Query psy14208
Match_columns 778
No_of_seqs 205 out of 1074
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 22:12:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14208.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14208hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2285|consensus 100.0 2E-117 4E-122 911.0 66.4 768 3-778 6-777 (777)
2 KOG2166|consensus 100.0 1E-117 3E-122 1015.0 63.6 708 2-776 2-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 1E-114 3E-119 944.3 62.6 721 5-778 15-773 (773)
4 KOG2284|consensus 100.0 9E-112 2E-116 861.0 47.8 703 4-778 5-728 (728)
5 KOG2167|consensus 100.0 3E-107 6E-112 866.7 48.5 651 55-778 1-661 (661)
6 PF00888 Cullin: Cullin family 100.0 2.2E-91 4.8E-96 820.6 59.1 585 14-671 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 2.5E-32 5.4E-37 258.8 17.9 141 442-584 1-142 (142)
8 KOG2165|consensus 99.9 2.1E-23 4.5E-28 228.3 25.3 299 436-765 442-755 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 4.1E-20 8.9E-25 150.5 3.3 68 705-772 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 96.9 0.012 2.7E-07 56.1 11.8 148 7-159 2-156 (158)
11 KOG2167|consensus 94.2 2.4 5.3E-05 48.0 17.4 199 13-244 113-324 (661)
12 PF09339 HTH_IclR: IclR helix- 92.3 0.21 4.6E-06 38.1 4.1 46 598-649 6-51 (52)
13 PF02082 Rrf2: Transcriptional 89.7 1.3 2.8E-05 37.5 6.8 61 596-670 11-71 (83)
14 TIGR01610 phage_O_Nterm phage 89.3 1.1 2.3E-05 39.1 6.2 67 591-671 21-93 (95)
15 PF12802 MarR_2: MarR family; 86.9 1.3 2.7E-05 34.9 4.8 53 593-650 3-55 (62)
16 PF13412 HTH_24: Winged helix- 85.8 1.7 3.7E-05 32.4 4.7 42 594-637 2-43 (48)
17 TIGR02698 CopY_TcrY copper tra 85.6 1.5 3.2E-05 40.7 5.2 60 714-778 6-65 (130)
18 COG3682 Predicted transcriptio 82.9 2.2 4.7E-05 38.8 4.8 62 712-778 6-67 (123)
19 PF13463 HTH_27: Winged helix 80.7 3.8 8.2E-05 32.8 5.2 51 593-650 1-52 (68)
20 PF01047 MarR: MarR family; I 79.0 2.5 5.3E-05 32.9 3.4 50 594-650 2-51 (59)
21 PF03965 Penicillinase_R: Peni 76.6 1.8 3.8E-05 39.2 2.2 60 714-778 5-64 (115)
22 PF09012 FeoC: FeoC like trans 76.6 1.4 3E-05 35.8 1.4 45 717-769 5-49 (69)
23 PRK10857 DNA-binding transcrip 76.4 7.8 0.00017 37.5 6.7 47 597-649 12-58 (164)
24 PF08220 HTH_DeoR: DeoR-like h 75.8 4.6 0.0001 31.4 4.1 40 597-638 2-41 (57)
25 PF01022 HTH_5: Bacterial regu 75.6 8 0.00017 28.6 5.2 39 597-638 4-42 (47)
26 PF04492 Phage_rep_O: Bacterio 75.5 9.6 0.00021 33.5 6.4 62 593-671 30-98 (100)
27 smart00346 HTH_ICLR helix_turn 74.6 6.6 0.00014 33.4 5.3 58 598-670 8-65 (91)
28 TIGR02010 IscR iron-sulfur clu 72.9 11 0.00023 35.2 6.6 46 597-648 12-57 (135)
29 smart00550 Zalpha Z-DNA-bindin 72.6 9.5 0.00021 30.9 5.3 43 596-638 7-49 (68)
30 PRK15090 DNA-binding transcrip 71.3 8.5 0.00018 40.2 6.1 47 597-650 16-62 (257)
31 PF12840 HTH_20: Helix-turn-he 70.5 10 0.00022 29.8 5.0 44 594-639 9-52 (61)
32 TIGR02337 HpaR homoprotocatech 70.5 7.6 0.00016 35.1 4.9 51 593-650 26-76 (118)
33 PRK11920 rirA iron-responsive 69.7 14 0.0003 35.3 6.6 46 598-650 13-58 (153)
34 PRK10163 DNA-binding transcrip 68.7 10 0.00022 39.9 6.1 59 597-670 27-85 (271)
35 PRK11569 transcriptional repre 68.6 9.7 0.00021 40.2 5.9 48 597-650 30-77 (274)
36 PF08279 HTH_11: HTH domain; 68.3 10 0.00023 28.9 4.6 29 610-638 14-42 (55)
37 TIGR02944 suf_reg_Xantho FeS a 68.1 11 0.00023 34.9 5.4 47 597-648 11-57 (130)
38 PF01978 TrmB: Sugar-specific 67.6 6 0.00013 31.8 3.2 49 594-649 7-55 (68)
39 PRK11512 DNA-binding transcrip 66.5 12 0.00026 35.2 5.5 51 593-650 38-88 (144)
40 PF05732 RepL: Firmicute plasm 65.8 8.9 0.00019 37.1 4.5 46 612-672 76-121 (165)
41 COG1414 IclR Transcriptional r 65.7 13 0.00028 38.6 6.0 47 598-650 7-53 (246)
42 PF13601 HTH_34: Winged helix 65.5 6.7 0.00015 32.9 3.2 39 599-639 4-42 (80)
43 PF01978 TrmB: Sugar-specific 65.3 6.8 0.00015 31.5 3.1 56 714-777 10-65 (68)
44 COG3355 Predicted transcriptio 63.5 12 0.00025 34.4 4.4 36 609-649 40-75 (126)
45 COG1959 Predicted transcriptio 62.2 21 0.00045 34.0 6.2 60 596-669 11-70 (150)
46 TIGR02431 pcaR_pcaU beta-ketoa 62.2 17 0.00037 37.6 6.2 45 598-648 12-56 (248)
