=94.61 E-value=0.047 Score=40.34 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=39.4
Q ss_pred HHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 499 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 499 ~~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+.||..|.+.+ .+|+.||++.+|+|...+.+.|..|. ..+++.++|
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 45788888776 58999999999999999999999999 888888754
No 12
>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=94.25 E-value=0.092 Score=37.97 Aligned_cols=46 Identities=15% Similarity=0.333 Sum_probs=38.4
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccce
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 542 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 542 (662)
+..+..||....+++.+|..||++.+|++...+.++|..|. +.+++
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 45677889888888899999999999999999999999998 66665
No 13
>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=93.97 E-value=0.15 Score=41.72 Aligned_cols=59 Identities=17% Similarity=0.287 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 497 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
+++.+.+..+..+ .+|.++|++.+++|+..+.+.+..|. +.+++...++ +++-|.++.+
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 3444555544444 49999999999999999999999999 9999876542 4567888775
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=93.84 E-value=0.076 Score=40.64 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=44.9
Q ss_pred ecHHHHHHHHHhcCCCC--CCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 57889999988887776 9999999999999999999999999 899998764
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=93.02 E-value=0.15 Score=38.46 Aligned_cols=47 Identities=23% Similarity=0.483 Sum_probs=41.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
|..|+...++.+.+|+++|++.+|+++..+++-|..|. +.+++.+.-
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 45688888999999999999999999999999999999 888887754
No 16
>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=92.32 E-value=0.2 Score=39.07 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=40.9
Q ss_pred ecHHHHHHHHHhc-CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|..|..||.... ..+.++..+|++.++++...+.+.+..|. ..+++.+.+
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 4678999999988 77899999999999999999999999999 889997654
No 17
>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=92.07 E-value=0.11 Score=39.32 Aligned_cols=51 Identities=14% Similarity=0.289 Sum_probs=45.3
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|..|+.+|....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 377899999998888899999999999999999999999999 889988754
No 18
>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=91.58 E-value=0.43 Score=34.32 Aligned_cols=44 Identities=14% Similarity=0.372 Sum_probs=36.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
...-||.++-+ ++.++.||++.+|++...+.++|..|. +.+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 45567777777 689999999999999999999999998 777764
No 19
>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=91.40 E-value=0.26 Score=37.71 Aligned_cols=49 Identities=12% Similarity=0.259 Sum_probs=42.0
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
++.-..||..+...++.|+.+|++.+|++...+..+|..|. +.+++...
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 45667788888777899999999999999999999999999 88888754
No 20
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=91.32 E-value=0.39 Score=42.24 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=47.5
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
.+|..|+.||..+..++.+|..+|++.+|++...+.+.+..|. +.+++.+.+
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 4588899999999888899999999999999999999999999 899998865
No 21
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=90.35 E-value=0.56 Score=42.85 Aligned_cols=54 Identities=22% Similarity=0.254 Sum_probs=48.0
Q ss_pred EEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 492 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
..+|..|+.||......+.+|..+|++.++++...+.+.+..|. +.+++.+.++
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~~ 89 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLPN 89 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEeccC
Confidence 35688899999887777789999999999999999999999999 9999998653
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.19 E-value=0.7 Score=36.24 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCCC--CCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 497 FQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..-.||..+.+.+. +|..||++.+|++...+.++|..|. +.+++.+.+
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 44567777777766 9999999999999999999999999 888887753
No 23
>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=88.79 E-value=1.1 Score=38.84 Aligned_cols=54 Identities=22% Similarity=0.333 Sum_probs=46.6
Q ss_pred EEecHHHHHHHHHhc----CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 492 LAVSLFQTVVLMLFN----DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+.+|..|..||.... ..+.+|..+|++.++++...+.+.+..|. +.+++.+.+.
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~~ 78 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKERS 78 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccCC
Confidence 346888998887765 55789999999999999999999999999 9999998653
No 24
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.78 E-value=1.2 Score=36.87 Aligned_cols=46 Identities=15% Similarity=0.306 Sum_probs=39.8
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 499 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 499 ~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..||..+... +.+|..+|++.+|++...+.+.|..|. +.+++.+.+
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 689999999999999999999999999 889998754
No 25
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=88.61 E-value=3.9 Score=37.87 Aligned_cols=85 Identities=12% Similarity=0.085 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCChHHHHHHHHHHHHHH-HHHHHHHHHHhhhhhhhhhccC----------------CC
Q 006074 7 QRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDL-CDQMLMIRGIALYLDRTYVKQT----------------PN 69 (662)
Q Consensus 7 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~L~~~~~~W~~~-~~~~~~l~~vf~YLdr~yv~~~----------------~~ 69 (662)
+.+++.+..-+......+... +++.+|.++++.|.-| ..-.-++..+|..|++.+-... ..
T Consensus 54 ~dl~elL~tg~~~L~~~l~~~--~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~ 131 (158)
T PF08539_consen 54 EDLEELLTTGMYILENQLNEV--PDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGS 131 (158)
T ss_pred HHHHHHHHHHHHHHHHHHhhc--chhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCC
Confidence 344555555444444434332 2368999999999995 4556689999999996443221 23
Q ss_pred cccHHHHHHHHHHHHhcCCcchHHHH
Q 006074 70 VRSLWDMGLQLFRKYLSSYSEVEHKT 95 (662)
Q Consensus 70 ~~~i~~l~l~~f~~~v~~~~~~~~~l 95 (662)
..+|..+++..||+.|+- +..+++
T Consensus 132 ~l~Vr~l~L~~FRD~IvL--P~y~~l 155 (158)
T PF08539_consen 132 ELDVRRLLLIAFRDSIVL--PYYQRL 155 (158)
T ss_pred CCcHHHHHHHHHHHHhhh--cchHhh
Confidence 589999999999999985 344443
No 26
>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=88.06 E-value=1.6 Score=37.02 Aligned_cols=62 Identities=19% Similarity=0.317 Sum_probs=48.6
Q ss_pred EecHHHHHHHHH-------hcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCC
Q 006074 493 AVSLFQTVVLML-------FNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 564 (662)
Q Consensus 493 ~vs~~Q~~iLl~-------Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 564 (662)
.+|.-|.-|++. ||.. +.+|..++++.||++...+.+++..|+ +.++|... +..+.+|.+.+
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 455666666655 4543 589999999999999999999999999 99999764 35677776654
No 27
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=87.06 E-value=0.47 Score=37.09 Aligned_cols=51 Identities=18% Similarity=0.259 Sum_probs=42.8
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|-.++.|+..+-..+..|..+|++.+|+|...+.+.|..|. +.+++.+.+
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 355666777666577789999999999999999999999999 888887754
No 28
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=86.97 E-value=1.1 Score=39.30 Aligned_cols=62 Identities=18% Similarity=0.285 Sum_probs=53.4
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
..++.|++||=.++..+.+|++.++.+. +.++...|+--|..|..||.|.+.-++ ..|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~--~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD--REWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc--ccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 4678899999999999999999888774 788999999999999999999998654 4677754
No 29
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=86.83 E-value=1.3 Score=39.69 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=46.3
Q ss_pred hhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 600 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 600 ~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
+..|++++-..+.++..+++....+ +..+....+...|..|.+||||+|..+.+ .|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~--~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAE--KKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhh--ccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEe
Confidence 4567888877788888877765543 35677889999999999999999986544 688865
No 30
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=86.44 E-value=1.3 Score=37.08 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=47.2
Q ss_pred EEEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 491 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 491 ~l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+..++..+..||......+.+|..+|++.++++...+.++|..|. +.+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 356788899999998888889999999999999999999999999 88888764
No 31
>PHA00738 putative HTH transcription regulator
Probab=86.29 E-value=1.6 Score=37.14 Aligned_cols=68 Identities=18% Similarity=0.171 Sum_probs=54.4
Q ss_pred EEEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCC
Q 006074 491 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 564 (662)
Q Consensus 491 ~l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 564 (662)
++...+.=-.||.++.+++.+++.+|++.++++.+.+-++|.-|- ..+|+.....|+ .-.|++|.+-.
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr----~vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGR----TLYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECC----EEEEEECCCcc
Confidence 455666666788777777789999999999999999999999998 899998765542 24678888743
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=86.20 E-value=1.5 Score=31.82 Aligned_cols=45 Identities=22% Similarity=0.478 Sum_probs=37.6
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
-.|+..+.+...++..+|++.++++...+.+.|..|. +.+++.+.
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 3466666666789999999999999999999999998 77777654
No 33
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=85.84 E-value=2.4 Score=39.19 Aligned_cols=57 Identities=16% Similarity=0.234 Sum_probs=43.3
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
+.+.|..+..+.+|..+|++..++|...|.+.|..|. +.+++....+ .++-|.++.+
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~rG-----~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVRG-----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeecC-----CCCCeeecCC
Confidence 3344555666678999999999999999999999999 9999886542 2345666554
No 34
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=85.73 E-value=2.5 Score=39.61 Aligned_cols=57 Identities=14% Similarity=0.285 Sum_probs=43.3
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 499 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 499 ~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
+.+.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.+|+....+ +++-|.+..+
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~rG-----~~GGy~Lar~ 70 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVRG-----PGGGYLLGKD 70 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCCC-----CCCCeeccCC
Confidence 4444556654 589999999999999999999999999 9999986422 2334666554
No 35
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=84.94 E-value=2 Score=43.51 Aligned_cols=143 Identities=9% Similarity=0.161 Sum_probs=84.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCC-------Ccc---
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTA-------PLY--- 568 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~-------~~~--- 568 (662)
+.||.+|.....+|+.||++.+|+|...+.+.|..|. ..+.|.+.+. +..|.+-..+-. ...
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~~------~~~Y~lG~~~~~lg~~~~~~~~l~~ 88 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEGE------SEKYSLTLKLFELGAKALQNVDLIR 88 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC------CCcEEecHHHHHHHHHHHhhCcHHH
Confidence 4588889888889999999999999999999999999 8999988642 345555433210 000
Q ss_pred ---------------eEEeccccccc----chhhh-hhh-hHHHHHhhHhhhhhhhhhhhcCCCCCChHHHHHHHHHhc-
Q 006074 569 ---------------RIKVNAIQMKE----TVEEN-TST-TERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL- 626 (662)
Q Consensus 569 ---------------~i~i~~~~~~~----~~~e~-~~~-~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l- 626 (662)
.+.+......+ ...+. ... ...-...|.+..-++.=|+|=+.-. - +-+..+....
T Consensus 89 ~a~p~l~~La~~~~etv~L~v~~g~~~v~l~~~~~~~~~~~~~~~G~~~Pl~~tA~GkalLA~~~--~-~~~~~~l~~~~ 165 (257)
T PRK15090 89 SADIQMREISRLTKETIHLGALDEDSIVYIHKIDSMYNLRMYSRIGRRNPLYSTAIGKVLLAWRD--R-DEVREILSGVE 165 (257)
T ss_pred HHHHHHHHHHHHhCCeEEEEEEECCEEEEEEEecCCCceEEEccCCCccchhhhhHHHHHHhCCC--H-HHHHHHHccCC
Confidence 00000000000 00000 000 0011234556666777777777643 2 2233444332
Q ss_pred --CCC----CChhhHHHHHHhhhhhccccccC
Q 006074 627 --KFP----IKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 627 --~F~----~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
+++ .+.+.+.+.++.--++||-.-++
T Consensus 166 ~~~~t~~t~~~~~~l~~~l~~iR~~Gya~~~~ 197 (257)
T PRK15090 166 FKRSTEKTITSTEALLPVLDQVREQGYGEDNE 197 (257)
T ss_pred CCcCCCCCCCCHHHHHHHHHHHHHhCCCcccc
Confidence 232 35678999999999999976544
No 36
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=84.19 E-value=2.2 Score=40.78 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=47.9
Q ss_pred EEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 492 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+.+|..|..||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45678899999999988999999999999999999999999999 889998865
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=84.16 E-value=2.9 Score=37.75 Aligned_cols=45 Identities=18% Similarity=0.334 Sum_probs=36.7
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 499 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 499 ~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s~ 58 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKSV 58 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEE
Confidence 3344555544 479999999999999999999999999 99998753
No 38
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=83.19 E-value=2.3 Score=38.68 Aligned_cols=54 Identities=24% Similarity=0.271 Sum_probs=46.8
Q ss_pred EEecHHHHHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 492 LAVSLFQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+.+|..|..||...... +.+|..+|++.++++...+.+.+..|. +.+++.+.++
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~~ 81 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQTC 81 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeecC
Confidence 45788899999888754 568999999999999999999999999 9999988653
No 39
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=82.86 E-value=2.5 Score=32.41 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=36.6
Q ss_pred HHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCC
Q 006074 501 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 548 (662)
Q Consensus 501 iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 548 (662)
||-.++. +.+++..||++.+|++....+..|..|. +.+.+.+.|.+
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~ 51 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVR 51 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-S
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 4555666 6789999999999999999999999999 88888876654
No 40
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=82.81 E-value=3.1 Score=36.76 Aligned_cols=38 Identities=13% Similarity=0.286 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 507 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 507 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
.++..|+++|++.++.+...+.++|+.|. ..|++.++.
