Query psy16234
Match_columns 609
No_of_seqs 257 out of 1013
Neff 8.3
Searched_HMMs 46136
Date Sat Aug 17 00:17:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16234hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2284|consensus 100.0 1E-120 2E-125 901.8 41.7 577 1-609 2-728 (728)
2 KOG2166|consensus 100.0 4E-106 8E-111 890.2 57.7 587 4-607 4-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 1E-106 3E-111 855.0 51.4 597 6-609 16-773 (773)
4 KOG2167|consensus 100.0 1.9E-97 4E-102 768.2 41.9 532 62-609 122-661 (661)
5 KOG2285|consensus 100.0 1.6E-90 3.4E-95 692.8 47.8 600 7-609 10-777 (777)
6 PF00888 Cullin: Cullin family 100.0 3.3E-80 7.2E-85 698.0 49.5 483 14-510 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 2.6E-34 5.6E-39 263.1 17.8 142 292-435 1-142 (142)
8 KOG2165|consensus 100.0 1.5E-28 3.1E-33 260.4 40.3 306 289-600 445-759 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 5E-20 1.1E-24 145.3 4.4 67 537-603 1-68 (68)
10 TIGR01610 phage_O_Nterm phage 96.2 0.014 3E-07 49.2 6.6 65 442-510 21-93 (95)
11 PF09339 HTH_IclR: IclR helix- 96.1 0.01 2.3E-07 43.9 4.4 46 449-494 6-52 (52)
12 PF13412 HTH_24: Winged helix- 95.8 0.022 4.7E-07 41.3 5.2 46 445-490 2-47 (48)
13 PF02082 Rrf2: Transcriptional 95.4 0.05 1.1E-06 44.6 6.6 59 447-508 11-70 (83)
14 PF12802 MarR_2: MarR family; 94.8 0.045 9.7E-07 41.8 4.4 50 444-493 3-54 (62)
15 PF08220 HTH_DeoR: DeoR-like h 94.5 0.1 2.3E-06 39.4 5.5 46 448-493 2-47 (57)
16 PF13463 HTH_27: Winged helix 94.1 0.15 3.3E-06 39.6 6.1 50 444-493 1-51 (68)
17 PF01022 HTH_5: Bacterial regu 94.1 0.13 2.8E-06 37.1 5.1 44 447-491 3-46 (47)
18 PF01047 MarR: MarR family; I 94.1 0.065 1.4E-06 40.6 3.7 50 444-493 1-50 (59)
19 PF12840 HTH_20: Helix-turn-he 93.5 0.16 3.5E-06 38.9 4.9 49 445-493 9-57 (61)
20 COG3355 Predicted transcriptio 93.3 0.22 4.7E-06 43.9 5.9 38 456-493 38-75 (126)
21 smart00550 Zalpha Z-DNA-bindin 93.0 0.2 4.3E-06 39.4 4.8 47 447-493 7-55 (68)
22 TIGR02337 HpaR homoprotocatech 92.5 0.23 4.9E-06 43.6 5.1 52 443-494 25-76 (118)
23 smart00346 HTH_ICLR helix_turn 92.3 0.42 9.1E-06 39.5 6.2 55 449-507 8-63 (91)
24 PF01978 TrmB: Sugar-specific 91.8 0.16 3.4E-06 39.8 2.9 49 445-493 7-55 (68)
25 PF04492 Phage_rep_O: Bacterio 91.7 0.62 1.3E-05 39.6 6.6 61 444-510 30-98 (100)
26 PRK11512 DNA-binding transcrip 91.5 0.37 8.1E-06 43.9 5.5 52 443-494 37-88 (144)
27 PRK15090 DNA-binding transcrip 91.2 0.47 1E-05 47.8 6.4 56 449-508 17-72 (257)
28 smart00347 HTH_MARR helix_turn 91.0 0.56 1.2E-05 39.2 5.8 52 442-493 6-57 (101)
29 PRK10857 DNA-binding transcrip 90.8 0.76 1.6E-05 42.9 6.9 58 448-508 12-70 (164)
30 PRK11920 rirA iron-responsive 90.8 0.74 1.6E-05 42.5 6.8 56 449-507 13-68 (153)
31 smart00419 HTH_CRP helix_turn_ 90.2 0.73 1.6E-05 32.8 5.0 34 460-493 8-41 (48)
32 smart00420 HTH_DEOR helix_turn 90.2 0.74 1.6E-05 33.4 5.1 44 450-493 4-47 (53)
33 TIGR02010 IscR iron-sulfur clu 89.5 0.99 2.1E-05 40.6 6.4 56 449-507 13-69 (135)
34 TIGR01889 Staph_reg_Sar staphy 89.5 0.9 1.9E-05 39.2 5.8 52 443-494 22-77 (109)
35 PF04703 FaeA: FaeA-like prote 89.4 0.87 1.9E-05 35.0 4.9 44 451-494 5-49 (62)
36 PF13601 HTH_34: Winged helix 88.8 0.51 1.1E-05 38.3 3.6 45 449-493 3-47 (80)
37 COG1414 IclR Transcriptional r 88.8 0.93 2E-05 45.4 6.2 56 449-508 7-63 (246)
38 PF05584 Sulfolobus_pRN: Sulfo 88.5 1.2 2.6E-05 35.0 5.3 46 446-493 6-51 (72)
39 PF09012 FeoC: FeoC like trans 88.5 0.44 9.5E-06 37.5 2.9 46 548-600 4-49 (69)
40 TIGR02431 pcaR_pcaU beta-ketoa 87.8 1.2 2.7E-05 44.5 6.4 54 449-508 12-66 (248)
41 PRK11569 transcriptional repre 87.8 1.1 2.4E-05 45.6 6.1 53 449-505 31-84 (274)
42 PF05732 RepL: Firmicute plasm 87.6 0.74 1.6E-05 43.0 4.3 49 460-513 75-123 (165)
43 PRK10163 DNA-binding transcrip 87.5 1.3 2.7E-05 45.1 6.4 56 449-508 28-84 (271)
44 COG1959 Predicted transcriptio 87.5 1.5 3.2E-05 40.4 6.1 59 447-508 11-70 (150)
45 PRK13777 transcriptional regul 87.4 1.3 2.9E-05 42.1 6.0 52 442-493 41-92 (185)
46 PF13730 HTH_36: Helix-turn-he 87.2 1.8 3.8E-05 32.1 5.4 29 462-490 27-55 (55)
47 TIGR00738 rrf2_super rrf2 fami 86.8 1.7 3.7E-05 38.7 6.1 46 448-493 12-58 (132)
48 PF08279 HTH_11: HTH domain; 86.5 1.7 3.6E-05 32.2 5.0 39 450-488 4-43 (55)
49 smart00345 HTH_GNTR helix_turn 86.2 2.1 4.5E-05 31.8 5.5 40 455-494 14-54 (60)
50 smart00344 HTH_ASNC helix_turn 85.8 1.6 3.4E-05 37.4 5.2 46 447-492 4-49 (108)
51 PHA00738 putative HTH transcri 85.7 2.1 4.5E-05 36.5 5.6 67 441-509 7-73 (108)
52 PRK03573 transcriptional regul 85.5 1.6 3.4E-05 39.7 5.3 53 442-494 27-80 (144)
53 TIGR01884 cas_HTH CRISPR locus 85.4 1.4 3.1E-05 42.6 5.2 51 443-493 140-190 (203)
54 cd00092 HTH_CRP helix_turn_hel 85.2 2.4 5.2E-05 32.5 5.5 35 459-493 24-58 (67)
55 PRK09834 DNA-binding transcrip 85.1 1.7 3.7E-05 43.9 5.8 54 449-506 14-68 (263)
56 PF01325 Fe_dep_repress: Iron 85.1 2 4.2E-05 32.8 4.7 44 451-494 13-56 (60)
57 cd00090 HTH_ARSR Arsenical Res 84.8 2.2 4.7E-05 33.2 5.2 48 445-493 6-53 (78)
58 TIGR02944 suf_reg_Xantho FeS a 84.4 2.4 5.2E-05 37.7 5.9 45 449-493 12-58 (130)
59 COG3682 Predicted transcriptio 84.1 2 4.4E-05 37.7 4.9 62 544-609 6-67 (123)
60 TIGR02698 CopY_TcrY copper tra 84.1 2.2 4.7E-05 38.2 5.4 60 546-609 6-65 (130)
61 PRK10870 transcriptional repre 83.5 2.5 5.5E-05 39.9 5.9 51 444-494 53-105 (176)
62 TIGR03879 near_KaiC_dom probab 83.4 1.2 2.7E-05 35.3 3.1 41 452-492 24-64 (73)
63 PF08784 RPA_C: Replication pr 82.0 2.6 5.6E-05 35.8 4.9 49 443-491 44-96 (102)
64 PF03965 Penicillinase_R: Peni 81.7 1.4 3.1E-05 38.4 3.2 60 546-609 5-64 (115)
65 smart00418 HTH_ARSR helix_turn 81.7 3 6.5E-05 31.2 4.7 36 458-493 8-43 (66)
66 COG2345 Predicted transcriptio 81.3 2.4 5.2E-05 41.3 4.8 44 449-492 14-57 (218)
67 PF01978 TrmB: Sugar-specific 81.1 1.1 2.3E-05 35.0 2.0 56 546-608 10-65 (68)
68 COG1846 MarR Transcriptional r 80.9 3.3 7.1E-05 35.8 5.3 51 444-494 20-70 (126)
69 PF09012 FeoC: FeoC like trans 80.8 1.9 4.2E-05 33.8 3.4 43 451-493 5-47 (69)
70 PF00325 Crp: Bacterial regula 80.5 3 6.5E-05 27.4 3.5 31 460-490 2-32 (32)
71 PRK11014 transcriptional repre 80.5 5.1 0.00011 36.3 6.5 49 455-506 20-68 (141)
72 PF08221 HTH_9: RNA polymerase 80.3 2.8 6E-05 32.2 4.0 35 457-491 24-58 (62)
73 PF01638 HxlR: HxlR-like helix 79.1 4 8.8E-05 33.8 4.9 44 449-493 8-52 (90)
74 PF01726 LexA_DNA_bind: LexA D 78.9 4.9 0.00011 31.2 5.0 51 444-494 4-60 (65)
75 cd07377 WHTH_GntR Winged helix 78.9 7.4 0.00016 29.4 6.1 38 456-493 20-58 (66)
76 COG4189 Predicted transcriptio 77.9 3.6 7.8E-05 39.9 4.7 50 444-493 21-70 (308)
77 PRK11179 DNA-binding transcrip 77.0 4.7 0.0001 37.1 5.2 48 444-491 7-54 (153)
78 PRK10141 DNA-binding transcrip 76.9 5.9 0.00013 34.7 5.5 48 446-493 16-63 (117)
79 smart00550 Zalpha Z-DNA-bindin 76.5 6.3 0.00014 30.8 5.1 54 545-605 7-62 (68)
80 PF08220 HTH_DeoR: DeoR-like h 76.4 3.5 7.7E-05 31.0 3.5 47 547-600 3-49 (57)
81 PF13463 HTH_27: Winged helix 76.4 6.4 0.00014 30.2 5.1 51 546-603 5-58 (68)
82 PRK11169 leucine-responsive tr 75.9 4.6 0.0001 37.6 4.9 48 444-491 12-59 (164)
83 PF13404 HTH_AsnC-type: AsnC-t 75.4 5.4 0.00012 28.0 3.9 36 449-484 6-41 (42)
84 PF02002 TFIIE_alpha: TFIIE al 75.1 2.8 6E-05 35.9 3.0 45 448-492 15-59 (105)
85 TIGR00373 conserved hypothetic 74.5 6.1 0.00013 36.6 5.2 44 449-492 17-60 (158)
86 PF08280 HTH_Mga: M protein tr 73.5 4.9 0.00011 30.4 3.6 38 448-485 7-44 (59)
87 PRK06266 transcription initiat 73.1 6.1 0.00013 37.4 5.0 45 448-492 24-68 (178)
88 PRK00215 LexA repressor; Valid 72.6 6.6 0.00014 37.9 5.3 51 444-494 2-58 (205)
89 PRK10434 srlR DNA-bindng trans 72.0 5.1 0.00011 40.3 4.4 46 448-493 7-52 (256)
90 PF09756 DDRGK: DDRGK domain; 71.2 3.8 8.3E-05 39.0 3.1 58 545-609 100-157 (188)
91 PF05158 RNA_pol_Rpc34: RNA po 70.9 4.4 9.5E-05 42.3 3.8 144 443-601 81-260 (327)
92 TIGR02702 SufR_cyano iron-sulf 70.8 6.4 0.00014 38.1 4.7 44 450-493 5-48 (203)
93 PF14947 HTH_45: Winged helix- 70.7 9.8 0.00021 30.5 5.0 43 449-492 9-51 (77)
94 PF08318 COG4: COG4 transport 69.7 1.3E+02 0.0027 31.6 14.4 85 145-229 12-110 (331)
95 COG1522 Lrp Transcriptional re 68.9 9.7 0.00021 34.7 5.3 49 444-492 6-54 (154)
96 PF14394 DUF4423: Domain of un 68.5 17 0.00037 34.1 6.9 55 440-494 18-75 (171)
97 TIGR00498 lexA SOS regulatory 68.0 6.5 0.00014 37.8 4.1 51 444-494 4-60 (199)
98 COG1349 GlpR Transcriptional r 67.6 6.8 0.00015 39.3 4.3 46 448-493 7-52 (253)
99 PF01726 LexA_DNA_bind: LexA D 66.9 14 0.00031 28.6 5.0 57 540-601 6-62 (65)
100 cd07153 Fur_like Ferric uptake 66.8 12 0.00026 32.3 5.2 58 548-607 5-63 (116)
101 PRK04424 fatty acid biosynthes 65.4 6.6 0.00014 37.4 3.5 47 447-493 8-54 (185)
102 PF01047 MarR: MarR family; I 65.2 4.7 0.0001 30.1 2.0 48 546-600 5-52 (59)
103 PF13545 HTH_Crp_2: Crp-like h 65.1 15 0.00032 28.9 5.0 34 460-493 28-61 (76)
104 PRK13509 transcriptional repre 64.5 11 0.00023 37.9 5.0 47 447-493 6-52 (251)
105 PF12802 MarR_2: MarR family; 64.2 7.5 0.00016 29.2 3.0 49 546-601 7-57 (62)
106 smart00418 HTH_ARSR helix_turn 63.9 13 0.00029 27.5 4.4 45 549-601 2-46 (66)
107 PRK04172 pheS phenylalanyl-tRN 63.9 12 0.00026 41.5 5.6 51 443-493 3-53 (489)
108 PF10163 EnY2: Transcription f 63.8 12 0.00026 30.8 4.2 56 11-66 29-86 (86)
109 TIGR02698 CopY_TcrY copper tra 63.5 55 0.0012 29.1 8.9 50 444-493 2-55 (130)
110 PRK03902 manganese transport t 63.4 18 0.0004 32.6 5.9 44 450-493 12-55 (142)
111 PF00392 GntR: Bacterial regul 62.2 18 0.00038 27.7 4.8 38 457-494 20-58 (64)
112 PF09681 Phage_rep_org_N: N-te 61.9 16 0.00034 32.3 4.9 38 456-493 49-86 (121)
113 PF13412 HTH_24: Winged helix- 61.8 12 0.00027 26.6 3.6 45 545-596 4-48 (48)
114 PRK09802 DNA-binding transcrip 61.5 11 0.00025 38.1 4.6 49 446-494 17-65 (269)
115 COG4742 Predicted transcriptio 61.3 13 0.00028 37.3 4.7 44 450-494 17-60 (260)
116 PRK10906 DNA-binding transcrip 61.2 12 0.00025 37.7 4.5 47 447-493 6-52 (252)
117 PF01399 PCI: PCI domain; Int 60.2 18 0.00039 30.2 5.0 45 447-491 47-91 (105)
118 PRK06474 hypothetical protein; 59.9 20 0.00043 33.9 5.6 53 442-494 7-61 (178)
119 COG1733 Predicted transcriptio 59.9 27 0.00058 30.7 6.0 45 449-494 26-71 (120)
120 PRK10411 DNA-binding transcrip 59.5 21 0.00046 35.5 6.0 46 448-493 6-51 (240)
121 PF10771 DUF2582: Protein of u 59.1 13 0.00027 28.9 3.3 39 449-487 11-49 (65)
122 PRK11050 manganese transport r 58.4 21 0.00046 32.7 5.4 44 450-493 41-84 (152)
123 PF11994 DUF3489: Protein of u 58.3 40 0.00086 26.7 6.0 43 445-487 9-51 (72)
124 COG1510 Predicted transcriptio 58.1 14 0.00031 34.3 4.1 57 452-510 34-91 (177)
125 smart00420 HTH_DEOR helix_turn 58.0 16 0.00036 26.0 3.8 46 548-600 4-49 (53)
126 PF02186 TFIIE_beta: TFIIE bet 57.9 11 0.00024 29.2 2.9 54 546-609 7-61 (65)
127 TIGR00122 birA_repr_reg BirA b 57.5 34 0.00074 26.5 5.8 41 451-492 5-45 (69)
128 PF06163 DUF977: Bacterial pro 57.0 26 0.00056 30.9 5.3 49 446-494 12-60 (127)
129 cd07153 Fur_like Ferric uptake 56.7 24 0.00053 30.3 5.3 57 450-507 5-67 (116)
130 KOG2167|consensus 56.6 2.2E+02 0.0048 31.9 13.3 36 76-113 289-324 (661)
131 PF04182 B-block_TFIIIC: B-blo 56.5 17 0.00037 28.9 3.9 49 446-494 2-52 (75)
132 PF04545 Sigma70_r4: Sigma-70, 55.9 36 0.00078 24.4 5.3 34 449-484 11-44 (50)
133 PF10007 DUF2250: Uncharacteri 55.8 24 0.00051 29.5 4.7 53 442-494 3-55 (92)
134 TIGR01714 phage_rep_org_N phag 55.3 20 0.00043 31.5 4.4 48 446-493 29-84 (119)
135 smart00088 PINT motif in prote 55.2 20 0.00042 29.2 4.2 35 457-491 21-55 (88)
136 smart00753 PAM PCI/PINT associ 55.2 20 0.00042 29.2 4.2 35 457-491 21-55 (88)
137 PRK00135 scpB segregation and 54.9 1.6E+02 0.0034 28.2 10.8 34 453-486 12-46 (188)
138 PF03444 HrcA_DNA-bdg: Winged 54.8 48 0.001 26.7 6.0 47 447-493 10-56 (78)
139 PRK00135 scpB segregation and 54.3 79 0.0017 30.2 8.7 109 397-510 34-153 (188)
140 PF13384 HTH_23: Homeodomain-l 53.5 14 0.0003 26.5 2.7 36 451-488 10-45 (50)
141 COG1654 BirA Biotin operon rep 53.1 34 0.00074 27.7 5.0 38 452-489 11-48 (79)
142 PRK14165 winged helix-turn-hel 52.4 29 0.00064 33.9 5.5 46 448-493 9-54 (217)
143 cd06170 LuxR_C_like C-terminal 52.1 37 0.0008 24.5 5.0 39 446-486 3-41 (57)
144 COG4190 Predicted transcriptio 51.3 48 0.001 29.5 6.0 63 448-510 66-133 (144)
145 smart00421 HTH_LUXR helix_turn 51.1 39 0.00084 24.3 5.0 39 445-485 5-43 (58)
146 smart00344 HTH_ASNC helix_turn 51.0 22 0.00048 30.2 4.0 47 545-598 4-50 (108)
147 PF02796 HTH_7: Helix-turn-hel 50.4 25 0.00054 24.8 3.5 31 450-482 13-43 (45)
148 PRK10430 DNA-binding transcrip 50.4 27 0.00059 34.3 5.2 36 457-492 175-210 (239)
149 PRK04214 rbn ribonuclease BN/u 50.3 41 0.00088 36.4 6.8 39 455-493 305-343 (412)
150 PHA02943 hypothetical protein; 48.9 35 0.00075 31.1 4.9 54 451-507 16-69 (165)
151 COG1321 TroR Mn-dependent tran 48.8 30 0.00064 31.9 4.7 45 450-494 14-58 (154)
152 PF09904 HTH_43: Winged helix- 48.6 27 0.00058 28.9 3.8 40 451-491 13-52 (90)
153 PF08281 Sigma70_r4_2: Sigma-7 48.2 33 0.00071 25.0 4.1 25 459-483 25-49 (54)
154 COG0735 Fur Fe2+/Zn2+ uptake r 48.0 33 0.00072 31.2 4.9 52 442-493 17-74 (145)
155 KOG3054|consensus 47.9 24 0.00052 34.5 4.0 56 547-609 203-258 (299)
156 TIGR00281 segregation and cond 47.8 2.1E+02 0.0046 27.2 10.4 33 453-485 9-43 (186)
157 PF09114 MotA_activ: Transcrip 47.7 53 0.0011 27.0 5.2 46 449-494 19-66 (96)
158 PF12324 HTH_15: Helix-turn-he 47.2 48 0.001 26.6 4.9 38 448-485 26-63 (77)
159 PF07106 TBPIP: Tat binding pr 46.6 2.4E+02 0.0053 26.1 11.2 58 449-508 4-64 (169)
160 PF01853 MOZ_SAS: MOZ/SAS fami 45.2 21 0.00046 33.9 3.1 26 459-484 149-174 (188)
161 COG1777 Predicted transcriptio 44.8 2.8E+02 0.006 26.9 10.4 41 451-492 20-60 (217)
162 TIGR02844 spore_III_D sporulat 44.3 36 0.00078 27.6 3.9 33 448-481 8-40 (80)
163 smart00531 TFIIE Transcription 43.2 32 0.00069 31.4 4.0 35 457-491 12-46 (147)
164 PRK10079 phosphonate metabolis 43.0 23 0.0005 35.1 3.3 54 545-606 21-75 (241)
165 PF03428 RP-C: Replication pro 43.0 36 0.00078 32.2 4.3 32 462-493 72-104 (177)
166 COG2996 Predicted RNA-bindinin 42.7 41 0.00088 33.7 4.8 35 460-494 246-280 (287)
167 TIGR01889 Staph_reg_Sar staphy 42.4 46 0.001 28.5 4.7 39 555-600 40-78 (109)
168 PF04157 EAP30: EAP30/Vps36 fa 41.7 64 0.0014 31.6 6.1 83 394-492 132-222 (223)
169 COG4565 CitB Response regulato 41.2 46 0.001 32.3 4.8 51 442-493 155-206 (224)
170 TIGR02716 C20_methyl_CrtF C-20 40.5 38 0.00082 34.9 4.6 35 459-493 22-56 (306)
171 PRK11512 DNA-binding transcrip 39.9 46 0.001 30.0 4.5 46 548-600 44-89 (144)
172 COG1378 Predicted transcriptio 39.8 40 0.00086 33.7 4.4 51 443-493 13-63 (247)
173 PRK09954 putative kinase; Prov 39.7 60 0.0013 34.3 6.1 43 449-491 6-48 (362)
174 PRK10681 DNA-binding transcrip 39.4 43 0.00094 33.5 4.6 41 447-487 8-48 (252)
175 PRK10046 dpiA two-component re 39.3 44 0.00095 32.5 4.6 44 450-493 166-210 (225)
176 KOG2905|consensus 39.1 48 0.001 32.5 4.6 56 449-510 189-244 (254)
177 smart00529 HTH_DTXR Helix-turn 38.9 40 0.00087 27.8 3.7 32 463-494 2-33 (96)
178 COG1318 Predicted transcriptio 38.5 35 0.00076 31.7 3.4 57 414-491 36-92 (182)
179 PF08672 APC2: Anaphase promot 38.4 65 0.0014 24.5 4.3 51 549-599 2-55 (60)
180 cd07977 TFIIE_beta_winged_heli 38.1 57 0.0012 26.1 4.2 57 544-609 9-70 (75)
181 PF02334 RTP: Replication term 37.8 36 0.00078 29.1 3.1 54 543-597 17-72 (122)
182 PF01475 FUR: Ferric uptake re 37.4 34 0.00074 29.7 3.1 63 444-507 6-74 (120)
183 PF04967 HTH_10: HTH DNA bindi 37.4 59 0.0013 24.1 3.8 30 455-484 18-47 (53)
184 smart00346 HTH_ICLR helix_turn 36.9 70 0.0015 25.9 4.8 45 549-600 10-55 (91)
185 PRK09462 fur ferric uptake reg 36.8 74 0.0016 28.9 5.4 59 547-607 20-80 (148)
186 PRK14999 histidine utilization 36.5 51 0.0011 32.6 4.6 47 552-606 29-76 (241)
187 PF10557 Cullin_Nedd8: Cullin 36.4 52 0.0011 25.6 3.7 49 446-494 8-64 (68)
188 TIGR02404 trehalos_R_Bsub treh 35.9 25 0.00055 34.5 2.3 31 575-606 34-64 (233)
189 smart00347 HTH_MARR helix_turn 35.9 62 0.0013 26.4 4.4 49 545-600 11-59 (101)
190 PF00165 HTH_AraC: Bacterial r 35.8 50 0.0011 22.7 3.2 28 458-485 6-33 (42)
191 PF09107 SelB-wing_3: Elongati 35.2 82 0.0018 23.0 4.2 41 453-493 3-43 (50)
192 TIGR02147 Fsuc_second hypothet 35.2 1.1E+02 0.0025 31.0 6.8 34 461-494 138-173 (271)
193 PHA03103 double-strand RNA-bin 35.2 73 0.0016 30.2 5.0 44 451-494 18-61 (183)
194 PF01475 FUR: Ferric uptake re 34.9 65 0.0014 27.9 4.5 59 547-607 11-70 (120)
195 PF09339 HTH_IclR: IclR helix- 34.8 57 0.0012 23.6 3.5 44 549-599 8-52 (52)
196 COG2512 Predicted membrane-ass 34.7 53 0.0012 33.0 4.4 48 446-493 196-243 (258)
197 PF12395 DUF3658: Protein of u 34.6 83 0.0018 27.1 5.0 62 544-607 48-109 (111)
198 PF13542 HTH_Tnp_ISL3: Helix-t 34.5 89 0.0019 22.4 4.5 35 448-484 17-51 (52)
199 PF00196 GerE: Bacterial regul 34.4 82 0.0018 23.3 4.4 40 445-486 5-44 (58)
200 PRK11402 DNA-binding transcrip 34.4 27 0.0006 34.5 2.3 31 575-606 43-73 (241)
201 PF13551 HTH_29: Winged helix- 34.4 76 0.0016 26.7 4.8 39 450-489 3-41 (112)
202 PF08820 DUF1803: Domain of un 34.2 24 0.00053 29.4 1.5 29 570-599 32-61 (93)
203 KOG2747|consensus 34.2 52 0.0011 34.9 4.3 65 420-484 282-353 (396)
204 PRK12423 LexA repressor; Provi 34.1 67 0.0015 30.9 4.9 51 444-494 4-60 (202)
205 TIGR03697 NtcA_cyano global ni 33.6 80 0.0017 29.5 5.3 34 460-493 143-176 (193)
206 PF08222 HTH_CodY: CodY helix- 33.3 43 0.00094 25.1 2.5 33 460-492 4-36 (61)
207 cd06171 Sigma70_r4 Sigma70, re 33.2 1.1E+02 0.0024 21.2 5.0 40 444-484 11-50 (55)
208 PRK11886 bifunctional biotin-- 33.0 1E+02 0.0022 32.0 6.4 42 450-491 8-49 (319)
209 PRK09462 fur ferric uptake reg 32.9 80 0.0017 28.6 5.0 52 442-493 13-71 (148)
210 PRK09334 30S ribosomal protein 32.8 33 0.00072 28.2 2.1 57 546-609 26-85 (86)
211 PRK11753 DNA-binding transcrip 32.8 78 0.0017 30.2 5.1 34 460-493 168-201 (211)
212 COG1522 Lrp Transcriptional re 32.4 65 0.0014 29.1 4.3 50 543-599 7-56 (154)
213 PF14493 HTH_40: Helix-turn-he 32.4 97 0.0021 25.5 4.9 37 451-489 6-42 (91)
214 PRK10434 srlR DNA-bindng trans 32.4 46 0.00099 33.4 3.5 46 546-598 7-52 (256)
215 smart00345 HTH_GNTR helix_turn 32.4 36 0.00077 24.9 2.1 26 575-600 30-55 (60)
216 PRK13918 CRP/FNR family transc 32.3 81 0.0018 29.8 5.2 34 460-493 149-182 (202)
217 PRK11161 fumarate/nitrate redu 32.2 78 0.0017 30.8 5.2 34 460-493 184-217 (235)
218 TIGR03433 padR_acidobact trans 32.1 1.2E+02 0.0026 25.5 5.5 53 544-597 4-57 (100)
219 TIGR02337 HpaR homoprotocatech 31.8 76 0.0016 27.4 4.4 48 546-600 30-77 (118)
220 PF08784 RPA_C: Replication pr 31.8 67 0.0015 27.0 4.0 47 543-596 46-96 (102)
221 TIGR01610 phage_O_Nterm phage 31.6 73 0.0016 26.6 4.1 39 555-600 44-82 (95)
222 COG2865 Predicted transcriptio 31.5 73 0.0016 34.9 5.0 59 544-609 402-460 (467)
223 PF09763 Sec3_C: Exocyst compl 31.4 6.9E+02 0.015 29.1 13.5 133 76-227 550-701 (701)
224 COG3355 Predicted transcriptio 31.4 80 0.0017 28.0 4.4 41 553-600 37-77 (126)
225 PRK13239 alkylmercury lyase; P 31.4 82 0.0018 30.5 4.8 39 447-485 23-61 (206)
226 PF06163 DUF977: Bacterial pro 31.0 99 0.0021 27.3 4.8 51 543-600 11-61 (127)
227 PF06784 UPF0240: Uncharacteri 30.5 74 0.0016 30.1 4.3 68 417-489 96-165 (179)
228 PRK10402 DNA-binding transcrip 30.5 1.2E+02 0.0026 29.5 6.1 33 461-493 170-202 (226)
229 TIGR02787 codY_Gpos GTP-sensin 30.3 92 0.002 30.9 5.0 43 451-493 188-231 (251)