47 TIGR00738 rrf2_super rrf2 fami 61.7 20 0.00044 32.9 6.0 48 596-649 11-58 (132)
48 TIGR01889 Staph_reg_Sar staphy 60.5 22 0.00047 31.7 5.8 54 592-650 22-77 (109)
49 smart00550 Zalpha Z-DNA-bindin 59.8 18 0.00039 29.3 4.6 54 713-774 7-62 (68)
50 PRK10870 transcriptional repre 58.5 25 0.00053 34.4 6.2 53 593-650 53-105 (176)
51 smart00347 HTH_MARR helix_turn 57.9 16 0.00035 31.3 4.4 52 591-649 6-57 (101)
52 PRK09834 DNA-binding transcrip 57.0 21 0.00045 37.4 5.8 47 598-650 14-60 (263)
53 smart00419 HTH_CRP helix_turn_ 55.0 28 0.00061 25.2 4.7 33 611-648 8-40 (48)
54 PF09763 Sec3_C: Exocyst compl 54.0 4.8E+02 0.01 31.6 19.0 140 209-361 552-701 (701)
55 PRK03573 transcriptional regul 53.9 24 0.00053 33.0 5.2 53 592-650 28-80 (144)
56 TIGR03879 near_KaiC_dom probab 53.8 16 0.00034 30.1 3.3 29 610-638 31-59 (73)
57 PF13404 HTH_AsnC-type: AsnC-t 52.2 20 0.00044 26.0 3.3 35 599-635 7-41 (42)
58 cd07153 Fur_like Ferric uptake 51.8 25 0.00054 31.5 4.7 58 716-776 5-63 (116)
59 PF13463 HTH_27: Winged helix 51.1 18 0.0004 28.7 3.3 54 714-775 5-61 (68)
60 PF08784 RPA_C: Replication pr 50.9 27 0.00058 30.7 4.6 48 592-639 44-93 (102)
61 PRK13777 transcriptional regul 50.0 34 0.00073 33.8 5.6 52 592-650 42-93 (185)
62 PF08280 HTH_Mga: M protein tr 50.0 23 0.00049 27.7 3.6 38 597-636 7-44 (59)
63 PF08281 Sigma70_r4_2: Sigma-7 49.8 27 0.00059 26.4 4.0 24 610-633 25-48 (54)
64 smart00418 HTH_ARSR helix_turn 48.7 28 0.0006 26.8 4.0 46 717-771 2-47 (66)
65 PF08220 HTH_DeoR: DeoR-like h 47.8 14 0.0003 28.7 2.1 46 715-768 3-48 (57)
66 PRK10141 DNA-binding transcrip 47.2 40 0.00087 30.6 5.2 36 610-650 29-64 (117)
67 PF08221 HTH_9: RNA polymerase 46.9 36 0.00077 27.0 4.3 36 600-638 19-54 (62)
68 PF06784 UPF0240: Uncharacteri 46.1 32 0.00069 33.8 4.7 65 567-636 97-161 (179)
69 TIGR01884 cas_HTH CRISPR locus 45.9 34 0.00074 34.2 5.1 52 592-650 140-191 (203)
70 PF05584 Sulfolobus_pRN: Sulfo 45.2 52 0.0011 27.0 4.9 40 594-637 5-44 (72)
71 PHA00738 putative HTH transcri 44.8 60 0.0013 28.8 5.6 65 593-671 10-74 (108)
72 PF10771 DUF2582: Protein of u 44.5 51 0.0011 26.5 4.7 40 598-639 11-50 (65)
73 PF01726 LexA_DNA_bind: LexA D 44.3 38 0.00083 27.2 4.1 55 709-770 7-62 (65)
74 PRK11014 transcriptional repre 44.2 75 0.0016 29.7 6.8 36 610-650 24-59 (141)
75 smart00420 HTH_DEOR helix_turn 44.0 39 0.00085 24.9 4.1 37 599-637 4-40 (53)
76 cd00092 HTH_CRP helix_turn_hel 43.3 57 0.0012 25.6 5.1 35 610-649 24-58 (67)
77 PF09756 DDRGK: DDRGK domain; 43.0 15 0.00032 36.3 1.8 58 713-778 100-157 (188)
78 COG2345 Predicted transcriptio 42.7 32 0.0007 34.8 4.2 41 594-637 11-51 (218)
79 PF04703 FaeA: FaeA-like prote 42.4 24 0.00052 28.0 2.6 39 600-639 5-43 (62)
80 PF13412 HTH_24: Winged helix- 42.3 35 0.00077 25.1 3.5 45 713-765 4-48 (48)
81 COG1318 Predicted transcriptio 42.2 30 0.00066 33.2 3.6 51 563-636 36-86 (182)
82 PF08318 COG4: COG4 transport 39.2 1.8E+02 0.0038 31.7 9.7 88 276-363 11-110 (331)
83 KOG2905|consensus 38.6 41 0.00088 34.2 4.1 58 596-671 187-244 (254)
84 smart00344 HTH_ASNC helix_turn 38.2 55 0.0012 28.8 4.7 39 597-637 5-43 (108)
85 PF09012 FeoC: FeoC like trans 37.4 43 0.00094 27.0 3.5 32 609-640 12-43 (69)
86 cd00090 HTH_ARSR Arsenical Res 37.3 68 0.0015 25.3 4.8 41 594-637 6-46 (78)
87 smart00344 HTH_ASNC helix_turn 37.2 45 0.00098 29.3 4.0 46 713-766 4-49 (108)
88 smart00345 HTH_GNTR helix_turn 36.5 71 0.0015 24.2 4.6 37 609-650 17-54 (60)
89 smart00418 HTH_ARSR helix_turn 36.4 80 0.0017 24.0 5.0 28 610-637 9-36 (66)
90 smart00420 HTH_DEOR helix_turn 36.2 55 0.0012 24.0 3.8 45 717-769 5-49 (53)
91 COG5090 TFG2 Transcription ini 35.4 50 0.0011 33.2 4.1 55 599-671 199-253 (297)
92 PF10163 EnY2: Transcription f 35.3 95 0.002 26.4 5.4 55 11-67 29-84 (86)
93 PF04967 HTH_10: HTH DNA bindi 35.2 90 0.0019 24.0 4.6 31 603-635 17-47 (53)
94 PF04545 Sigma70_r4: Sigma-70, 35.2 79 0.0017 23.5 4.4 35 597-635 10-44 (50)
95 PF01638 HxlR: HxlR-like helix 35.0 72 0.0016 27.2 4.7 44 598-649 8-52 (90)