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Rek 76 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVEREK 76 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeeee
Confidence 67899999999999999999999999999 999998753
No 41
>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=82.23 E-value=3.4 Score=32.49 Aligned_cols=42 Identities=21% Similarity=0.448 Sum_probs=35.7
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
||+..... ..|+++|.+.||++.+.+...|.-|. +.+++.+.
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 44455554 99999999999999999999999999 88888763
No 42
>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=81.92 E-value=2.9 Score=30.93 Aligned_cols=36 Identities=17% Similarity=0.506 Sum_probs=29.4
Q ss_pred HHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 500 VVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 500 ~iLl~F-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.||..+ +..+.+|.++|++.+|++...+.+.|..|-
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 445444 666679999999999999999999999997
No 43
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=81.77 E-value=2.7 Score=39.40 Aligned_cols=48 Identities=17% Similarity=0.421 Sum_probs=41.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCCC
Q 006074 510 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAP 566 (662)
Q Consensus 510 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~ 566 (662)
-+|..+|++.+|++...+.+++..|. +.++|.+. ..+.|.+|++|--+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~-------~~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKI-------RNGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEc-------cCCeEEECcHHhee
Confidence 47889999999999999999999999 89999875 34689999997644
No 44
>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=81.59 E-value=0.83 Score=35.70 Aligned_cols=56 Identities=18% Similarity=0.354 Sum_probs=42.0
Q ss_pred hhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeec
Q 006074 600 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 661 (662)
Q Consensus 600 ~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yi 661 (662)
++.|-..|-.++.++..+|...+ ..+...+-+.++.|.++|+++|.++++..|..+
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEEL------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHH------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 44455555567778888876554 456889999999999999999998776566554
No 45
>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=80.96 E-value=0.76 Score=40.25 Aligned_cols=61 Identities=15% Similarity=0.249 Sum_probs=46.2
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
.+..|++++=..+.++..+++..+.+. ..+....|...+..|.+||||.+...++ .|.|-|
T Consensus 4 ~E~~IM~~lW~~~~~t~~eI~~~l~~~--~~~~~sTv~t~L~rL~~Kg~l~~~~~gr-~~~Y~p 64 (115)
T PF03965_consen 4 LELEIMEILWESGEATVREIHEALPEE--RSWAYSTVQTLLNRLVEKGFLTREKIGR-AYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHCTT--SS--HHHHHHHHHHHHHTTSEEEEEETT-CEEEEE
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhc--cccchhHHHHHHHHHHhCCceeEeecCC-ceEEEe
Confidence 355677777777778888877665443 5678999999999999999999986543 688865
No 46
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=80.86 E-value=3.7 Score=29.09 Aligned_cols=34 Identities=26% Similarity=0.433 Sum_probs=31.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 510 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 510 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+|..+|++.+|++...+.+.|..|. +.+++...
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 57899999999999999999999999 88998764
No 47
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=80.67 E-value=4.2 Score=37.42 Aligned_cols=59 Identities=14% Similarity=0.282 Sum_probs=45.0
Q ss_pred HHHHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 497 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|. +.+++....+ +++-|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 3444555555555 68899999999999999999999999 9999987543 3455666654
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=80.64 E-value=3.5 Score=32.13 Aligned_cols=48 Identities=15% Similarity=0.327 Sum_probs=40.5
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+..+..|+..+.+.+ ++..+|++.+|++...+.+.|..|. ..+++...
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 456777888777766 9999999999999999999999998 77787754
No 49
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=80.61 E-value=1.3 Score=36.02 Aligned_cols=44 Identities=20% Similarity=0.458 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
..|+...+..+.+++.+|.+.+|+++..+.++|..|. +.+.+..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le--~~GyV~~ 46 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLE--EAGYVEV 46 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEE
Confidence 4566666667889999999999999999999999999 7777654
No 50
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=80.58 E-value=5.9 Score=43.74 Aligned_cols=201 Identities=10% Similarity=0.032 Sum_probs=106.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCc
Q 006074 32 VVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEA 111 (662)
Q Consensus 32 ~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~~i~~l~l~~f~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~ 111 (662)
..+...+...|-....... +++-+|-.=+ ++....+.++-..+-...-.-+...+-+.+....++..++.++.
T Consensus 191 atV~~~LL~~hL~~IL~kg----l~~lvDm~q~---~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk~ 263 (661)
T KOG2167|consen 191 ATVERCLLSRHLDLILTKG----LDSLVDMRQT---SDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDKD 263 (661)
T ss_pred HHHHHHHHHHHHHHHHhcc----hHHhhhhhhc---cchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhHH
Confidence 3455566666655533322 2333333211 12344555544444111100123444555555556666665554
Q ss_pred CC--hHHHHHHHHHHhhhhccHHhhhHHHHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 006074 112 VD--RTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPL 189 (662)
Q Consensus 112 i~--~~~ik~~i~ml~~l~~Y~~~fE~~~l~~t~~yY~~~s~~~~~~~~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l 189 (662)
.. ....|.-+++......+..+- .+|+..++++|...++. ....+.+|+.+.....-.+-+. ..+-+.+
T Consensus 264 mVqELL~FK~k~Dii~~~sF~~~v~-e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~gnk------~~~d~~l 334 (661)
T KOG2167|consen 264 MVQELLDFKKKVDIIVDESFLKYVA-EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRAGNK------ETSDEEL 334 (661)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHhhH-HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHhccc------cccchhH
Confidence 22 234667777777776555444 89999999999999984 6667999999888755444111 1112223
Q ss_pred HHHHHHHHH----------------HHHHHHHH-------HhHHHHhhccCCHHHHHHHHHHhcccchHHHHHHHHHHHH
Q 006074 190 IATAERQLL----------------ERHISAIL-------DKGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYI 246 (662)
Q Consensus 190 ~~~l~~~LI----------------~~~~~~il-------~~gl~~ll~~~~~~~L~~ly~l~~~~~~l~~l~~~~~~~i 246 (662)
-.++.++++ ..-..+++ +.|+--+-+-......+..|+|.+-.+..+...+..+.|.
T Consensus 335 ~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~ 414 (661)
T KOG2167|consen 335 EFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFK 414 (661)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 333333331 11111222 2333333344456778889999887755555555555554
Q ss_pred HH
Q 006074 247 RR 248 (662)
Q Consensus 247 ~~ 248 (662)
..
T Consensus 415 ~~ 416 (661)
T KOG2167|consen 415 QS 416 (661)
T ss_pred HH
Confidence 44
No 51
>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=80.26 E-value=4.3 Score=36.28 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=36.7
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 498 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 498 Q~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
++.+.+.-+++ ..+|.++|++.+++|...+.+.|..|. +.+++...
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 34444444433 389999999999999999999999999 88998754
No 52
>PRK10870 transcriptional repressor MprA; Provisional
Probab=79.99 E-value=4.3 Score=38.48 Aligned_cols=53 Identities=11% Similarity=0.155 Sum_probs=45.4
Q ss_pred EecHHHHHHHHHhcC--CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 493 AVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
.+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+.
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 356778888877764 4579999999999999999999999999 9999998653
No 53
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=79.65 E-value=3.6 Score=36.05 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=46.4
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 496 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 496 ~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
+.-..||.+.-+.++.++.||++.+|++...+.++|.-|. +.+++.....|+ .-.|++|.+
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~~ 76 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECch
Confidence 3344566655555679999999999999999999999999 899998765442 234777654
No 54
>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=79.42 E-value=2.4 Score=33.63 Aligned_cols=39 Identities=21% Similarity=0.271 Sum_probs=31.1
Q ss_pred HhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 504 LFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 504 ~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
++...+.+|+.||++.+|+++..++..+..+. +.++|.+
T Consensus 26 L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~~ 64 (73)
T TIGR03879 26 LAREEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLVK 64 (73)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHHH
Confidence 33444678999999999999999999998877 6666643
No 55
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=79.29 E-value=3.6 Score=30.61 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=34.3
Q ss_pred hcCCCCC-CHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 505 FNDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 505 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+..++.+ |..+|++.+|++...+.++|..|. +.+++...+
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 4455567 899999999999999999999999 888887654
No 56
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=79.21 E-value=1.7 Score=34.10 Aligned_cols=45 Identities=24% Similarity=0.409 Sum_probs=35.4
Q ss_pred hhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 603 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 603 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
|-.+|+.++.++.++|-. .|..+++.+...|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAR------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHH------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHH------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 456788899999888764 378899999999999999999998654
No 57
>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=78.69 E-value=3.3 Score=40.23 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=47.3
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
.++..|..||..+.+++.++..+|++.+|++...+.++|..|. +.+++.+.+
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 5688899999999887889999999999999999999999999 889998764
No 58
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=78.65 E-value=4.5 Score=40.65 Aligned_cols=46 Identities=22% Similarity=0.446 Sum_probs=41.1
Q ss_pred HHHHHHhcCCCC-CCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 499 TVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 499 ~~iLl~Fn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..||.+|..... +++.||++.+|+|...+.+.|..|. ..+++.+++
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 468888987654 7899999999999999999999999 999999976
No 59
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=78.11 E-value=4.4 Score=30.42 Aligned_cols=36 Identities=11% Similarity=0.303 Sum_probs=32.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 508 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 508 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+..|..+|++.+|++...+.+.|..|. +.+++...
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 5678999999999999999999999999 78888754
No 60
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=77.13 E-value=6.1 Score=30.88 Aligned_cols=54 Identities=11% Similarity=0.258 Sum_probs=42.5
Q ss_pred hhhhhhhhhcCCCC--CChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCce
Q 006074 599 VDAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 658 (662)
Q Consensus 599 i~A~IVRimK~~k~--l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 658 (662)
.+..|...||.++. ++-.+|-.++ ..+...+.+.+..|.++||+.++++.|..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH------CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 45568888999876 9988877554 446778999999999999999987665554
No 61
>PRK11569 transcriptional repressor IclR; Provisional
Probab=77.09 E-value=4.9 Score=41.13 Aligned_cols=46 Identities=9% Similarity=0.299 Sum_probs=40.9
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 499 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 499 ~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..||.+|.+. ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 4588889875 579999999999999999999999999 999998764
No 62
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=77.05 E-value=5.3 Score=40.78 Aligned_cols=56 Identities=14% Similarity=0.103 Sum_probs=45.6
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 499 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 499 ~~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
..||.+|... ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+++. +..|.+...
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~~------~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDSQ------LGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC------CCeEEecHH
Confidence 4588899865 479999999999999999999999999 8999988642 345655433
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=76.75 E-value=6.1 Score=35.28 Aligned_cols=44 Identities=23% Similarity=0.392 Sum_probs=36.3
Q ss_pred HHHHHhc--CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 500 VVLMLFN--DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 500 ~iLl~Fn--~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+|..+. ..+.+|..+|++.+|+|...+.+.|..|. +.+++...