230 PF13601 HTH_34: Winged helix 30.0 57 0.0012 26.3 3.0 46 547-599 3-48 (80)
231 TIGR02325 C_P_lyase_phnF phosp 29.8 36 0.00077 33.5 2.2 31 575-606 42-72 (238)
232 COG1497 Predicted transcriptio 29.3 1.7E+02 0.0037 29.0 6.6 48 445-493 11-58 (260)
233 PLN03238 probable histone acet 29.3 83 0.0018 32.0 4.6 42 447-491 209-251 (290)
234 TIGR00721 tfx DNA-binding prot 28.4 1.2E+02 0.0026 27.3 5.1 40 444-485 7-46 (137)
235 PRK09391 fixK transcriptional 28.4 1E+02 0.0022 30.2 5.2 34 460-493 179-212 (230)
236 PRK03573 transcriptional regul 28.2 45 0.00097 30.0 2.4 26 575-600 56-81 (144)
237 PF03965 Penicillinase_R: Peni 28.0 84 0.0018 27.1 4.0 49 445-493 2-54 (115)
238 PHA02701 ORF020 dsRNA-binding 27.8 1.2E+02 0.0025 28.8 5.0 44 450-493 8-52 (183)
239 PRK15431 ferrous iron transpor 27.6 84 0.0018 25.3 3.5 37 457-493 13-49 (78)
240 PRK10906 DNA-binding transcrip 27.3 64 0.0014 32.3 3.6 46 546-598 7-52 (252)
241 PRK11534 DNA-binding transcrip 26.9 1.4E+02 0.0031 28.9 5.9 42 453-494 23-64 (224)
242 PF13518 HTH_28: Helix-turn-he 26.7 1.6E+02 0.0036 20.7 4.8 28 462-489 14-41 (52)
243 cd00090 HTH_ARSR Arsenical Res 26.1 1.1E+02 0.0023 23.1 4.1 45 549-601 12-56 (78)
244 TIGR03338 phnR_burk phosphonat 26.1 1.3E+02 0.0027 28.9 5.3 41 454-494 28-68 (212)
245 PF10826 DUF2551: Protein of u 26.0 72 0.0016 25.9 2.8 66 444-509 9-79 (83)
246 smart00762 Cog4 COG4 transport 26.0 4.1E+02 0.0089 27.6 9.4 76 145-220 12-94 (324)
247 PF09940 DUF2172: Domain of un 26.0 2.9E+02 0.0064 29.3 8.0 120 370-491 256-386 (386)
248 TIGR02989 Sig-70_gvs1 RNA poly 25.1 1.2E+02 0.0026 27.3 4.7 38 444-483 112-150 (159)
249 COG2188 PhnF Transcriptional r 24.9 48 0.001 32.8 2.2 31 575-606 41-71 (236)
250 COG1349 GlpR Transcriptional r 24.9 71 0.0015 32.0 3.3 45 547-598 8-52 (253)
251 smart00526 H15 Domain in histo 24.8 2E+02 0.0044 21.9 5.2 53 544-598 10-64 (66)
252 cd07377 WHTH_GntR Winged helix 24.3 62 0.0013 24.1 2.2 26 575-600 35-60 (66)
253 PRK11169 leucine-responsive tr 24.2 1.2E+02 0.0026 28.0 4.6 47 544-597 14-60 (164)
254 PF14502 HTH_41: Helix-turn-he 24.2 1.3E+02 0.0028 21.9 3.5 33 461-493 7-39 (48)
255 TIGR02018 his_ut_repres histid 24.0 51 0.0011 32.3 2.1 47 552-606 18-65 (230)
256 PF12793 SgrR_N: Sugar transpo 23.9 1.8E+02 0.0039 25.3 5.3 36 459-494 18-53 (115)
257 PRK11179 DNA-binding transcrip 23.8 1.2E+02 0.0026 27.7 4.4 47 544-597 9-55 (153)
258 PF00356 LacI: Bacterial regul 23.7 86 0.0019 22.4 2.6 22 462-483 1-22 (46)
259 PHA02591 hypothetical protein; 23.6 1E+02 0.0022 24.8 3.1 25 459-483 58-82 (83)
260 COG2771 CsgD DNA-binding HTH d 23.4 2.3E+02 0.005 20.8 5.4 41 443-485 4-44 (65)
261 PLN03239 histone acetyltransfe 23.2 1.1E+02 0.0025 31.9 4.4 43 447-492 267-313 (351)
262 PRK09764 DNA-binding transcrip 23.2 58 0.0013 32.2 2.4 36 570-606 33-69 (240)
263 PF00538 Linker_histone: linke 23.1 1.2E+02 0.0025 24.2 3.7 55 544-599 8-65 (77)
264 cd04761 HTH_MerR-SF Helix-Turn 22.5 1.2E+02 0.0026 21.2 3.3 27 461-491 1-27 (49)
265 PF08511 COQ9: COQ9; InterPro 22.4 66 0.0014 26.0 2.0 26 3-28 50-75 (79)
266 PLN00104 MYST -like histone ac 22.3 1.2E+02 0.0027 32.9 4.6 41 449-492 362-403 (450)
267 PF02270 TFIIF_beta: Transcrip 22.1 93 0.002 31.6 3.6 57 447-509 217-273 (275)
268 PF00392 GntR: Bacterial regul 22.0 56 0.0012 24.8 1.6 26 575-600 34-59 (64)
269 PRK11414 colanic acid/biofilm 22.0 1.4E+02 0.003 28.9 4.8 42 453-494 27-68 (221)
270 KOG3341|consensus 21.8 3.7E+02 0.0081 26.1 7.2 141 346-493 54-223 (249)
271 PF04760 IF2_N: Translation in 21.7 62 0.0013 23.7 1.7 22 460-481 3-24 (54)
272 TIGR02983 SigE-fam_strep RNA p 21.5 1.3E+02 0.0028 27.3 4.2 41 444-485 111-151 (162)
273 PF04539 Sigma70_r3: Sigma-70 21.5 99 0.0022 24.3 3.0 27 459-485 19-45 (78)
274 PF05331 DUF742: Protein of un 21.3 1.8E+02 0.0039 25.3 4.6 50 441-492 38-87 (114)
275 PF01316 Arg_repressor: Argini 21.2 2.6E+02 0.0056 22.0 5.1 59 544-608 5-63 (70)
276 PRK11642 exoribonuclease R; Pr 21.1 2E+02 0.0044 34.1 6.6 44 450-493 23-71 (813)
277 PRK03975 tfx putative transcri 21.0 2E+02 0.0044 26.0 5.1 39 443-483 6-44 (141)
278 PF08766 DEK_C: DEK C terminal 20.9 1.6E+02 0.0035 21.6 3.8 46 544-592 4-51 (54)
279 PF08461 HTH_12: Ribonuclease 20.8 1.8E+02 0.0039 22.5 4.2 50 548-599 2-52 (66)
280 PF09202 Rio2_N: Rio2, N-termi 20.8 2.2E+02 0.0048 23.2 4.8 46 448-493 8-57 (82)
281 COG5090 TFG2 Transcription ini 20.8 1.3E+02 0.0029 29.3 4.0 56 450-511 199-254 (297)
282 PRK04217 hypothetical protein; 20.7 2.2E+02 0.0047 24.7 5.0 41 444-485 43-83 (110)
283 PF04297 UPF0122: Putative hel 20.6 1.8E+02 0.0039 24.7 4.4 38 445-483 19-56 (101)
284 PRK14999 histidine utilization 20.5 1.6E+02 0.0034 29.0 4.9 37 458-494 33-70 (241)
285 PF06969 HemN_C: HemN C-termin 20.4 1.6E+02 0.0036 22.2 3.9 43 458-506 18-61 (66)
286 TIGR01884 cas_HTH CRISPR locus 20.4 1.7E+02 0.0036 28.2 4.8 47 547-600 146-192 (203)
287 PRK12529 RNA polymerase sigma 20.2 1.3E+02 0.0028 28.0 4.0 37 444-482 128-165 (178)
288 PRK09464 pdhR transcriptional 20.2 1.6E+02 0.0035 29.2 4.9 40 455-494 28-68 (254)
289 COG0735 Fur Fe2+/Zn2+ uptake r 20.2 2.2E+02 0.0048 25.8 5.3 60 546-607 23-83 (145)
No 1
>KOG2284|consensus
Probab=100.00 E-value=1e-120 Score=901.79 Aligned_cols=577 Identities=43% Similarity=0.769 Sum_probs=561.8
Q ss_pred CCCCCCccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh------------
Q psy16234 1 MSLKPKQVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH------------ 68 (609)
Q Consensus 1 ~~~~~~~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~------------ 68 (609)
|||+|+.+|||++|..|.++|..++.++++++..|..+|++||++|++.|.|+|+.||+.++.++.+|
T Consensus 2 ~slkp~vv~fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~ 81 (728)
T KOG2284|consen 2 YSLKPKVVEFDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVD 81 (728)
T ss_pred CCCCceeeeHHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred --------------------------------------------------------------------------------
Q psy16234 69 -------------------------------------------------------------------------------- 68 (609)
Q Consensus 69 -------------------------------------------------------------------------------- 68 (609)
T Consensus 82 p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~i~~~l 161 (728)
T KOG2284|consen 82 PDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKTILPQL 161 (728)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred --------------------------------------------------------ccHHhhHHHHHHHHHHHHHHHHHH
Q psy16234 69 --------------------------------------------------------LYVDIFETQFLEMSGEWYKSEASK 92 (609)
Q Consensus 69 --------------------------------------------------------~Y~~~FE~~~L~~t~~yY~~~s~~ 92 (609)
+|++.||.|||-+|..||+.+|+.
T Consensus 162 v~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~ 241 (728)
T KOG2284|consen 162 VKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQK 241 (728)
T ss_pred HHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHH
Confidence 899999999999999999999999
Q ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhccc
Q psy16234 93 LLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVR 172 (609)
Q Consensus 93 ~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~ 172 (609)
.+.+.+|++||.+|..++++|+-||..|||+||..|++..|++++|.+|.+.++..|..++++++..||+.||.|++.+.
T Consensus 242 ~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~lha~ch~~i~~e~~~d~~nmy~ll~~i~ 321 (728)
T KOG2284|consen 242 MLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKLHAVCHDLITNEENKDLRNMYRLLKPIQ 321 (728)
T ss_pred HHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCC
Q psy16234 173 EGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMP 252 (609)
Q Consensus 173 ~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~ 252 (609)
.|++.+...|++||.++|.++++.+++.+.|..||+.+|.+|.||.+++...|++|..|..++|+|+..++|....+++.
T Consensus 322 ~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv 401 (728)
T KOG2284|consen 322 AGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSV 401 (728)
T ss_pred cCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998666777
Q ss_pred CCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHH
Q psy16234 253 SKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQA 332 (609)
Q Consensus 253 ~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~ 332 (609)
+++||.||+|||.+|||+.||+++.|++.+|+..+.+|+|++|||+|+++|.++||+|||.+.|.|+|.|+.||++||+.
T Consensus 402 ~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqa 481 (728)
T KOG2284|consen 402 PKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQA 481 (728)
T ss_pred cchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHh
Q psy16234 333 CGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYH 412 (609)
Q Consensus 333 ~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~ 412 (609)
||++||+++. +.|++.|.+++++| .+.+ .+|.+|.+|+...+.|+.||.
T Consensus 482 cgyefts~~~--~td~~~s~~lnn~f-~~~i----------------------------~nf~~pq~l~~~iq~fe~fyt 530 (728)
T KOG2284|consen 482 CGYEFTSSWP--LTDPQLSTNLNNQF-AQDI----------------------------ANFHLPQILQPVIQEFEKFYT 530 (728)
T ss_pred hCceecccCC--CCChhhccccchhH-HHHH----------------------------HhccchHHHHHHHHHHHHHhc
Confidence 9999999999 99999999999999 5533 258999999999999999999
Q ss_pred hcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 413 GQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 413 ~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
++|+||+|+|++.+|+++++++|.++.|.-.|.+|||++||+||..+.+++.+|.+.+|++.+.|.+.+.++.+.++|..
T Consensus 531 ~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tildv~~~~~ 610 (728)
T KOG2284|consen 531 GKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILDVTLLTC 610 (728)
T ss_pred cccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHhceeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCEEEEecCCCCCcceEEecccc-ccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHh
Q psy16234 493 NKEELTEDTEIRLNLGYNNKRTKLKISGAV-QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ 571 (609)
Q Consensus 493 ~~~~~~~~~~f~lN~~F~~~~~ki~i~~~~-~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~ 571 (609)
++.++..+..|++|++|++++.|+++.+|+ ++.+++|.+.+...+.+||+.+++||||||||+||.+.|+.|+++|+.|
T Consensus 611 d~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~q 690 (728)
T KOG2284|consen 611 DDQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQ 690 (728)
T ss_pred cccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHh
Confidence 887888889999999999999999999876 8889999999999999999999999999999999999999999999999
Q ss_pred hcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 572 SKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 572 l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
.++ |.|++++||+|||.||+|.||+|.+.+ +.|.|+|
T Consensus 691 t~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 691 TKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred hcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 999 999999999999999999999999887 9999997
No 2
>KOG2166|consensus
Probab=100.00 E-value=3.8e-106 Score=890.17 Aligned_cols=587 Identities=32% Similarity=0.601 Sum_probs=530.3
Q ss_pred CCCccChHhhHHHHHHHHHHHHhcC-CCChhhhhhhhhhhhhhcc------cCC-cccHHHHHHHHHhhhhhh-------
Q psy16234 4 KPKQVDFNKTWGSLQETIQGVITLG-NVRRATWNDRFSDIYSLCV------AYP-EPLADRLYQETKLFLDQH------- 68 (609)
Q Consensus 4 ~~~~~~fe~~W~~l~~~i~~i~~~~-~~~~~~~~~~y~~vy~~c~------~~~-~~~~~~Ly~~~~~~l~~~------- 68 (609)
.+++++|+.+|+.+++|+..+.+.. .++ ..+|..|+.+|.+|+ +.+ .+.+++||+++++++.+|
T Consensus 4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s-~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~ 82 (725)
T KOG2166|consen 4 APKEIDLEVGWSYIETGITKLKRIIEGLS-EPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLP 82 (725)
T ss_pred cccccchhccHHHHHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988863 444 455666666555555 332 234499999998888766
Q ss_pred --------------------------------------------------------------------------------
Q psy16234 69 -------------------------------------------------------------------------------- 68 (609)
Q Consensus 69 -------------------------------------------------------------------------------- 68 (609)
T Consensus 83 ~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~ 162 (725)
T KOG2166|consen 83 ALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIH 162 (725)
T ss_pred HHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred -----------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhh
Q psy16234 69 -----------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVR 119 (609)
Q Consensus 69 -----------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~ 119 (609)
+|..+||++|+++|..||..++..|+...++.+||.+|+.++.+|..|+..
T Consensus 163 ~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~ 242 (725)
T KOG2166|consen 163 KEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTH 242 (725)
T ss_pred hhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHh
Confidence 799999999999999999999999999999999999999999999999998
Q ss_pred hcCCCchhHHHHHHHHHHHHHH----HHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhh
Q psy16234 120 FLHVSSYPKVKAKCEQHMVADH----LNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAIS 195 (609)
Q Consensus 120 yL~~~t~~kl~~~l~~~LI~~~----~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~ 195 (609)
||+..+..++.+.++..++..| .+.+++||..|+++++.+||.+||+|+++++.|++++.+.|+.|++.+|..++.
T Consensus 243 yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~ 322 (725)
T KOG2166|consen 243 YLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVA 322 (725)
T ss_pred hhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhh
Confidence 8877766666666666665555 455569999999999999999999999999999999999999999999988888
Q ss_pred cccCC--CchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCC
Q psy16234 196 GLSGD--NISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKG 273 (609)
Q Consensus 196 ~~~~~--~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~ 273 (609)
..... ..|..+|..+++++++|..++..||.++..|..+++.||..|+|.+.. ..+|+||+|||.+||++.++
T Consensus 323 r~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~-----~~~E~la~y~D~~lkk~~k~ 397 (725)
T KOG2166|consen 323 RPAETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA-----TSAELLATYCDDILKKGSKK 397 (725)
T ss_pred hhhhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC-----CcHHHHHHHhHHHhcccccC
Confidence 66433 689999999999999999999999999999999999999999998842 22699999999999999999
Q ss_pred CChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHH
Q psy16234 274 LSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGG 353 (609)
Q Consensus 274 ~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~ 353 (609)
.++.+++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|+|+|++||++|+++||.+||.||++|++|+..|++
T Consensus 398 ~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~ 477 (725)
T KOG2166|consen 398 LSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRE 477 (725)
T ss_pred CchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEE
Q psy16234 354 LNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKL 433 (609)
Q Consensus 354 l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~ 433 (609)
++..| +++ .+.+...+++|.|.|||+|+||.+++ .++.||++|.++++.|..||.++|+||+|+|+|++|+|+|.+
T Consensus 478 l~~~F-~~~-~~~~~~~~~df~v~VLt~g~WP~~~~--~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~ 553 (725)
T KOG2166|consen 478 LQTAF-ADY-ANYSANLGIDFTVTVLTTGFWPSYKS--TDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEING 553 (725)
T ss_pred HHHHH-Hhh-hchhccCCCceeEEEeecCCcCCccC--CCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEE
Confidence 99999 765 22333367999999999999999775 469999999999999999999999999999999999999999
Q ss_pred EEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc--CccccCC--CCCCCCCEEEEecCC
Q psy16234 434 SYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC--KLLTSNK--EELTEDTEIRLNLGY 509 (609)
Q Consensus 434 ~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~--~iL~~~~--~~~~~~~~f~lN~~F 509 (609)
+|.+++|+++||++||+||++||+.+.+|+++|.++|+++.+++.++|+||... +++.. | +. ++++.|.+|.+|
T Consensus 554 ~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f 631 (725)
T KOG2166|consen 554 KFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKF 631 (725)
T ss_pred EecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccc
Confidence 999999999999999999999999999999999999999999999999999543 34444 3 33 789999999999
Q ss_pred CCCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHH
Q psy16234 510 NNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIES 588 (609)
Q Consensus 510 ~~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~ 588 (609)
+++..|++++.+..+ |.+.+.+.+++||+.+|+||||||||+||.|.|++|+.||++|+++ |.|++.+||+|||.
T Consensus 632 ~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~ 707 (725)
T KOG2166|consen 632 TSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIED 707 (725)
T ss_pred cCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHH
Confidence 999999999876544 6778889999999999999999999999999999999999999999 99999999999999
Q ss_pred hhhhccccccCCCCCceee
Q psy16234 589 LIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 589 LIekeyl~r~~~~~~~y~Y 607 (609)
|||||||+|| +|+++|+|
T Consensus 708 LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 708 LIEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHHhcc-CCCCcccC
Confidence 9999999999 89999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-106 Score=854.98 Aligned_cols=597 Identities=32% Similarity=0.536 Sum_probs=539.8
Q ss_pred CccChHhhHHHHHHHHHHHHhc--CCCChhhhhhhhhhhhhhcccCCc-------------ccHHHHHHHHHhhhhhh--
Q psy16234 6 KQVDFNKTWGSLQETIQGVITL--GNVRRATWNDRFSDIYSLCVAYPE-------------PLADRLYQETKLFLDQH-- 68 (609)
Q Consensus 6 ~~~~fe~~W~~l~~~i~~i~~~--~~~~~~~~~~~y~~vy~~c~~~~~-------------~~~~~Ly~~~~~~l~~~-- 68 (609)
...||+.+|+.++.||.+|... .++....+|+.|+.+|++|+.... .+++.||+++..+.+++
T Consensus 16 ~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~i~ 95 (773)
T COG5647 16 SEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNYIE 95 (773)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999954 567788999999999999995422 26777888885444332
Q ss_pred --------------------------------------------------------------------------------
Q psy16234 69 -------------------------------------------------------------------------------- 68 (609)
Q Consensus 69 -------------------------------------------------------------------------------- 68 (609)
T Consensus 96 ~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~~lin~ 175 (773)
T COG5647 96 EYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVDSLINP 175 (773)
T ss_pred HhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhHHHHHH
Confidence
Q ss_pred -----------------------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Q psy16234 69 -----------------------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVL 107 (609)
Q Consensus 69 -----------------------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~ 107 (609)
+|...||++||+.|.+||..+++..+..+++.+||.+|.