96 PF02186 TFIIE_beta: TFIIE bet 35.0 40 0.00086 27.1 2.8 55 713-778 6-61 (65)
97 PF12802 MarR_2: MarR family; 34.8 23 0.0005 27.5 1.5 48 714-769 7-56 (62)
98 PF13730 HTH_36: Helix-turn-he 34.8 1.1E+02 0.0025 23.0 5.4 25 613-637 27-51 (55)
99 PF02002 TFIIE_alpha: TFIIE al 32.8 38 0.00083 29.8 2.7 39 597-637 15-53 (105)
100 PF01047 MarR: MarR family; I 32.8 28 0.0006 26.8 1.6 46 715-768 6-51 (59)
101 PF04001 Vhr1: Transcription f 32.4 1.9E+02 0.0042 24.4 6.4 52 452-503 23-84 (95)
102 TIGR03433 padR_acidobact trans 32.3 1.2E+02 0.0025 26.6 5.7 53 713-766 5-57 (100)
103 cd07977 TFIIE_beta_winged_heli 32.1 54 0.0012 27.2 3.3 26 712-737 9-36 (75)
104 PF02796 HTH_7: Helix-turn-hel 31.7 66 0.0014 23.5 3.4 30 600-633 14-43 (45)
105 PF02270 TFIIF_beta: Transcrip 31.5 63 0.0014 34.1 4.5 59 595-671 216-274 (275)
106 PF01325 Fe_dep_repress: Iron 31.3 1E+02 0.0022 24.2 4.6 37 609-650 20-56 (60)
107 TIGR02404 trehalos_R_Bsub treh 30.5 36 0.00079 34.7 2.5 37 738-775 28-64 (233)
108 PRK10079 phosphonate metabolis 30.3 56 0.0012 33.6 3.9 55 713-775 21-75 (241)
109 smart00345 HTH_GNTR helix_turn 29.4 44 0.00096 25.4 2.3 29 741-769 27-55 (60)
110 PF01726 LexA_DNA_bind: LexA D 29.1 80 0.0017 25.3 3.7 52 594-650 5-60 (65)
111 smart00421 HTH_LUXR helix_turn 29.0 1.2E+02 0.0025 22.5 4.6 39 594-636 5-43 (58)
112 COG1846 MarR Transcriptional r 28.8 1E+02 0.0023 27.1 5.0 51 593-650 20-70 (126)
113 PRK09334 30S ribosomal protein 27.7 56 0.0012 27.8 2.6 39 740-778 47-85 (86)
114 PRK11402 DNA-binding transcrip 27.7 43 0.00094 34.4 2.5 37 738-775 37-73 (241)
115 smart00347 HTH_MARR helix_turn 27.2 1.1E+02 0.0024 25.8 4.8 48 713-768 11-58 (101)
116 PLN03238 probable histone acet 27.2 1.2E+02 0.0026 31.9 5.5 40 596-636 209-248 (290)
117 PF04182 B-block_TFIIIC: B-blo 27.1 1.2E+02 0.0026 24.9 4.6 51 595-650 2-52 (75)
118 COG1510 Predicted transcriptio 27.0 77 0.0017 30.6 3.7 39 597-638 30-68 (177)
119 PF09339 HTH_IclR: IclR helix- 27.0 95 0.0021 23.3 3.6 44 717-768 8-52 (52)
120 cd06171 Sigma70_r4 Sigma70, re 26.7 1.1E+02 0.0024 22.1 4.1 39 594-635 12-50 (55)
121 PRK13713 conjugal transfer pro 26.6 1.4E+02 0.003 26.9 5.0 43 156-204 3-46 (118)
122 PF00392 GntR: Bacterial regul 26.1 45 0.00097 26.3 1.8 30 740-769 30-59 (64)
123 cd06170 LuxR_C_like C-terminal 26.1 1.4E+02 0.0031 22.1 4.6 38 595-636 3-40 (57)
124 PRK00215 LexA repressor; Valid 26.0 1.1E+02 0.0023 30.6 5.0 53 593-650 2-58 (205)
125 PF01853 MOZ_SAS: MOZ/SAS fami 25.8 70 0.0015 31.5 3.4 26 611-636 150-175 (188)
126 TIGR01889 Staph_reg_Sar staphy 25.7 60 0.0013 28.8 2.7 46 723-776 40-88 (109)
127 PF13730 HTH_36: Helix-turn-he 25.5 52 0.0011 24.9 2.0 21 744-764 35-55 (55)
128 PRK10434 srlR DNA-bindng trans 25.0 99 0.0021 32.2 4.6 41 596-638 6-46 (256)
129 TIGR02325 C_P_lyase_phnF phosp 24.9 51 0.0011 33.6 2.4 36 739-775 37-72 (238)
130 PF06163 DUF977: Bacterial pro 24.9 1.2E+02 0.0026 27.8 4.3 52 710-769 10-61 (127)
131 PF08328 ASL_C: Adenylosuccina 24.9 48 0.001 29.7 1.8 30 8-38 46-75 (115)
132 KOG2747|consensus 24.8 89 0.0019 34.4 4.2 69 568-636 281-354 (396)
133 PRK11169 leucine-responsive tr 24.7 1.1E+02 0.0024 29.4 4.6 44 594-639 13-56 (164)
134 COG4742 Predicted transcriptio 24.6 1.3E+02 0.0028 31.4 5.2 42 600-649 18-59 (260)
135 PRK11179 DNA-binding transcrip 24.0 1.2E+02 0.0027 28.6 4.7 45 593-639 7-51 (153)
136 smart00346 HTH_ICLR helix_turn 23.6 1.3E+02 0.0029 25.2 4.4 45 717-769 10-55 (91)
137 PRK09416 lstR lineage-specific 23.6 2.4E+02 0.0052 26.3 6.2 56 710-767 41-96 (135)
138 PRK06266 transcription initiat 23.5 96 0.0021 30.4 3.9 40 597-638 24-63 (178)
139 PF00196 GerE: Bacterial regul 22.9 1.3E+02 0.0029 23.0 3.9 40 594-637 5-44 (58)
140 PRK14999 histidine utilization 22.7 58 0.0012 33.5 2.3 48 720-775 29-76 (241)
141 PF12395 DUF3658: Protein of u 22.5 1.5E+02 0.0033 26.5 4.7 62 712-776 48-109 (111)
142 PF13542 HTH_Tnp_ISL3: Helix-t 22.4 1.8E+02 0.0039 21.5 4.5 35 596-634 16-50 (52)
143 PF00165 HTH_AraC: Bacterial r 22.2 1E+02 0.0022 21.9 2.8 28 609-636 6-33 (42)