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 3444444 33579999999999999999999999999 89999754
No 64
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=75.86 E-value=4.8 Score=34.48 Aligned_cols=46 Identities=11% Similarity=0.314 Sum_probs=40.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
..-.||..+......|+.+|++.+|+++..+.+.+..|. +.+++.+
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeec
Confidence 345678888888899999999999999999999999999 7888863
No 65
>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=75.50 E-value=4.3 Score=34.55 Aligned_cols=48 Identities=21% Similarity=0.391 Sum_probs=39.6
Q ss_pred EecHHHHHHHHHhcC----CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccce
Q 006074 493 AVSLFQTVVLMLFND----AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 542 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 542 (662)
.++..|-.||-.+.. .+.+++++|++.+++++.+++.+|..|+ ..+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~--~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLS--NEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHH--HTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--hCCeE
Confidence 678999999999887 3589999999999999999999999999 54444
No 66
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=75.28 E-value=5.6 Score=40.37 Aligned_cols=47 Identities=19% Similarity=0.304 Sum_probs=40.9
Q ss_pred HHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 499 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 499 ~~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+.||..|.+.+ .+|..||++.+|+|...+.+.|..|. ..+++.+.+.
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 35788887655 59999999999999999999999999 9999988653
No 67
>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=74.00 E-value=6.4 Score=29.95 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=36.8
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
|..+-.+...++..+|++.+|+++..+...+..|. +.+++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577899999999999999999999999999 888888765
No 68
>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=73.84 E-value=4.3 Score=31.12 Aligned_cols=35 Identities=23% Similarity=0.473 Sum_probs=28.6
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 507 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 507 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
..+..|+.+|...|++|.+.++.+|-.|+ +.+++.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCee
Confidence 44689999999999999999999999999 777764
No 69
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=73.48 E-value=6.8 Score=33.97 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=45.7
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+++.|..+|......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788899999888887777668999999999999999999999 999998865
No 70
>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=73.33 E-value=7.6 Score=39.00 Aligned_cols=45 Identities=24% Similarity=0.406 Sum_probs=39.6
Q ss_pred HHHHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 499 TVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 499 ~~iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|. ..+.|.++
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 458888986 4589999999999999999999999999 88898763
No 71
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=73.19 E-value=9.8 Score=34.53 Aligned_cols=50 Identities=6% Similarity=0.292 Sum_probs=39.6
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEec
Q 006074 505 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 561 (662)
Q Consensus 505 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 561 (662)
+..+..+|..+|++.+|+|...++++|..|. +.+++...++ .+.-|.+..
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~G-----~~GG~~l~~ 69 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVRG-----KNGGIRLGK 69 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEecC-----CCCCeeecC
Confidence 4444578999999999999999999999999 9999987653 234455543
No 72
>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=72.63 E-value=6.5 Score=27.50 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=27.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
-.||..+......++.+|++.+|+++..+.+-+..|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 357777777789999999999999999998877654
No 73
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=72.42 E-value=1e+02 Score=32.41 Aligned_cols=159 Identities=13% Similarity=0.234 Sum_probs=90.3
Q ss_pred HHHHHHhHHHHhhccCCHHHHHHHHHHhccc----chHHHHHHHHHHHHHHHhchhccCc-------cchHHHHHHHHHH
Q 006074 202 ISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLLEF 270 (662)
Q Consensus 202 ~~~il~~gl~~ll~~~~~~~L~~ly~l~~~~----~~l~~l~~~~~~~i~~~g~~~~~~~-------~~~~~~i~~ll~l 270 (662)
+..++.+.|......+|.+.+.+.++||-.+ .|++....-+.+.|.....+.+... ..+.-|+..|..+
T Consensus 8 L~~~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~L 87 (331)
T PF08318_consen 8 LCEIFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKL 87 (331)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHH
Confidence 3445566788888999999999999999765 5777777777777766666655432 1233455555555
Q ss_pred HHHH-------HHHHHHhcCCCHHH--HHHHHH--------HHHHHhhcCC-CCcHHHHHHHHHHHhhc-----------
Q 006074 271 KASL-------DTIWEQSFSKNEAF--CNTIKD--------AFEYLINLRQ-NRPAELIAKFLDEKLRA----------- 321 (662)
Q Consensus 271 ~~~~-------~~l~~~~F~~~~~~--~~~~~~--------af~~~ln~~~-~~~~e~La~y~d~~lk~----------- 321 (662)
++.. ..++..+|+..... ...+.. -+..|..... .+....+-.|-...+.+
T Consensus 88 Fe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 167 (331)
T PF08318_consen 88 FEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSR 167 (331)
T ss_pred HHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhccccccccccccc
Confidence 5554 45567788765421 111111 1222221111 01112233333222222
Q ss_pred -------CCCCCCHHHHHhhhhccceeeEeccChhHHHHHHHHHHHHHhcCCC
Q 006074 322 -------GNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 367 (662)
Q Consensus 322 -------~~~~~~~~e~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~ 367 (662)
+..+.+-.+++..|+++..+..... .|.++++.|.-...
T Consensus 168 ~~~~~~~~~~~~d~reld~lL~Eis~i~~~w~-------lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 168 AASSSQSEDEGIDPRELDALLNEISLILQRWS-------LYCRFISRKWNEFS 213 (331)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhccc
Confidence 0011233567788888777775443 79999999987743
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=72.16 E-value=7.1 Score=30.26 Aligned_cols=55 Identities=18% Similarity=0.339 Sum_probs=37.6
Q ss_pred hHhhhhhhhhhhhcCCC-CCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCC
Q 006074 595 RQYQVDAAIVRIMKTRK-VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNN 654 (662)
Q Consensus 595 r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~ 654 (662)
|+..|=.+|...++.++ .-+ +.|+.+.+.+. ++.-+...++.|.++|||+|+++-
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt----~rEIa~~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPT----VREIAEALGLK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS-------HHHHHHHHTSS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHcCCCCC----HHHHHHHhCCC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 44455566666666554 333 34445666665 788899999999999999999864
No 75
>PF13730 HTH_36: Helix-turn-helix domain
Probab=71.64 E-value=9 Score=28.20 Aligned_cols=29 Identities=14% Similarity=0.404 Sum_probs=25.9
Q ss_pred CHHHHHHHhCCCHHHHHHHhhHhhcCCccce
Q 006074 512 SFQDIKDATGIEDKELRRTLQSLACGKVRVL 542 (662)
Q Consensus 512 t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 542 (662)
|.+.|++.+|++...+.+++..|. +.++|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~--~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE--EKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH--HCcCC
Confidence 899999999999999999999998 65543
No 76
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=69.57 E-value=7.1 Score=38.13 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=38.3
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
..||.+.+..+++|.+||++.+||+...++++|..|. ..+++..
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 3577778888899999999999999999999999999 7776654
No 77
>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=69.37 E-value=6.1 Score=30.92 Aligned_cols=43 Identities=14% Similarity=0.327 Sum_probs=32.7
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
|.-...+++.+|++||+..++++++.+...|..|+ +.+-+.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~--~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLI--RKGYIRKV 47 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH--CCTSCEEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEEe
Confidence 34445567889999999999999999999999999 76666653
No 78
>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=67.59 E-value=7.4 Score=29.41 Aligned_cols=38 Identities=13% Similarity=0.348 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
|.-+|-++-+.+.+|+++|++.+|++...++.-+.-|-
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 55566555557899999999999999999998887775
No 79
>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=66.76 E-value=9.4 Score=29.18 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..+|..+|++.+|++...+.+.|..|. +.+++...+
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 479999999999999999999999999 889998753
No 80
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=65.59 E-value=7.9 Score=39.15 Aligned_cols=49 Identities=14% Similarity=0.179 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
-|..|+-..++++.+++.||++.+|+++..+++-|..|- +.+++.+.-+
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~G 54 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTYG 54 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEEC
Confidence 367889999999999999999999999999999999998 8888877543
No 81
>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=64.07 E-value=5 Score=34.34 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=32.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
.+.|+..+..++.++-++|++.+|++..++++.|..|. ..+++.
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 45567666666789999999999999999999999999 777774
No 82
>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=63.78 E-value=13 Score=26.56 Aligned_cols=45 Identities=13% Similarity=0.313 Sum_probs=35.7
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhcccc
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 649 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~ 649 (662)
.+-.|+..+..+..++..+|-..+ ..+.+.+.+.+..|.+.|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHHHHHCcCcC
Confidence 455677888888889998887655 567899999999999999985
No 83
>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=63.35 E-value=13 Score=28.54 Aligned_cols=51 Identities=14% Similarity=0.315 Sum_probs=34.5
Q ss_pred hhhhhhhhc-CCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhcccccc--CCCCC
Q 006074 600 DAAIVRIMK-TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD--KNNPQ 656 (662)
Q Consensus 600 ~A~IVRimK-~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~--~~~~~ 656 (662)
+..|.+.+. ....++..+|...+ ..+.+.+-+.|+.|+++|||++. +.|..
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~------~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERL------GISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHT------T--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHHHHHHHHccCCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 456677777 67788777766443 45678888999999999999764 44444
No 84
>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=62.10 E-value=15 Score=27.72 Aligned_cols=39 Identities=18% Similarity=0.440 Sum_probs=31.9
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 506 NDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 506 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
.....+ |..+|++.+|++...+.++|..|. +.+++...+
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 499999999999999999999999 888887643
No 85
>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=61.44 E-value=14 Score=34.36 Aligned_cols=43 Identities=21% Similarity=0.285 Sum_probs=36.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
..|+..+-.++.+|-+||+..+|++..++++.|..|. ..+++.
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 4466555556689999999999999999999999999 888874
No 86
>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=61.04 E-value=11 Score=29.19 Aligned_cols=52 Identities=19% Similarity=0.360 Sum_probs=38.0
Q ss_pred ecHHHHHHHHHhcC-----CCCCCHHHHHHHhCCC-HHHHHHHhhHhhcCCccceecCCC
Q 006074 494 VSLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+|.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.|.
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 45567777755433 2366999999999996 999999999999 8999988763
No 87
>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=61.00 E-value=14 Score=28.61 Aligned_cols=37 Identities=35% Similarity=0.466 Sum_probs=32.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
..|-.+.++...+|+.+|++.|++++.++..++--|.
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLa 47 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLA 47 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHH
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHh
Confidence 3466778898999999999999999999999999998
No 88
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=60.90 E-value=22 Score=33.52 Aligned_cols=55 Identities=20% Similarity=0.154 Sum_probs=43.0
Q ss_pred EEEEecHHHHHHHHHhcCCCCC-CHHHHHHHh--CCCHHHHHHHhhHhhcCCccceecCC
Q 006074 490 KELAVSLFQTVVLMLFNDAQKL-SFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 490 ~~l~vs~~Q~~iLl~Fn~~~~~-t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++.+|..|. +.|+|.++.
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 3344455666666665544433 899999999 999999999999999 999999864
No 89
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=60.77 E-value=11 Score=37.96 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=43.9
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCC
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 548 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 548 (662)
|-.|+.+.++++.++++||++.+|+++..++|=|..|. +.++|.+..+|
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGG 55 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGG 55 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCC
Confidence 56788999999999999999999999999999999999 88888885443
No 90
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=60.23 E-value=15 Score=33.86 Aligned_cols=50 Identities=4% Similarity=0.243 Sum_probs=43.6
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
.++..--.||..+..+...|+.+|++.+|+++..+.+-++.|. ..|++..
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~--~~GvI~~ 55 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK--QAGIITG 55 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeee
Confidence 3456677788888888999999999999999999999999999 7888763
No 91
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=59.61 E-value=14 Score=35.88 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=44.1
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
|..-..||.++..++.+.+.||++.+|+|...+..+++.|. +.+++..+.