T Consensus 176 LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL~ka~ 255 (773)
T COG5647 176 LLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAH 255 (773)
T ss_pred HHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHH
Confidence 799999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHh---hhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHH
Q psy16234 108 QVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQG---ECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRD 184 (609)
Q Consensus 108 ~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~---~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~ 184 (609)
.++++|..++..|++.++..++.++++++||+.|.+.+.. ++..+++..+.+.|+.||+++++++.|+.+|.+.|++
T Consensus 256 ~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~~~f~~ 335 (773)
T COG5647 256 KILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPLQEVFER 335 (773)
T ss_pred HHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHH
Confidence 9999999999999999999999999999999999999975 9999999999999999999999999999999999999
Q ss_pred HHHHHH--H-HHhhc---cc--------CCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCCC
Q psy16234 185 HICKQG--L-EAISG---LS--------GDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPK 250 (609)
Q Consensus 185 ~i~~~g--~-~~~~~---~~--------~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~ 250 (609)
||++.| . ..... .+ ....|..||+.++.+|+.+..++...|.+|..+.+++++||+.|+|.+..
T Consensus 336 yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~s-- 413 (773)
T COG5647 336 YVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNES-- 413 (773)
T ss_pred HHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccc--
Confidence 999999 1 11110 01 12368899999999999999999999999999999999999999998632
Q ss_pred CCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Q psy16234 251 MPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLK 330 (609)
Q Consensus 251 ~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk 330 (609)
....+||+||+|+|.+||++.+.....+++..+.+++.||+|+.+||+|+++|++.||||||+++|+|.++|.+||++||
T Consensus 414 a~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LK 493 (773)
T COG5647 414 ADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLK 493 (773)
T ss_pred cccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHH
Confidence 22578999999999999998865555678888999999999999999999999999999999999999999999999999
Q ss_pred HHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHH
Q psy16234 331 QACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKF 410 (609)
Q Consensus 331 ~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~ 410 (609)
+.||.+||+|+++||+||+.|.++...|++. ++. ....+|+.|.||+..+||.+++ ...++||++|.+.++.|++|
T Consensus 494 k~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s--~~s-~~~~~Dl~v~VLt~a~WP~sp~-~~~~~lP~~l~p~le~f~~~ 569 (773)
T COG5647 494 KVCGQEFTSKLEGMFRDISLSSEFTEAFQHS--PQS-YNKYLDLFVWVLTQAYWPLSPE-EVSIRLPKELVPILEGFKKF 569 (773)
T ss_pred HHhhhHHHHHHHHHHHhcchhHHHHHHHhhC--chh-hccccchhHHHHHHhcCCCCcc-ccccCCChHHHHHHHHHHHH
Confidence 9999999999999999999999999999333 221 1257899999999999998876 46999999999999999999
Q ss_pred HhhcCCCcceeeecccceEEEEEEEeCccE---EEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc
Q psy16234 411 YHGQFNGRKLSWLHNISQVELKLSYLKRPY---FVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487 (609)
Q Consensus 411 Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~---~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~ 487 (609)
|.+||+||+|.|.||||+|+|+++|+.+.+ ..+++++|+.|+++||+++++|+++|.+.|+|+.++++++|+||+++
T Consensus 570 Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~a 649 (773)
T COG5647 570 YSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCA 649 (773)
T ss_pred HHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhh
Confidence 999999999999999999999999987653 33478999999999999999999999999999999999999999998
Q ss_pred CccccCC--CCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCCChHHHH
Q psy16234 488 KLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALI 565 (609)
Q Consensus 488 ~iL~~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~ 565 (609)
+++...+ +.++|++.|.+|.+|+++..+|+++.+...+..++..++++.+++||+..+|||||||||+||.|+|++|+
T Consensus 650 k~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv 729 (773)
T COG5647 650 KLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLV 729 (773)
T ss_pred heeeeccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHH
Confidence 8765443 67889999999999999999999998876666667788889999999999999999999999999999999
Q ss_pred HHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 566 QEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 566 ~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
++|+.|.++ |.|++.+||++|+.|||||||+|.++| ..|+|+|
T Consensus 730 ~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 730 KEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999 999999999999999999999999988 8999997
No 4
>KOG2167|consensus
Probab=100.00 E-value=1.9e-97 Score=768.24 Aligned_cols=532 Identities=31% Similarity=0.539 Sum_probs=500.6
Q ss_pred HhhhhhhccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHH
Q psy16234 62 KLFLDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADH 141 (609)
Q Consensus 62 ~~~l~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~ 141 (609)
+.+...++|.+.|+..|++.+.++|.+++.+..++..+++||++++.++.+|..|+..|++.+|..++..+++.+|+..|
T Consensus 122 ~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~h 201 (661)
T KOG2167|consen 122 KMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRH 201 (661)
T ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHH
Confidence 34444559999999999999999999999999999999999999999999999999999999997779999999999999
Q ss_pred HHHHH-hhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHH
Q psy16234 142 LNFLQ-GECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAF 220 (609)
Q Consensus 142 ~~~l~-~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~l 220 (609)
++.+. .|+..+++.++..|+.+||.|++++.+|...++..|.+|+++-|..++....+ ...+|..++.++++.+-+
T Consensus 202 L~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~k---Dk~mVqELL~FK~k~Dii 278 (661)
T KOG2167|consen 202 LDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEK---DKDMVQELLDFKKKVDII 278 (661)
T ss_pred HHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchh---hHHHHHHHHHHHHHhhHH
Confidence 99975 79999999999999999999999999899999999999999999999876543 356999999999999999
Q ss_pred HHHhcCCC--hhHHHHHHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHH
Q psy16234 221 VKELFSGD--QSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDV 298 (609)
Q Consensus 221 i~~~F~~~--~~f~~~l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~ 298 (609)
+..+|..+ ..|..++.+||+.|+|.. ..++||++|+|.|.+|+.|+++.++++++..++.++.||+||..||+
T Consensus 279 ~~~sF~~~v~e~f~~~~~~afe~fink~-----~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdv 353 (661)
T KOG2167|consen 279 VDESFLKYVAEKFLNSMSKAFETFINKR-----RNRPAELIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDV 353 (661)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHhcc-----cCCHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHH
Confidence 99999999 899999999999999965 37899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhcc-CCCCCcceEEE
Q psy16234 299 FHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN-EIDLGIHFSIN 377 (609)
Q Consensus 299 F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~-~~~~~~~f~~~ 377 (609)
|+.+|++-||+|||.++|+|.|+|.+|+.+||.+||..||+||++||+||..|++++..| +++...+ ....++ +.+.
T Consensus 354 feA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f-~~~~~~~~~~~~~l-~~v~ 431 (661)
T KOG2167|consen 354 FEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAF-KQSKGANNRLEGNL-LTVN 431 (661)
T ss_pred HHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHH-HHHHHhhccCcCCc-eEEE
Confidence 999999999999999999999999999999999999999999999999999999999999 7764333 333445 9999
Q ss_pred eeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcC
Q psy16234 378 ILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEK 457 (609)
Q Consensus 378 VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~ 457 (609)
|||.|+||.+++ ..+.||++|..+++.|..||-.+|.||+|.|.+.+|+|.+++.|..|+.++.+|++|++||++||+
T Consensus 432 vlt~~yWpty~~--~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~ 509 (661)
T KOG2167|consen 432 VLTMGYWPTYPP--MEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNE 509 (661)
T ss_pred eecccccCCCCc--hhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCC
Confidence 999999999987 689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHh--cCccccCC--CCCCCCCEEEEecCCCCCcceEEeccccccCChhHHhhh
Q psy16234 458 NDAMTCGDIQTVLSLSQDQIGRHIASLVE--CKLLTSNK--EELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERT 533 (609)
Q Consensus 458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~--~~iL~~~~--~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~~~e~~~~ 533 (609)
++.+|++||.+.|+|.+-+|.++|++|.+ .++|.+.| +.+.+++.|.+|.+|+.|..||+|+++..|++.+|...|
T Consensus 510 ~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~ 589 (661)
T KOG2167|consen 510 GEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKST 589 (661)
T ss_pred CCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhh
Confidence 99999999999999999999999999996 46888887 678899999999999999999999999989999999999
Q ss_pred hhhHHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 534 VSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 534 ~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
.++|.+||.+.|+||||||||+||+|+|+.|+.++.+|++ |++.+ ++|++||+||+|||++|| +| +.|+|||
T Consensus 590 ~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk-fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 590 TERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK-FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC-CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999999999999999999999999999999999 99888 999999999999999999 44 9999998
No 5
>KOG2285|consensus
Probab=100.00 E-value=1.6e-90 Score=692.78 Aligned_cols=600 Identities=32% Similarity=0.543 Sum_probs=537.1
Q ss_pred ccChHhhHHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccC---CcccHHHHHHHHHhhhhhh---------------
Q psy16234 7 QVDFNKTWGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAY---PEPLADRLYQETKLFLDQH--------------- 68 (609)
Q Consensus 7 ~~~fe~~W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~---~~~~~~~Ly~~~~~~l~~~--------------- 68 (609)
...||+.|+..++.|.++++.+++++..|.++|.+||..|+|. |..+.+-|-..+.+|+.+-
T Consensus 10 r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL~ 89 (777)
T KOG2285|consen 10 RDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTDGALLI 89 (777)
T ss_pred hhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence 3479999999999999999999999999999999999999986 3334444555555554321
Q ss_pred --------------------------------------------------------------------------------
Q psy16234 69 -------------------------------------------------------------------------------- 68 (609)
Q Consensus 69 -------------------------------------------------------------------------------- 68 (609)
T Consensus 90 ~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklVhaER~G~a 169 (777)
T KOG2285|consen 90 GYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLVHAERDGNA 169 (777)
T ss_pred HHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccch
Confidence
Q ss_pred -------------------------ccHHhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCC
Q psy16234 69 -------------------------LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHV 123 (609)
Q Consensus 69 -------------------------~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~ 123 (609)
+|.+.||..||+.|.+||+..+..+++++++.+||+.|...+++|+.|+.+||.+
T Consensus 170 ~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~ 249 (777)
T KOG2285|consen 170 IDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEM 249 (777)
T ss_pred hhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhcc
Confidence 8999999999999999999999999999999999999999999999999999977
Q ss_pred --CchhHHHHHHHHHHHHHHHHHHHhhhHHHHhcccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcc--cC
Q psy16234 124 --SSYPKVKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGL--SG 199 (609)
Q Consensus 124 --~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~--~~ 199 (609)
.|..++++.|.+.||.+|.+.|+.+|..|+...+++-|++||+|+.+++.|++++...+..||...|.+-+... .-
T Consensus 250 ~~~s~~~lme~~VnaLv~sf~~tIlAEC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~i 329 (777)
T KOG2285|consen 250 NSPSSGKLMEKAVNALVESFEDTILAECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENI 329 (777)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhc
Confidence 68899999999999999999999999999999999999999999999999999999999999999999877533 22
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHhhcCCCCC-------------C--CCCCchhHhHHHHH
Q psy16234 200 DNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP-------------K--MPSKSPEYLAKYCD 264 (609)
Q Consensus 200 ~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~-------------~--~~~~~~e~La~y~D 264 (609)
..++..||+.||.++++|.+++.++|..|+.|..+-|.||+.++|..... + -..++||+||.|||
T Consensus 330 ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCD 409 (777)
T KOG2285|consen 330 TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCD 409 (777)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHH
Confidence 35788999999999999999999999999999999999999999986321 1 24689999999999
Q ss_pred HHHhccC--CCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCc--hhHHH
Q psy16234 265 MLLKKSS--KGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGY--EFTNK 340 (609)
Q Consensus 265 ~~lkk~~--k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~--~~t~k 340 (609)
.+||+.. |.++.++++.+|.+++-+++|+++||+|..+++.+|++|||.+.|++.+.|+.|+..|+ +||. +|++|
T Consensus 410 mLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNk 488 (777)
T KOG2285|consen 410 MLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNK 488 (777)
T ss_pred HHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHH
Confidence 9999974 67788999999999999999999999999999999999999999999999999999998 5885 89999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhcc-CCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcc
Q psy16234 341 FHRMLTDIKISGGLNEKFHSEFVKTN-EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRK 419 (609)
Q Consensus 341 l~~M~~Di~~S~~l~~~f~~~~~~~~-~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~Rk 419 (609)
|.+||+||+.|+++++.| +..+... +....-.+++.||+.|.|...+. ...+.||.+|++.+-..+.||+++|+||+
T Consensus 489 LaRMfQDIkvseDlN~~F-k~~~~~~~~~~~aDsiNiKiLNaGAW~R~SE-rv~vSLP~ELED~iPdveEfykk~hsgrk 566 (777)
T KOG2285|consen 489 LARMFQDIKVSEDLNSSF-KKALTGTNNNSIADSINIKILNAGAWGRGSE-RVRVSLPRELEDFIPDVEEFYKKKHSGRK 566 (777)
T ss_pred HHHHHhhccccHHHHHHH-HHHHhCCCCCCcccceeeeeecccccccccc-eEEEeCchhHHHhCccHHHHHhcccCccc
Confidence 999999999999999999 5545433 33334567899999999998865 46899999999999999999999999999
Q ss_pred eeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHh-----cCcccc
Q psy16234 420 LSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVE-----CKLLTS 492 (609)
Q Consensus 420 L~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~-----~~iL~~ 492 (609)
|.|.|++|.++|++.-.-|.|.+.|+|+||+||.+||+ ++.+|++.+.-+|.+|+.+|.+.|-||+. ..||..
T Consensus 567 l~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ 646 (777)
T KOG2285|consen 567 LQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLC 646 (777)
T ss_pred hhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeee
Confidence 99999999999988666689999999999999999997 58999999999999999999999999984 457666
Q ss_pred CC------CCCCCCCEEEEecCCC-------CCcceEEeccccccCChhHHhhhhhhHHHHhhhhhhhhhhhhhccccCC
Q psy16234 493 NK------EELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI 559 (609)
Q Consensus 493 ~~------~~~~~~~~f~lN~~F~-------~~~~ki~i~~~~~~~~~~e~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l 559 (609)
+| +++.++..|.+|.+|. .+++|+++....+-.+....++.++.+-+-|....|-+||+|||.||++
T Consensus 647 ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~ 726 (777)
T KOG2285|consen 647 EPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTY 726 (777)
T ss_pred cCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHh
Confidence 54 6788899999999995 4567788766555544444445567788899999999999999999999
Q ss_pred ChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 560 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 560 ~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
+..+|..+.++.++. |-|+..+||++||.|||..|++||++|-++|+|+|
T Consensus 727 ~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 727 TNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred hHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999999 99999999999999999999999999999999997
No 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=3.3e-80 Score=698.05 Aligned_cols=483 Identities=36% Similarity=0.667 Sum_probs=431.9
Q ss_pred HHHHHHHHHHHHhcCCCChhhhhhhhhhhhhhcccCCcccHHHHHHHHHhhhhhh-------------------------
Q psy16234 14 WGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQH------------------------- 68 (609)
Q Consensus 14 W~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~~~~~~~~~Ly~~~~~~l~~~------------------------- 68 (609)
|+.|++||..|+ .+.+++..||++|+.||++|... .|++||+.+++++..|
T Consensus 1 W~~l~~~i~~i~-~~~~~~~~~~~lY~~vy~l~~~~---~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~ 76 (588)
T PF00888_consen 1 WEILEEAIDQIF-KKSISKLSYMELYTCVYNLCDNK---YGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWE 76 (588)
T ss_dssp HHHHHHHHHHHH-TT-GCCSHHHHHHHHHHHHHHTT---THHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHH
T ss_pred ChHHHHHHHHHH-cCCCChhHHHHHHHHHHhhcCCc---ccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHH
Confidence 999999999999 45778999999999999996544 8899999998777655
Q ss_pred --------------------------------------------------------------------------ccHHhh
Q psy16234 69 --------------------------------------------------------------------------LYVDIF 74 (609)
Q Consensus 69 --------------------------------------------------------------------------~Y~~~F 74 (609)
+|.+.|
T Consensus 77 ~~~~~~~~i~~if~yLdr~yv~~~~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~~~~~y~~~f 156 (588)
T PF00888_consen 77 KYKKAIKYISDIFSYLDRNYVKRNLFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELGSLEVYEEEF 156 (588)
T ss_dssp HHHHHHHHHHHHTHHHHHTSTTTTHHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTTHTHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccchHHhhHHHH
Confidence 489999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHh
Q psy16234 75 ETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVA 154 (609)
Q Consensus 75 E~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~ 154 (609)
|++||+.|.+||+.++ +++.++.+||.+|+.++++|.+|+..||+++|..++.+++.++||.+|.+.|.+++..|++
T Consensus 157 e~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l~~~~~~ll~ 233 (588)
T PF00888_consen 157 EKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDELSSGFRDLLE 233 (588)
T ss_dssp HHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHHHTCHHHHHH
T ss_pred HHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999 7777999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHH
Q psy16234 155 EERRHDLANMYPLLRSVREGINILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGA 234 (609)
Q Consensus 155 ~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~V~~ll~~~~k~~~li~~~F~~~~~f~~~ 234 (609)
+++.++|++||+|+++++++++.+++.|++||.+.|.++++.......|..||+.++++|++|..++..||++++.|..+
T Consensus 234 ~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~ 313 (588)
T PF00888_consen 234 EDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKA 313 (588)
T ss_dssp TT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHH
T ss_pred hhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHH
Confidence 99999999999999999999999999999999999999999876556788999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCCCCCchhHhHHHHHHHHhccCCCCChhhHhhhhhhhhheeeccCChHHHHHHHHHHHHHHhcCC
Q psy16234 235 LDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQ 314 (609)
Q Consensus 235 l~~af~~~~N~~~~~~~~~~~~e~La~y~D~~lkk~~k~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~ 314 (609)
+++||+.++|.+ ..++|++||+|||.+++++.++.++++++..++.++.||+|+++||+|+.+|+++||+|||.+
T Consensus 314 l~~af~~~~n~~-----~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~ 388 (588)
T PF00888_consen 314 LDEAFEEFLNKN-----NNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSN 388 (588)
T ss_dssp HHHHHHHHHHCS-----TSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT
T ss_pred HHHhHHHHHHcC-----CcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcc
Confidence 999999999986 378999999999999999987778888999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCC--CcceEEEeeecCCCCCCCCCCC
Q psy16234 315 QSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDL--GIHFSINILQAGSWPLGPTVIS 392 (609)
Q Consensus 315 ~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~--~~~f~~~VLt~~~WP~~~~~~~ 392 (609)
++.+.+.|+.+|++|+.+||.++|++|++|++|+..|+++++.| ++.....+... +++|+|.||++|+||..+.. .
T Consensus 389 ~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f-~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~-~ 466 (588)
T PF00888_consen 389 KSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEF-KQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSE-N 466 (588)
T ss_dssp -BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTT-SS--CCEEEEEEEETTTS-S-S-S-S
T ss_pred cccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHH-HHHhhhccccccCCCceEEEEecCCCCCCCCCC-c
Confidence 99999999999999999999999999999999999999999999 77666554333 89999999999999999863 2
Q ss_pred CccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCC
Q psy16234 393 SFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSL 472 (609)
Q Consensus 393 ~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i 472 (609)
++.+|++|+.+++.|++||+++|+||+|+|++++|+|+|+++++++.++++||++||+||++||+++++|+++|++.||+
T Consensus 467 ~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~ 546 (588)
T PF00888_consen 467 NIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGI 546 (588)
T ss_dssp -----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC--
T ss_pred cccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHhcCccc--cCC--CCCCCCCEEEEecCCC
Q psy16234 473 SQDQIGRHIASLVECKLLT--SNK--EELTEDTEIRLNLGYN 510 (609)
Q Consensus 473 ~~~~l~~~L~~L~~~~iL~--~~~--~~~~~~~~f~lN~~F~ 510 (609)
++++++++|.+|++.|++. +.+ +++.+++.|.+|.+|+
T Consensus 547 ~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 547 SEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp -HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred CHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999987 333 6789999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.6e-34 Score=263.08 Aligned_cols=142 Identities=47% Similarity=0.845 Sum_probs=132.1
Q ss_pred ccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHHHhhccCCCCC
Q psy16234 292 YIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTNEIDLG 371 (609)
Q Consensus 292 ~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~~~~~~~~~~~ 371 (609)
|++|||+|+.+|+++||+|||..++++.+.|..||++||.+||.++|++|++|++|+..|+++++.| ++++..++...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f-~~~~~~~~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSF-KDMLENNSNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhccCCCC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999 776655433367
Q ss_pred cceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEE
Q psy16234 372 IHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSY 435 (609)
Q Consensus 372 ~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~ 435 (609)
++|+|.|||+++||..+.. .++.||++|+.+++.|++||.++|+||+|+|+|++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTE-VEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCC-CceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 8999999999999988753 58999999999999999999999999999999999999999875
No 8
>KOG2165|consensus
Probab=99.97 E-value=1.5e-28 Score=260.39 Aligned_cols=306 Identities=20% Similarity=0.282 Sum_probs=243.8
Q ss_pred eeeccCChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhHHHHHHHHHH-Hhhc-c
Q psy16234 289 VFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSE-FVKT-N 366 (609)
Q Consensus 289 lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~Di~~S~~l~~~f~~~-~~~~-~ 366 (609)
|...+.+|+.|.+.||.+||.||++....+.+.|..-++.||-.+|....+.|++|++|+..|+++++.+|+. .... .
T Consensus 445 LVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~~ 524 (765)
T KOG2165|consen 445 LVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRGA 524 (765)
T ss_pred HHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhccc
Confidence 3445599999999999999999999999999999999999999999999999999999999999999999553 2211 1
Q ss_pred CCCCCcceEEEeeecCCCCCCCCCCCCccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEEecH
Q psy16234 367 EIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVTMQT 446 (609)
Q Consensus 367 ~~~~~~~f~~~VLt~~~WP~~~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~ 446 (609)
...+.+.+++.||++.+||.... ..+.+|..++..++.+.+-|.+...+|+|.|++++|+|++++++.+++.+++||+
T Consensus 525 e~~~~~~i~~~IlS~~fWP~~~~--~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp 602 (765)
T KOG2165|consen 525 EEVPDFGISATILSSLFWPPLCD--EAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSP 602 (765)
T ss_pred ccCCCCchhhhhhhhhcCCcccc--ccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCH
Confidence 11235788999999999998765 6899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCcceEEeccccccCC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISGAVQKET 526 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~~ki~i~~~~~~~~ 526 (609)
.||+|+.+|.+.++||++++++.+|+|...+++.|..|++.|+|..+|. +++.++|++++.=.+. .+-+....-+.