144 PRK03573 transcriptional regul 21.9 72 0.0016 29.7 2.6 26 743-768 55-80 (144)
145 PF14164 YqzH: YqzH-like prote 21.8 3.9E+02 0.0084 21.5 6.1 39 29-69 25-63 (64)
146 PF01399 PCI: PCI domain; Int 21.7 1.6E+02 0.0034 25.2 4.7 31 609-639 58-88 (105)
147 PF07106 TBPIP: Tat binding pr 21.7 1.7E+02 0.0037 28.3 5.2 60 597-669 3-64 (169)
148 cd07377 WHTH_GntR Winged helix 21.5 1.8E+02 0.004 22.3 4.6 33 612-649 26-58 (66)
149 PRK04217 hypothetical protein; 21.5 1.4E+02 0.003 26.8 4.1 40 594-636 44-83 (110)
150 COG1522 Lrp Transcriptional re 21.3 98 0.0021 29.1 3.4 46 713-766 9-54 (154)
151 cd07377 WHTH_GntR Winged helix 21.2 80 0.0017 24.4 2.4 29 740-768 31-59 (66)
152 TIGR02337 HpaR homoprotocatech 21.2 1.5E+02 0.0032 26.5 4.5 46 715-768 31-76 (118)
153 PRK09462 fur ferric uptake reg 21.0 1.7E+02 0.0036 27.6 4.9 50 716-768 21-72 (148)
154 PF02334 RTP: Replication term 20.9 1.1E+02 0.0025 27.1 3.3 55 711-766 17-72 (122)
155 PF00392 GntR: Bacterial regul 20.9 1.5E+02 0.0032 23.3 3.9 37 609-650 21-58 (64)
156 TIGR00373 conserved hypothetic 20.7 1.6E+02 0.0036 28.2 4.8 38 598-637 17-54 (158)
157 PRK13509 transcriptional repre 20.2 1.6E+02 0.0034 30.6 4.9 40 596-637 6-45 (251)
158 PF08820 DUF1803: Domain of un 20.1 74 0.0016 27.5 2.0 27 740-767 34-60 (93)
159 COG2188 PhnF Transcriptional r 20.1 71 0.0015 32.8 2.3 37 738-775 35-71 (236)
No 1
>KOG2285|consensus
Probab=100.00 E-value=1.8e-117 Score=910.99 Aligned_cols=768 Identities=68% Similarity=1.059 Sum_probs=720.7
Q ss_pred CCCCCCcHHhhhhHHHHHHHHHHhcCCCChhHHHHHHHHHHhhcccCCCChhHHHHHHHHHHHHHHHHHHHHHhhccchH
Q psy14208 3 KDKGTQTFEDKWPSMRPIVLKLLQQEPVSQNEWQNLFYAVHVVCLWDEKGPSKIVDALKEDIMNFIRHAQQRVLAHEEDQ 82 (778)
Q Consensus 3 ~~~~~~~fe~~W~~L~~ai~~i~~~~~~~~~sy~~lY~~vY~lc~~~~~~~~~LY~~l~~~i~~~l~~~~~~l~~~~~~~ 82 (778)
|.+...-||+.|...++.+.++++++.+++..|++||..||.+|.+..+++.++|+-++..|.+|+.+...++.+..++.
T Consensus 6 ~~r~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~ 85 (777)
T KOG2285|consen 6 GKRDRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTDG 85 (777)
T ss_pred cccchhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 55566689999999999999999999999999999999999999998889999999999999999998877777766778
Q ss_pred HHHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCCccccccccchhHHHHHHHhhhhhHHHhhHHHHHHHH
Q psy14208 83 ALLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISAEESTVRVLMLDSWNQSIFNDIKQRLQDSA 162 (778)
Q Consensus 83 ~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~~~~~i~~l~l~~f~~~v~~~~~~~l~~~l 162 (778)
.+|..|...|.+|..++.++..-|..|+..-....++ . .+.|. +-.+|..+.+..|.+.+|..++++|....
T Consensus 86 aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs--~-----kk~~~-eds~vRklMLd~WNe~IF~nIk~rLq~sA 157 (777)
T KOG2285|consen 86 ALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGS--V-----KKTPT-EDSSVRKLMLDKWNEIIFMNIKERLQVSA 157 (777)
T ss_pred HHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCC--C-----CCCCC-cchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999875544321 0 12222 23789999999999999999999999999
Q ss_pred HHHHHHHhcCCcCChHhHHHHHHHHHhhcCCCCchhhhhHHhHHHHHHHHHHHHHHHHHHHHHHccChhHHHHHHHHHHH
Q psy14208 163 MKLVQSERNGEAFDSQLVIGVRESYVNLCSNPEDKLQIYREHFEKAYIAATESFYTVKAAEFLQNNGVESYMKYADAKLH 242 (778)
Q Consensus 163 l~~I~~~R~g~~id~~~i~~v~~~~~~l~~~~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~ 242 (778)
+.++..+|+|+.+|.+++.+|.++||.|++++++++.+|.+.||..||+.|.+||+..+..+++++++.+|+++|+..++
T Consensus 158 mklVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~ 237 (777)
T KOG2285|consen 158 MKLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLE 237 (777)
T ss_pred HHHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCC-ccHHHHHHHHHHHHHHHHHHHHHHhhHHHhccchHHHHHHHHHhhhhhcCCchHHHHHHHHHHHHH
Q psy14208 243 EEELRACKYLESS-SSVQLLTDCCVTVLVSSFKNTILAECPKMIKMNETLKLELMMKLLDRIKDGITPMLQDLEAHIVNA 321 (778)
Q Consensus 243 eE~~r~~~yL~~~-~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~ 321 (778)
+|+.|+.+||... .|..++++++.++||.+|.+.|+.+|..||..++.+.|.+||+|+.|+..|++++...+..||...