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~t 71 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTET 71 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeeee
Confidence 45556689899999999999999999999999999999999 999998653
No 92
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.54 E-value=15 Score=34.84 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
...||.++-.++.+|-++|+..+||+...++++|..|. ..+++.
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 45567666677799999999999999999999999999 788876
No 93
>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=59.22 E-value=11 Score=24.63 Aligned_cols=30 Identities=27% Similarity=0.447 Sum_probs=23.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccc
Q 006074 510 KLSFQDIKDATGIEDKELRRTLQSLACGKVRV 541 (662)
Q Consensus 510 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~i 541 (662)
.+|-+||++.+|++.+.+-+.|..|- +.++
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~--~~gl 31 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE--RQGL 31 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH--HTTS
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH--HcCC
Confidence 36789999999999999999999887 5554
No 94
>PRK00215 LexA repressor; Validated
Probab=58.59 E-value=21 Score=34.63 Aligned_cols=52 Identities=21% Similarity=0.329 Sum_probs=43.5
Q ss_pred ecHHHHHHHHHhcC-----CCCCCHHHHHHHhCC-CHHHHHHHhhHhhcCCccceecCCC
Q 006074 494 VSLFQTVVLMLFND-----AQKLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~-----~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+|.-|..||..+.+ ....|..||++.+|+ +...+.+.|..|. +.+++.+.+.
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 46778888866652 347899999999999 9999999999999 8899988764
No 95
>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=58.14 E-value=23 Score=34.33 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=37.7
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 456555555679999999999999999999999999 88898765
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=58.08 E-value=16 Score=34.17 Aligned_cols=49 Identities=10% Similarity=0.199 Sum_probs=43.4
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
+.-.-..||..+.++..+|+.+|++.+|++...+.+-++.|. +.|++..
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~~ 60 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQG 60 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEE
Confidence 455667789999999999999999999999999999999999 8888863
No 97
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=57.41 E-value=17 Score=36.68 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 548 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 548 (662)
-|..|+..+++++.+++.||++.+|+++..+++-|..|. +.+++.+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gg 55 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 356788899999999999999999999999999999998 77888775544
No 98
>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=54.57 E-value=31 Score=24.75 Aligned_cols=32 Identities=25% Similarity=0.532 Sum_probs=23.7
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhH
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 533 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 533 (662)
.|-+.| ...+|++||++.+|++...+.+....
T Consensus 12 vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 12 VIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 344556 45789999999999999988776543
No 99
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=54.44 E-value=17 Score=36.57 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=43.6
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 548 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~ 548 (662)
-|..|+...++.+.+++.||++.++++...++|-|..|. +.++|.+.-+|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~GG 55 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHGG 55 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 356788888999999999999999999999999999999 88888876444
No 100
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=54.05 E-value=14 Score=35.37 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=41.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
-+..|+...+.++.+++++|++.+|+++..+++-|..|. ..+++.+.
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~--~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG--IPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh--cchHHHHH
Confidence 467789899999999999999999999999999999999 77777653
No 101
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=53.38 E-value=27 Score=25.89 Aligned_cols=46 Identities=13% Similarity=0.255 Sum_probs=32.9
Q ss_pred hhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCC
Q 006074 603 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNP 655 (662)
Q Consensus 603 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~ 655 (662)
|++.+. .+.++..++.... ..+...+.+.|+.|.++|++....+.+
T Consensus 2 il~~l~-~~~~~~~~i~~~l------~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 2 ILKLLA-EGELCVCELAEIL------GLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHHhh-cCCccHHHHHHHH------CCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 344555 6667777655432 356788999999999999999876443
No 102
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=52.98 E-value=18 Score=36.81 Aligned_cols=50 Identities=12% Similarity=0.169 Sum_probs=43.9
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 496 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 496 ~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
--|..|+...+.++.+++.||++.+|++...++|-|..|- ..+++.+..+
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~G 66 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAYG 66 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEeC
Confidence 4577899999999999999999999999999999999998 7788877543
No 103
>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=52.85 E-value=19 Score=27.00 Aligned_cols=47 Identities=17% Similarity=0.368 Sum_probs=40.3
Q ss_pred hhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 601 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 601 A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
..|+..++.++.++..+|.+. |.++...|.+=+..|.++|.|.|.-+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~------~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE------FGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 357888899999999888753 68899999999999999999998644
No 104
>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=52.00 E-value=23 Score=29.28 Aligned_cols=45 Identities=18% Similarity=0.370 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHh-CCCHHHHHHHhhHhhcCCccceecC
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
-+.||..... +...+.||.+.+ |++...|.+.|..|. ..+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 3567766666 689999999999 999999999999999 88999764
No 105
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=52.00 E-value=26 Score=32.04 Aligned_cols=49 Identities=14% Similarity=0.341 Sum_probs=43.1
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
++-.-.-||..+.+....++.+|++.+|++...+.+.+..|. +.|++..
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 345566788888888889999999999999999999999999 8888875
No 106
>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=51.58 E-value=29 Score=25.32 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
+++|++||++.+|+++..++..+.
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 368999999999999998887764
No 107
>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=51.51 E-value=31 Score=33.26 Aligned_cols=51 Identities=22% Similarity=0.300 Sum_probs=43.2
Q ss_pred ecHHHHHHHHHhcCC-----CCCCHHHHHHHhCCC-HHHHHHHhhHhhcCCccceecCC
Q 006074 494 VSLFQTVVLMLFNDA-----QKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~-----~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|..|..||....+. -..|..||++.+|++ ...+.++|..|. +.+++.+.+
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 477899998776632 358899999999998 999999999999 899998864
No 108
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=51.07 E-value=30 Score=28.91 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=45.7
Q ss_pred EEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 492 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+..+.....||..+...+.=...-|+..+++|.+++...|..|. ..|+|.+..
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 44567778899998888777778899999999999999999999 999998864
No 109
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=51.01 E-value=34 Score=29.65 Aligned_cols=62 Identities=21% Similarity=0.201 Sum_probs=46.1
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceee
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 660 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 660 (662)
.+|+.|.+-- ...=.....++.+|+.+....++...+--||+.||+.|.++-.++-.++-+|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 5777777722 2333456788999999886557889999999999999999998765555444
No 110
>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=50.77 E-value=31 Score=29.82 Aligned_cols=58 Identities=16% Similarity=0.128 Sum_probs=43.1
Q ss_pred hhhhhhcC-CCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceee
Q 006074 602 AIVRIMKT-RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 660 (662)
Q Consensus 602 ~IVRimK~-~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 660 (662)
+|..+|.. .+-++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 35555555 56799999998887653 467889999999999999999986543333444
No 111
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=50.62 E-value=25 Score=39.18 Aligned_cols=51 Identities=10% Similarity=0.219 Sum_probs=46.0
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+|..|..||..+...+.+|..+|++.+|++...+.+++.+|. +.+++...
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 4688999999999988899999999999999999999999999 77777653
No 112
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.69 E-value=26 Score=35.05 Aligned_cols=46 Identities=15% Similarity=0.295 Sum_probs=39.7
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
|..|+..+++++.++.+||++.+|+++..+++-|..|. ..+.+.+.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~--~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQ--TQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 56688888888999999999999999999999999997 55666654
No 113
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.57 E-value=24 Score=30.11 Aligned_cols=46 Identities=15% Similarity=0.340 Sum_probs=39.8
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccc
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 650 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r 650 (662)
+|-.|++.+.....++..+|-..+ ..+.+.+.+++..|.++|+|.|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l------~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKV------GLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeec
Confidence 567889999998899998887554 6789999999999999999995
No 114
>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=48.87 E-value=36 Score=26.88 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=39.7
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccc
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 541 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~i 541 (662)
.+=|+.++-++...+..|+++|++.||-....++-+|..++-.+.++
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 45689999999998999999999999999999999999986334444
No 115
>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=47.95 E-value=47 Score=26.65 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.-.+|-+.-++..+|.++|+..+|.+.+++...|..+-
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 44577778889999999999999999999999998775
No 116
>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=47.77 E-value=26 Score=24.74 Aligned_cols=31 Identities=19% Similarity=0.393 Sum_probs=22.1
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
.|+-++.++ .|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 345556554 8999999999999999988775
No 117
>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=47.63 E-value=52 Score=24.36 Aligned_cols=30 Identities=13% Similarity=0.472 Sum_probs=24.4
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 505 FNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 505 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
|+.-...|.+||++.+||+...+..+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 444458999999999999999888777643
No 118
>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=47.20 E-value=29 Score=30.62 Aligned_cols=50 Identities=10% Similarity=0.121 Sum_probs=39.7
Q ss_pred ecHHHHHHHHH--hc--------CCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 494 VSLFQTVVLML--FN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 494 vs~~Q~~iLl~--Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+-.+.-..++. .| +.-+.|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34455555555 33 34589999999999999999999999999 99998764
No 119
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=47.19 E-value=30 Score=34.76 Aligned_cols=43 Identities=12% Similarity=0.299 Sum_probs=36.9
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
||++.-+ ++.|++||.+.++++...+..+|.-|. +.+++.++.
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~~ 60 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQEG 60 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEecC
Confidence 5555555 688999999999999999999999999 889988753
No 120
>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=46.89 E-value=21 Score=26.73 Aligned_cols=48 Identities=15% Similarity=0.299 Sum_probs=34.1
Q ss_pred hhhhhhhhcCCCC--CChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 600 DAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 600 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
+..|...+..+.. ++..+|...+ ..+.+.+.+.|..|+++|||+|..+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l------~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERL------GISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4455555666655 7777766443 4568899999999999999999753
No 121
>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=46.75 E-value=20 Score=34.11 Aligned_cols=27 Identities=37% Similarity=0.613 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
..+|+++|++.|||..+++..+|+.|-
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 379999999999999999999998774
No 122
>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=46.60 E-value=18 Score=37.86 Aligned_cols=145 Identities=13% Similarity=0.177 Sum_probs=41.5
Q ss_pred EEecHHHHHHHHHhcC--CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCCCCcce
Q 006074 492 LAVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYR 569 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~ 569 (662)
-.++..+..|.-+..+ ..++-..+|...||++...+.++|.+|. ..++++... +.+.+.+|
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le--~k~lIK~vk---------------sv~~~~rK 142 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLE--SKKLIKSVK---------------SVKNPNRK 142 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHH--HTTSEEEE-----------------SS-SS--
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHH--hCCCEEEec---------------CcCCCCeE
Confidence 3567778888877765 4588899999999999999999999998 556666432 12233334
Q ss_pred EEecc-c-cccc-chhhhhhhhHHHHHhhHhhhhhhhhhhhcCCCC-----------------------------CChHH
Q 006074 570 IKVNA-I-QMKE-TVEENTSTTERVFQDRQYQVDAAIVRIMKTRKV-----------------------------LSHTL 617 (662)
Q Consensus 570 i~i~~-~-~~~~-~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~ 617 (662)
+-+-. + +.++ |. ..=-+..+.+.+=-..+...|.+.+.++.. .+.++
T Consensus 143 ~Yml~~l~Ps~eiTG-G~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~e 221 (327)
T PF05158_consen 143 VYMLYDLEPSEEITG-GPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEE 221 (327)
T ss_dssp EEEESSS-------------------------------------------------------------------------
T ss_pred EEEEccCCcCcccCC-CCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHH
Confidence 43311 0 0000 00 000001122222233455555555555544 33444
Q ss_pred HHHHHHHhc--CCCCChhhHHHHHHhhhhhccccccCCC
Q 006074 618 LITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNN 654 (662)
Q Consensus 618 L~~~v~~~l--~F~~~~~~ik~~Ie~Liereyi~r~~~~ 654 (662)
+...+.+.- +-..+.++|...++-|+=.|-|++-...