T Consensus 603 ~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~-~s~tgt~T~iEse~d~---~q~~~~~~~e~ 678 (765)
T KOG2165|consen 603 EQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPI-ISDTGTLTVIESEMDF---DQAEGTVLLEA 678 (765)
T ss_pred HHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCC-CCCCceeeeccccccc---cccCCCccccc
Confidence 9999999999999999999999999999999999999999999998863 3778999999853322 22111111121
Q ss_pred hhHHhh--hhhhHHHHh--hhhhhhhhhhhhccccCCChHHHHHHHHHhhc--C-CCCChHHHHHHHHHhhhhccccccC
Q psy16234 527 PQEIER--TVSSVDEDR--KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSK--S-FAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 527 ~~e~~~--~~~~v~~~R--~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~--~-F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
.++..+ ....+++-+ -..-...||-.+-.-+.|+.+-+.+...--.. + ..++-++++..+..++..|-|+-.+
T Consensus 679 eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~~ 758 (765)
T KOG2165|consen 679 EEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFIA 758 (765)
T ss_pred ccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEec
Confidence 111111 112222211 12334578887777788988777754322221 1 5567788999999999888888766
Q ss_pred C
Q psy16234 600 N 600 (609)
Q Consensus 600 ~ 600 (609)
+
T Consensus 759 G 759 (765)
T KOG2165|consen 759 G 759 (765)
T ss_pred c
Confidence 3
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=99.79 E-value=5e-20 Score=145.27 Aligned_cols=67 Identities=51% Similarity=0.819 Sum_probs=61.2
Q ss_pred HHHHhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCC
Q psy16234 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTD 603 (609)
Q Consensus 537 v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~ 603 (609)
|+++|...|+|+||||||++|+++|++|+.+|.+++++ |.|+..+||++||.||++|||+||++|+|
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 35789999999999999999999999999999999997 99999999999999999999999999875
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=96.23 E-value=0.014 Score=49.24 Aligned_cols=65 Identities=18% Similarity=0.231 Sum_probs=54.9
Q ss_pred EEecHHHHHHHHhhc--------CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCC
Q psy16234 442 VTMQTFQMAILLLFE--------KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYN 510 (609)
Q Consensus 442 l~~s~~Q~~iLllFn--------~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~ 510 (609)
..++.-|+.+|+..- ..+.+|-.||++.+|++.+.+.+.|..|.+.|+|.... ....|++|.+++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~----~~~~~~~n~~~~ 93 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG----MMGIVGVNTPLS 93 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec----CCceeecCCCcc
Confidence 457788898888655 46789999999999999999999999999999998652 247899998864
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=96.05 E-value=0.01 Score=43.90 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=39.7
Q ss_pred HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 449 MAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 449 ~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+.||..|.+.+ .+|+.||++.+|+|...+.+.|..|...|++.++|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecCc
Confidence 46888888765 48999999999999999999999999999998764
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=95.83 E-value=0.022 Score=41.30 Aligned_cols=46 Identities=24% Similarity=0.319 Sum_probs=39.7
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLL 490 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL 490 (609)
+..+..||....+++.+|..+|++.+|++...+.++|..|.+.|++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 4567788988888899999999999999999999999999999987
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=95.43 E-value=0.05 Score=44.57 Aligned_cols=59 Identities=15% Similarity=0.261 Sum_probs=43.5
Q ss_pred HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 447 FQMAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 447 ~Q~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
+++.+.+..+..+ .+|.++|++.+++|...+.+.++.|.+.|++.... .+++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~---G~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSR---GRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET---STTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC---CCCCceeecCC
Confidence 3444555544443 49999999999999999999999999999987543 23577888764
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=94.85 E-value=0.045 Score=41.84 Aligned_cols=50 Identities=16% Similarity=0.337 Sum_probs=44.4
Q ss_pred ecHHHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 444 MQTFQMAILLLFEKNDA--MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 47789999988887776 999999999999999999999999999999765
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=94.47 E-value=0.1 Score=39.37 Aligned_cols=46 Identities=20% Similarity=0.318 Sum_probs=41.7
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|..|+...++++.+|+++|++.+|++...+++-|..|.+.|++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4467888888999999999999999999999999999999998765
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=94.14 E-value=0.15 Score=39.61 Aligned_cols=50 Identities=24% Similarity=0.324 Sum_probs=40.7
Q ss_pred ecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 444 MQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 444 ~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+|..|..||.... ....++..+|++.++++...+.+.+..|+..|+|.+.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 3677899998888 7789999999999999999999999999999999655
No 17
>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=94.13 E-value=0.13 Score=37.14 Aligned_cols=44 Identities=27% Similarity=0.465 Sum_probs=37.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
...-||.++-+ .+.++.||++.+|++...+.++|..|.+.|++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 34567777766 679999999999999999999999999999875
No 18
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=94.10 E-value=0.065 Score=40.55 Aligned_cols=50 Identities=22% Similarity=0.334 Sum_probs=44.9
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+|..|+.+|....+.+.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 36789999998888888999999999999999999999999999999765
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=93.51 E-value=0.16 Score=38.85 Aligned_cols=49 Identities=27% Similarity=0.434 Sum_probs=42.3
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
++.-..||.++...+.+|+.+|++.+|++...+..+|..|.+.|++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 4566778888877789999999999999999999999999999998643
No 20
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=93.26 E-value=0.22 Score=43.90 Aligned_cols=38 Identities=24% Similarity=0.456 Sum_probs=35.5
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 456 EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 456 n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.++.+|+++|++.++.+...+.+.|+.|+.+|++.+.
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 36789999999999999999999999999999999876
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.95 E-value=0.2 Score=39.38 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 447 FQMAILLLFEKNDA--MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 447 ~Q~~iLllFn~~~~--lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..-.||.++.+... +|..+|++.+|++...+.++|..|.+.|++...
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 44567777777655 999999999999999999999999999999775
No 22
>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=92.50 E-value=0.23 Score=43.58 Aligned_cols=52 Identities=17% Similarity=0.189 Sum_probs=47.3
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.++..|+.||..+..++.+|..+|++.++++...+.+.+..|.+.|++...+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 4578899999998888899999999999999999999999999999998753
No 23
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.26 E-value=0.42 Score=39.52 Aligned_cols=55 Identities=20% Similarity=0.329 Sum_probs=44.1
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
..||..+... +.+|..+|++.+|++...+.+.|..|.+.|+|...+ .++.|.+..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~----~~~~y~l~~ 63 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG----QNGRYRLGP 63 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC----CCCceeecH
Confidence 4567777766 689999999999999999999999999999997653 234565543
No 24
>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=91.79 E-value=0.16 Score=39.80 Aligned_cols=49 Identities=24% Similarity=0.296 Sum_probs=42.0
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|-.++.|+..+-..+..|..+|++.+|++...+.+.|..|.+.|++...
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4456666666557788999999999999999999999999999999765
No 25
>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=91.75 E-value=0.62 Score=39.55 Aligned_cols=61 Identities=21% Similarity=0.393 Sum_probs=47.9
Q ss_pred ecHHHHHHHHh-------hcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCC
Q psy16234 444 MQTFQMAILLL-------FEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYN 510 (609)
Q Consensus 444 ~s~~Q~~iLll-------Fn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~ 510 (609)
+|.-|..|++. ||. .+.+|..++++.||++...+.+++..|++.|+|..+ +..+.+|.+.+
T Consensus 30 ls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~------g~~~G~N~~i~ 98 (100)
T PF04492_consen 30 LSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRD------GKRIGVNKNIS 98 (100)
T ss_pred ccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC------CcEEeeecccc
Confidence 44455555544 554 478999999999999999999999999999999776 46777777653
No 26
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=91.52 E-value=0.37 Score=43.86 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=46.8
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.++..|+.||......+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4677899999887777889999999999999999999999999999998763
No 27
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.16 E-value=0.47 Score=47.83 Aligned_cols=56 Identities=13% Similarity=0.245 Sum_probs=47.1
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
+.||.+|.+...+|+.||++.+|+|...+.+.|..|+..|+|.+++ .++.|.+-..
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~----~~~~Y~lG~~ 72 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEG----ESEKYSLTLK 72 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEEecHH
Confidence 4688889887789999999999999999999999999999997753 2456666544
No 28
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=90.98 E-value=0.56 Score=39.17 Aligned_cols=52 Identities=13% Similarity=0.262 Sum_probs=46.9
Q ss_pred EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.++..+..||......+.+|..+|++.++++...+.++|..|.+.|++...
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 4567889999988888788999999999999999999999999999999764
No 29
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=90.83 E-value=0.76 Score=42.90 Aligned_cols=58 Identities=12% Similarity=0.114 Sum_probs=43.8
Q ss_pred HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
.+++.+.|+. ...+|.++|++.+++|...+.+.|..|.++||+.... .+++.|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~r---G~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVR---GPGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC---CCCCCeeccCC
Confidence 3444555665 3589999999999999999999999999999997531 12445666543
No 30
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=90.78 E-value=0.74 Score=42.47 Aligned_cols=56 Identities=16% Similarity=0.193 Sum_probs=43.1
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
+.+.|..+..+.+|..+|++..++|...|.+.|..|.++||+.... ..++-|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r---G~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR---GRNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec---CCCCCeeecC
Confidence 3344555555678999999999999999999999999999987542 2345566654
No 31
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=90.19 E-value=0.73 Score=32.82 Aligned_cols=34 Identities=21% Similarity=0.423 Sum_probs=31.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|..+|++.+|++...+.+.|..|.+.|++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4789999999999999999999999999999765
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.15 E-value=0.74 Score=33.37 Aligned_cols=44 Identities=27% Similarity=0.382 Sum_probs=37.9
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.|+..+.++..+|..+|++.++++...+.+.|..|.+.|++...
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45656666677999999999999999999999999999988654
No 33
>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=89.50 E-value=0.99 Score=40.63 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=41.4
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|.++||+.... ..++.|.+..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~---G~~Ggy~l~~ 69 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVR---GPGGGYQLGR 69 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEe---CCCCCEeccC
Confidence 3444555543 479999999999999999999999999999986431 1234465554
No 34
>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=89.46 E-value=0.9 Score=39.22 Aligned_cols=52 Identities=15% Similarity=0.243 Sum_probs=45.2
Q ss_pred EecHHHHHHHHhhc----CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 443 TMQTFQMAILLLFE----KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 443 ~~s~~Q~~iLllFn----~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.+|..|..||.... ..+.+|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 45778888887665 55789999999999999999999999999999998763
No 35
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=89.37 E-value=0.87 Score=34.97 Aligned_cols=44 Identities=20% Similarity=0.194 Sum_probs=36.3
Q ss_pred HHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 451 ILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 451 iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
||-.+++ +.++|..||++++|++.......|..|.+.|.+...|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4555565 6789999999999999999999999999999887655
No 36
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=88.82 E-value=0.51 Score=38.35 Aligned_cols=45 Identities=24% Similarity=0.449 Sum_probs=37.3
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..|+...+..+.+++.+|.+.+|+++..+.++|..|.+.|++...
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence 456666666788999999999999999999999999999998643
No 37
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=88.81 E-value=0.93 Score=45.38 Aligned_cols=56 Identities=25% Similarity=0.401 Sum_probs=46.3
Q ss_pred HHHHHhhcCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 449 MAILLLFEKNDA-MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 449 ~~iLllFn~~~~-lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
+.||.+|...+. +++.||++.+|+|...+.+.|..|+..|++..++ .++.|.+-..
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~----~~g~Y~Lg~~ 63 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP----EDGRYRLGPR 63 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEeehHH
Confidence 468888987654 7899999999999999999999999999999875 2346776443
No 38
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=88.55 E-value=1.2 Score=35.03 Aligned_cols=46 Identities=15% Similarity=0.273 Sum_probs=37.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..|. ||+..... +.|+++|.+.||++...+...|..|.+.|++...
T Consensus 6 ~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 3444 44444444 8999999999999999999999999999999764
No 39
>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=88.48 E-value=0.44 Score=37.46 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=36.7
Q ss_pred hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
.|-.+|+.++.++..+|-.+ |..+++.+..-|+.|+.+|||++.+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~-------~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELARE-------FGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHH-------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 35567899999999887754 88999999999999999999998764
No 40
>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=87.85 E-value=1.2 Score=44.50 Aligned_cols=54 Identities=22% Similarity=0.301 Sum_probs=45.1
Q ss_pred HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 449 MAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 449 ~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|+..|.|..+ +..|.+-..
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~------~~~Y~lG~~ 66 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD------GRLFWLTPR 66 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC------CCEEEecHH
Confidence 468888986 567999999999999999999999999999999764 356766443
No 41
>PRK11569 transcriptional repressor IclR; Provisional
Probab=87.76 E-value=1.1 Score=45.58 Aligned_cols=53 Identities=8% Similarity=0.148 Sum_probs=44.6
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEE
Q psy16234 449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRL 505 (609)
Q Consensus 449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~l 505 (609)
..||.+|.+. ..+|+.||++.+|++...+.+.|.+|+..|+|..++ .++.|.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~----~~~~Y~l 84 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG----ELGHWAI 84 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEec
Confidence 4688889874 579999999999999999999999999999998753 2456665
No 42
>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=87.61 E-value=0.74 Score=42.98 Aligned_cols=49 Identities=20% Similarity=0.263 Sum_probs=42.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCc
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKR 513 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~ 513 (609)
.+|.++|++.+|++...+.+.+..|.+.++|.+.. .+.|.||++|--+.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~-----~G~Y~iNP~~~~kG 123 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR-----NGAYMINPNFFFKG 123 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc-----CCeEEECcHHheeC
Confidence 36889999999999999999999999999998763 57999999975443
No 43
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=87.51 E-value=1.3 Score=45.09 Aligned_cols=56 Identities=23% Similarity=0.282 Sum_probs=46.4
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 449 MAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 449 ~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
..||.+|... ..+|+.||++.+|+|...+.+.|.+|+..|.|..++ .++.|.+...
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~----~~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS----QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEEecHH
Confidence 4688889865 579999999999999999999999999999998763 2456766544
No 44
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=87.51 E-value=1.5 Score=40.37 Aligned_cols=59 Identities=14% Similarity=0.211 Sum_probs=44.7
Q ss_pred HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 447 FQMAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 447 ~Q~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|.++|++.... .+++-|.++..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~r---G~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVR---GKGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeec---CCCCCccCCCC
Confidence 3444555555544 68899999999999999999999999999997543 23566777653
No 45
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=87.37 E-value=1.3 Score=42.10 Aligned_cols=52 Identities=13% Similarity=0.029 Sum_probs=47.4
Q ss_pred EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.++..|..||.....++.+|..+|++.++++...+.+.+..|.+.|++.+.
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence 3466789999999998899999999999999999999999999999999875
No 46
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.18 E-value=1.8 Score=32.07 Aligned_cols=29 Identities=24% Similarity=0.302 Sum_probs=27.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234 462 TCGDIQTVLSLSQDQIGRHIASLVECKLL 490 (609)
Q Consensus 462 t~~ei~~~t~i~~~~l~~~L~~L~~~~iL 490 (609)
|.+.|++.+|++...+.+++..|.+.|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 89999999999999999999999999875
No 47
>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=86.80 E-value=1.7 Score=38.73 Aligned_cols=46 Identities=13% Similarity=0.212 Sum_probs=36.8
Q ss_pred HHHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
++.+.+.-++ ...+|.++|++.+++|...+.+.|..|.+.|+|...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 3344444333 348999999999999999999999999999998653
No 48
>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=86.47 E-value=1.7 Score=32.20 Aligned_cols=39 Identities=31% Similarity=0.445 Sum_probs=31.9
Q ss_pred HHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcC
Q psy16234 450 AILLLF-EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488 (609)
Q Consensus 450 ~iLllF-n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~ 488 (609)
.||.++ +..+.+|.++|++.+|++...+.+.|..|-..+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 344444 666669999999999999999999999998877
No 49
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=86.21 E-value=2.1 Score=31.84 Aligned_cols=40 Identities=13% Similarity=0.250 Sum_probs=34.6
Q ss_pred hcCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 455 FEKNDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 455 Fn~~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+...+.+ |..+|++.+|++...+.++|..|.+.|+|...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4455667 999999999999999999999999999986543
No 50
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.81 E-value=1.6 Score=37.40 Aligned_cols=46 Identities=15% Similarity=0.274 Sum_probs=40.9
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
..-.||..+..+...|+.+|++.+|++...+.+.+..|.+.|++..
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 3456788888878899999999999999999999999999999873
No 51
>PHA00738 putative HTH transcription regulator
Probab=85.68 E-value=2.1 Score=36.54 Aligned_cols=67 Identities=19% Similarity=0.157 Sum_probs=52.2
Q ss_pred EEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234 441 FVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY 509 (609)
Q Consensus 441 ~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F 509 (609)
++...+.=-.||.++.+++.+++.+|++.++++...+-++|..|-.+||+.... ....-.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK--~Gr~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYK--EGRTLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEE--ECCEEEEEECCCc
Confidence 455566666778777777789999999999999999999999999999997542 0113457777764
No 52
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.50 E-value=1.6 Score=39.66 Aligned_cols=53 Identities=11% Similarity=0.149 Sum_probs=45.8
Q ss_pred EEecHHHHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 442 VTMQTFQMAILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+.++..|..||...... +..|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34677898888887754 568999999999999999999999999999998763
No 53
>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=85.40 E-value=1.4 Score=42.60 Aligned_cols=51 Identities=18% Similarity=0.277 Sum_probs=46.9
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.++..|..||..+.+++..+..+|++.+|++...+.++|..|.+.|++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 467889999999988788999999999999999999999999999999875
No 54
>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=85.20 E-value=2.4 Score=32.52 Aligned_cols=35 Identities=23% Similarity=0.367 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..+|..+|++.+|++...+.+.|..|.+.|+|...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 56999999999999999999999999999999865
No 55
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=85.09 E-value=1.7 Score=43.91 Aligned_cols=54 Identities=20% Similarity=0.342 Sum_probs=44.3
Q ss_pred HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234 449 MAILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN 506 (609)
Q Consensus 449 ~~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN 506 (609)
+.||.+|.+++ .+|..||++.+|++...+.+.|..|...|+|.+++ .++.|.+-
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~----~~~~Y~Lg 68 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA----SDDSFRLT 68 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec----CCCcEEEc
Confidence 45788887654 59999999999999999999999999999998763 23456664
No 56
>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=85.06 E-value=2 Score=32.81 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=37.4
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
|..+-.+...++..+|++.+|++...+...+..|.+.|++...+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 44444577899999999999999999999999999999998764
No 57
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=84.78 E-value=2.2 Score=33.16 Aligned_cols=48 Identities=29% Similarity=0.453 Sum_probs=41.2
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+..+..|+..+.+.+ ++..+|++.+|++...+.+.|..|...|++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence 345777887777766 999999999999999999999999999998754
No 58
>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=84.40 E-value=2.4 Score=37.74 Aligned_cols=45 Identities=13% Similarity=0.253 Sum_probs=36.9
Q ss_pred HHHHHhhc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 449 MAILLLFE--KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 449 ~~iLllFn--~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..+|..+. ..+.+|..+|++.+|+|...+.+.|..|.+.|++...
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 34454554 3457999999999999999999999999999999643
No 59
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=84.12 E-value=2 Score=37.68 Aligned_cols=62 Identities=19% Similarity=0.287 Sum_probs=52.7
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
..++.|++||=+++..+.++++.++... +.++...|+--|..|..||.|.|.-+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~---~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD---REWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc---ccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 4578899999999999999888777665 67889999999999999999999875 47777754
No 60
>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=84.10 E-value=2.2 Score=38.20 Aligned_cols=60 Identities=18% Similarity=0.250 Sum_probs=45.0
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
+..|++++-..+.++..+++....+. ..+....+...|+.|.+||+|+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~---~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEK---KDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhc---cCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 45677888777788777666443322 56788999999999999999999854 35788854
No 61
>PRK10870 transcriptional repressor MprA; Provisional
Probab=83.53 E-value=2.5 Score=39.88 Aligned_cols=51 Identities=14% Similarity=0.203 Sum_probs=44.1
Q ss_pred ecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+|..|..||..... ..++|..+|++.++++...+.+.+..|.+.|++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 55678888877764 4679999999999999999999999999999998763
No 62
>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=83.40 E-value=1.2 Score=35.25 Aligned_cols=41 Identities=15% Similarity=0.193 Sum_probs=33.3
Q ss_pred HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 452 LLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 452 LllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
+.++.....+|+.||++.+|+|...++..+..+.+.|+|.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHHH
Confidence 33333346789999999999999999999999888887754
No 63
>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=82.03 E-value=2.6 Score=35.82 Aligned_cols=49 Identities=12% Similarity=0.281 Sum_probs=41.6
Q ss_pred EecHHHHHHHHhhcC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 443 TMQTFQMAILLLFEK----NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~----~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
.++..|-.||-.+.+ .+.+++++|++.++++..+++.+|..|+..|.+-
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 578899999988887 4679999999999999999999999999988774
No 64
>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=81.73 E-value=1.4 Score=38.36 Aligned_cols=60 Identities=13% Similarity=0.263 Sum_probs=45.5
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
+..|++++=..+.++..+++..+.+. ..+....|...+..|.+||||.|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l~~~---~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEALPEE---RSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHCTT---SS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhc---cccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 56678888888888888776554333 56889999999999999999999865 46888864
No 65
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=81.68 E-value=3 Score=31.25 Aligned_cols=36 Identities=25% Similarity=0.457 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 458 NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.++.|..+|++.+|++...+.+.|..|.+.|++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 567899999999999999999999999999998644
No 66
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=81.33 E-value=2.4 Score=41.27 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=39.6
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
..||.+.+..++.|.+||++.+|++..-+++||+.|...|++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceee
Confidence 34777888889999999999999999999999999999998864
No 67
>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=81.15 E-value=1.1 Score=35.01 Aligned_cols=56 Identities=21% Similarity=0.260 Sum_probs=41.3
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 608 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yi 608 (609)
++.|-+.|-.++.++..+|... + ..+...+-+.++.|.++|+++|.++++..|..+
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~----l---~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEE----L---GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHH----H---TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 4455555556777777766533 3 467899999999999999999999876555544
No 68
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=80.86 E-value=3.3 Score=35.78 Aligned_cols=51 Identities=18% Similarity=0.290 Sum_probs=45.5
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+++.|..+|......+..+..+|++.++++...+.+.+..|.+.|++...+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 678999999888887776669999999999999999999999999998763
No 69
>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=80.83 E-value=1.9 Score=33.76 Aligned_cols=43 Identities=7% Similarity=0.186 Sum_probs=34.1
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|.-...++..+|+++|+..++++.+.+...|..|+..|-+.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 3344556788999999999999999999999999999988754
No 70
>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=80.52 E-value=3 Score=27.42 Aligned_cols=31 Identities=29% Similarity=0.428 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCcc
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLL 490 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL 490 (609)
.+|-+||++.+|++.+.+-+.|..|-+.|++
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 3678999999999999999999999988875
No 71
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=80.50 E-value=5.1 Score=36.28 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=38.8
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234 455 FEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLN 506 (609)
Q Consensus 455 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN 506 (609)
+..+..+|.++|++..|+|...+.++|..|.+.|++...+ ..++.|.+.
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~---G~~GG~~l~ 68 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR---GKNGGIRLG 68 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec---CCCCCeeec
Confidence 4445578999999999999999999999999999997653 123445554
No 72
>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=80.34 E-value=2.8 Score=32.21 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=29.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
.++.+|+.+|.+.|++|.+.++..|..|++.+++.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 45688999999999999999999999999999874
No 73
>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=79.05 E-value=4 Score=33.78 Aligned_cols=44 Identities=20% Similarity=0.326 Sum_probs=37.5
Q ss_pred HHHHHhhcCCCCCCHHHHHHHh-CCCHHHHHHHHHHHHhcCccccC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVL-SLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t-~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.||..... +...+.||.+.+ |++...|.+.|..|...||+.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcc
Confidence 456666666 688999999999 99999999999999999999765
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=78.95 E-value=4.9 Score=31.20 Aligned_cols=51 Identities=18% Similarity=0.270 Sum_probs=37.7
Q ss_pred ecHHHHHHHHhhcC-----CCCCCHHHHHHHhCCC-HHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEK-----NDAMTCGDIQTVLSLS-QDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~-----~~~lt~~ei~~~t~i~-~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+|.-|.-||...-+ +-+-|+.||++.+|+. ...+..+|..|.+.|.|...+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 34567767655432 3456999999999997 999999999999999998764
No 75
>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=78.89 E-value=7.4 Score=29.44 Aligned_cols=38 Identities=13% Similarity=0.234 Sum_probs=32.1
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 456 EKNDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 456 n~~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.....+ |..+|++.+|++...+.++|..|.+.|+|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 333444 49999999999999999999999999998654
No 76
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=77.90 E-value=3.6 Score=39.90 Aligned_cols=50 Identities=22% Similarity=0.414 Sum_probs=44.5
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.|..-..||.+......+.+.||++++|+|...+..++..|.++||+...
T Consensus 21 aS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 21 ASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 34555678989999999999999999999999999999999999999754
No 77
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=76.96 E-value=4.7 Score=37.09 Aligned_cols=48 Identities=13% Similarity=0.266 Sum_probs=43.5
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
++..--.||..+..+...|+.+|++.+|++...+.+.+..|...|++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 455667788888888999999999999999999999999999999986
No 78
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=76.94 E-value=5.9 Score=34.69 Aligned_cols=48 Identities=33% Similarity=0.472 Sum_probs=39.7
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.-..||.+.-+.+..++.+|++.+|++...+-+||.-|.++|++...
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDR 63 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 344456655545567999999999999999999999999999999754
No 79
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.51 E-value=6.3 Score=30.78 Aligned_cols=54 Identities=13% Similarity=0.162 Sum_probs=42.0
Q ss_pred hhhhhhhhhccccC--CChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCce
Q psy16234 545 LQAAIVRIMKSRKQ--IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY 605 (609)
Q Consensus 545 i~A~IVRiMK~~k~--l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y 605 (609)
.+..|...|+.++. ++-.+|- +++ ..+...+.+.+..|.++|||.++++.+..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa----~~l---gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLA----KNL---GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHH----HHH---CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 35568888998866 8877665 443 467789999999999999999988665554
No 80
>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=76.37 E-value=3.5 Score=30.96 Aligned_cols=47 Identities=21% Similarity=0.399 Sum_probs=41.0
Q ss_pred hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
..|+..++.++.++..+|.+. |.++...|.+-+..|-++|.|.|.-+
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 468888999999999888754 78999999999999999999998653
No 81
>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=76.37 E-value=6.4 Score=30.25 Aligned_cols=51 Identities=22% Similarity=0.333 Sum_probs=34.3
Q ss_pred hhhhhhhhc-cccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc--CCCCC
Q psy16234 546 QAAIVRIMK-SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT--ANSTD 603 (609)
Q Consensus 546 ~A~IVRiMK-~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~--~~~~~ 603 (609)
+..|.+.+. +...++..+|... +..+.+.+-+.|+.|+++|||++. +.|+.