T Consensus 238 EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlAEC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~sa 317 (777)
T KOG2285|consen 238 EEEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILAECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSA 317 (777)
T ss_pred HHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhh
Confidence 9999999999864 678999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhhhhccCHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhccccccccccCCccccCC-CCCCCC
Q psy14208 322 GLADMIASADIITQDSEKYVERLLELFNQFSKLVKDAFKDDPRFLTARDKAYKNVVNDTTVFKLELPTKQCTG-IKTLPE 400 (778)
Q Consensus 322 g~~~~~~~~~~~~~~~~~~V~~ll~l~~~~~~l~~~~F~~~~~~~~~l~~af~~~lN~~~~~~~~~~~~~~~~-~~~~~~ 400 (778)
|...|....+.++.|+.+||+.|+.++++|..++.++|++||.|..|-+.||+.++|...+|..++|++.++- -...++
T Consensus 318 GLaDM~~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pE 397 (777)
T KOG2285|consen 318 GLADMRNAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPE 397 (777)
T ss_pred hHHHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999754222 122356
Q ss_pred CchhHHHHHHhHHhhccCCCCCCCChHHHHHHHHhHHHhhhcccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHH
Q psy14208 401 SKCPELLANYCDMLLRKTPLSKRLTADEIESKLRNVLLVLKYVQNKDVFMRFHKAHLTRRLILDTSADSEKEENMVEWLR 480 (778)
Q Consensus 401 ~~~~e~La~y~D~~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk 480 (778)
.++||+||.|||.+||+.+.++.++.+|++.+|++++-+++|+.+||+|..|++.||.+||+.+.|++.+.|..|+..|+
T Consensus 398 SKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR 477 (777)
T KOG2285|consen 398 SKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR 477 (777)
T ss_pred cccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH
Confidence 79999999999999999998999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccCC-CCCCCceEEEeccCCCCCCCCCCccccCChHHHHHHHHHHHH
Q psy14208 481 DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGSK-GSIGDSINIKILNAGAWARGSERVTVSLPLELEDYIPEVEDF 559 (778)
Q Consensus 481 ~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~-~~~~~~~~v~VLt~~~WP~~~~~~~~~lP~~l~~~~~~f~~~ 559 (778)
+||+|++|++||.+||+|++.|++++..|+....+.+ .+....+++.||+.|.|...++...+.||.+|++.+-..+.|
T Consensus 478 EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEf 557 (777)
T KOG2285|consen 478 EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEF 557 (777)
T ss_pred HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHH
Confidence 9999999999999999999999999999999886543 234467899999999999987778999999999999999999
Q ss_pred HHhhCCCceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 560 YKKKHSGRKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 560 Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
|+++|+||+|+|.|+++.|+|+|....|.|+|.|+|+||+||.+||+.+++.+|++.+.-+|.+|+.+|.++|-||+..|
T Consensus 558 ykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfP 637 (777)
T KOG2285|consen 558 YKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFP 637 (777)
T ss_pred HhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhh
Confidence 99999999999999999999999877899999999999999999999888999999999999999999999999999999
Q ss_pred ccccceeecccCC-CCCCCCCCCCeEEEccccccccccccccceeeeeccccccccchhhhhhhHhHHHhhhhhhhhhhh
Q psy14208 640 KIKRQILLYSEEV-QSPKDFTEHTSFWINQEFALVKMGKILKRGKINLIGRLQLSTEKSKEEDNESIVQLRILRVQEAII 718 (778)
Q Consensus 640 k~k~~iL~~~~~~-~~~~~~~~~~~f~lN~~F~~~~~~k~~~~~ki~~~~~~~~~~~~~~~~~~~~v~~~R~~~i~A~IV 718 (778)
|.|.+||...|+. .+++||.+++.|.+|.+|+..+|+|.++|.||++++.+|.+++...++..+++.+-|-...|.+||
T Consensus 638 K~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIi 717 (777)
T KOG2285|consen 638 KMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAII 717 (777)
T ss_pred hhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHH
Confidence 9999999998853 578899999999999999999999988999999999999999888888899999999999999999
Q ss_pred hhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 719 KILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 719 RiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
+|||.||+++..+|-.|+++.|+..|-|+..+||..||.|||..|++||++|-++|+|+|
T Consensus 718 kImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 718 KIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999999999999999999999999999999999999999999999999997
No 2
>KOG2166|consensus
Probab=100.00 E-value=1.3e-117 Score=1014.99 Aligned_cols=708 Identities=30% Similarity=0.514 Sum_probs=625.3
Q ss_pred CCCCCCCcHHhhhhHHHHHHHHHHhcC------CCChhHHHHHHHHHHhhcccCCCCh----hHHHHHHHHHHHHHHHHH
Q psy14208 2 LKDKGTQTFEDKWPSMRPIVLKLLQQE------PVSQNEWQNLFYAVHVVCLWDEKGP----SKIVDALKEDIMNFIRHA 71 (778)
Q Consensus 2 ~~~~~~~~fe~~W~~L~~ai~~i~~~~------~~~~~sy~~lY~~vY~lc~~~~~~~----~~LY~~l~~~i~~~l~~~ 71 (778)
+..+.+.+|+.+|+.+++++.++.+.. .++..+|+.+|+++|++|++ ++| ++||+++++++.+|+.+.
T Consensus 2 ~~~~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~--k~~~~~~~~lY~~l~~~~~~yl~~~ 79 (725)
T KOG2166|consen 2 MMAPKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQ--KPPHDYSQQLYDKYREVIEEYLIQT 79 (725)
T ss_pred CccccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhc--cCCCcchHHHHHHHHHHHHHHHHHH
Confidence 455678889999999998888877643 57889999999999999998 555 999999999999999998
Q ss_pred HHHHhhccchHHHHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCCccccccccchhHHHHHHHhhhhhHH
Q psy14208 72 QQRVLAHEEDQALLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISAEESTVRVLMLDSWNQSIF 151 (778)
Q Consensus 72 ~~~l~~~~~~~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~~~~~i~~l~l~~f~~~v~ 151 (778)
+........++.+|+.+...|.+|+.++.+++++|+||||+||.+.. |+. ++.++.. +.+|+..++
T Consensus 80 ~~~~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~--------~~~----~v~~~~~--l~l~r~~v~ 145 (725)
T KOG2166|consen 80 VLPALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSR--------RKL----PTLNEVG--LTCFRDLVY 145 (725)
T ss_pred HHHHHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhc--------CCC----Cccccee--eEEeehHHH
Confidence 75555445678999999999999999999999999999999998741 111 1233333 555555554
Q ss_pred H-hhHHHHHHHHHHHHHHHhcCCcCChHhHHHHHHHHHhhcCCCCchhhhhHHhHHHHHHHHHHHHHHHHHHHHHHccCh
Q psy14208 152 N-DIKQRLQDSAMKLVQSERNGEAFDSQLVIGVRESYVNLCSNPEDKLQIYREHFEKAYIAATESFYTVKAAEFLQNNGV 230 (778)
Q Consensus 152 ~-~~~~~l~~~ll~~I~~~R~g~~id~~~i~~v~~~~~~l~~~~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~ 230 (778)
. ++.+++++++|.+|..+|.|+.||+..|++++++++.+|.+. +++|.+.||++|+++|..||..++..|+...++
T Consensus 146 ~~~~~~~~~~all~lI~~eR~ge~in~~~i~~~~~~~~~lg~~~---~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~ 222 (725)
T KOG2166|consen 146 KFEMQSEAIDALLALIHKEREGEQIDRELIRNVIDVYVELGMGE---LSFYEEDFERKFLQDTASYYSEEASEWLEENSC 222 (725)
T ss_pred HHHHHHHHHHHHHHHHHhhcccccccHHHHhhHHHHHHhccccc---hhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccH
Confidence 4 699999999999999999999999999999999999998654 789999999999999999999999999998899
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHH----HHHhhHHHhccchHHHHHHHHHhhhhhcCC
Q psy14208 231 ESYMKYADAKLHEEELRACKYLESSSSVQLLTDCCVTVLVSSFKNT----ILAECPKMIKMNETLKLELMMKLLDRIKDG 306 (778)
Q Consensus 231 ~~Yl~~v~~~l~eE~~r~~~yL~~~~t~~kl~~~l~~~LI~~~~~~----l~~~~~~ll~~~~~~~L~~ly~l~~~~~~~ 306 (778)
++|+.+|+.++.+|..|+..|++. .+.+++...++.+++..+++. +.+++..|+.+++.++|.+||++++|+++|
T Consensus 223 ~~yl~k~e~~l~~e~~r~~~yl~~-~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~g 301 (725)
T KOG2166|consen 223 LDYLKKIEECLKEERERVTHYLHS-STEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPG 301 (725)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhh-cccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhccccc
Confidence 999999999999999999988877 666666666666666655544 445799999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHhHHHHHhhhhhhccCHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhcccccccccc
Q psy14208 307 ITPMLQDLEAHIVNAGLADMIASADIITQDSEKYVERLLELFNQFSKLVKDAFKDDPRFLTARDKAYKNVVNDTTVFKLE 386 (778)
Q Consensus 307 ~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~V~~ll~l~~~~~~l~~~~F~~~~~~~~~l~~af~~~lN~~~~~~~~ 386 (778)
++++++.|+.|+..+|...+....+....+|..+|+.+++++++|..++..||.+|..|.++++.||..|+|.++.