T Consensus 222 I~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 222 IAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp ---------------------------------------
T ss_pred HHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 443332221 2457889999999999999988886543
No 123
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=46.51 E-value=33 Score=32.53 Aligned_cols=64 Identities=19% Similarity=0.316 Sum_probs=49.3
Q ss_pred CeeeEeccCCceEEEEEEecCceEEEEecHHHHHHHHHhcCC--CCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 467 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 467 ~R~L~w~~~l~~~~i~~~~~~~~~~l~vs~~Q~~iLl~Fn~~--~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.|.-.|.+.+|..+++ +.+.|+ ||+.||.-|+.-... ..||.+-|++..+++.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~-~vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPE-KVPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCcc-cCCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3344578888888876 344454 678898887664433 489999999999999999999998887
No 124
>PHA02943 hypothetical protein; Provisional
Probab=46.06 E-value=37 Score=30.94 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=40.4
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEec
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 561 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 561 (662)
||-.+ ..+..|..||++.+|++-....-+|.-|- +-|.+.+..-| ....+.+|+
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 55555 66678899999999999999999999998 77777765432 234555555
No 125
>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=46.00 E-value=19 Score=26.76 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=34.3
Q ss_pred hhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 600 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 600 ~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
+..+..++-....++..+|-... ..+.+.+-+.+..|..+|||+|..
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~------~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKL------GISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH------CCChhHHHHHHHHHHHCCCEEecc
Confidence 34555556666777777765433 557899999999999999999954
No 126
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=45.86 E-value=18 Score=28.09 Aligned_cols=55 Identities=24% Similarity=0.243 Sum_probs=33.3
Q ss_pred hhhhhhhhhcCC-CCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 599 VDAAIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 599 i~A~IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
.=|.||..||++ ..++.+||..++. +..+ +..++.|-+.+-|+-|++ .++|.|.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~----~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLS----LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHT----SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHc----CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 347889999997 6788888776653 4443 234456668889999874 36899976
No 127
>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=45.27 E-value=24 Score=26.91 Aligned_cols=39 Identities=18% Similarity=0.421 Sum_probs=32.1
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 506 NDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 506 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..++.+ |..+|++..|++...++++|..|. ..+++...|
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~--~~g~i~~~~ 58 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLE--AEGLIERRP 58 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHH--HCCcEEEEC
Confidence 345688 999999999999999999999999 888988765
No 128
>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=44.82 E-value=30 Score=25.13 Aligned_cols=44 Identities=18% Similarity=0.411 Sum_probs=31.5
Q ss_pred hhhhhcCC-CCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 603 IVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 603 IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
|.+.+... ..++..+|...+ ..+...+-+.+..|.+.||++|||
T Consensus 8 iL~~l~~~~~~~t~~eia~~~------gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARAL------GLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHcCCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCcCeecCc
Confidence 44445554 447777776554 345778999999999999999985
No 129
>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=44.71 E-value=33 Score=27.34 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=41.8
Q ss_pred cHHHHHHHHHhcCC--CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 495 SLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~--~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
|..|.++|...-.. .+++-.+|...+|++...+-..++.|. +.+++.+.+
T Consensus 1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 1 TDIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred CchHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 34677888777643 588999999999999999999999999 888988754
No 130
>PRK06474 hypothetical protein; Provisional
Probab=44.39 E-value=60 Score=30.77 Aligned_cols=52 Identities=12% Similarity=0.200 Sum_probs=42.3
Q ss_pred EecHHHHHHHHHhcCCCC-CCHHHHHHHh-CCCHHHHHHHhhHhhcCCccceecCC
Q 006074 493 AVSLFQTVVLMLFNDAQK-LSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~-~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
-.++.-..||..+...++ +|..+|++.+ +++...+-++|..|. +.+++...+
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 345666778866655544 9999999999 799999999999999 999998754
No 131
>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=44.13 E-value=50 Score=23.78 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=28.7
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
|..|..++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 458999999999999998888877654
No 132
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.04 E-value=50 Score=23.71 Aligned_cols=39 Identities=23% Similarity=0.398 Sum_probs=29.7
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
|.-+..++.++. ..++..+|++.+|++...+...+..+.
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 455555665553 357999999999999999988887654
No 133
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.74 E-value=30 Score=31.54 Aligned_cols=50 Identities=18% Similarity=0.359 Sum_probs=43.4
Q ss_pred hhhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 597 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 597 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
..+|..|.+++....+++..+|-..+ ..+++.+..||+.|.++|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 35788999999999999999988766 467899999999999999998853
No 134
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=43.73 E-value=21 Score=34.01 Aligned_cols=58 Identities=21% Similarity=0.323 Sum_probs=39.5
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
+-...|...|.+|.+..++|-.. |..+++++-.+|..|...|-|.=--+|++.|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~------f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAE------FGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHH------H-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHH------cCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 33445588899999999887643 67789999999999999998887777889999984
No 135
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=43.48 E-value=6e+02 Score=29.79 Aligned_cols=112 Identities=14% Similarity=0.232 Sum_probs=58.7
Q ss_pred CChhHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccC-----------CHHHHHHH
Q 006074 157 SDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGH-----------RTEDLQRM 225 (662)
Q Consensus 157 ~~~~~Yl~~v~~~i~eE~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~il~~gl~~ll~~~-----------~~~~L~~l 225 (662)
..+..+.+.+...++++.+..-..+-.....++.+.+ .|+..++... ....|+.+
T Consensus 570 ~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~--------------~gve~l~~~~~~~ei~~~~~ySk~~l~kv 635 (701)
T PF09763_consen 570 SVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFF--------------EGVEALLQTVSPEEISYQAAYSKQELKKV 635 (701)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHH--------------HHHHHHHhccCchhcccchhccHHHHHHH
Confidence 4556666666666666665543332222223333222 2333333321 23455555
Q ss_pred HHHhcc--c-chHHHHHHHHHHHHHHHhc------hhccCccchHHHHHHHHHHHHHHHHHHHHhcCC
Q 006074 226 YSLFSR--V-NALESLRQALAMYIRRTGH------GIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSK 284 (662)
Q Consensus 226 y~l~~~--~-~~l~~l~~~~~~~i~~~g~------~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~ 284 (662)
-.-+.. + .+++.+.+.+.+|+..-+. .++...+ ..+-+.++..|.++..++..|+.|
T Consensus 636 l~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW--~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 636 LKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVVW--SAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHHH--HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 544322 2 5667777777777622111 1110001 256677889999999999999864
No 136
>PRK11050 manganese transport regulator MntR; Provisional
Probab=43.03 E-value=48 Score=30.49 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=37.1
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.|+.++..++.++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le--~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLA--RDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 455567777889999999999999999999999999 66777653
No 137
>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=42.81 E-value=43 Score=27.18 Aligned_cols=35 Identities=6% Similarity=0.130 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
=++.|+-.... +.+|+.+|++.+|++...+.+.|.
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 36778888888 899999999999999999888663
No 138
>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=41.91 E-value=34 Score=30.05 Aligned_cols=49 Identities=18% Similarity=0.301 Sum_probs=39.4
Q ss_pred cHHHHHHHHHhcCC--------CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 495 SLFQTVVLMLFNDA--------QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~--------~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
..+.-..|+..|.. -+.+.++|+..++-+.+.++.+|..|. +.+++...
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34555555555544 478999999999999999999999999 99998764
No 139
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.43 E-value=43 Score=23.75 Aligned_cols=45 Identities=13% Similarity=0.261 Sum_probs=34.3
Q ss_pred hhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 603 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 603 IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 4455555667777776654 35688999999999999999998653
No 140
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=41.24 E-value=45 Score=30.18 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=36.3
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
.|..+.+.++..++.+|++.++++...+.+.|..|. +.+++.+
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEE
Confidence 344555677788999999999999999999999999 7788864
No 141
>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=41.23 E-value=89 Score=25.18 Aligned_cols=48 Identities=13% Similarity=0.349 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+++.|=+.-..+..+.-.+|++.++.++..++..+..|- ..++|...|
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 444444555667799999999999999999999999998 889997654
No 142
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=40.95 E-value=97 Score=27.57 Aligned_cols=68 Identities=22% Similarity=0.303 Sum_probs=50.5
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCC---CCeEEEecCCC
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVED---DDSFVFNEGFT 564 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~---~~~~~~N~~f~ 564 (662)
|+---.+|-+..+.+..|+.|+++.+|=+.+.+.+.|..|. +.+|+..+.+|+...+ -+.+.++-.|.
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 33344567778888999999999999999999999999999 9999987654432222 24455555554
No 143
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=40.70 E-value=48 Score=26.48 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=32.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
+-||.... .++.+..+|+..++++...+.+.|..|. +.+++..
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 45666665 5678899999999999999999999999 8888854
No 144
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=39.35 E-value=48 Score=30.88 Aligned_cols=47 Identities=15% Similarity=0.323 Sum_probs=42.3
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccc
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 650 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r 650 (662)
.+|-.|.+++....+++..+|-..| ..+.+.+.+||..|.+.|.|++
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeEE
Confidence 4788999999999999999988766 5689999999999999999986
No 145
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.81 E-value=38 Score=24.19 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=21.9
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
++.++.+ .+|..+|++.+|++...+.+-+..+.
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4445544 78999999999999999988877665
No 146
>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=37.30 E-value=47 Score=27.27 Aligned_cols=47 Identities=11% Similarity=0.245 Sum_probs=36.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHHh--CCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 499 TVVLMLFNDAQKLSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+.|+-..-+++-+|.+++.+.+ .++...+..++..|+ |.+++.++++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSGD 67 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSGD 67 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEETT
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccCC
Confidence 4566666677788999999976 788999999999999 9999998653
No 147
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=36.87 E-value=94 Score=29.75 Aligned_cols=111 Identities=16% Similarity=0.161 Sum_probs=61.9
Q ss_pred ChhHHHHHHHHHHHHhhcCCCeeeEeccCCceEEEEEE--ec-------CceEEEEecHHHHHHHHHhcCCCCCCHHHHH
Q 006074 447 PHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAE--FP-------KGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 517 (662)
Q Consensus 447 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~--~~-------~~~~~l~vs~~Q~~iLl~Fn~~~~~t~~ei~ 517 (662)
|.++..+++....-|.....+ +.-...=|...+..+ +. .....-..|...+-+|-..--+.++|-.+|.
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 357899999999999865333 332222222222111 00 0011123444444455444445689999999
Q ss_pred HHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCC
Q 006074 518 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 564 (662)
Q Consensus 518 ~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 564 (662)
+.+|++. ..++..|. ..+++...+..........|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999986 45677777 777876533221111334566677664
No 148
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.73 E-value=83 Score=27.78 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 496 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 496 ~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+.+-|+-+--+++.+|+.++...||++-..+++.+.-|+ ..+-|...
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLV--a~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELV--ARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCCeEeC
Confidence 3567788888889999999999999999999999999999 66666554
No 149
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=36.24 E-value=45 Score=35.51 Aligned_cols=67 Identities=27% Similarity=0.349 Sum_probs=41.1
Q ss_pred eeEeccCCceEEEEEEecCceE-EE-E---ecHHHHHHHHHhcC-CC-CCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 469 RLMWQNSLGHCVLKAEFPKGKK-EL-A---VSLFQTVVLMLFND-AQ-KLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 469 ~L~w~~~l~~~~i~~~~~~~~~-~l-~---vs~~Q~~iLl~Fn~-~~-~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
-+.+.+.||..|=++--|.+.. +| . -+-+-..||-.+-+ .+ .+|+++|++.|||..+++..+|++|-
T Consensus 281 LIdFSYeLSr~E~~~GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhhcccCcCCCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 3567777887665543332211 00 0 02233334433333 22 39999999999999999999999885
No 150
>smart00753 PAM PCI/PINT associated module.
Probab=36.07 E-value=64 Score=26.17 Aligned_cols=36 Identities=11% Similarity=0.223 Sum_probs=30.2
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 506 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 506 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
.....+++++|++.++++.+++...+..++ ..+.|.
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l~ 55 (88)
T smart00753 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEIS 55 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCeE
Confidence 345789999999999999999999999998 555553
No 151
>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=36.07 E-value=64 Score=26.17 Aligned_cols=36 Identities=11% Similarity=0.223 Sum_probs=30.2
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 506 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 506 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
.....+++++|++.++++.+++...+..++ ..+.|.