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~-------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER-------LGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH-------TT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHHHHHHHHccCCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 456667777 6677777665533 567788999999999999999764 44444
No 82
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=75.93 E-value=4.6 Score=37.59 Aligned_cols=48 Identities=13% Similarity=0.186 Sum_probs=43.6
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
+.-.-..||..+.++...|+.+|++.+|++...+.+.++.|.+.|++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 445667789899999999999999999999999999999999999986
No 83
>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=75.39 E-value=5.4 Score=27.96 Aligned_cols=36 Identities=25% Similarity=0.416 Sum_probs=28.0
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
-.||-.+.+....++.+|++.+|++...+.+-+..|
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 457777777788999999999999999999887765
No 84
>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=75.10 E-value=2.8 Score=35.87 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=33.3
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
.+.|+..+..+..++-++|++.+|++..++++.|..|...|++..
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~ 59 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSY 59 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEE
Confidence 345666666667899999999999999999999999999999853
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=74.53 E-value=6.1 Score=36.62 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=37.2
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
..|+..+-.+..+|-++|++.+|++...+++.|..|...||+..
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~ 60 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADY 60 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcee
Confidence 34555444556899999999999999999999999999999853
No 86
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=73.53 E-value=4.9 Score=30.41 Aligned_cols=38 Identities=29% Similarity=0.378 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
|.-+|-++-+.+.+|+++|++.+|++...++.-+.-|-
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 45566555447899999999999999999999888875
No 87
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.11 E-value=6.1 Score=37.39 Aligned_cols=45 Identities=13% Similarity=0.212 Sum_probs=39.2
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
...||.+.-.+..+|-++|++.+|++...++++|..|...|++..
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 445666666777899999999999999999999999999999873
No 88
>PRK00215 LexA repressor; Validated
Probab=72.61 E-value=6.6 Score=37.94 Aligned_cols=51 Identities=18% Similarity=0.241 Sum_probs=43.1
Q ss_pred ecHHHHHHHHhhcC-----CCCCCHHHHHHHhCC-CHHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEK-----NDAMTCGDIQTVLSL-SQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~-----~~~lt~~ei~~~t~i-~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
++.-|..||..+.+ ....|+.||++.+|+ +...+.+.|..|.+.|+|...+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence 45678888866652 456899999999999 9999999999999999998764
No 89
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=72.01 E-value=5.1 Score=40.33 Aligned_cols=46 Identities=15% Similarity=0.235 Sum_probs=42.6
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|..|+-+.++++.+++.||++.+|++...+++-|..|-+.|+|.+.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 6678989999999999999999999999999999999999988765
No 90
>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=71.22 E-value=3.8 Score=38.96 Aligned_cols=58 Identities=16% Similarity=0.287 Sum_probs=40.8
Q ss_pred hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
+-...|...|.+|.+..++|-.+ |.++.+++-.+|..|...|-|.-.-+|++.|+||+
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 34445588899999999887644 88999999999999999999998888899999984
No 91
>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=70.89 E-value=4.4 Score=42.30 Aligned_cols=144 Identities=19% Similarity=0.208 Sum_probs=44.4
Q ss_pred EecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCCCcceEEecc
Q psy16234 443 TMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNNKRTKLKISG 520 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~~~~ki~i~~ 520 (609)
.++..+..|.-+..+ ...+-..+|...|||+...+.++|.+|...++++... +.+.+++|+-+..
T Consensus 81 ~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk-------------sv~~~~rK~Yml~ 147 (327)
T PF05158_consen 81 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK-------------SVKNPNRKVYMLY 147 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE---------------SS-SS--EEEES
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec-------------CcCCCCeEEEEEc
Confidence 456677888877765 5678999999999999999999999999988886431 2233445555432
Q ss_pred ccccCChhHHhh----hhhhHHHHhhhhhhhhhhhhhccccC-----------------------------CChHHHHHH
Q psy16234 521 AVQKETPQEIER----TVSSVDEDRKLYLQAAIVRIMKSRKQ-----------------------------IRHNALIQE 567 (609)
Q Consensus 521 ~~~~~~~~e~~~----~~~~v~~~R~~~i~A~IVRiMK~~k~-----------------------------l~~~~L~~~ 567 (609)
.. +...|... +..+.+.+=...|...|.+.+.++.. .+.+++...
T Consensus 148 ~l--~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~f 225 (327)
T PF05158_consen 148 DL--EPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEF 225 (327)
T ss_dssp SS------------------------------------------------------------------------------
T ss_pred cC--CcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHH
Confidence 11 00000000 11233444445566666666666544 333444433
Q ss_pred HHHh-hcCCCCChHHHHHHHHHhhhhccccccCCC
Q psy16234 568 VLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANS 601 (609)
Q Consensus 568 v~~~-l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~ 601 (609)
+.+. +..-..+.++|...|+.||=-|-|++....
T Consensus 226 I~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 226 INKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp -----------------------------------
T ss_pred HHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 3322 111347789999999999999988886654
No 92
>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=70.76 E-value=6.4 Score=38.07 Aligned_cols=44 Identities=23% Similarity=0.332 Sum_probs=37.9
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.||......+.+|..+|++.+|++...+.++|..|.+.|++...
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 45555555567999999999999999999999999999999764
No 93
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=70.67 E-value=9.8 Score=30.51 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=32.9
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
+-||.... .+..+..+|+..+|++...+.+.|..|.+.|++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence 45666665 56788999999999999999999999999999954
No 94
>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=69.67 E-value=1.3e+02 Score=31.56 Aligned_cols=85 Identities=7% Similarity=0.215 Sum_probs=58.7
Q ss_pred HHhhhHHHHhcccHHHHHHHHHhhhcc---cccHHHHHHHHHHHHHHHHHHHhhcccC----CCchHHHHHHHHHHHHHH
Q psy16234 145 LQGECVPMVAEERRHDLANMYPLLRSV---REGINILIDAVRDHICKQGLEAISGLSG----DNISTQFVENMLAVHKKY 217 (609)
Q Consensus 145 l~~~~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~V~~ll~~~~k~ 217 (609)
+...|..-.+.++.+.+.|.++||-.+ ..|++....-+.+.|.......+..... ...+.-|+..|..+++..
T Consensus 12 f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~i 91 (331)
T PF08318_consen 12 FLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEHI 91 (331)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHHH
Confidence 346788888889999999988888654 4688888888888887777776665422 223445666666666665
Q ss_pred HHH-------HHHhcCCCh
Q psy16234 218 KAF-------VKELFSGDQ 229 (609)
Q Consensus 218 ~~l-------i~~~F~~~~ 229 (609)
..+ |..+|+...
T Consensus 92 a~ii~~h~~lI~~~yG~~~ 110 (331)
T PF08318_consen 92 ATIIEQHQPLIEKYYGPGY 110 (331)
T ss_pred HHHHHHccHHHHHHcCCcH
Confidence 554 456887654
No 95
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=68.85 E-value=9.7 Score=34.67 Aligned_cols=49 Identities=18% Similarity=0.328 Sum_probs=43.2
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
+.-.-.-||..+.+....++.+|++.+|++...+.+.+..|.+.|++..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceee
Confidence 3445667888888888899999999999999999999999999999864
No 96
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=68.55 E-value=17 Score=34.11 Aligned_cols=55 Identities=15% Similarity=0.070 Sum_probs=42.7
Q ss_pred EEEEecHHHHHHHHhhcCCCC-CCHHHHHHHh--CCCHHHHHHHHHHHHhcCccccCC
Q psy16234 440 YFVTMQTFQMAILLLFEKNDA-MTCGDIQTVL--SLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 440 ~~l~~s~~Q~~iLllFn~~~~-lt~~ei~~~t--~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+++--+.+..+|+-+..-.+. -+.++|++.+ +++.++++..|..|.+.|+|.+++
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECC
Confidence 344445566666666554333 2899999999 999999999999999999999874
No 97
>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=68.00 E-value=6.5 Score=37.77 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=43.4
Q ss_pred ecHHHHHHHHhhcC-----CCCCCHHHHHHHhCCC-HHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEK-----NDAMTCGDIQTVLSLS-QDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~-----~~~lt~~ei~~~t~i~-~~~l~~~L~~L~~~~iL~~~~ 494 (609)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|.+.|+|...+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 46788888877663 2358899999999999 999999999999999998764
No 98
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=67.61 E-value=6.8 Score=39.34 Aligned_cols=46 Identities=22% Similarity=0.332 Sum_probs=42.6
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|-.|+-+.++++.++++||++.+|+++..++|=|..|.+.|+|.+.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 5568889999999999999999999999999999999999998875
No 99
>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=66.87 E-value=14 Score=28.55 Aligned_cols=57 Identities=16% Similarity=0.268 Sum_probs=37.0
Q ss_pred HhhhhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCC
Q psy16234 540 DRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 601 (609)
Q Consensus 540 ~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~ 601 (609)
+|+..|=.+|...++..+--+. +.|+.+.+. +. +..-+...++.|.++|||+|+++.
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt---~rEIa~~~g-~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPT---VREIAEALG-LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS------HHHHHHHHT-SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHHcCCCCC---HHHHHHHhC-CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 3555555666666666543332 234444443 32 588889999999999999999864
No 100
>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=66.82 E-value=12 Score=32.29 Aligned_cols=58 Identities=12% Similarity=0.233 Sum_probs=44.3
Q ss_pred hhhhhhcc-ccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234 548 AIVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 548 ~IVRiMK~-~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y 607 (609)
+|..+|.. .+.++.++|.+.+.++. ..++...|=+.|+.|.+.|+|.+-..+.....|
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 45566655 56799999998887664 357899999999999999999987654344444
No 101
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=65.42 E-value=6.6 Score=37.41 Aligned_cols=47 Identities=21% Similarity=0.091 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-+..|+.+.+.+..+++.+|++.+|++...++|-|..|...|++.+.
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence 46678889999999999999999999999999999999998887653
No 102
>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=65.24 E-value=4.7 Score=30.13 Aligned_cols=48 Identities=27% Similarity=0.382 Sum_probs=35.5
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|..|..++-....++..+|-.. +..+.+.+-+.+..|.++|||+|..+
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~-------~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEK-------LGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHH-------HTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH-------HCCChhHHHHHHHHHHHCCCEEeccC
Confidence 4455666667777777765533 45788999999999999999998654
No 103
>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=65.06 E-value=15 Score=28.92 Aligned_cols=34 Identities=18% Similarity=0.369 Sum_probs=31.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-++|++.+|++...+.+.|..|.+.|++...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence 4799999999999999999999999999999754
No 104
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=64.47 E-value=11 Score=37.86 Aligned_cols=47 Identities=21% Similarity=0.179 Sum_probs=42.6
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-|..|+..++++..+++.||++.+|++...+++-|..|.+.|++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 35678888999999999999999999999999999999999988765
No 105
>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=64.17 E-value=7.5 Score=29.22 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=34.5
Q ss_pred hhhhhhhhccccC--CChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCC
Q psy16234 546 QAAIVRIMKSRKQ--IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 601 (609)
Q Consensus 546 ~A~IVRiMK~~k~--l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~ 601 (609)
+..|...+..+.. ++..+|... +..+.+.+.+.|..|+++|||+|..+.
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~-------l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAER-------LGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHH-------HTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4455566666655 666665533 346789999999999999999997653
No 106
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=63.90 E-value=13 Score=27.54 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=32.4
Q ss_pred hhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCC
Q psy16234 549 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 601 (609)
Q Consensus 549 IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~ 601 (609)
|++.+. .+.++..++... +..+.+.+.+.|+.|.++|++.+..+.
T Consensus 2 il~~l~-~~~~~~~~i~~~-------l~is~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 2 ILKLLA-EGELCVCELAEI-------LGLSQSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred HHHHhh-cCCccHHHHHHH-------HCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence 344555 566676655433 346778999999999999999987643
No 107
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=63.85 E-value=12 Score=41.53 Aligned_cols=51 Identities=16% Similarity=0.182 Sum_probs=46.8
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|..|..||......+.+|..+|++.+|++...+.+.+.+|.+.|++...
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~ 53 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVE 53 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEE
Confidence 467899999999998889999999999999999999999999999988654
No 108
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=63.80 E-value=12 Score=30.82 Aligned_cols=56 Identities=21% Similarity=0.421 Sum_probs=43.7
Q ss_pred HhhH-HHHHHHHHHHHhcCCCChhhhhhhhhhhhhhccc-CCcccHHHHHHHHHhhhh
Q psy16234 11 NKTW-GSLQETIQGVITLGNVRRATWNDRFSDIYSLCVA-YPEPLADRLYQETKLFLD 66 (609)
Q Consensus 11 e~~W-~~l~~~i~~i~~~~~~~~~~~~~~y~~vy~~c~~-~~~~~~~~Ly~~~~~~l~ 66 (609)
+.+| +.++.....++...+.++..+.+++..|--.+.+ .|..+..+|...++.||+
T Consensus 29 e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L~ 86 (86)
T PF10163_consen 29 ECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFLD 86 (86)
T ss_dssp HTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHH
T ss_pred HCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhC
Confidence 5688 5677777777776667777899999999888774 588899999999999874
No 109
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=63.54 E-value=55 Score=29.15 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=40.9
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHhcCccccC
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVL----SLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t----~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+|..+..|+..+=+.+..|..+|.+.+ +++...+...|..|.+.|+|...
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 466778888777666789999977765 78899999999999999998643
No 110
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=63.39 E-value=18 Score=32.61 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=37.6
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.|..+.+.++..++.+|++.++++...+.+.|..|.+.|++...
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 34455566778899999999999999999999999999998643
No 111
>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=62.23 E-value=18 Score=27.68 Aligned_cols=38 Identities=11% Similarity=0.188 Sum_probs=32.5
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 457 KNDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 457 ~~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.++.+ |..+|++..|++...+.++|..|...|++...+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence 45788 999999999999999999999999999997654
No 112
>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=61.87 E-value=16 Score=32.26 Aligned_cols=38 Identities=13% Similarity=0.100 Sum_probs=34.1
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 456 EKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 456 n~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
++.-++|.++||..++-+.+.++.+|..|.+.|++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34568999999999999999999999999999999654
No 113
>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=61.79 E-value=12 Score=26.59 Aligned_cols=45 Identities=20% Similarity=0.375 Sum_probs=34.7
Q ss_pred hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccc
Q psy16234 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE 596 (609)
Q Consensus 545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~ 596 (609)
.+-.|+..+.....++..+|-.. ...+.+.+.+.|..|.++|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~-------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEK-------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHH-------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHH-------hCCCHHHHHHHHHHHHHCcCcC
Confidence 35567788888888988877644 3478899999999999999985
No 114
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=61.49 E-value=11 Score=38.10 Aligned_cols=49 Identities=12% Similarity=0.161 Sum_probs=43.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
--|..|+.+.+.+..+++.||++.+|++...++|-|..|-..|++.+..
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 3477889899999899999999999999999999999999999887653
No 115
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=61.29 E-value=13 Score=37.27 Aligned_cols=44 Identities=25% Similarity=0.344 Sum_probs=38.0
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
-+|++.-+ ++.|++||...++++...+..+|..|.+.|++.+++
T Consensus 17 ~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~~ 60 (260)
T COG4742 17 DLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQEG 60 (260)
T ss_pred HHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEecC
Confidence 35555555 678999999999999999999999999999998774
No 116
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=61.24 E-value=12 Score=37.68 Aligned_cols=47 Identities=19% Similarity=0.264 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-|..|+-+.+++..+++.||++.++++...++|-|..|.+.|+|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35668888889999999999999999999999999999999998765
No 117
>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=60.21 E-value=18 Score=30.17 Aligned_cols=45 Identities=16% Similarity=0.279 Sum_probs=37.0
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
...++.-++....++++++|++.++++.+++...+..++..|.|.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~ 91 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIK 91 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSE
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEE
Confidence 334455555577899999999999999999999999999998875
No 118
>PRK06474 hypothetical protein; Provisional
Probab=59.94 E-value=20 Score=33.90 Aligned_cols=53 Identities=23% Similarity=0.408 Sum_probs=42.9
Q ss_pred EEecHHHHHHHHhhcCCCC-CCHHHHHHHh-CCCHHHHHHHHHHHHhcCccccCC
Q psy16234 442 VTMQTFQMAILLLFEKNDA-MTCGDIQTVL-SLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~~~-lt~~ei~~~t-~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+-.++.-..||..+-.++. +|..+|++.+ +++...+-++|..|.+.|||....
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3445667778866655444 9999999999 799999999999999999997643
No 119
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=59.91 E-value=27 Score=30.73 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=37.4
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHhcCccccCC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLS-LSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~-i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+.||....+ ...-++||...++ |+...|.+.|..|...|++.+..
T Consensus 26 ~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~ 71 (120)
T COG1733 26 LLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVV 71 (120)
T ss_pred HHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeee
Confidence 345544444 7789999999998 99999999999999999998764
No 120
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.48 E-value=21 Score=35.47 Aligned_cols=46 Identities=24% Similarity=0.311 Sum_probs=40.9
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|..|+..++++..++.+||++.+|++...+++-|..|...|.|...
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 5568888888899999999999999999999999999988877654
No 121
>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=59.05 E-value=13 Score=28.93 Aligned_cols=39 Identities=15% Similarity=0.209 Sum_probs=33.6
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~ 487 (609)
..|-.+.++...+|+.+|++.|+++++++..+|--|.+-
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE 49 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARE 49 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCT
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhcc
Confidence 346677888899999999999999999999999999873
No 122
>PRK11050 manganese transport regulator MntR; Provisional
Probab=58.37 E-value=21 Score=32.74 Aligned_cols=44 Identities=20% Similarity=0.188 Sum_probs=38.2
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.|+.++...+.++..+|++.++++...+.+.|..|.+.|++...
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45556777788999999999999999999999999999988654
No 123
>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=58.28 E-value=40 Score=26.70 Aligned_cols=43 Identities=12% Similarity=0.217 Sum_probs=38.6
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~ 487 (609)
.+=|+.++-++...+.-|+++|+++||-....++-.|..+++.
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kK 51 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKK 51 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 4568999999998889999999999999999999999999754
No 124
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=58.14 E-value=14 Score=34.29 Aligned_cols=57 Identities=12% Similarity=0.239 Sum_probs=41.7
Q ss_pred HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC-CCCCCCCEEEEecCCC
Q psy16234 452 LLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK-EELTEDTEIRLNLGYN 510 (609)
Q Consensus 452 LllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~-~~~~~~~~f~lN~~F~ 510 (609)
++.+ ..+++|++||+++||++...+-..+.-|...+|+.+.- ++. -.+.|..-.+|.
T Consensus 34 ilyl-s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~-Rk~~F~a~~df~ 91 (177)
T COG1510 34 ILYL-SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGD-RKDYFEAEKDFS 91 (177)
T ss_pred hhee-cCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCc-chhhhcccchHH
Confidence 3344 44789999999999999999999999999999887642 111 124566666654
No 125
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=57.96 E-value=16 Score=25.98 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=34.8
Q ss_pred hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
.|.+.+.....++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~-------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQGKVSVEELAEL-------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 35555666666777766644 45788999999999999999998764
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=57.88 E-value=11 Score=29.23 Aligned_cols=54 Identities=19% Similarity=0.277 Sum_probs=33.5
Q ss_pred hhhhhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 546 QAAIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 546 ~A~IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
=|.||..||.+ +.++.++|..++ + +.++ ++.++.|-+-+=|+-+++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l----~-~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYL----S-LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHH----T-SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHH----c-CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 46899999998 668888777554 3 3333 345566668888999875 37999976
No 127
>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=57.48 E-value=34 Score=26.45 Aligned_cols=41 Identities=22% Similarity=0.377 Sum_probs=33.0
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
|+-.+.+. ..|..+|++.+|++...+.+.+..|-..|+...
T Consensus 5 il~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 5 LLALLADN-PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred HHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 34344444 478999999999999999999999998888543
No 128
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=57.04 E-value=26 Score=30.87 Aligned_cols=49 Identities=16% Similarity=0.194 Sum_probs=42.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.+.+-|+-+--++..+|+.++...||++-..+.+++.-|+..|-|...+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeCC
Confidence 3566778788889999999999999999999999999999998777654
No 129
>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=56.66 E-value=24 Score=30.34 Aligned_cols=57 Identities=25% Similarity=0.267 Sum_probs=41.7
Q ss_pred HHHHhhcC-CCCCCHHHHHHHh-----CCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 450 AILLLFEK-NDAMTCGDIQTVL-----SLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 450 ~iLllFn~-~~~lt~~ei~~~t-----~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
.||..+.+ ...+|.+||.+.+ +++...+-++|..|++.|++.+...+ +....|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~-~~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG-DGKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC-CCceEEEeCC
Confidence 45555554 4579999999998 68999999999999999999764200 1124566654
No 130
>KOG2167|consensus
Probab=56.64 E-value=2.2e+02 Score=31.95 Aligned_cols=36 Identities=6% Similarity=0.135 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q psy16234 76 TQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEE 113 (609)
Q Consensus 76 ~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E 113 (609)
.+|+..++++|..+++ ...+.+.+|+.+....+-.+
T Consensus 289 e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 289 EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 7899999999999997 56677999999888755444
No 131
>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=56.52 E-value=17 Score=28.91 Aligned_cols=49 Identities=16% Similarity=0.260 Sum_probs=42.0
Q ss_pred HHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 446 TFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 446 ~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
..|.++|...-. ...++-.+|...+|++...+-..+..|.+.|++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEE
Confidence 467778877764 4678999999999999999999999999999998763
No 132
>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=55.95 E-value=36 Score=24.41 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=25.1
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
..|-+.| ...+|++||++.+|++...+.+....-
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 3444556 457899999999999999888776543
No 133
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=55.84 E-value=24 Score=29.48 Aligned_cols=53 Identities=17% Similarity=0.272 Sum_probs=45.3
Q ss_pred EEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 442 VTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+..+.....||..+...+.=...-|+..+++|.+++...|..|...|+|....
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 34566777899888887777788899999999999999999999999998763
No 134
>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=55.31 E-value=20 Score=31.48 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=39.2
Q ss_pred HHHHHHHHhhcC--------CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 446 TFQMAILLLFEK--------NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 446 ~~Q~~iLllFn~--------~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+.-..|+..|. .-+++.++|+..++-+.+.++.+|..|.+.|++...
T Consensus 29 I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~ 84 (119)
T TIGR01714 29 IWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKK 84 (119)
T ss_pred HHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 455555555553 457999999999999999999999999999998754
No 135
>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=55.24 E-value=20 Score=29.22 Aligned_cols=35 Identities=11% Similarity=0.275 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
...++++++|++.++++.+++...+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999988774
No 136
>smart00753 PAM PCI/PINT associated module.
Probab=55.24 E-value=20 Score=29.22 Aligned_cols=35 Identities=11% Similarity=0.275 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
...++++++|++.++++.+++...+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999988774
No 137
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=54.87 E-value=1.6e+02 Score=28.17 Aligned_cols=34 Identities=21% Similarity=0.447 Sum_probs=30.0
Q ss_pred HhhcCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHh
Q psy16234 453 LLFEKNDA-MTCGDIQTVLSLSQDQIGRHIASLVE 486 (609)
Q Consensus 453 llFn~~~~-lt~~ei~~~t~i~~~~l~~~L~~L~~ 486 (609)
++|-..++ +|+++|++.++++...+...|..|..
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~ 46 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQE 46 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56777776 99999999999999999999999964
No 138
>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=54.77 E-value=48 Score=26.73 Aligned_cols=47 Identities=23% Similarity=0.285 Sum_probs=38.8
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+++.|=+.-..+..+.-.+|++.++++...++..+..|-..|+|...
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 34444444556788999999999999999999999999999999754
No 139
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=54.27 E-value=79 Score=30.18 Aligned_cols=109 Identities=14% Similarity=0.197 Sum_probs=62.5
Q ss_pred chHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEE---------eCccEEEEecHHHHHHHHhhcCCCCCCHHHHH
Q psy16234 397 PQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSY---------LKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQ 467 (609)
Q Consensus 397 P~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~---------~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~ 467 (609)
|.++..+++....-|... +|-+.-...=|.-.+..+- ......-..|...+-+|-..--+.++|-.+|.
T Consensus 34 ~~~v~~~l~~L~~~y~~~--~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGD--DRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhC--CCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 357889999999999765 3333332211212121110 00001112333344444333334689999999
Q ss_pred HHhCCCHHHHHHHHHHHHhcCccccCC--CCCCCCCEEEEecCCC
Q psy16234 468 TVLSLSQDQIGRHIASLVECKLLTSNK--EELTEDTEIRLNLGYN 510 (609)
Q Consensus 468 ~~t~i~~~~l~~~L~~L~~~~iL~~~~--~~~~~~~~f~lN~~F~ 510 (609)
+.+|++. ..++..|+..|++...+ ........|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999996 67888999999987543 1112345566777763
No 140
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=53.52 E-value=14 Score=26.52 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=22.5
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcC
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECK 488 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~ 488 (609)
++.++.+ .+|..+|++.+|++...+.+-+..+...|
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4555555 78999999999999999999888776555
No 141
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=53.09 E-value=34 Score=27.67 Aligned_cols=38 Identities=24% Similarity=0.342 Sum_probs=33.0
Q ss_pred HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234 452 LLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKL 489 (609)
Q Consensus 452 LllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~i 489 (609)
++..++.+.+|-++|++.+|++...+-++++.|-+.|+
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGV 48 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCC
Confidence 34455667899999999999999999999999998876
No 142
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=52.35 E-value=29 Score=33.89 Aligned_cols=46 Identities=13% Similarity=0.185 Sum_probs=38.7
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.+.+-..++...+|..+|++.++++...+.+.|..|.+.|++.+.