T Consensus 302 l~~l~~~~~~~~~~eg~~l~~r~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~---- 377 (725)
T KOG2166|consen 302 LEPLASVFKQHVREEGNALVARPAETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA---- 377 (725)
T ss_pred chhHHHHHHHHHHhhHHHHhhhhhhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC----
Confidence 9999999999999999877766554433789999999999999999999999999999999999999999998632
Q ss_pred CCccccCCCCCCCCCchhHHHHHHhHHhhccCCCCCCCChHHHHHHHHhHHHhhhcccChhHHHHHHHHHHHHHHcCCCC
Q psy14208 387 LPTKQCTGIKTLPESKCPELLANYCDMLLRKTPLSKRLTADEIESKLRNVLLVLKYVQNKDVFMRFHKAHLTRRLILDTS 466 (778)
Q Consensus 387 ~~~~~~~~~~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~LakRLL~~~s 466 (778)
..+|+||+|||.+||++ .++.++++++..|++++.+|+|+++||+|+.+|+++||||||+++|
T Consensus 378 ---------------~~~E~la~y~D~~lkk~--~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S 440 (725)
T KOG2166|consen 378 ---------------TSAELLATYCDDILKKG--SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRS 440 (725)
T ss_pred ---------------CcHHHHHHHhHHHhccc--ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCc
Confidence 12699999999999996 4678899999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccCCCCCCCceEEEeccCCCCCCCCCCccccC
Q psy14208 467 ADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGSKGSIGDSINIKILNAGAWARGSERVTVSL 545 (778)
Q Consensus 467 ~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~~l 545 (778)
.|+|+|+.||++|+ +||+ +||+||++|++|+..|++++..|.++ .+.....+++|.|.|||+|+||.++ +.++.|
T Consensus 441 ~sdd~E~~mIsklk~~~g~--~~T~kL~~Mf~D~~~s~~l~~~F~~~-~~~~~~~~~df~v~VLt~g~WP~~~-~~~~~L 516 (725)
T KOG2166|consen 441 ASDDHEKSLITKLKNLCGE--QFTSKLEGMFTDLTLSRELQTAFADY-ANYSANLGIDFTVTVLTTGFWPSYK-STDINL 516 (725)
T ss_pred cchHHHHHHHHHHHHHHHh--HHHHHHHhhcccHHHHHHHHHHHHhh-hchhccCCCceeEEEeecCCcCCcc-CCCCCC
Confidence 99999999999999 9995 99999999999999999999999987 2222223689999999999999974 567999
Q ss_pred ChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCCh
Q psy14208 546 PLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATELPD 625 (778)
Q Consensus 546 P~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~ 625 (778)
|++|..+++.|..||.++|+||+|+|+|++|.|+|.+++.+++|+|+|||+||||||+||+ .+.+|+++|.++|+++.
T Consensus 517 P~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~--~d~lt~~eI~~~t~i~~ 594 (725)
T KOG2166|consen 517 PSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNN--TEKLTYEEILEQTNLGH 594 (725)
T ss_pred ChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccc--hhhccHHHHHHHhCCCH
Confidence 9999999999999999999999999999999999999999999999999999999999999 58999999999999999
Q ss_pred HHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccccccccccccceeeeeccccccccchhhhhhhHhH
Q psy14208 626 PELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFALVKMGKILKRGKINLIGRLQLSTEKSKEEDNESI 705 (778)
Q Consensus 626 ~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~~~~~~k~~~~~ki~~~~~~~~~~~~~~~~~~~~v 705 (778)
+++.+.|+||+.. | .+++.. |. +.+ ++++.|.+|.+|++ + .+|++|+..+. .+.+.+.+.+
T Consensus 595 ~~l~~~L~Sl~~~-K--~~v~~~-~~---s~~-~~~~~~~~N~~f~s----k-~~Rv~i~~~~~------~e~~~~~~~v 655 (725)
T KOG2166|consen 595 EDLARLLQSLSCL-K--YKILLK-PM---SRT-SPNDEFAFNSKFTS----K-MRRVKIPLPPM------DERKKVVEDV 655 (725)
T ss_pred HHHHHHHHHHHHH-h--HhhccC-cc---ccC-CCCcEEEeeccccC----c-ceeeccCCCCc------hhHHHHHhhh
Confidence 9999999999853 3 235554 43 333 68999999999994 3 36778775432 1567888999
Q ss_pred HHhhhhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEe
Q psy14208 706 VQLRILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVY 776 (778)
Q Consensus 706 ~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Y 776 (778)
++||++.|+||||||||+||.|.|++|+.||++|+++||.|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 656 e~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 656 DKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred hhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 99999999999999999999999999999999999999999999999999999999999999 89999998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-114 Score=944.32 Aligned_cols=721 Identities=25% Similarity=0.427 Sum_probs=630.6
Q ss_pred CCCCcHHhhhhHHHHHHHHHHhc--CCCChhHHHHHHHHHHhhcccCCC--------------ChhHHHHHHHHHHHHHH
Q psy14208 5 KGTQTFEDKWPSMRPIVLKLLQQ--EPVSQNEWQNLFYAVHVVCLWDEK--------------GPSKIVDALKEDIMNFI 68 (778)
Q Consensus 5 ~~~~~fe~~W~~L~~ai~~i~~~--~~~~~~sy~~lY~~vY~lc~~~~~--------------~~~~LY~~l~~~i~~~l 68 (778)
.+..||+++|+.++.||++|+.. ..+...+||++|+.+|+.|+++.+ .|+.+|+++....++++
T Consensus 15 ~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~i 94 (773)
T COG5647 15 LSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNYI 94 (773)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999931 356789999999999999998632 37889999999999998
Q ss_pred HHHHHHHhhccchHHHHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCCccccccccchhHHHHHHHhhhh
Q psy14208 69 RHAQQRVLAHEEDQALLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISAEESTVRVLMLDSWNQ 148 (778)
Q Consensus 69 ~~~~~~l~~~~~~~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~~~~~i~~l~l~~f~~ 148 (778)
........ ......||..|+..|++|..++.+++++|.||||+|++..+. +......+.++++..|+.