T Consensus 20 ~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l~ 55 (88)
T smart00088 20 EPYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEIS 55 (88)
T ss_pred HHhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCeE
Confidence 345789999999999999999999999998 555553
No 152
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=36.05 E-value=65 Score=29.74 Aligned_cols=45 Identities=13% Similarity=0.270 Sum_probs=38.3
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 500 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 500 ~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+|..+..+.......+|++.+++++..+...++-|. +.+++...|
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 344556577789999999999999999999999999 888888754
No 153
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=35.60 E-value=52 Score=33.09 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
-|..|+...+.++.+++.+|++.+|+++..+++=|..|-
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 477899999999999999999999999999999999886
No 154
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.59 E-value=51 Score=30.27 Aligned_cols=47 Identities=13% Similarity=0.268 Sum_probs=41.5
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccc
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 650 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r 650 (662)
.+|-.|.+.|....+.++.+|-.++ ..+++.+..||+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeee
Confidence 4678899999999999999988665 5689999999999999999985
No 155
>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=35.52 E-value=68 Score=23.79 Aligned_cols=40 Identities=20% Similarity=0.347 Sum_probs=31.7
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.|.-+..||.++..+ .+..+|++.+|+++..+..++..+.
T Consensus 4 LT~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHH
Confidence 356677788777664 7899999999999999999988876
No 156
>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=34.90 E-value=57 Score=27.15 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
....+.-.+....++++++|++.++++.+++...+..++ ..+.|.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I--~~~~i~ 91 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLI--SNGLIK 91 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHH--HTTSSE
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHH--HCCCEE
Confidence 344455555677899999999999999999999999998 555543
No 157
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=34.68 E-value=60 Score=28.79 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=33.6
Q ss_pred hhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 606 IMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 606 imK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
+|..++.++.++|-+.+ ..+.+.+.+++.+|++.|.+.|..
T Consensus 36 LL~~~~~~tvdelae~l------nr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 36 LLEENGPLTVDELAEIL------NRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHhhcCCcCHHHHHHHH------CccHHHHHHHHHHHHHcCCeeeee
Confidence 34478888888877665 557899999999999999999964
No 158
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=34.44 E-value=65 Score=24.97 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=41.2
Q ss_pred hhhhhhcCC-CCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 602 AIVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 602 ~IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
.|.++++.. +.++..+|....... .+..+.+.|..++..|-++||+++..
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~-g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR-GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc-ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 366777776 669999988776554 78899999999999999999998754
No 159
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=34.35 E-value=64 Score=32.82 Aligned_cols=39 Identities=36% Similarity=0.520 Sum_probs=30.4
Q ss_pred HHHHHHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 497 FQTVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 497 ~Q~~iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
+...|+-.+.+ ...+|+++|+..|||..+++..+|+.|-
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 44455544433 5689999999999999999999998774
No 160
>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=34.26 E-value=40 Score=28.54 Aligned_cols=45 Identities=9% Similarity=0.252 Sum_probs=32.4
Q ss_pred hhhhhhhhhhcC----CCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccc
Q 006074 598 QVDAAIVRIMKT----RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYL 648 (662)
Q Consensus 598 ~i~A~IVRimK~----~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi 648 (662)
.++..|..++|. ...++.++|... + ..+..+|+++|+.|++.|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~----l--~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQ----L--GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHH----S--TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHH----h--CcCHHHHHHHHHHHHhCCeE
Confidence 345556666666 567887777644 3 44699999999999999976
No 161
>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=33.84 E-value=52 Score=25.77 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=30.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 510 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 510 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+|-++|++.+|++...+.+.|..|. +.+++...
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 47899999999999999999999999 88888753
No 162
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=33.33 E-value=44 Score=27.47 Aligned_cols=36 Identities=28% Similarity=0.247 Sum_probs=32.0
Q ss_pred CCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 627 KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 627 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
|+....+.-++.|..|.++|.|..-..++..-+|.|
T Consensus 50 rlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 50 KYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 567889999999999999999998888888899976
No 163
>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=33.26 E-value=93 Score=21.70 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=28.6
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
++..+..++.++- .+.+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555555554442 246899999999999999988877654
No 164
>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=33.00 E-value=1.1e+02 Score=27.27 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=40.6
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHh----CCCHHHHHHHhhHhhcCCccceecC
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t----~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+|..+..|+..+=+.+..|..+|.+.+ +.+...+...|.-|. +.|++.+.
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 466788888777667789999977765 788899999999999 88888753
No 165
>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=32.60 E-value=1e+02 Score=25.54 Aligned_cols=40 Identities=15% Similarity=0.414 Sum_probs=26.6
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
+..+..+... ++..|.+.||||.-.++.+|.+|- ..+|-.
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~--~~~I~~ 52 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALP--ELGIEC 52 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGG--GGT-EE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhh--cCCeEE
Confidence 3344555556 999999999999999999999998 666643
No 166
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=32.55 E-value=1.1e+02 Score=33.28 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=35.4
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 505 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 505 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+..++.+|.++|++.+++|+..+.+.|..|. +.+++.+.
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 5667799999999999999999999999999 99999863
No 167
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=31.98 E-value=83 Score=25.78 Aligned_cols=48 Identities=19% Similarity=0.313 Sum_probs=36.9
Q ss_pred hhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 599 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 599 i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
.+..|...+.....++..+|...+ .++.+.+.+.|..|.++|+|.+..
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~~------~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKRL------GVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHH------CCCchhHHHHHHHHHHCCCeEecC
Confidence 355667777777778888876443 556788999999999999998764
No 168
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.93 E-value=55 Score=29.90 Aligned_cols=29 Identities=28% Similarity=0.397 Sum_probs=26.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 507 DAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 507 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.++.+|-++|++.+|++...+++.|..|.
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ 40 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLY 40 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45689999999999999999999999998
No 169
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=31.20 E-value=67 Score=22.00 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 508 AQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 508 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
...+++++|++..|++..-+.+..+...
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 4579999999999999999988887665
No 170
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=31.18 E-value=96 Score=25.09 Aligned_cols=34 Identities=21% Similarity=0.343 Sum_probs=29.5
Q ss_pred HHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 502 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 502 Ll~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
++..++.+.+|=++|++.+|++...+-++++.|-
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHH
Confidence 3445566789999999999999999999999997
No 171
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=31.07 E-value=1.2e+02 Score=24.12 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=42.1
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCC----hhhHHHHHHhhhhhccccccC
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK----PADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~----~~~ik~~Ie~Liereyi~r~~ 652 (662)
.|-.|| .-|+.++..+...+...+...-+...+ ...++++|..++++|-|.+..
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 344555 688999999999999998886542222 367999999999999998865
No 172
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=30.94 E-value=1.2e+02 Score=21.74 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhH
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 533 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 533 (662)
+.+.|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344455444333 69999999999999999988764
No 173
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.88 E-value=89 Score=30.68 Aligned_cols=45 Identities=22% Similarity=0.301 Sum_probs=37.6
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
.+.+-..++...+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 10 iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~ 54 (217)
T PRK14165 10 LALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRT 54 (217)
T ss_pred HHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 3444455566689999999999999999999999999 88999875
No 174
>PRK13239 alkylmercury lyase; Provisional
Probab=30.73 E-value=89 Score=30.33 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
+...||.++-++..+|+++|+..+|.+.+.+.+.|..|-
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 455677778899999999999999999999999999875
No 175
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=30.51 E-value=61 Score=25.89 Aligned_cols=58 Identities=21% Similarity=0.298 Sum_probs=33.6
Q ss_pred hhhhhhhhhhhcCCC--CCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccc---cccCCCCCceeecC
Q 006074 597 YQVDAAIVRIMKTRK--VLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYL---ERDKNNPQIYNYLA 662 (662)
Q Consensus 597 ~~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi---~r~~~~~~~y~Yia 662 (662)
...=|.||..||++. .++.+|+..++.. +... ..+++-+. +-.-+ +.++. .++|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~---~d~~-~~~~~~L~---~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL---LDIG-PKLKEWLK---SEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc---cCcc-HHHHHHHH---hhhhccCceeccC-CCEEEecc
Confidence 345688999999975 7888888776642 3322 22233332 22222 33433 45899876
No 176
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=30.42 E-value=1.1e+02 Score=29.06 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=37.6
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
++.-++.++..|..+|+..+|++..++.++|=.|. +.+.+...+
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 55666777899999999999999999999999998 777776654
No 177
>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=30.35 E-value=1e+02 Score=22.48 Aligned_cols=42 Identities=14% Similarity=0.278 Sum_probs=34.5
Q ss_pred HHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 502 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 502 Ll~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
--+|++++.+|+++..+.+|++-+.....|.-|= +.++..+.
T Consensus 2 ~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD--~~g~T~R~ 43 (50)
T PF09107_consen 2 RELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLD--REGITRRV 43 (50)
T ss_dssp HHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred hHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHh--ccCCEEEe
Confidence 3467788999999999999999999988898886 77777664
No 178
>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=29.91 E-value=74 Score=32.52 Aligned_cols=58 Identities=21% Similarity=0.362 Sum_probs=32.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCC
Q 006074 496 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 563 (662)
Q Consensus 496 ~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 563 (662)
-+--.|.-+|.++..|++.+|.+.|+-|+..|+..|..++ ++.+.++ -...|.+=..|
T Consensus 216 eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 216 ELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 3445677899999999999999999999999999999776 5655432 12456665544
No 179
>smart00526 H15 Domain in histone families 1 and 5.
Probab=29.45 E-value=1.7e+02 Score=22.41 Aligned_cols=53 Identities=21% Similarity=0.130 Sum_probs=38.6
Q ss_pred hhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCC--hhhHHHHHHhhhhhcccccc
Q 006074 598 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIK--PADLKKRIESLIDREYLERD 651 (662)
Q Consensus 598 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~--~~~ik~~Ie~Liereyi~r~ 651 (662)
.|..||.. |+.+++.+...+..-+...-...|. ...++..|..++++|-|.+-
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 46666665 6999999999988888765332222 25688889999999988754
No 180
>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=29.23 E-value=1.2e+02 Score=26.06 Aligned_cols=57 Identities=18% Similarity=0.325 Sum_probs=41.7
Q ss_pred HHHHHhcC-CCCCCHHHHHHHh-----CCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEec
Q 006074 500 VVLMLFND-AQKLSFQDIKDAT-----GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 561 (662)
Q Consensus 500 ~iLl~Fn~-~~~~t~~ei~~~t-----~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 561 (662)
.||..+.+ ...+|.+||.+.+ +++...+-++|..|. ..+++.+...+. ....|..+.
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 4579999999988 689999999999999 999998753211 124566664
No 181
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.22 E-value=85 Score=30.96 Aligned_cols=49 Identities=16% Similarity=0.205 Sum_probs=37.9
Q ss_pred ecHHHHHHHHHh---cCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 494 VSLFQTVVLMLF---NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 494 vs~~Q~~iLl~F---n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
.|.-+.-+++.+ +...++|.++|++.+++++..++.++..|+ +++++..
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 345554444332 334689999999999999999999999999 8888854
No 182
>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=29.19 E-value=1.1e+02 Score=26.20 Aligned_cols=41 Identities=27% Similarity=0.434 Sum_probs=30.9
Q ss_pred CCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhcccccc--CCCC
Q 006074 609 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD--KNNP 655 (662)
Q Consensus 609 ~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~--~~~~ 655 (662)
....++..+|...+ ..+.+.+-+.|..|.++|||.|. ++|+
T Consensus 40 ~~~~~t~~eL~~~l------~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKEI------LIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHHH------CCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 44677877776443 45688899999999999999974 4443
No 183
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=28.85 E-value=71 Score=32.25 Aligned_cols=49 Identities=16% Similarity=0.333 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
-|..+-..-+.++.++-+||.+.+|+|...+-++|..|- +.+++.+...