T Consensus 9 ~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 9 KLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3344455556667999999999999999999999999999999765
No 143
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=52.06 E-value=37 Score=24.46 Aligned_cols=39 Identities=18% Similarity=0.395 Sum_probs=29.2
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHh
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVE 486 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~ 486 (609)
..|..++.++- +.+|..+|++.+|++...+...+..+.+
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34455554443 4579999999999999999998887653
No 144
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=51.34 E-value=48 Score=29.46 Aligned_cols=63 Identities=11% Similarity=0.318 Sum_probs=47.6
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC--C---CCCCCCEEEEecCCC
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK--E---ELTEDTEIRLNLGYN 510 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~--~---~~~~~~~f~lN~~F~ 510 (609)
-..+|-+..+.+..|+.|+++.+|-+.+.+.+.|..|.+.||+..+. + ..-.-+.+.|+-.|.
T Consensus 66 nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 66 NLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEecCCcccCceeeccccEEeeecC
Confidence 33566777788999999999999999999999999999999987653 1 111224455666664
No 145
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=51.10 E-value=39 Score=24.25 Aligned_cols=39 Identities=18% Similarity=0.398 Sum_probs=30.1
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
|.-+..++.++. ..+|..+|++.+|++...+.+.+..+.
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 445555665553 347999999999999999999888764
No 146
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.98 E-value=22 Score=30.18 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=39.2
Q ss_pred hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc
Q psy16234 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 598 (609)
Q Consensus 545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~ 598 (609)
++-.|++.+.....++..+|-.. +..+.+.+.++|..|.++|+|.|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~-------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK-------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeece
Confidence 46678889998888898877644 457899999999999999999953
No 147
>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=50.38 E-value=25 Score=24.84 Aligned_cols=31 Identities=19% Similarity=0.352 Sum_probs=22.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIA 482 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~ 482 (609)
.|+-++.++ +|+.+|++.+|++...+.+.|.
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 8999999999999999998774
No 148
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=50.35 E-value=27 Score=34.28 Aligned_cols=36 Identities=14% Similarity=0.368 Sum_probs=32.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
....+|.++|++.++++...++.++..|+++|++..
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~ 210 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFT 210 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEE
Confidence 357899999999999999999999999999999954
No 149
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=50.33 E-value=41 Score=36.43 Aligned_cols=39 Identities=18% Similarity=0.359 Sum_probs=35.7
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 455 FEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 455 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.....+|.++|++.++++.+.+.+.|..|.+.|++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEec
Confidence 566779999999999999999999999999999999754
No 150
>PHA02943 hypothetical protein; Provisional
Probab=48.92 E-value=35 Score=31.14 Aligned_cols=54 Identities=15% Similarity=0.145 Sum_probs=40.1
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
||-.+ ..+.-|..+|++++|++-..++-+|..|-+-|.+.+.. ++....+.+|.
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~--~G~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVE--IGRAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEe--ecceEEEEECh
Confidence 44444 56778899999999999999999999999988876542 22234455554
No 151
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=48.77 E-value=30 Score=31.92 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=39.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+|..+..+.......+|++.++++...+...++-|.+.|++...+
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 455566677889999999999999999999999999999998764
No 152
>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=48.64 E-value=27 Score=28.87 Aligned_cols=40 Identities=13% Similarity=0.215 Sum_probs=27.3
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
+..+..+... ++..|.+.||||...++.+|.+|-..+|-.
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT-EE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCCeEE
Confidence 3344555556 999999999999999999999999877643
No 153
>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=48.18 E-value=33 Score=24.98 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~ 483 (609)
+.+|++||++.+|++...+...+..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3589999999999999988887654
No 154
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=47.99 E-value=33 Score=31.19 Aligned_cols=52 Identities=17% Similarity=0.263 Sum_probs=43.5
Q ss_pred EEecHHHHHHHHhhcCC-CCCCHHHHHHHh-----CCCHHHHHHHHHHHHhcCccccC
Q psy16234 442 VTMQTFQMAILLLFEKN-DAMTCGDIQTVL-----SLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~~-~~lt~~ei~~~t-----~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.+|..+.+||-.+.+. +.+|.++|-+.+ +++...+-++|..|...|++..-
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~ 74 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL 74 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE
Confidence 46788899999777754 569999998876 48899999999999999999754
No 155
>KOG3054|consensus
Probab=47.85 E-value=24 Score=34.53 Aligned_cols=56 Identities=16% Similarity=0.301 Sum_probs=46.7
Q ss_pred hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
+--|-..|..|.+..++|-.+ |....++.-.+|..|+..|.|.-.-+|+..|+||.
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 344567788888888877644 77778888889999999999999999999999984
No 156
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=47.84 E-value=2.1e+02 Score=27.22 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=25.4
Q ss_pred HhhcCCCC-CCHHHHHHHhCCC-HHHHHHHHHHHH
Q psy16234 453 LLFEKNDA-MTCGDIQTVLSLS-QDQIGRHIASLV 485 (609)
Q Consensus 453 llFn~~~~-lt~~ei~~~t~i~-~~~l~~~L~~L~ 485 (609)
++|-..++ +|.++|++.++++ .+.+...+.-|.
T Consensus 9 lLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~ 43 (186)
T TIGR00281 9 LLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLE 43 (186)
T ss_pred HHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHH
Confidence 56777777 9999999999998 446666666654
No 157
>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=47.65 E-value=53 Score=27.05 Aligned_cols=46 Identities=17% Similarity=0.390 Sum_probs=36.4
Q ss_pred HHHHHhhcCCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhcCccccCC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVL--SLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t--~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+.||...-+++-+|..++++.+ .++...+.+.+..|++.|++.+++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSG 66 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLIEKSG 66 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccccC
Confidence 4456666677788999999976 889999999999999999998874
No 158
>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=47.22 E-value=48 Score=26.61 Aligned_cols=38 Identities=16% Similarity=0.308 Sum_probs=28.7
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
.-.+|-+.-....+|..+|+.++|.+.+++...|..+-
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 44577778889999999999999999999999998875
No 159
>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=46.64 E-value=2.4e+02 Score=26.11 Aligned_cols=58 Identities=22% Similarity=0.239 Sum_probs=43.7
Q ss_pred HHHHHhhcC-CCCCCHHHHHHHh--CCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecC
Q psy16234 449 MAILLLFEK-NDAMTCGDIQTVL--SLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLG 508 (609)
Q Consensus 449 ~~iLllFn~-~~~lt~~ei~~~t--~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~ 508 (609)
..|+-.+.. +.++|..+|...+ +++...+.++|..|+..|-|... .++..-.|..|.+
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K--~~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEK--EYGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeee--eecceEEEeeCcc
Confidence 456766664 5689999999988 59999999999999998866543 2444556666654
No 160
>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=45.18 E-value=21 Score=33.88 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
..+|+++|++.||+..+++..+|+.|
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 37999999999999999999998886
No 161
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=44.81 E-value=2.8e+02 Score=26.92 Aligned_cols=41 Identities=27% Similarity=0.375 Sum_probs=33.9
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
||.+..... .=+.+|+..+|++.+-+..||..|.++||+..
T Consensus 20 Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 20 ILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 444444444 66789999999999999999999999999975
No 162
>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=44.32 E-value=36 Score=27.61 Aligned_cols=33 Identities=12% Similarity=0.216 Sum_probs=29.5
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHI 481 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L 481 (609)
++.|+-...+ ...|+.+|++.+|++...+.+.|
T Consensus 8 ~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 6678888888 99999999999999999999866
No 163
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.21 E-value=32 Score=31.37 Aligned_cols=35 Identities=26% Similarity=0.412 Sum_probs=30.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
.+..+|-++|++.+|++...+++.|..|...|++.
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~ 46 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIK 46 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcch
Confidence 34579999999999999999999999999866654
No 164
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=43.03 E-value=23 Score=35.05 Aligned_cols=54 Identities=13% Similarity=0.314 Sum_probs=39.1
Q ss_pred hhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
|...|...++....|+-+ .+|.. |.++...+.++|+.|++.|+|.|..+ +++|+
T Consensus 21 L~~~I~~~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 21 LEQELRQHYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHHHhcccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 444454456766666643 22333 89999999999999999999999887 36654
No 165
>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=43.02 E-value=36 Score=32.15 Aligned_cols=32 Identities=28% Similarity=0.493 Sum_probs=29.4
Q ss_pred CHHHHHHHh-CCCHHHHHHHHHHHHhcCccccC
Q psy16234 462 TCGDIQTVL-SLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 462 t~~ei~~~t-~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|-..|++.+ |+++..+.++|..|+..|||...
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeec
Confidence 567899999 99999999999999999999865
No 166
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=42.73 E-value=41 Score=33.75 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=31.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.=|-++|.+..|+|...++++|..|.++|++..++
T Consensus 246 KSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q~g 280 (287)
T COG2996 246 KSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQDG 280 (287)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEEcC
Confidence 44789999999999999999999999999887753
No 167
>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=42.42 E-value=46 Score=28.45 Aligned_cols=39 Identities=21% Similarity=0.339 Sum_probs=29.1
Q ss_pred cccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 555 SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 555 ~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
....++-.+|... ...+.+.+-+.|+.|.++|||.|..+
T Consensus 40 ~~~~~t~~eL~~~-------l~~~~stvs~~i~~Le~kg~I~r~~~ 78 (109)
T TIGR01889 40 NEGKLTLKEIIKE-------ILIKQSALVKIIKKLSKKGYLSKERS 78 (109)
T ss_pred cCCcCcHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEeccCC
Confidence 3456776665533 45678999999999999999997443
No 168
>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=41.73 E-value=64 Score=31.65 Aligned_cols=83 Identities=17% Similarity=0.157 Sum_probs=56.1
Q ss_pred ccCchHHHHHHHHHHHHHhhcCCCcceeeecccceEEEEEEEeCccEEEE-ec-----HHHHHHHHhh--cCCCCCCHHH
Q psy16234 394 FSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNISQVELKLSYLKRPYFVT-MQ-----TFQMAILLLF--EKNDAMTCGD 465 (609)
Q Consensus 394 ~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~-~s-----~~Q~~iLllF--n~~~~lt~~e 465 (609)
..-|..+..+.+.|+. +|.+---.+|+++...+. ++ ..|..||-.- .....+|..+
T Consensus 132 lISp~Di~~A~~~l~~----------------lg~g~~l~~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~~ 195 (223)
T PF04157_consen 132 LISPEDILRACKLLEV----------------LGLGFRLRKFGSGVKVVQSVPYSELSKDQSRILELAEEENGGGVTASE 195 (223)
T ss_dssp T--HHHHHHHHHHHCC----------------CTSSEEEEEETTTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHHH
T ss_pred CcCHHHHHHHHHHHHH----------------cCCCeEEEEeCCCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHHH
Confidence 4557778777776654 343311123443433332 33 5677788777 6678899999
Q ss_pred HHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 466 IQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 466 i~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
+++.+|.+....+..|..+...|++..
T Consensus 196 l~~~~~ws~~~a~~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 196 LAEKLGWSVERAKEALEELEREGLLWR 222 (223)
T ss_dssp HHHHHTB-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHhCCCHHHHHHHHHHHHhCCCEee
Confidence 999999999999999999999998753
No 169
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=41.19 E-value=46 Score=32.29 Aligned_cols=51 Identities=18% Similarity=0.242 Sum_probs=40.2
Q ss_pred EEecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 442 VTMQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 442 l~~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.-+|+|... ..|. ....+|.+|+++++|++....++-|.-|++.|+|..+
T Consensus 155 i~~~Tl~~i~-~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 155 LDELTLQKVR-EALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred cCHHHHHHHH-HHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence 4455666533 3343 3468999999999999999999999999999998654
No 170
>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=40.46 E-value=38 Score=34.86 Aligned_cols=35 Identities=3% Similarity=0.069 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
...|.++|++.+|+++..+.+.|..|+..|+|.+.
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~ 56 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLE 56 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEec
Confidence 57899999999999999999999999999999875
No 171
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.90 E-value=46 Score=29.97 Aligned_cols=46 Identities=17% Similarity=0.326 Sum_probs=32.2
Q ss_pred hhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 548 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 548 ~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
.|...+-....++..+|... +..+.+.+-+.|+.|.++|||+|.++
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~-------l~i~~~tvsr~l~~Le~~GlI~R~~~ 89 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKV-------LSVDLGALTRMLDRLVCKGWVERLPN 89 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEeccC
Confidence 33333334555666655533 45788999999999999999999653
No 172
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=39.81 E-value=40 Score=33.73 Aligned_cols=51 Identities=12% Similarity=0.133 Sum_probs=43.1
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-.|-++|-+-+..=..++.|..||++.+|+|..-+-..|.+|.+.|++...
T Consensus 13 Glt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~ 63 (247)
T COG1378 13 GLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVI 63 (247)
T ss_pred CCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEee
Confidence 346677777666666678999999999999999999999999999988654
No 173
>PRK09954 putative kinase; Provisional
Probab=39.75 E-value=60 Score=34.26 Aligned_cols=43 Identities=21% Similarity=0.417 Sum_probs=38.4
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
.-||..+.++..+|..+|++.+|++...+.+.|..|.+.|++.
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 3477788888899999999999999999999999999988774
No 174
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=39.36 E-value=43 Score=33.51 Aligned_cols=41 Identities=17% Similarity=0.206 Sum_probs=37.3
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhc
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~ 487 (609)
=|..|+.+.+++..+++.+|++.+|+++..++|-|..|-..
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~ 48 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAP 48 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcC
Confidence 46789999999999999999999999999999999998743
No 175
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=39.28 E-value=44 Score=32.48 Aligned_cols=44 Identities=18% Similarity=0.255 Sum_probs=36.9
Q ss_pred HHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKN-DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~-~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-||.++.+. ...|.+||++.++++...+++++..|...|++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEE
Confidence 466666553 36899999999999999999999999999988654
No 176
>KOG2905|consensus
Probab=39.05 E-value=48 Score=32.54 Aligned_cols=56 Identities=14% Similarity=0.200 Sum_probs=42.8
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCC
Q psy16234 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYN 510 (609)
Q Consensus 449 ~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~ 510 (609)
..++-+|.++..||+.+|.+.|+=|...|+.+|..++ ++.+.+ +...+|++-.+|.
T Consensus 189 d~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic---v~NkKg---~~k~tyeLKPEYK 244 (254)
T KOG2905|consen 189 DMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC---VLNKKG---PYKNTYELKPEYK 244 (254)
T ss_pred HHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH---HHhccC---cccCceecCHHHh
Confidence 3567889999999999999999999999999999876 444332 1235677766663
No 177
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=38.87 E-value=40 Score=27.78 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=29.2
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 463 CGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 463 ~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
..+|++.+|++...+.+.|..|.+.|++...+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 46899999999999999999999999998764
No 178
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=38.53 E-value=35 Score=31.71 Aligned_cols=57 Identities=16% Similarity=0.305 Sum_probs=42.2
Q ss_pred cCCCcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 414 QFNGRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 414 k~~~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
+++.++|+|.++|. .-|.++-. +.-..|+++|++.+|.++.+++++|..=.++|=|.
T Consensus 36 ~~~~~~lTWvdSLa-------------------vAAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~lv 92 (182)
T COG1318 36 KDPYERLTWVDSLA-------------------VAAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQLV 92 (182)
T ss_pred hCcccccchhhHHH-------------------HHHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcchhhhhHH
Confidence 45789999987653 12223323 44568999999999999999999999887766443
No 179
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=38.38 E-value=65 Score=24.54 Aligned_cols=51 Identities=10% Similarity=0.236 Sum_probs=34.9
Q ss_pred hhhhhccccCCChHHHHHHHHHh--hcC-CCCChHHHHHHHHHhhhhccccccC
Q psy16234 549 IVRIMKSRKQIRHNALIQEVLSQ--SKS-FAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 549 IVRiMK~~k~l~~~~L~~~v~~~--l~~-F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
|+..+..-..|+.+.+.+-..-. -.+ |+++.++++..++.+++.|-|+-++
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~ 55 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSG 55 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--T
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecC
Confidence 56666667778887777554433 123 9999999999999999999999884
No 180
>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=38.10 E-value=57 Score=26.07 Aligned_cols=57 Identities=19% Similarity=0.251 Sum_probs=33.9
Q ss_pred hhhhhhhhhhcccc--CCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccc---cccCCCCCceeecC
Q psy16234 544 YLQAAIVRIMKSRK--QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV---ERTANSTDEYSYVA 609 (609)
Q Consensus 544 ~i~A~IVRiMK~~k--~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl---~r~~~~~~~y~Yia 609 (609)
..=|.||..||+|. .++.+|+..++.. +... ..++ +.|-+-.-+ +.++. .++|.|.|
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls~----~d~~-~~~~---~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLSL----LDIG-PKLK---EWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHhc----cCcc-HHHH---HHHHhhhhccCceeccC-CCEEEecc
Confidence 44578999999986 6888887766542 2222 2223 333333333 44444 37999875
No 181
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=37.82 E-value=36 Score=29.14 Aligned_cols=54 Identities=19% Similarity=0.417 Sum_probs=35.0
Q ss_pred hhhhhhhhhhhccccCCChHHHHHHHHHhhcC--CCCChHHHHHHHHHhhhhccccc
Q psy16234 543 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS--FAPSISMIKKCIESLIDKNYVER 597 (609)
Q Consensus 543 ~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~--F~~~~~~ik~~Ie~LIekeyl~r 597 (609)
..+.-.|+.+.-+++.-.. ++..+..+..++ |.|+.++|=+++-.|++.||+.|
T Consensus 17 aFlKlYiitm~e~~r~Yg~-q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 17 AFLKLYIITMVEQERGYGL-QLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHHHTT-EBCT-CHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhhhhcccchHH-HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 3566667777666663322 344455566666 99999999999999999999965
No 182
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=37.41 E-value=34 Score=29.74 Aligned_cols=63 Identities=21% Similarity=0.284 Sum_probs=44.7
Q ss_pred ecHHHHHHHHhhcC-CCCCCHHHHHHHh-----CCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEec
Q psy16234 444 MQTFQMAILLLFEK-NDAMTCGDIQTVL-----SLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNL 507 (609)
Q Consensus 444 ~s~~Q~~iLllFn~-~~~lt~~ei~~~t-----~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~ 507 (609)
+|....+||..+.+ ...+|.++|.+.+ +++...+-++|..|.+.|++.+.... +....|.++.
T Consensus 6 ~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~~~~~Y~~~~ 74 (120)
T PF01475_consen 6 LTPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-TSEEEEEESS
T ss_pred CCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-CCcceEeecC
Confidence 35556677777765 3589999999987 67889999999999999999765311 2235566665
No 183
>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=37.39 E-value=59 Score=24.12 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=24.8
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 455 FEKNDAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 455 Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
|+.-...|++||++.+|++...+..+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555567999999999999999888887653
No 184
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.86 E-value=70 Score=25.90 Aligned_cols=45 Identities=18% Similarity=0.327 Sum_probs=34.3
Q ss_pred hhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 549 IVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 549 IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|...+... ..++..+|..++ ..+...+.+.+..|.+.|||.+++.
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 44445544 678888777553 4678999999999999999999854
No 185
>PRK09462 fur ferric uptake regulator; Provisional
Probab=36.75 E-value=74 Score=28.88 Aligned_cols=59 Identities=8% Similarity=0.231 Sum_probs=43.6
Q ss_pred hhhhhhhcc--ccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234 547 AAIVRIMKS--RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 547 A~IVRiMK~--~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y 607 (609)
-+|.+++.. .+.++.++|...+.+.. ..++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~--~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y 80 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG--EEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEE
Confidence 355666664 36899999998887654 457889999999999999999886432233444
No 186
>PRK14999 histidine utilization repressor; Provisional
Probab=36.51 E-value=51 Score=32.59 Aligned_cols=47 Identities=15% Similarity=0.367 Sum_probs=36.1
Q ss_pred hhccccCC-ChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 552 IMKSRKQI-RHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 552 iMK~~k~l-~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
..+....| +-.+|.++ |.++...+.++|+.|.+.|+|.|..+ +++|+
T Consensus 29 ~~~~G~~LPsE~eLa~~-------~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVAQ-------YGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 45556666 44455433 88999999999999999999999887 46664
No 187
>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=36.42 E-value=52 Score=25.56 Aligned_cols=49 Identities=16% Similarity=0.342 Sum_probs=38.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHh--------CCCHHHHHHHHHHHHhcCccccCC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVL--------SLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t--------~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.+||+|.-..-...+++.++|...+ ..+...+++.|..|+..+.|..++
T Consensus 8 ~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 8 QIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 5789999888888888888887654 456789999999999999998764
No 188
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=35.91 E-value=25 Score=34.54 Aligned_cols=31 Identities=13% Similarity=0.389 Sum_probs=27.8
Q ss_pred CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
|.++...+.++|+.|++.|+|.|..+ +++|+
T Consensus 34 ~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 34 YGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 89999999999999999999999887 46664
No 189
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.86 E-value=62 Score=26.41 Aligned_cols=49 Identities=18% Similarity=0.306 Sum_probs=36.8
Q ss_pred hhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 545 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 545 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
.+..|...+.....++..+|... +.++.+.+.+.|..|.++|+|.+..+
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~-------~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKR-------LGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH-------HCCCchhHHHHHHHHHHCCCeEecCC
Confidence 35567777777777777766543 34677889999999999999987643
No 190
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=35.84 E-value=50 Score=22.67 Aligned_cols=28 Identities=18% Similarity=0.183 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 458 NDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 458 ~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
...+|+++|++..|++...+.+......
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 4579999999999999999988877654
No 191
>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=35.20 E-value=82 Score=23.03 Aligned_cols=41 Identities=20% Similarity=0.201 Sum_probs=35.4
Q ss_pred HhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 453 LLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 453 llFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-+|++++.+|++++.+.+|++-+.....|.-|=+.|+....
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEe
Confidence 46778899999999999999999999999999888887665
No 192
>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=35.17 E-value=1.1e+02 Score=30.96 Aligned_cols=34 Identities=15% Similarity=0.168 Sum_probs=30.8
Q ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHHhcCccccCC
Q psy16234 461 MTCGDIQTVLS--LSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 461 lt~~ei~~~t~--i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.+.++|++.++ |+.++++..|..|++.|+|.+++
T Consensus 138 ~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~ 173 (271)
T TIGR02147 138 DDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE 173 (271)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC
Confidence 36789999998 89999999999999999999874
No 193
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=35.17 E-value=73 Score=30.21 Aligned_cols=44 Identities=9% Similarity=0.183 Sum_probs=37.9
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
++.-.+.++..|..+|+..+|++..++.++|-.|.+.|.+...+
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~ 61 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSD 61 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCC
Confidence 45556677889999999999999999999999999998876553
No 194
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=34.90 E-value=65 Score=27.95 Aligned_cols=59 Identities=12% Similarity=0.276 Sum_probs=42.9
Q ss_pred hhhhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234 547 AAIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 547 A~IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y 607 (609)
-+|..+|+.. +.++.++|...+.+.- ..++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~--~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 11 LAILELLKESPEHLTAEEIYDKLRKKG--PRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHHSSSEEHHHHHHHHHHTT--TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHhhhcc--CCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 3455566664 6899999998877543 467889999999999999999987655444444
No 195
>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=34.83 E-value=57 Score=23.65 Aligned_cols=44 Identities=16% Similarity=0.376 Sum_probs=30.7
Q ss_pred hhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234 549 IVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 549 IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
|.+.+... ..++..+|.. .+ ..+...+-+.+..|.+.||++||+
T Consensus 8 iL~~l~~~~~~~t~~eia~----~~---gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIAR----AL---GLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHH----HH---TS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHcCCCCCCHHHHHH----HH---CcCHHHHHHHHHHHHHCcCeecCc
Confidence 44444444 3367776653 33 356788999999999999999986
No 196
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=34.71 E-value=53 Score=33.03 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=40.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 446 TFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 446 ~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.-|..+-+.-+.++.++-+||.+++|+|+..+-|+|..|-+.|++.+.
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~ 243 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEE
Confidence 345555566677788999999999999999999999999999998654
No 197
>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=34.57 E-value=83 Score=27.14 Aligned_cols=62 Identities=21% Similarity=0.235 Sum_probs=45.1
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y 607 (609)
.+|+.|.+-- ...=.+...++.+|+.....+ ++...+--||+.||+.|.|+-.++..+.-+|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSDQG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcCcC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 4667777611 223345678899999887534 7789999999999999999988765555444
No 198
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=34.49 E-value=89 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=26.0
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 448 Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
...|+.+.-+. .|+.+|+..+|++...+.+.+...