T Consensus 95 ~~~~~~~s-~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~-----------~~~~~~E~~slcl~~~~~ 162 (773)
T COG5647 95 EEYNRGRS-QENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARY-----------DKTLVFEVYSLCLVKEKI 162 (773)
T ss_pred HHhccccc-chhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccC-----------CCccceeeehhhhhHHHH
Confidence 87543311 123478999999999999999999999999999999994321 111347788899999999
Q ss_pred hHHHhhHHHHHHHHHHHHHHHhcCCcCChHhHHHHHHHHHhhcCCC---CchhhhhHHhHHHHHHHHHHHHHHHHHHHHH
Q psy14208 149 SIFNDIKQRLQDSAMKLVQSERNGEAFDSQLVIGVRESYVNLCSNP---EDKLQIYREHFEKAYIAATESFYTVKAAEFL 225 (778)
Q Consensus 149 ~v~~~~~~~l~~~ll~~I~~~R~g~~id~~~i~~v~~~~~~l~~~~---~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l 225 (778)
.+|.++.+.+++.+|..+.+.|.|+.||+..+..++.|+.+|+... ..++++|.+.|||.||+.|.+||..++++.+
T Consensus 163 ~~f~~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i 242 (773)
T COG5647 163 ESFRLIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVI 242 (773)
T ss_pred HHHHhhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999996311 1236899999999999999999999999999
Q ss_pred HccChhHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHHHHH---hhHHHhccchHHHHHHHHHhhhh
Q psy14208 226 QNNGVESYMKYADAKLHEEELRACKYLESSSSVQLLTDCCVTVLVSSFKNTILA---ECPKMIKMNETLKLELMMKLLDR 302 (778)
Q Consensus 226 ~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~~t~~kl~~~l~~~LI~~~~~~l~~---~~~~ll~~~~~~~L~~ly~l~~~ 302 (778)
+.+++.+||.+|+.++++|.++++.|++. ++..+|.++++++||..|.+.+.+ ++..+++..+.+.|..||+++++
T Consensus 243 ~~~~~~eyL~ka~~~~~~E~~~v~~yl~~-~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se 321 (773)
T COG5647 243 ELLSVTEYLEKAHKILEREEELVEIYLKV-STKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSE 321 (773)
T ss_pred HHcCHHHHHHHHHHHHHHHHHHHHHHHhc-cccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhh
Confidence 99999999999999999999999999999 999999999999999999999998 79999999999999999999999
Q ss_pred hcCCchHHHHHHHHHHHHHhH--HH-HHhhhh---------hhccCHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHH
Q psy14208 303 IKDGITPMLQDLEAHIVNAGL--AD-MIASAD---------IITQDSEKYVERLLELFNQFSKLVKDAFKDDPRFLTARD 370 (778)
Q Consensus 303 ~~~~~~~l~~~~~~~i~~~g~--~~-~~~~~~---------~~~~~~~~~V~~ll~l~~~~~~l~~~~F~~~~~~~~~l~ 370 (778)
++.|+.+|.+.|.+||+..|. .+ ...... .....|..||+.++..++.+..++.+.|.+|..+.++++
T Consensus 322 ~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~ 401 (773)
T COG5647 322 TKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALG 401 (773)
T ss_pred hhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHH
Confidence 999999999999999999992 11 110100 012357889999999999999999999999999999999
Q ss_pred HHHHHhccccccccccCCccccCCCCCCCCCchhHHHHHHhHHhhccCCCCCCCChHHHHHHHHhHHHhhhcccChhHHH
Q psy14208 371 KAYKNVVNDTTVFKLELPTKQCTGIKTLPESKCPELLANYCDMLLRKTPLSKRLTADEIESKLRNVLLVLKYVQNKDVFM 450 (778)
Q Consensus 371 ~af~~~lN~~~~~~~~~~~~~~~~~~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~Kd~F~ 450 (778)
+||..|+|.+. +++...||+||+|+|.+||++. +......++..+.+++.||+|+.+||+|+
T Consensus 402 ~AF~~fin~~~----------------sa~~~~~e~Laky~D~~lkk~~--k~s~~~~i~~~l~~iitLfryv~~KDvFe 463 (773)
T COG5647 402 NAFKTFINGNE----------------SADSGPSEYLAKYIDGLLKKDG--KQSFIGKIKDLLQDIITLFRYVEEKDVFE 463 (773)
T ss_pred HHHHHHhcccc----------------ccccccHHHHHHHhHHHhhccc--cccccccHHHHHHHHHHHHHHhhhhHHHH
Confidence 99999999852 2345789999999999999985 33334568888999999999999999999
Q ss_pred HHHHHHHHHHHcCCCCCChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccCCCCCCCceEEEec
Q psy14208 451 RFHKAHLTRRLILDTSADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGSKGSIGDSINIKIL 529 (778)
Q Consensus 451 ~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~v~VL 529 (778)
++|+++||||||+++|+|.++|..||++|| .|| .+||+|+++||+||..|.+++..|++...+.+ ...++.|.||
T Consensus 464 ~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g--~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~--~~~Dl~v~VL 539 (773)
T COG5647 464 KYYKKLLAKRLLNGRSASAQAELKMISMLKKVCG--QEFTSKLEGMFRDISLSSEFTEAFQHSPQSYN--KYLDLFVWVL 539 (773)
T ss_pred HHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhh--hHHHHHHHHHHHhcchhHHHHHHHhhCchhhc--cccchhHHHH
Confidence 999999999999999999999999999999 999 59999999999999999999999987653222 2468999999
Q ss_pred cCCCCCCCCCCccccCChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEecCeeEEEE---ecHHHHHHHHhhcC
Q psy14208 530 NAGAWARGSERVTVSLPLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSNEVGKYDLD---VTTFQMAVLFAWNE 606 (778)
Q Consensus 530 t~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~---~s~~Q~~ILl~FN~ 606 (778)
++.+||.+++...+.||++|.+.++.|++||.+||+||+|.|.|+||+|+|++.|+.+++.+. ++++|+.|+++||+
T Consensus 540 t~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~ 619 (773)
T COG5647 540 TQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFND 619 (773)
T ss_pred HHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcC
Confidence 999999887788999999999999999999999999999999999999999999988765444 56789999999999
Q ss_pred CCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccccccccccccceeeee
Q psy14208 607 RPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFALVKMGKILKRGKINL 686 (778)
Q Consensus 607 ~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~~~~~~k~~~~~ki~~ 686 (778)
++++|+++|.+.|+|+..++++.|+||+.+ |.. +|.+. ++..++++.|.+|.+|++ + ..|++|+.