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 445555666677789999999999999999999999999 9999887543
No 184
>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=28.69 E-value=1.8e+02 Score=22.40 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=30.5
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccce
Q 006074 501 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 542 (662)
Q Consensus 501 iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 542 (662)
|+-.+.+. ..+..+|++.+|++...+.+.+..|- ..++.
T Consensus 5 il~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~--~~g~~ 43 (69)
T TIGR00122 5 LLALLADN-PFSGEKLGEALGMSRTAVNKHIQTLR--EWGVD 43 (69)
T ss_pred HHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCe
Confidence 34344444 57899999999999999999999997 55553
No 185
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=28.44 E-value=3.7e+02 Score=28.17 Aligned_cols=54 Identities=15% Similarity=0.382 Sum_probs=39.4
Q ss_pred HHHHHHHhHHHHhhccCCHHHHHHHHHHhccc----chHHHHHHHHHHHHHHHhchhc
Q 006074 201 HISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIV 254 (662)
Q Consensus 201 ~~~~il~~gl~~ll~~~~~~~L~~ly~l~~~~----~~l~~l~~~~~~~i~~~g~~~~ 254 (662)
.+..++.+.|....+++|...+.+.++||-.+ .|++....-+.+.|......+.
T Consensus 7 ~L~~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~ 64 (324)
T smart00762 7 TLTELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLL 64 (324)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHh
Confidence 34445567788889999999999999999766 4677766666666666555444
No 186
>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=28.39 E-value=95 Score=25.93 Aligned_cols=38 Identities=16% Similarity=0.230 Sum_probs=31.2
Q ss_pred CCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 609 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 609 ~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
....+++.+|-..+ -.+.+.+-+.|..|.++|+|+|..
T Consensus 44 ~~~~is~~eLa~~~------g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAELT------GLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeeeec
Confidence 56788888877554 447788999999999999999876
No 187
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=27.37 E-value=82 Score=31.02 Aligned_cols=57 Identities=16% Similarity=0.303 Sum_probs=42.5
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecCCC
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 564 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 564 (662)
-..+.-+|.++..||+.+|.+.|+=|+..|+..|..++ ++.+-++ -..+|.+-..|.
T Consensus 188 ld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 188 LDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 34466789999999999999999999999999999887 4443221 125666666553
No 188
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.14 E-value=1.3e+02 Score=26.60 Aligned_cols=52 Identities=17% Similarity=0.286 Sum_probs=44.1
Q ss_pred HhhhhhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 596 QYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 596 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
+..|.+-||-..+.++.++..++.... -.+...++..+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~T------GasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAKT------GASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHHH------CCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 346899999999999999999988654 4578889999999999999888653
No 189
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=26.68 E-value=1.1e+02 Score=24.71 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=35.0
Q ss_pred hhhhhcCC-CCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC
Q 006074 603 IVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 653 (662)
Q Consensus 603 IVRimK~~-k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~ 653 (662)
|...+... ..++..+|..++ ..+...+.+.+..|.+.|||.+++.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 34445444 678888887665 4578889999999999999999753
No 190
>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=26.49 E-value=1.1e+02 Score=27.82 Aligned_cols=38 Identities=16% Similarity=0.266 Sum_probs=28.8
Q ss_pred EecHHHHHHHHH-hcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 493 AVSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 493 ~vs~~Q~~iLl~-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
.+|+.|..|+.+ +- ++++++||++.+|+|...++..+.
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 346666666655 43 468999999999999988887654
No 191
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=26.19 E-value=77 Score=29.63 Aligned_cols=57 Identities=19% Similarity=0.456 Sum_probs=40.5
Q ss_pred HHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC-CCCCCCCCeEEEecCCC
Q 006074 502 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK-GRDVEDDDSFVFNEGFT 564 (662)
Q Consensus 502 Ll~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~-~~~~~~~~~~~~N~~f~ 564 (662)
+|.++ .+++|++||++.||++...+-..+.-|. ..+|..+.-. | ...+.|..-.+|.
T Consensus 34 ilyls-~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~--~~~lV~~~~~~G---~Rk~~F~a~~df~ 91 (177)
T COG1510 34 ILYLS-RKPLTLDEIAEALGMSKSNVSMGLKKLQ--DWNLVKKVFEKG---DRKDYFEAEKDFS 91 (177)
T ss_pred hheec-CCCccHHHHHHHHCCCcchHHHHHHHHH--hcchHHhhhccC---cchhhhcccchHH
Confidence 34444 4699999999999999999999999888 7777765321 1 1234566666664
No 192
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=26.08 E-value=97 Score=28.23 Aligned_cols=52 Identities=27% Similarity=0.375 Sum_probs=43.5
Q ss_pred EEecHHHHHHHHHhcCC-CCCCHHHHHHHh-----CCCHHHHHHHhhHhhcCCccceecC
Q 006074 492 LAVSLFQTVVLMLFNDA-QKLSFQDIKDAT-----GIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~-~~~t~~ei~~~t-----~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+.+|..+..||..+.+. +.+|.++|-+.+ +++...+-++|..|. ..|++.+.
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~--e~Glv~~~ 74 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLE--EAGLVHRL 74 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHH--HCCCEEEE
Confidence 56788999999777755 569999998765 588999999999999 89998874
No 193
>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=26.06 E-value=82 Score=25.92 Aligned_cols=54 Identities=24% Similarity=0.301 Sum_probs=39.2
Q ss_pred hhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCC--CCCceee
Q 006074 601 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN--NPQIYNY 660 (662)
Q Consensus 601 A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~--~~~~y~Y 660 (662)
+.|++.+.. +.+.+++|...+. ..++..+-+++..|.+.|.|.|... .|....|
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~-----~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y 63 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLP-----GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY 63 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHST-----TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcc-----hhHHHHHHHHHHHHHHcchhhcccccCCCCCCcc
Confidence 456777777 7888888876542 4578999999999999999999642 3333444
No 194
>PRK12423 LexA repressor; Provisional
Probab=25.81 E-value=1.1e+02 Score=29.69 Aligned_cols=52 Identities=19% Similarity=0.378 Sum_probs=41.4
Q ss_pred ecHHHHHHHHHhcCC---C--CCCHHHHHHHhCC-CHHHHHHHhhHhhcCCccceecCCC
Q 006074 494 VSLFQTVVLMLFNDA---Q--KLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~---~--~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
+|.-|-.||..+.+. . .-|..||++.+|+ +...+..+|..|. +.++|...|.
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~--~~G~l~~~~~ 61 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALA--EAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEecCC
Confidence 366777777655542 2 3499999999995 8999999999999 8999998765
No 195
>PLN03239 histone acetyltransferase; Provisional
Probab=25.62 E-value=99 Score=32.46 Aligned_cols=39 Identities=21% Similarity=0.338 Sum_probs=29.4
Q ss_pred HHHHHHHHhcCC----CCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 497 FQTVVLMLFNDA----QKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 497 ~Q~~iLl~Fn~~----~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|-
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~ 309 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLG 309 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 444555444222 469999999999999999999988773
No 196
>PHA02591 hypothetical protein; Provisional
Probab=25.60 E-value=86 Score=25.09 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhH
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQS 533 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~~ 533 (662)
.++|.++|++.+|++.+.+++.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3789999999999999999888765
No 197
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=25.27 E-value=1.4e+02 Score=29.73 Aligned_cols=44 Identities=18% Similarity=0.272 Sum_probs=38.9
Q ss_pred HHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 501 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 501 iLl~Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
||-.++. ...++..+|++.+|++...+.+++..|. ..+++...|
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE--~aGvIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLE--SAGVIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 6777777 3689999999999999999999999999 889998765
No 198
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.14 E-value=88 Score=30.76 Aligned_cols=56 Identities=23% Similarity=0.383 Sum_probs=44.3
Q ss_pred hhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccCCCCCceeecC
Q 006074 601 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 662 (662)
Q Consensus 601 A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 662 (662)
+--|-..|+.|.+..+||-.+ |....++.-.+|..|+..|.|.=.-+|++.|+||.
T Consensus 203 ~eFv~YIk~nKvV~ledLas~------f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 203 SEFVEYIKKNKVVPLEDLASE------FGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHhcCeeeHHHHHHH------hCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 344567788888888887643 55567777779999999999998888999999984
No 199
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=24.88 E-value=1.7e+02 Score=29.81 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=31.1
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHhhHhhcCCccceecCC
Q 006074 510 KLSFQDIKDATG--IEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 510 ~~t~~ei~~~t~--i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
..+.++|++.++ |+.++++.+|..|. +.|+|.++.
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~--~~glikk~~ 173 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLE--RLGLIKKNE 173 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHH--HCCCeeECC
Confidence 346889999998 89999999999999 999999863
No 200
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=24.87 E-value=1.2e+02 Score=27.32 Aligned_cols=45 Identities=11% Similarity=0.256 Sum_probs=32.1
Q ss_pred hhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 602 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 602 ~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
.|...+-....++..+|-.. +..+.+.+-+.|+.|.++|||+|.+
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~------l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKV------LSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecc
Confidence 33333334566777776544 3567888999999999999999964
No 201
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=24.72 E-value=1.3e+02 Score=28.00 Aligned_cols=59 Identities=17% Similarity=0.283 Sum_probs=42.7
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHHh--CCCHHHHHHHhhHhhcCCccceecCCCCCCCCCCCeEEEecC
Q 006074 498 QTVVLMLFNDA-QKLSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 562 (662)
Q Consensus 498 Q~~iLl~Fn~~-~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 562 (662)
...|+-.|... .+.|..+|.+.+ +++...+.++|..|+ ..|-|..- .+...-+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~--~~g~i~~K----~~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLV--EEGKIVEK----EYGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHH--hCCCeeee----eecceEEEeeCcc
Confidence 35677777665 489999999988 589999999999999 54444321 2334567888876
No 202
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=24.32 E-value=1e+02 Score=30.90 Aligned_cols=52 Identities=17% Similarity=0.330 Sum_probs=43.0
Q ss_pred EEecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 492 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 492 l~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
|-.|-++|-+-+..=..+..|..||++.+|+|..-+-..|.+|. +.|++...
T Consensus 12 lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe--~kG~v~~~ 63 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLE--KKGLVEVI 63 (247)
T ss_pred cCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHH--HCCCEEee
Confidence 44567777776666666789999999999999999999999999 77777654
No 203
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=24.04 E-value=1.9e+02 Score=21.36 Aligned_cols=41 Identities=17% Similarity=0.292 Sum_probs=35.4
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
.+|.-+..++.++..+ .+..||+...+++...+..++....
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 4677888899888876 8999999999999999998888775
No 204
>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=23.66 E-value=1.5e+02 Score=26.81 Aligned_cols=40 Identities=18% Similarity=0.075 Sum_probs=31.8
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
.+|.-|..|+.++ ..++|.+||++.+|++...+...+...
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 3577888888886 367999999999999998887655443
No 205
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=23.48 E-value=97 Score=25.52 Aligned_cols=32 Identities=16% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 513 FQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 513 ~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
+.+|++.+|++...+.+.|..|. +.+++.+.|
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~--~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLE--KDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHH--HCCCEEEcC
Confidence 46899999999999999999999 888988754
No 206
>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=22.98 E-value=53 Score=24.10 Aligned_cols=22 Identities=23% Similarity=0.517 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHh
Q 006074 510 KLSFQDIKDATGIEDKELRRTL 531 (662)
Q Consensus 510 ~~t~~ei~~~t~i~~~~l~~~L 531 (662)
.+++.||++.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5788999999999999988877
No 207
>PRK09462 fur ferric uptake regulator; Provisional
Probab=22.73 E-value=1.6e+02 Score=26.70 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=40.1
Q ss_pred hhhhhhhcC--CCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 601 AAIVRIMKT--RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 601 A~IVRimK~--~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
-+|.+++.. .+-++.++|...+.+.. ..++...|=+.|+.|.+.|.|.+-.