T Consensus 17 ~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLRES--RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34444444332 699999999999999999988753
No 199
>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=34.45 E-value=82 Score=23.31 Aligned_cols=40 Identities=18% Similarity=0.362 Sum_probs=31.8
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHh
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVE 486 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~ 486 (609)
|.-+..||.++.. ..|..+|++.+|++...+..++..+.+
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 4566777777766 468899999999999999999998874
No 200
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=34.40 E-value=27 Score=34.50 Aligned_cols=31 Identities=19% Similarity=0.290 Sum_probs=27.8
Q ss_pred CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
|.++...+.++|+.|++.|+|.|..+ +++|+
T Consensus 43 ~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 43 YNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 88999999999999999999999887 46654
No 201
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.37 E-value=76 Score=26.70 Aligned_cols=39 Identities=26% Similarity=0.351 Sum_probs=32.2
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKL 489 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~i 489 (609)
.+++++.++.+ |..+++..+|++...+.+.+..+-..|+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYREGGI 41 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHcccH
Confidence 45666666544 7999999999999999999999988774
No 202
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=34.23 E-value=24 Score=29.40 Aligned_cols=29 Identities=34% Similarity=0.517 Sum_probs=21.9
Q ss_pred HhhcC-CCCChHHHHHHHHHhhhhccccccC
Q psy16234 570 SQSKS-FAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 570 ~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
+++++ | |...-+.+.||.||.-|||.|++
T Consensus 32 R~iKk~f-~~qk~~D~fie~li~~GYI~re~ 61 (93)
T PF08820_consen 32 RFIKKDF-PKQKRLDIFIEALIKLGYIEREE 61 (93)
T ss_pred HHHHHhh-ccccchhHHHHHHHHcCCeEecC
Confidence 33444 5 45667788999999999999943
No 203
>KOG2747|consensus
Probab=34.22 E-value=52 Score=34.91 Aligned_cols=65 Identities=18% Similarity=0.309 Sum_probs=40.1
Q ss_pred eeeecccceEEEEEEEeCccEE-E---E-ecHHHHHHHHhhcC-C-CCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 420 LSWLHNISQVELKLSYLKRPYF-V---T-MQTFQMAILLLFEK-N-DAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 420 L~W~~~l~~~~l~~~~~~~~~~-l---~-~s~~Q~~iLllFn~-~-~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
+.+.+.||..|=++--+.+... | . -+-+-..||-++-+ + ..+|+++|++.|||..+++..+|++|
T Consensus 282 IdFSYeLSr~E~~~GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L 353 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSL 353 (396)
T ss_pred hhhhhhhhcccCcCCCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhh
Confidence 4666778877765533333211 0 0 01233334433332 2 23999999999999999999999987
No 204
>PRK12423 LexA repressor; Provisional
Probab=34.06 E-value=67 Score=30.92 Aligned_cols=51 Identities=18% Similarity=0.310 Sum_probs=40.5
Q ss_pred ecHHHHHHHHhhcCC---C--CCCHHHHHHHhCC-CHHHHHHHHHHHHhcCccccCC
Q psy16234 444 MQTFQMAILLLFEKN---D--AMTCGDIQTVLSL-SQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~---~--~lt~~ei~~~t~i-~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
+|.-|-.||-...+. . .-|..||++.+|+ +...+..+|..|.+.|+|...+
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecC
Confidence 356677777655542 2 3499999999995 8999999999999999998765
No 205
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=33.57 E-value=80 Score=29.52 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=31.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-++|++.+|++.+.+-+.|..|.+.|++...
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 5799999999999999999999999999999764
No 206
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=33.27 E-value=43 Score=25.14 Aligned_cols=33 Identities=12% Similarity=0.237 Sum_probs=27.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
.++...|++..|+.-..+..+|..|-.+|++..
T Consensus 4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIes 36 (61)
T PF08222_consen 4 RLVASKIADRVGITRSVIVNALRKLESAGVIES 36 (61)
T ss_dssp EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred eehHHHHHHHhCccHHHHHHHHHHHHhcCceee
Confidence 467889999999999999999999999999863
No 207
>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=33.21 E-value=1.1e+02 Score=21.17 Aligned_cols=40 Identities=13% Similarity=0.321 Sum_probs=28.7
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASL 484 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L 484 (609)
++..+..++.++- .+.+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444555554443 145899999999999999998877664
No 208
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=33.04 E-value=1e+02 Score=31.96 Aligned_cols=42 Identities=26% Similarity=0.313 Sum_probs=36.1
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
.||..+.+....+.++|++.+|++...+.++|..|...|+..
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i 49 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDI 49 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 356666677789999999999999999999999999999833
No 209
>PRK09462 fur ferric uptake regulator; Provisional
Probab=32.92 E-value=80 Score=28.64 Aligned_cols=52 Identities=13% Similarity=0.281 Sum_probs=41.8
Q ss_pred EEecHHHHHHHHhhcC--CCCCCHHHHHHHh-----CCCHHHHHHHHHHHHhcCccccC
Q psy16234 442 VTMQTFQMAILLLFEK--NDAMTCGDIQTVL-----SLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 442 l~~s~~Q~~iLllFn~--~~~lt~~ei~~~t-----~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+.+|.-..+||-.+.+ .+.+|.++|.+.+ +++...+-|+|..|...|++.+-
T Consensus 13 lr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 13 LKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 3466677788877754 3689999998877 47889999999999999999754
No 210
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=32.80 E-value=33 Score=28.19 Aligned_cols=57 Identities=21% Similarity=0.280 Sum_probs=41.1
Q ss_pred hhhhhhhhccc---cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 546 QAAIVRIMKSR---KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 546 ~A~IVRiMK~~---k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
++..=|++|.= |-++...|. +. +.++.+.-++.|..|.++|.|.....++..-+|.|
T Consensus 26 k~t~dkl~kEV~~~K~ITps~ls----er---lkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 26 EELLKRVAKEVKKEKIVTPYTLA----SK---YGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHHHHHHHhccCcEEcHHHHH----HH---hcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 34444555553 444444333 22 67889999999999999999998888888888876
No 211
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=32.76 E-value=78 Score=30.16 Aligned_cols=34 Identities=21% Similarity=0.407 Sum_probs=31.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-.+|++.+|++.+.+-+.|..|.+.|++...
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH 201 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence 5888999999999999999999999999999765
No 212
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.42 E-value=65 Score=29.12 Aligned_cols=50 Identities=18% Similarity=0.269 Sum_probs=41.8
Q ss_pred hhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234 543 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 543 ~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
..++..|.+++.....++..+|-..+ ..+.+.+.++|+.|.+.|.|++-.
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 35678899999999889998777553 377899999999999999998854
No 213
>PF14493 HTH_40: Helix-turn-helix domain
Probab=32.38 E-value=97 Score=25.49 Aligned_cols=37 Identities=27% Similarity=0.424 Sum_probs=32.0
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKL 489 (609)
Q Consensus 451 iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~i 489 (609)
.+-+|++ .+|+++|++.-|++...+..||..++..|-
T Consensus 6 T~~l~~~--G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 6 TYELFQK--GLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred HHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 4567775 589999999999999999999999997654
No 214
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=32.38 E-value=46 Score=33.45 Aligned_cols=46 Identities=28% Similarity=0.283 Sum_probs=40.1
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 598 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~ 598 (609)
+..|+..++.++.++..+|.+. |.++...|.+-|+.|-++|.|.|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~-------l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQY-------FDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEE
Confidence 4568888999999999988744 789999999999999999999884
No 215
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.35 E-value=36 Score=24.90 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=23.7
Q ss_pred CCCChHHHHHHHHHhhhhccccccCC
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|..+.+.+.+.+..|.+.|+|.+.++
T Consensus 30 ~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 30 LGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 67899999999999999999998765
No 216
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=32.34 E-value=81 Score=29.81 Aligned_cols=34 Identities=12% Similarity=0.194 Sum_probs=31.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-++|++.+|++.+.+-+.|..|.+.|++...
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence 4789999999999999999999999999999754
No 217
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=32.17 E-value=78 Score=30.83 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=31.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-++|++.+|++.+.+.+.|..|.+.|++...
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 4788999999999999999999999999999765
No 218
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=32.09 E-value=1.2e+02 Score=25.47 Aligned_cols=53 Identities=9% Similarity=0.182 Sum_probs=43.6
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCCChHHHHHHHHHhhhhccccc
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVER 597 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~~~~~ik~~Ie~LIekeyl~r 597 (609)
.++-+|..++. .+.+.=-+|.+++.+.... +.++.+.+=..+..|-++|+|++
T Consensus 4 ~l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 4 TLDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred hHHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 35566777776 4677888999998877655 78999999999999999999998
No 219
>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=31.80 E-value=76 Score=27.38 Aligned_cols=48 Identities=17% Similarity=0.184 Sum_probs=33.9
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
+..|...+.....++..+|... ...+.+.+-+.|..|.++|||+|..+
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~-------~~~~~~tvs~~l~~Le~~GlI~r~~~ 77 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQ-------ACILRPSLTGILARLERDGLVTRLKA 77 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH-------hCCCchhHHHHHHHHHHCCCEEeccC
Confidence 4445555666777776655533 23566788999999999999998653
No 220
>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=31.77 E-value=67 Score=27.03 Aligned_cols=47 Identities=15% Similarity=0.236 Sum_probs=32.2
Q ss_pred hhhhhhhhhhhcc----ccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccc
Q psy16234 543 LYLQAAIVRIMKS----RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE 596 (609)
Q Consensus 543 ~~i~A~IVRiMK~----~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~ 596 (609)
.-++..|..++|. .-.++.++|. +++ ..+..+|+++|+.|++.|+|=
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~----~~l---~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIA----QQL---GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHH----HHS---TS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHH----HHh---CcCHHHHHHHHHHHHhCCeEe
Confidence 3455566666666 4457777665 444 356899999999999999763
No 221
>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=31.63 E-value=73 Score=26.58 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=30.6
Q ss_pred cccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 555 SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 555 ~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
....+++.+|... ...+.+.+.+.|..|.++|+|+|..+
T Consensus 44 ~~~~is~~eLa~~-------~g~sr~tVsr~L~~Le~~GlI~r~~~ 82 (95)
T TIGR01610 44 KQDRVTATVIAEL-------TGLSRTHVSDAIKSLARRRIIFRQGM 82 (95)
T ss_pred cCCccCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeeeecC
Confidence 4566777766643 34678899999999999999998774
No 222
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=31.46 E-value=73 Score=34.87 Aligned_cols=59 Identities=19% Similarity=0.278 Sum_probs=49.5
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeecC
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 609 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yia 609 (609)
..+.+|++.++....++-.+|-+. |..+...+-+.|..|+++|++++-+....-+.||.
T Consensus 402 ~~~~~il~~~~en~~~T~~~L~~~-------l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~ 460 (467)
T COG2865 402 ERQEKILELIKENGKVTARELREI-------LGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVK 460 (467)
T ss_pred HHHHHHHHHHhhccccCHHHHHHH-------hCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEec
Confidence 345899999999999998877643 45788999999999999999999987777787763
No 223
>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=31.43 E-value=6.9e+02 Score=29.06 Aligned_cols=133 Identities=15% Similarity=0.302 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhHHHHhc
Q psy16234 76 TQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPKVKAKCEQHMVADHLNFLQGECVPMVAE 155 (609)
Q Consensus 76 ~~~L~~t~~yY~~~s~~~l~~~s~~eYl~~v~~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~ 155 (609)
-..++...-||...+..-. ...+..+.+.|....+++.+..-..+-.....|+.+-++ |+..++..
T Consensus 550 v~~leN~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~-------------gve~l~~~ 615 (701)
T PF09763_consen 550 VVLLENYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFE-------------GVEALLQT 615 (701)
T ss_pred HHHHHHHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHH-------------HHHHHHhc
Confidence 3455666666666664322 256788999999998888876554444445555554443 22222222
Q ss_pred c-----------cHHHHHHHHHhh--hcccccHHHHHHHHHHHHHHHHH------HHhhcccCCCchHHHHHHHHHHHHH
Q psy16234 156 E-----------RRHDLANMYPLL--RSVREGINILIDAVRDHICKQGL------EAISGLSGDNISTQFVENMLAVHKK 216 (609)
Q Consensus 156 ~-----------~~~~L~~ly~L~--~~~~~~l~~l~~~~~~~i~~~g~------~~~~~~~~~~~~~~~V~~ll~~~~k 216 (609)
. ....|+.+-.-+ +.+..|++.+.+.+++|+...+. .++.. .=..+-+..+..|.+
T Consensus 616 ~~~~ei~~~~~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~-----vW~~~q~~~i~~~~~ 690 (701)
T PF09763_consen 616 VSPEEISYQAAYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQV-----VWSAMQEEFIRQYER 690 (701)
T ss_pred cCchhcccchhccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHH-----HHHHHHHHHHHHHHH
Confidence 1 234555555543 33556788888888888822111 11110 112345567799999
Q ss_pred HHHHHHHhcCC
Q psy16234 217 YKAFVKELFSG 227 (609)
Q Consensus 217 ~~~li~~~F~~ 227 (609)
+..++..|+.|
T Consensus 691 l~~li~~~Y~g 701 (701)
T PF09763_consen 691 LETLIQKCYPG 701 (701)
T ss_pred HHHHHHHhCCC
Confidence 99999999865
No 224
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=31.41 E-value=80 Score=28.00 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=31.7
Q ss_pred hccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 553 MKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 553 MK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|..++.++-++|-+.+ ..+.+.+-+++.+|++.|.++|...
T Consensus 37 L~~~~~~tvdelae~l-------nr~rStv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 37 LEENGPLTVDELAEIL-------NRSRSTVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HhhcCCcCHHHHHHHH-------CccHHHHHHHHHHHHHcCCeeeeee
Confidence 3467778877666442 4678999999999999999998643
No 225
>PRK13239 alkylmercury lyase; Provisional
Probab=31.37 E-value=82 Score=30.50 Aligned_cols=39 Identities=10% Similarity=0.287 Sum_probs=34.9
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
+...||.++-++...|.++|++.+|.+.+.+.+.|..|-
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 555677788899999999999999999999999999975
No 226
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.97 E-value=99 Score=27.33 Aligned_cols=51 Identities=20% Similarity=0.330 Sum_probs=44.7
Q ss_pred hhhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 543 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 543 ~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
..|.+-||-..+.++.++..++... +-.+...+++.+..|++.|.|-+.+.
T Consensus 11 ~eLk~rIvElVRe~GRiTi~ql~~~-------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 11 EELKARIVELVREHGRITIKQLVAK-------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHcCCccHHHHHHH-------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 5689999999999999999988855 46788999999999999999988764
No 227
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=30.51 E-value=74 Score=30.10 Aligned_cols=68 Identities=13% Similarity=0.031 Sum_probs=50.0
Q ss_pred CcceeeecccceEEEEEEEeCccEEEEecHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234 417 GRKLSWLHNISQVELKLSYLKRPYFVTMQTFQMAILLLFEK--NDAMTCGDIQTVLSLSQDQIGRHIASLVECKL 489 (609)
Q Consensus 417 ~RkL~W~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~--~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~i 489 (609)
.|.-.|.+.+|..+++- .+.| .||+.||.-|+.-.. -..||.+.|++..+|..+++...|..+.-..+
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~~F~v 165 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFKPFEV 165 (179)
T ss_pred CCCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcCCcee
Confidence 34456778888887753 3444 467789987766443 35799999999999999999998888764433
No 228
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=30.49 E-value=1.2e+02 Score=29.46 Aligned_cols=33 Identities=12% Similarity=0.099 Sum_probs=30.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 461 MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 461 lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.|-++|++.+|++.+.+.+.|..|.+.|++...
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 478999999999999999999999999999765
No 229
>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=30.34 E-value=92 Score=30.88 Aligned_cols=43 Identities=12% Similarity=0.219 Sum_probs=37.7
Q ss_pred HHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 451 ILLLFEK-NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 451 iLllFn~-~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
||-.++. ...++..+|++.+|++...+.+++..|...|++...
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 6666666 368999999999999999999999999999999754
No 230
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=29.95 E-value=57 Score=26.31 Aligned_cols=46 Identities=20% Similarity=0.309 Sum_probs=35.5
Q ss_pred hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234 547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
-+|+-.+.....+++.+|... ...+.+.+.+.+..|.+.|||++..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~-------l~lt~g~Ls~hL~~Le~~GyV~~~k 48 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEE-------LGLTDGNLSKHLKKLEEAGYVEVEK 48 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHH-------TT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHH-------hCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 356777778888888877643 3578999999999999999999754
No 231
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=29.85 E-value=36 Score=33.47 Aligned_cols=31 Identities=10% Similarity=0.388 Sum_probs=27.6
Q ss_pred CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
|.++...+.++|+.|.+.|+|.|..+ +++|+
T Consensus 42 ~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 42 FGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 89999999999999999999999887 46654
No 232
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=29.32 E-value=1.7e+02 Score=28.96 Aligned_cols=48 Identities=19% Similarity=0.316 Sum_probs=40.0
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
+-+|..+.+.-+. ....-.||++.+|++.+-+..++..|++-|++...
T Consensus 11 t~fqIL~ei~~~q-p~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~ 58 (260)
T COG1497 11 TRFQILSEIAVRQ-PRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKE 58 (260)
T ss_pred hHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeec
Confidence 3467666665543 67899999999999999999999999999998765
No 233
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=29.28 E-value=83 Score=31.96 Aligned_cols=42 Identities=14% Similarity=0.272 Sum_probs=31.6
Q ss_pred HHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 447 FQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 447 ~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
+...|+-.+. ....+|+++|++.|||..+++..+|+.| |++.
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l---~~l~ 251 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL---NLIK 251 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CcEE
Confidence 3445554443 3578999999999999999999888875 5554
No 234
>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=28.39 E-value=1.2e+02 Score=27.35 Aligned_cols=40 Identities=13% Similarity=0.175 Sum_probs=32.5
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
+|.-|..|+.++ ...+|.+||++.+|++...+...+....
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 567788888886 4678999999999999988887666554
No 235
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=28.39 E-value=1e+02 Score=30.16 Aligned_cols=34 Identities=24% Similarity=0.383 Sum_probs=31.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+|-++|++.+|++.+.+-+.|..|.+.|+|...
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence 4688999999999999999999999999999654
No 236
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=28.21 E-value=45 Score=29.97 Aligned_cols=26 Identities=12% Similarity=0.253 Sum_probs=22.5
Q ss_pred CCCChHHHHHHHHHhhhhccccccCC
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
+..+.+.+.+.|+.|.++|||+|..+
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~~ 81 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQTC 81 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeecC
Confidence 45778899999999999999998654
No 237
>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=28.00 E-value=84 Score=27.10 Aligned_cols=49 Identities=18% Similarity=0.303 Sum_probs=38.4
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhC----CCHHHHHHHHHHHHhcCccccC
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLS----LSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~----i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
|..+..|+..+=+.+.+|..||.+.++ .+...+...|..|++.|+|...
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence 455677776666666699999999885 4489999999999999999764
No 238
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=27.77 E-value=1.2e+02 Score=28.80 Aligned_cols=44 Identities=20% Similarity=0.349 Sum_probs=36.0
Q ss_pred HHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEKND-AMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~~~-~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.||..+...+ .+|.-+|+..+||+...+.++|-.|.+.+.+...
T Consensus 8 ~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 8 LILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 4555554444 6999999999999999999999999998887554
No 239
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=27.60 E-value=84 Score=25.35 Aligned_cols=37 Identities=16% Similarity=0.113 Sum_probs=32.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 457 KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 457 ~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
.+...+..+|+..+++|.+.+...|.-|+..|-+.+.
T Consensus 13 ~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 13 LRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 4567899999999999999999999999988766543
No 240
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.35 E-value=64 Score=32.29 Aligned_cols=46 Identities=22% Similarity=0.434 Sum_probs=40.3
Q ss_pred hhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc
Q psy16234 546 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 598 (609)
Q Consensus 546 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~ 598 (609)
+..|..+++.++.++..+|.+. |.++...|.+-|+.|-++|.|.|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~-------l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEH-------FSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHHH-------hCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4568888899999999888753 789999999999999999999985
No 241
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=26.93 E-value=1.4e+02 Score=28.89 Aligned_cols=42 Identities=14% Similarity=0.224 Sum_probs=36.9
Q ss_pred HhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 453 LLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 453 llFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
-.|..++.++..+|++.+|++-.-++.+|..|...|++...|
T Consensus 23 g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~ 64 (224)
T PRK11534 23 GNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVN 64 (224)
T ss_pred CCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeC
Confidence 345567889999999999999999999999999999997654
No 242
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.73 E-value=1.6e+02 Score=20.72 Aligned_cols=28 Identities=18% Similarity=0.264 Sum_probs=24.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhcCc
Q psy16234 462 TCGDIQTVLSLSQDQIGRHIASLVECKL 489 (609)
Q Consensus 462 t~~ei~~~t~i~~~~l~~~L~~L~~~~i 489 (609)
|+.+++...|++...+.+-+..+-..|+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 9999999999999988888887776664
No 243
>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=26.09 E-value=1.1e+02 Score=23.09 Aligned_cols=45 Identities=18% Similarity=0.317 Sum_probs=31.5
Q ss_pred hhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCC
Q psy16234 549 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS 601 (609)
Q Consensus 549 IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~ 601 (609)
|...+.... ++..++.. . +..+...+.+.++.|.++|+|.+..+.
T Consensus 12 il~~l~~~~-~~~~ei~~----~---~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 12 ILRLLLEGP-LTVSELAE----R---LGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHCC-cCHHHHHH----H---HCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 444444444 66666543 2 456789999999999999999986543
No 244
>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=26.07 E-value=1.3e+02 Score=28.95 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=36.3
Q ss_pred hhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 454 LFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 454 lFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
.+.-++.++-.+|++..|++..-++.+|..|...|++...|
T Consensus 28 ~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 28 ELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred CCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence 34557789999999999999999999999999999997654
No 245
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=26.05 E-value=72 Score=25.94 Aligned_cols=66 Identities=27% Similarity=0.307 Sum_probs=40.3
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH-----hcCccccCCCCCCCCCEEEEecCC
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV-----ECKLLTSNKEELTEDTEIRLNLGY 509 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~-----~~~iL~~~~~~~~~~~~f~lN~~F 509 (609)
.+..-=++|-+|-+..++|+++|.+.+.-.-+.-.+...+|+ +.|||.-..........|++-++|
T Consensus 9 ~~GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y 79 (83)
T PF10826_consen 9 KDGIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKY 79 (83)
T ss_pred CccHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHh
Confidence 344556789999999999999998876322222333444444 458886521122334677776555
No 246
>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=26.01 E-value=4.1e+02 Score=27.64 Aligned_cols=76 Identities=12% Similarity=0.288 Sum_probs=49.6
Q ss_pred HHhhhHHHHhcccHHHHHHHHHhhhcc---cccHHHHHHHHHHHHHHHHHHHhhcccCC----CchHHHHHHHHHHHHHH
Q psy16234 145 LQGECVPMVAEERRHDLANMYPLLRSV---REGINILIDAVRDHICKQGLEAISGLSGD----NISTQFVENMLAVHKKY 217 (609)
Q Consensus 145 l~~~~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~----~~~~~~V~~ll~~~~k~ 217 (609)
+...|..-+++++...+.+.++||..+ ..|++....-+.+.|............+. ..+.-|+..+..+++..
T Consensus 12 ~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~~~~~~~~~a~~lt~Lfe~i 91 (324)
T smart00762 12 FKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASDDTRAAVFYADTLTHLFENV 91 (324)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccccccccchHHHHHHHHHHHH
Confidence 346788888999999999999998655 45777777777777766665555443221 12344666666665554
Q ss_pred HHH
Q psy16234 218 KAF 220 (609)
Q Consensus 218 ~~l 220 (609)
..+
T Consensus 92 a~i 94 (324)
T smart00762 92 ATI 94 (324)
T ss_pred HHH
Confidence 443
No 247
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=25.97 E-value=2.9e+02 Score=29.32 Aligned_cols=120 Identities=19% Similarity=0.191 Sum_probs=60.1
Q ss_pred CCcceEEEeeecCC---CCCCCCC--CCCccCchHHHHHHHHHHHHHhhcCCCccee-----eecccceEEEEEEEeCcc
Q psy16234 370 LGIHFSINILQAGS---WPLGPTV--ISSFSVPQELEKCIHMFEKFYHGQFNGRKLS-----WLHNISQVELKLSYLKRP 439 (609)
Q Consensus 370 ~~~~f~~~VLt~~~---WP~~~~~--~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~-----W~~~l~~~~l~~~~~~~~ 439 (609)
+++++-|--++... .|.+.++ +.++.=|..|+...+...+...---++|.-. =-++||.=-+=-+..++
T Consensus 256 PG~dLPv~~~~Rs~yg~ypEYHTS~Dnl~fi~p~~L~~s~~~~~~~i~~lE~n~~~~~~~~~gEPqLgkrgLY~~~~~~- 334 (386)
T PF09940_consen 256 PGFDLPVGSLMRSKYGEYPEYHTSLDNLDFISPEGLEGSFEVLLEAIEILENNRIYRNLKPLGEPQLGKRGLYPTISGK- 334 (386)
T ss_dssp TTT---EEEEESS-TT--TTTTBTTSSGGG--HHHHHHHHHHHHHHHHHHHH--EEEES--SS---TTS-----------
T ss_pred CCcCCceeeeecccccCCcccccCCCccccCCHHHHHHHHHHHHHHHHHHhcCCceecCCcccCCCCCcccCccccCCC-
Confidence 67787777777655 5666543 3568889999888877777765422222111 12344443331111111
Q ss_pred EEEEecHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 440 YFVTMQTFQMAILLLFE-KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 440 ~~l~~s~~Q~~iLllFn-~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
-... ...++++|-..| ....-|+-||++..|+|-..+...+..|.++|||.
T Consensus 335 ~~~~-~~~~~~~l~~L~~~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 335 SDAG-KAQQMAMLWVLNYSDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp --------HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred cchh-HHHHHHHHHHHHhccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 1110 113344443333 22467999999999999999999999999999873
No 248
>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=25.07 E-value=1.2e+02 Score=27.31 Aligned_cols=38 Identities=11% Similarity=0.235 Sum_probs=28.8
Q ss_pred ecHHHHHHHHh-hcCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy16234 444 MQTFQMAILLL-FEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 444 ~s~~Q~~iLll-Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~ 483 (609)
+|+-|..|+.+ |- ..+|.+||++.+|+|...+...+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45566666655 43 4689999999999999888877654
No 249
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=24.93 E-value=48 Score=32.76 Aligned_cols=31 Identities=16% Similarity=0.433 Sum_probs=27.8
Q ss_pred CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
|.++...+.++|..|.+.|+|.|..+ +++|+
T Consensus 41 f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 41 FGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 89999999999999999999999877 36664
No 250
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=24.88 E-value=71 Score=32.03 Aligned_cols=45 Identities=18% Similarity=0.331 Sum_probs=40.3
Q ss_pred hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhcccccc
Q psy16234 547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT 598 (609)
Q Consensus 547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~ 598 (609)
-.|+.+++.++.++.++|.+. |.++...|.+=|..|-++|+|.|.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~-------~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEKGKVSVEELAEL-------FGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHHH-------hCCCHHHHHHhHHHHHHCCcEEEE
Confidence 468889999999999888744 889999999999999999999994
No 251
>smart00526 H15 Domain in histone families 1 and 5.
Probab=24.76 E-value=2e+02 Score=21.95 Aligned_cols=53 Identities=21% Similarity=0.301 Sum_probs=38.5
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCC--hHHHHHHHHHhhhhcccccc
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS--ISMIKKCIESLIDKNYVERT 598 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~--~~~ik~~Ie~LIekeyl~r~ 598 (609)
.|..||.. |+.++..+...+..-+...-. ..|. ...++.+|..++++|-|.+.
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~-~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYK-VLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCC-CChHHHHHHHHHHHHHHHhcCceeec
Confidence 56666666 688999999988877766522 1122 36688899999999988764
No 252
>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=24.26 E-value=62 Score=24.11 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=23.2
Q ss_pred CCCChHHHHHHHHHhhhhccccccCC
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|..+.+.+.+.|..|.++|+|.+.++
T Consensus 35 ~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 35 LGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 66889999999999999999998764
No 253
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=24.24 E-value=1.2e+02 Score=28.04 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=40.4
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccc
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVER 597 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r 597 (609)
.+|..|.+++.....++..+|-..| ..+.+.+.++|..|.+.|.|++
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 4688899999999999998776443 4788999999999999999986
No 254
>PF14502 HTH_41: Helix-turn-helix domain
Probab=24.16 E-value=1.3e+02 Score=21.87 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=29.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 461 MTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 461 lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
-|++|+++..+++--.++.+|..|...|.+...
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le 39 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKLE 39 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEee
Confidence 589999999999999999999999998876544
No 255
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=24.00 E-value=51 Score=32.28 Aligned_cols=47 Identities=15% Similarity=0.316 Sum_probs=34.8
Q ss_pred hhccccCC-ChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 552 IMKSRKQI-RHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 552 iMK~~k~l-~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
.++....| +-.+|.++ |.++...+.++|+.|.+.|+|.|..+ +++|+
T Consensus 18 ~~~~g~~LPsE~eLa~~-------~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 18 EWPPGHRIPSEHELVAQ-------YGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred CCCCCCcCcCHHHHHHH-------HCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 34555556 34444422 89999999999999999999999887 45553
No 256
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=23.85 E-value=1.8e+02 Score=25.28 Aligned_cols=36 Identities=14% Similarity=0.108 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
-.+|++||++....+...++..|..|...|.|.=.|
T Consensus 18 ~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 18 VEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQP 53 (115)
T ss_pred cceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeC
Confidence 368999999999999999999999999999997655
No 257
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.81 E-value=1.2e+02 Score=27.69 Aligned_cols=47 Identities=13% Similarity=0.143 Sum_probs=39.6
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccc
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVER 597 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r 597 (609)
.++-.|.+.|......++.+|-.+ + ..+.+.+..+|+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~----l---glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQ----F---GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCeee
Confidence 357788899999999999877644 3 4789999999999999999985
No 258
>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=23.69 E-value=86 Score=22.41 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy16234 462 TCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 462 t~~ei~~~t~i~~~~l~~~L~~ 483 (609)
|+.||++..|++...+-+.|+.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6889999999999988887754
No 259
>PHA02591 hypothetical protein; Provisional
Probab=23.57 E-value=1e+02 Score=24.80 Aligned_cols=25 Identities=24% Similarity=0.396 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~ 483 (609)
..+|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 4689999999999999999988765
No 260
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=23.44 E-value=2.3e+02 Score=20.83 Aligned_cols=41 Identities=17% Similarity=0.363 Sum_probs=35.5
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
.+|.-+..++.++.++ .|..+|+...+++...+..++....
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 4567788888888876 7999999999999999999998875
No 261
>PLN03239 histone acetyltransferase; Provisional
Probab=23.22 E-value=1.1e+02 Score=31.93 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=31.5
Q ss_pred HHHHHHHhhcC----CCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 447 FQMAILLLFEK----NDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 447 ~Q~~iLllFn~----~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
+...|+-.+-+ ...+|+++|++.|||..+++..+|+.| |+|..
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l---~~l~~ 313 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL---GILKF 313 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC---CcEEE
Confidence 44455544322 246999999999999999999988875 56653
No 262
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=23.21 E-value=58 Score=32.17 Aligned_cols=36 Identities=17% Similarity=0.394 Sum_probs=0.0
Q ss_pred HhhcC-CCCChHHHHHHHHHhhhhccccccCCCCCcee
Q psy16234 570 SQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS 606 (609)
Q Consensus 570 ~~l~~-F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~ 606 (609)
.+|.. |.++...+.++|+.|.+.|+|.|..+ +++|+
T Consensus 33 ~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 33 SALQTEFGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
No 263
>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=23.08 E-value=1.2e+02 Score=24.19 Aligned_cols=55 Identities=20% Similarity=0.285 Sum_probs=41.7
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcC-CCC--ChHHHHHHHHHhhhhccccccC
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAP--SISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-F~~--~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
.|..|| +-|+.|+..+...+...+...-.- ..+ -...++++|..++++|-|.+..
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 455555 578999999999999888876431 222 1367999999999999998876
No 264
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.49 E-value=1.2e+02 Score=21.18 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=21.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHhcCccc
Q psy16234 461 MTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491 (609)
Q Consensus 461 lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~ 491 (609)
+|..|+++.+|++...+ ..|.+.|+|.
T Consensus 1 ~~~~e~a~~~gv~~~tl----r~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTL----RYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHH----HHHHHCCCCC
Confidence 57899999999998754 4677888875
No 265
>PF08511 COQ9: COQ9; InterPro: IPR013718 COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q []. It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role. ; PDB: 3NI7_B.
Probab=22.36 E-value=66 Score=26.03 Aligned_cols=26 Identities=38% Similarity=0.750 Sum_probs=17.8
Q ss_pred CCCCccChHhhHHHHHHHHHHHHhcC
Q psy16234 3 LKPKQVDFNKTWGSLQETIQGVITLG 28 (609)
Q Consensus 3 ~~~~~~~fe~~W~~l~~~i~~i~~~~ 28 (609)
+..++-+|+++|.+|+.-|+.+..++
T Consensus 50 l~d~S~~~~~T~~Fl~rri~~v~~~~ 75 (79)
T PF08511_consen 50 LQDKSPDFEDTWAFLDRRIDDVMQFG 75 (79)
T ss_dssp HT--SGGGHHHHHHHHHHHHHH----
T ss_pred hhCCCCCHHHHHHHHHHHHHhhhccc
Confidence 34567899999999999999988764
No 266
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=22.26 E-value=1.2e+02 Score=32.90 Aligned_cols=41 Identities=12% Similarity=0.280 Sum_probs=31.0
Q ss_pred HHHHHh-hcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 449 MAILLL-FEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 449 ~~iLll-Fn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
..|+-. .+....+|+++|++.|||..+++..+|+.| ++|..
T Consensus 362 ~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l---~~l~~ 403 (450)
T PLN00104 362 RVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL---NLIQY 403 (450)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CCEEe
Confidence 344433 344468999999999999999999998885 56643
No 267
>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=22.08 E-value=93 Score=31.64 Aligned_cols=57 Identities=14% Similarity=0.223 Sum_probs=32.0
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCC
Q psy16234 447 FQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY 509 (609)
Q Consensus 447 ~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F 509 (609)
+--.|+-+|.++..||+.+|.+.|+-|+..|+.+|...+ ++.+.+ .-...|.|=.+|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa---~~~k~g---~~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA---VLNKRG---PHKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-----EE--T---T---EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH---HHhccC---CcCCcEecchHH
Confidence 445678899999999999999999999999999999876 444442 112456655544
No 268
>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=22.02 E-value=56 Score=24.82 Aligned_cols=26 Identities=15% Similarity=0.379 Sum_probs=23.3
Q ss_pred CCCChHHHHHHHHHhhhhccccccCC
Q psy16234 575 FAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 575 F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
|.++...+.+++..|.+.|+|.+.++
T Consensus 34 ~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 34 YGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred hccCCcHHHHHHHHHHHCCcEEEECC
Confidence 78999999999999999999999875
No 269
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=21.99 E-value=1.4e+02 Score=28.89 Aligned_cols=42 Identities=12% Similarity=0.173 Sum_probs=36.9
Q ss_pred HhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 453 LLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 453 llFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
-.+..++.++..+|++..|++-.-++.+|..|...|++...|
T Consensus 27 g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 27 GALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence 445567889999999999999999999999999999997654
No 270
>KOG3341|consensus
Probab=21.82 E-value=3.7e+02 Score=26.13 Aligned_cols=141 Identities=13% Similarity=0.078 Sum_probs=88.7
Q ss_pred HHHHHhHHHHHHHHHHHhhccCCCCCcceEEEeeecCCCCCCCC----------CCCCccC--------chHHHHHHHHH
Q psy16234 346 TDIKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPT----------VISSFSV--------PQELEKCIHMF 407 (609)
Q Consensus 346 ~Di~~S~~l~~~f~~~~~~~~~~~~~~~f~~~VLt~~~WP~~~~----------~~~~~~l--------P~~l~~~~~~F 407 (609)
.+|+.+.++...| ++.+. .+.+.|..+.+|.|-.... +...+.+ --+++++.+.+
T Consensus 54 ~ei~knsqFR~~F-q~Mca------~IGvDPlas~kgfw~~~lgvgdFYYelgVqviEvC~at~~~nGGlislqel~~~l 126 (249)
T KOG3341|consen 54 TEIRKNSQFRNQF-QEMCA------SIGVDPLASGKGFWAELLGVGDFYYELGVQVIEVCLATKHTNGGLISLQELCNHL 126 (249)
T ss_pred HHHhhCHHHHHHH-HHHHH------HcCCCccccCcchHHHHhhhHHHHHHHhhHHHHHHHHhhcccCCeeeHHHHHHHH
Confidence 5777788888888 66543 4667788999999972110 0000000 01244444444
Q ss_pred HHHHhhcCC-------CcceeeecccceEEEEEEEeCccEEE----EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHH
Q psy16234 408 EKFYHGQFN-------GRKLSWLHNISQVELKLSYLKRPYFV----TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQ 476 (609)
Q Consensus 408 ~~~Y~~k~~-------~RkL~W~~~l~~~~l~~~~~~~~~~l----~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~ 476 (609)
-.+=+..|. -|-+.=+..||++=.-+...++.+.= .+|.-|-.||-+-....-+|...|...++-....
T Consensus 127 ~~~R~~~~e~vt~dD~lrAi~kLk~LG~gFev~~iggK~~vrSVP~ELn~Dht~ILela~~~gyvt~s~l~~~l~We~~R 206 (249)
T KOG3341|consen 127 LQRRKKDHEAVTEDDLLRAIDKLKVLGSGFEVIKIGGKKLVRSVPTELNMDHTVILELAEILGYVTISLLKANLGWERSR 206 (249)
T ss_pred HHHhcccchhccHHHHHHHHHHhhccCCCeEEEEecCEEeeecCcchhcccHHHHHHHHHhcCceeHHHHHHhccchHHH
Confidence 443322211 12233455678754445555544332 3455677888777777779999999999999999
Q ss_pred HHHHHHHHHhcCccccC
Q psy16234 477 IGRHIASLVECKLLTSN 493 (609)
Q Consensus 477 l~~~L~~L~~~~iL~~~ 493 (609)
...+|.-|++.|++-.+
T Consensus 207 a~qaLe~lv~egL~WiD 223 (249)
T KOG3341|consen 207 AIQALEHLVKEGLAWID 223 (249)
T ss_pred HHHHHHHHHhccceeee
Confidence 99999999999998655
No 271
>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=21.68 E-value=62 Score=23.74 Aligned_cols=22 Identities=9% Similarity=0.311 Sum_probs=18.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q psy16234 460 AMTCGDIQTVLSLSQDQIGRHI 481 (609)
Q Consensus 460 ~lt~~ei~~~t~i~~~~l~~~L 481 (609)
.+++.||++.+|++..++.+.|
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 5789999999999999888877
No 272
>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=21.53 E-value=1.3e+02 Score=27.28 Aligned_cols=41 Identities=12% Similarity=0.242 Sum_probs=29.1
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
++.-|-.|+.+.- -..+|.+||++.+|+|...++..+..-.
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~ 151 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRAL 151 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3445555554432 3468999999999999998888776544
No 273
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.46 E-value=99 Score=24.31 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 459 DAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 459 ~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
..-|.+||++.+|++.+.+...+....
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~~ 45 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQASR 45 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHHS
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhCC
Confidence 456999999999999999999887643
No 274
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=21.31 E-value=1.8e+02 Score=25.34 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=43.3
Q ss_pred EEEecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCcccc
Q psy16234 441 FVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492 (609)
Q Consensus 441 ~l~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~ 492 (609)
.-..++-|..|+-+... ..|+.||+..+++|-..++-.+.-|+..|.+.-
T Consensus 38 ~~~l~pE~~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 38 PAGLGPEHRAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred CCCCCHHHHHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 35667888889887776 899999999999999999999999999998754
No 275
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=21.20 E-value=2.6e+02 Score=22.01 Aligned_cols=59 Identities=15% Similarity=0.285 Sum_probs=39.1
Q ss_pred hhhhhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceeec
Q psy16234 544 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV 608 (609)
Q Consensus 544 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Yi 608 (609)
.-+++|-.+.+.+..-+..+|+....+. +|.++-+.|-+=|..| +-++ .++..+.|.|.
T Consensus 5 ~R~~~I~~li~~~~i~sQ~eL~~~L~~~--Gi~vTQaTiSRDLkeL---~~vK-v~~~~g~~~Y~ 63 (70)
T PF01316_consen 5 KRQELIKELISEHEISSQEELVELLEEE--GIEVTQATISRDLKEL---GAVK-VPDGNGKYRYV 63 (70)
T ss_dssp HHHHHHHHHHHHS---SHHHHHHHHHHT--T-T--HHHHHHHHHHH---T-EE-EECTTSSEEEE
T ss_pred HHHHHHHHHHHHCCcCCHHHHHHHHHHc--CCCcchhHHHHHHHHc---CcEE-eeCCCCCEEEE
Confidence 3478899999999999999999887665 4999999998888776 3333 33445788885
No 276
>PRK11642 exoribonuclease R; Provisional
Probab=21.15 E-value=2e+02 Score=34.09 Aligned_cols=44 Identities=14% Similarity=0.198 Sum_probs=35.9
Q ss_pred HHHHhhcC-CCCCCHHHHHHHhCCCH----HHHHHHHHHHHhcCccccC
Q psy16234 450 AILLLFEK-NDAMTCGDIQTVLSLSQ----DQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 450 ~iLllFn~-~~~lt~~ei~~~t~i~~----~~l~~~L~~L~~~~iL~~~ 493 (609)
.||-.|.+ ...+++.+|++.++++. +.|.+.|..|.+.|+|.+.
T Consensus 23 ~Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~ 71 (813)
T PRK11642 23 FILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT 71 (813)
T ss_pred HHHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEc
Confidence 46766665 47899999999999973 4599999999999988754
No 277
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=21.00 E-value=2e+02 Score=26.01 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=30.8
Q ss_pred EecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy16234 443 TMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 443 ~~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~ 483 (609)
.+|.-|..||.++ ...+|.+||++.+|++...+......
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4577888888776 35799999999999999776666554
No 278
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=20.92 E-value=1.6e+02 Score=21.61 Aligned_cols=46 Identities=24% Similarity=0.406 Sum_probs=28.2
Q ss_pred hhhhhhhhhhccc--cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhh
Q psy16234 544 YLQAAIVRIMKSR--KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDK 592 (609)
Q Consensus 544 ~i~A~IVRiMK~~--k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIek 592 (609)
.|.++|..||+.- .+++..++...+.+. |..+...-|..|..+|..
T Consensus 4 ~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~---~~~dL~~~K~~I~~~I~~ 51 (54)
T PF08766_consen 4 EIREAIREILREADLDTVTKKQVREQLEER---FGVDLSSRKKFIKELIDE 51 (54)
T ss_dssp HHHHHHHHHHTTS-GGG--HHHHHHHHHHH----SS--SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHhHhhHHHHHHHHHHH---HCCCcHHHHHHHHHHHHH
Confidence 5788899999986 556666555555554 556666777777777754
No 279
>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=20.82 E-value=1.8e+02 Score=22.46 Aligned_cols=50 Identities=14% Similarity=0.244 Sum_probs=40.2
Q ss_pred hhhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccC
Q psy16234 548 AIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA 599 (609)
Q Consensus 548 ~IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~ 599 (609)
.|-++++.. +.+...+|....... ++.++...+..++..|=++||+++..
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 669999888776544 38888999999999999999998765
No 280
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=20.80 E-value=2.2e+02 Score=23.17 Aligned_cols=46 Identities=20% Similarity=0.357 Sum_probs=35.0
Q ss_pred HHHHHHhhc----CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccC
Q psy16234 448 QMAILLLFE----KNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSN 493 (609)
Q Consensus 448 Q~~iLllFn----~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~ 493 (609)
..-||.... +++-+..+.|.+.+|++...+...|..|++.|++...
T Consensus 8 d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~ 57 (82)
T PF09202_consen 8 DFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRR 57 (82)
T ss_dssp HHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCcccc
Confidence 334454444 3567899999999999999999999999999999764
No 281
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=20.78 E-value=1.3e+02 Score=29.33 Aligned_cols=56 Identities=13% Similarity=0.176 Sum_probs=42.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhcCccccCCCCCCCCCEEEEecCCCC
Q psy16234 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGYNN 511 (609)
Q Consensus 450 ~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN~~F~~ 511 (609)
.++-+|.+.+.||+..|++.+|-|+..|+.+|...+ +|.+.+ .-...|++-..|+.
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia---vLnKkg---pya~kY~LrPEYK~ 254 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA---VLNKKG---PYANKYELRPEYKQ 254 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH---hhhccC---cccceeecCHHHHh
Confidence 466789999999999999999999999999998865 454432 01245677666653
No 282
>PRK04217 hypothetical protein; Provisional
Probab=20.73 E-value=2.2e+02 Score=24.67 Aligned_cols=41 Identities=17% Similarity=0.219 Sum_probs=29.0
Q ss_pred ecHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy16234 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLV 485 (609)
Q Consensus 444 ~s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~L~ 485 (609)
++.-|..++.+.. .+.+|+++|++.+|++...+.+.|....
T Consensus 43 Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 43 MTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4455554443332 2457999999999999998888777644
No 283
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.63 E-value=1.8e+02 Score=24.73 Aligned_cols=38 Identities=21% Similarity=0.301 Sum_probs=22.8
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy16234 445 QTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIAS 483 (609)
Q Consensus 445 s~~Q~~iLllFn~~~~lt~~ei~~~t~i~~~~l~~~L~~ 483 (609)
|--|-.++-++-. +.+|++||++..|++..-+...+..
T Consensus 19 T~kQ~~~l~lyy~-eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 19 TEKQREILELYYE-EDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp -HHHHHHHHHHCT-S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHc-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4456667766554 3589999999999997655544443
No 284
>PRK14999 histidine utilization repressor; Provisional
Probab=20.53 E-value=1.6e+02 Score=29.02 Aligned_cols=37 Identities=16% Similarity=0.253 Sum_probs=33.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 458 NDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 458 ~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
++.+ |-.+|++..|++-..++++|..|+..|+|.+..
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4556 999999999999999999999999999997654
No 285
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=20.43 E-value=1.6e+02 Score=22.19 Aligned_cols=43 Identities=16% Similarity=0.383 Sum_probs=30.8
Q ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHHHHHhcCccccCCCCCCCCCEEEEe
Q psy16234 458 NDAMTCGDIQTVLSLS-QDQIGRHIASLVECKLLTSNKEELTEDTEIRLN 506 (609)
Q Consensus 458 ~~~lt~~ei~~~t~i~-~~~l~~~L~~L~~~~iL~~~~~~~~~~~~f~lN 506 (609)
...++++++.+..|.+ .+.+.+.|..+...|++..+ ++.+.+.
T Consensus 18 ~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~------~~~l~lT 61 (66)
T PF06969_consen 18 NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEID------GGRLRLT 61 (66)
T ss_dssp HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-------SSEEEE-
T ss_pred HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEe------CCEEEEC
Confidence 4578999999999998 45558889999999999876 3555554
No 286
>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=20.35 E-value=1.7e+02 Score=28.16 Aligned_cols=47 Identities=17% Similarity=0.342 Sum_probs=35.6
Q ss_pred hhhhhhhccccCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCC
Q psy16234 547 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN 600 (609)
Q Consensus 547 A~IVRiMK~~k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~ 600 (609)
..|...+..+..++..+|... +..+.+.+-+.|..|.++|+|+|.++
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~-------l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKK-------LGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 355566666667777766644 34677889999999999999999974
No 287
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.21 E-value=1.3e+02 Score=27.97 Aligned_cols=37 Identities=19% Similarity=0.250 Sum_probs=27.2
Q ss_pred ecHHHHHHHHh-hcCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy16234 444 MQTFQMAILLL-FEKNDAMTCGDIQTVLSLSQDQIGRHIA 482 (609)
Q Consensus 444 ~s~~Q~~iLll-Fn~~~~lt~~ei~~~t~i~~~~l~~~L~ 482 (609)
+|.-|-.|+.+ +- +.+|++||++.+|+|...++..|.
T Consensus 128 Lp~~~R~v~~L~~~--~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMATL--DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555544 33 468999999999999988887655
No 288
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=20.19 E-value=1.6e+02 Score=29.19 Aligned_cols=40 Identities=13% Similarity=0.221 Sum_probs=35.7
Q ss_pred hcCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhcCccccCC
Q psy16234 455 FEKNDAM-TCGDIQTVLSLSQDQIGRHIASLVECKLLTSNK 494 (609)
Q Consensus 455 Fn~~~~l-t~~ei~~~t~i~~~~l~~~L~~L~~~~iL~~~~ 494 (609)
|..++.+ |-.+|++..|++-..++.+|..|...|+|...|
T Consensus 28 l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 28 LRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred CCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4456788 899999999999999999999999999997664
No 289
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=20.17 E-value=2.2e+02 Score=25.79 Aligned_cols=60 Identities=13% Similarity=0.242 Sum_probs=46.2
Q ss_pred hhhhhhhhccc-cCCChHHHHHHHHHhhcCCCCChHHHHHHHHHhhhhccccccCCCCCceee
Q psy16234 546 QAAIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY 607 (609)
Q Consensus 546 ~A~IVRiMK~~-k~l~~~~L~~~v~~~l~~F~~~~~~ik~~Ie~LIekeyl~r~~~~~~~y~Y 607 (609)
..+|.++|... ..++..+|..++.+.- ...+...|=+.++.|.+.|+|.+-....+...|
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~--p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEG--PGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhC--CCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 34666777754 6699999998887754 457789999999999999999998765444444
Done!