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 345556654 36899999998887653 4678899999999999999998854
No 208
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=22.73 E-value=2.4e+02 Score=27.71 Aligned_cols=81 Identities=20% Similarity=0.271 Sum_probs=54.1
Q ss_pred ccCChhHHHHHHHHHHHHhhcCCCeeeEeccCCce-EEEEEEecCceEEEE-e-----cHHHHHHHHHh--cCCCCCCHH
Q 006074 444 VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGH-CVLKAEFPKGKKELA-V-----SLFQTVVLMLF--NDAQKLSFQ 514 (662)
Q Consensus 444 ~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~-~~i~~~~~~~~~~l~-v-----s~~Q~~iLl~F--n~~~~~t~~ 514 (662)
..=|..+..+.+.++. +|. +.+ .+|++|..-+. + +..|..||-.. ...+.+|..
T Consensus 132 lISp~Di~~A~~~l~~----------------lg~g~~l-~~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~ 194 (223)
T PF04157_consen 132 LISPEDILRACKLLEV----------------LGLGFRL-RKFGSGVKVVQSVPYSELSKDQSRILELAEEENGGGVTAS 194 (223)
T ss_dssp T--HHHHHHHHHHHCC----------------CTSSEEE-EEETTTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHH
T ss_pred CcCHHHHHHHHHHHHH----------------cCCCeEE-EEeCCCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHH
Confidence 4557788888876653 232 222 23554433332 2 35677888777 667799999
Q ss_pred HHHHHhCCCHHHHHHHhhHhhcCCcccee
Q 006074 515 DIKDATGIEDKELRRTLQSLACGKVRVLQ 543 (662)
Q Consensus 515 ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 543 (662)
++++.+|.+....+..|..+. ..+++.
T Consensus 195 ~l~~~~~ws~~~a~~~L~~~~--~~G~l~ 221 (223)
T PF04157_consen 195 ELAEKLGWSVERAKEALEELE--REGLLW 221 (223)
T ss_dssp HHHHHHTB-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHhCCCHHHHHHHHHHHH--hCCCEe
Confidence 999999999999999999888 666664
No 209
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=22.70 E-value=1.2e+02 Score=29.55 Aligned_cols=43 Identities=21% Similarity=0.259 Sum_probs=35.5
Q ss_pred HHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceec
Q 006074 500 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 544 (662)
Q Consensus 500 ~iLl~Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 544 (662)
.||.++.++ ...|.+||++.+++++..+++++..|. ..+++..
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~--~~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCA--SRHLIIA 209 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHH--hCCeEEE
Confidence 566666554 268999999999999999999999999 7777765
No 210
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=22.52 E-value=1.1e+02 Score=28.92 Aligned_cols=32 Identities=22% Similarity=0.442 Sum_probs=29.1
Q ss_pred CHHHHHHHh-CCCHHHHHHHhhHhhcCCccceecC
Q 006074 512 SFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 512 t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
|-.+|+..+ |+++..++++|..|+ ..+++.+.
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~Lv--eaGLI~rr 104 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLV--EAGLIVRR 104 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHH--HCCCeeec
Confidence 567899999 999999999999999 99998874
No 211
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=22.00 E-value=5.4e+02 Score=22.49 Aligned_cols=39 Identities=18% Similarity=0.382 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhCCCcCChH-HHHHHHHHHhhhh--ccH
Q 006074 93 HKTVTGLLRMIERERLGEAVDRT-LLNHLLKMFTALG--IYS 131 (662)
Q Consensus 93 ~~l~~~ll~~I~~~R~g~~i~~~-~ik~~i~ml~~l~--~Y~ 131 (662)
.++.+.|-+++...|...+.+.+ -+.++..||.+|| ||+
T Consensus 3 ~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGLRVYe 44 (118)
T PRK13713 3 NEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYE 44 (118)
T ss_pred hHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhHHHHH
Confidence 45667777888888876653322 3668899999998 554
No 212
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=21.84 E-value=1.6e+02 Score=25.87 Aligned_cols=44 Identities=23% Similarity=0.411 Sum_probs=36.9
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhC-CCHHHHHHHhhHhhcCCccceecC
Q 006074 499 TVVLMLFNDAQKLSFQDIKDATG-IEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 499 ~~iLl~Fn~~~~~t~~ei~~~t~-i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
+.||-...+ +..-+.||...++ |+..-|.+.|+.|. ..+++.+.
T Consensus 26 ~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le--~~Glv~R~ 70 (120)
T COG1733 26 LLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELE--EDGLVERV 70 (120)
T ss_pred HHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHH--HCCCEEee
Confidence 346655544 7889999999998 99999999999999 88998874
No 213
>PRK00118 putative DNA-binding protein; Validated
Probab=21.55 E-value=1.5e+02 Score=25.35 Aligned_cols=39 Identities=10% Similarity=0.171 Sum_probs=26.9
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 495 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 495 s~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
+.-|-.++.+. ..++.|+.||++.+|++...+.+.+..-
T Consensus 19 ~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44444444332 2236899999999999999888777543
No 214
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=21.27 E-value=1.4e+02 Score=32.68 Aligned_cols=38 Identities=29% Similarity=0.501 Sum_probs=29.3
Q ss_pred HHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHhhHhh
Q 006074 498 QTVVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLA 535 (662)
Q Consensus 498 Q~~iLl~F-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 535 (662)
-..|+-.+ +....+|+++|++.|||..+++..+|+.|-
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~ 399 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLN 399 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 33455333 344689999999999999999999998774
No 215
>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=21.14 E-value=1.2e+02 Score=21.64 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHHhh
Q 006074 512 SFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 512 t~~ei~~~t~i~~~~l~~~L~ 532 (662)
|+.||++..|++...+-+.|+
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 688999999999998887775
No 216
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=21.13 E-value=2.2e+02 Score=27.03 Aligned_cols=45 Identities=24% Similarity=0.331 Sum_probs=35.7
Q ss_pred HHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCC
Q 006074 500 VVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 546 (662)
Q Consensus 500 ~iLl~Fn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 546 (662)
.||..+...+ .+|.-+|+..+||+...+.++|=.|. +.+.+..+|
T Consensus 8 ~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~--~~~~v~~~~ 53 (183)
T PHA02701 8 LILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLL--ESDAVSCED 53 (183)
T ss_pred HHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHh--hcCcEecCC
Confidence 4555555444 69999999999999999999999998 776666544
No 217
>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=21.03 E-value=1.6e+02 Score=25.44 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=33.1
Q ss_pred hhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhccccccC
Q 006074 600 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 652 (662)
Q Consensus 600 ~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~~ 652 (662)
+..|...+.....++..+|-..+ ..+.+.+-+.|..|.++|||+|..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~~------~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQA------CILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHh------CCCchhHHHHHHHHHHCCCEEecc
Confidence 33455555667777777665432 345567889999999999999954
No 218
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=20.88 E-value=1.1e+02 Score=28.09 Aligned_cols=50 Identities=22% Similarity=0.284 Sum_probs=41.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCC-------CHHH-------HHHHhhHhhcCCccceecCCCC
Q 006074 497 FQTVVLMLFNDAQKLSFQDIKDATGI-------EDKE-------LRRTLQSLACGKVRVLQKLPKG 548 (662)
Q Consensus 497 ~Q~~iLl~Fn~~~~~t~~ei~~~t~i-------~~~~-------l~~~L~~L~~~k~~iL~~~~~~ 548 (662)
=.|+||-.+-....+.+..+...+|. |... ++.+|+.|- +.+++.+++.|
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE--~~glVek~~~G 117 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLE--KAGLVEKTKKG 117 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHH--HCCCeeeCCCC
Confidence 46889988877789999999999998 5555 999999999 89999876543
No 219
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=20.85 E-value=1.2e+02 Score=29.34 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=36.5
Q ss_pred HhcCCCCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecCCC
Q 006074 504 LFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 547 (662)
Q Consensus 504 ~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 547 (662)
.+..++.++..+|++.+|++-.-++.+|..|. ..|++...|+
T Consensus 28 ~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~--~eGlv~~~~~ 69 (212)
T TIGR03338 28 ELPPGAKLNESDIAARLGVSRGPVREAFRALE--EAGLVRNEKN 69 (212)
T ss_pred CCCCCCEecHHHHHHHhCCChHHHHHHHHHHH--HCCCEEEecC
Confidence 35556789999999999999999999999999 8899987654
No 220
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=1.2e+02 Score=28.47 Aligned_cols=38 Identities=11% Similarity=0.160 Sum_probs=27.3
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
++.-|-.|+.+. .-+++|++||++.+|+|+..++..|.
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 12468999999999999988877664
No 221
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.80 E-value=1.4e+02 Score=27.21 Aligned_cols=37 Identities=22% Similarity=0.170 Sum_probs=25.7
Q ss_pred ecHHHHHHH-HHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 494 VSLFQTVVL-MLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 494 vs~~Q~~iL-l~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
+|.-|-.|+ +.+- +++|++||++.+|+++..++..|.
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 344444444 3333 358999999999999998876654
No 222
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.59 E-value=1.5e+02 Score=27.37 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 498 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 498 Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
+.++.|.+- +++|++||++.+|+|...++..|.
T Consensus 124 r~v~~L~~~--eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 124 RAAFLMSQL--EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 333444343 458999999999999988776653
No 223
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=20.52 E-value=61 Score=26.17 Aligned_cols=45 Identities=22% Similarity=0.373 Sum_probs=34.9
Q ss_pred hhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhcccccc
Q 006074 601 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 651 (662)
Q Consensus 601 A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~ 651 (662)
-+|+-.+.....+++.+|...+ ..+...+-+.+..|.+.|||++.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l------~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEEL------GLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHT------T--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHh------CcCHHHHHHHHHHHHHCCCEEEE
Confidence 3566667777888888877554 45789999999999999999985
No 224
>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=20.32 E-value=1.4e+02 Score=27.26 Aligned_cols=40 Identities=23% Similarity=0.249 Sum_probs=28.3
Q ss_pred ecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhHh
Q 006074 494 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 534 (662)
Q Consensus 494 vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 534 (662)
++.-|-.|+.+.- ..++|.+||++.+|+|...++..+.--
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 3455555554422 347899999999999999888776543
No 225
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.25 E-value=1.7e+02 Score=20.43 Aligned_cols=24 Identities=25% Similarity=0.415 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
..+|..+|++.+|.+...+.+.|.
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 458999999999999988877653
No 226
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.20 E-value=83 Score=31.66 Aligned_cols=46 Identities=20% Similarity=0.484 Sum_probs=39.8
Q ss_pred hhhhhhhhcCCCCCChHHHHHHHHHhcCCCCChhhHHHHHHhhhhhcccccc
Q 006074 600 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 651 (662)
Q Consensus 600 ~A~IVRimK~~k~l~~~~L~~~v~~~l~F~~~~~~ik~~Ie~Liereyi~r~ 651 (662)
...|..++++++.++..+|.+ +|.++...|.+-|..|-++|.|.|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 346778889999999999875 4688999999999999999999985
No 227
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=20.20 E-value=1.9e+02 Score=26.28 Aligned_cols=38 Identities=24% Similarity=0.199 Sum_probs=30.2
Q ss_pred EecHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 006074 493 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 532 (662)
Q Consensus 493 ~vs~~Q~~iLl~Fn~~~~~t~~ei~~~t~i~~~~l~~~L~ 532 (662)
.+|.-|..||.++ ...+|.+||++.+|++...+.....
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4578888888776 3579999999999999876665554
No 228
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=20.03 E-value=1.3e+02 Score=31.07 Aligned_cols=35 Identities=20% Similarity=0.256 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhHhhcCCccceecC
Q 006074 509 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 545 (662)
Q Consensus 509 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 545 (662)
...|.+||++.+|+++..+.+-|..|+ -.+++.+.
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~--~lgll~~~ 56 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLR--QMRVINLE 56 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHH--hCCCeEec
Confidence 588999999999999999999999999 88999864
Done!