T Consensus 620 --~e~lt~eei~e~T~l~~~dl~~~L~sl~~a-k~~--~l~~~-----~~~~~p~~~fy~ne~f~~----~-~~rIki~~ 684 (773)
T COG5647 620 --HEELTFEEILELTKLSTDDLKRVLQSLSCA-KLV--VLLKD-----DKLVSPNTKFYVNENFSS----K-LERIKINY 684 (773)
T ss_pred --ccceeHHHHHhhcCCChhhHHHHHHHHHhh-hee--eeccc-----cccCCCCceEEEcccccc----c-cceeeecc
Confidence 699999999999999999999999999964 322 34332 344568999999999994 2 36788876
Q ss_pred ccccccccchhhhhhhHhHHHhhhhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc
Q psy14208 687 IGRLQLSTEKSKEEDNESIVQLRILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR 766 (778)
Q Consensus 687 ~~~~~~~~~~~~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R 766 (778)
+.. .....++.++++.+++||+..+|||||||||+||+|.|++|+++|+.+.++||.|++.+||++|+.|||||||+|
T Consensus 685 ~~~--~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR 762 (773)
T COG5647 685 IAE--SECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLER 762 (773)
T ss_pred ccc--chhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHh
Confidence 632 222234566778999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCceEecC
Q psy14208 767 DDDDINVFVYLA 778 (778)
Q Consensus 767 d~~d~~~y~Yia 778 (778)
.++| .+|+|+|
T Consensus 763 ~~dd-~iY~YLa 773 (773)
T COG5647 763 QADD-EIYVYLA 773 (773)
T ss_pred ccCC-ceeeecC
Confidence 9888 8999997
No 4
>KOG2284|consensus
Probab=100.00 E-value=9.5e-112 Score=861.00 Aligned_cols=703 Identities=27% Similarity=0.479 Sum_probs=633.3
Q ss_pred CCCCCcHHhhhhHHHHHHHHHHhcCCCChhHHHHHHHHHHhhcccC-CCChhHHHHHHHHHHHHHHHHHHHHHhhccchH
Q psy14208 4 DKGTQTFEDKWPSMRPIVLKLLQQEPVSQNEWQNLFYAVHVVCLWD-EKGPSKIVDALKEDIMNFIRHAQQRVLAHEEDQ 82 (778)
Q Consensus 4 ~~~~~~fe~~W~~L~~ai~~i~~~~~~~~~sy~~lY~~vY~lc~~~-~~~~~~LY~~l~~~i~~~l~~~~~~l~~~~~~~ 82 (778)
.|.+++||+.|..|.+.|..|+.-+++++..|.+-|+.||.+|+.. .+-||+||..++.++++|+++.+......+ .+
T Consensus 5 kp~vv~fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~-p~ 83 (728)
T KOG2284|consen 5 KPKVVEFDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVD-PD 83 (728)
T ss_pred CceeeeHHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCC-HH
Confidence 4677899999999999999999888999999999999999999986 567999999999999999998776555433 35
Q ss_pred HHHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCC---ccccccccchhHHHHHHHhhhhhHHHhhHHHHH
Q psy14208 83 ALLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNN---NKQKISAEESTVRVLMLDSWNQSIFNDIKQRLQ 159 (778)
Q Consensus 83 ~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~---~~~~~~~~~~~i~~l~l~~f~~~v~~~~~~~l~ 159 (778)
.+|..|.+.|+.|..+..++..+|.|||..||+++.+| ..++. |.-...+++..|..+|+.+|++.+..++...|+
T Consensus 84 ~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t-~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~i~~~lv 162 (728)
T KOG2284|consen 84 LLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCT-DLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKTILPQLV 162 (728)
T ss_pred HHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhccc-chhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999987543 33332 112233366889999999999999999999999
Q ss_pred HHHHHHHHHHhcCCcCC-hHhHHHHHHHHHhhcCC--------------CCchhhhhHHhHHHHHHHHHHHHHHHHHHHH
Q psy14208 160 DSAMKLVQSERNGEAFD-SQLVIGVRESYVNLCSN--------------PEDKLQIYREHFEKAYIAATESFYTVKAAEF 224 (778)
Q Consensus 160 ~~ll~~I~~~R~g~~id-~~~i~~v~~~~~~l~~~--------------~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~ 224 (778)
..+|..|.++|.|+..+ ...+.+|+.+||.+... .+.++.+|++.||.|||.+|..||+.+|+..
T Consensus 163 ~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~ 242 (728)
T KOG2284|consen 163 KLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQKM 242 (728)
T ss_pred HHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHHH
Confidence 99999999999999998 67899999999988631 1235889999999999999999999999999
Q ss_pred HHccChhHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHHHHHhhHHHhccchHHHHHHHHHhhhhhc
Q psy14208 225 LQNNGVESYMKYADAKLHEEELRACKYLESSSSVQLLTDCCVTVLVSSFKNTILAECPKMIKMNETLKLELMMKLLDRIK 304 (778)
Q Consensus 225 l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~l~~~~~ 304 (778)
+.+.+|++|+.+|..++++|+-||++|||+ ++..+++..|.+.+|.+|.+.|...|..+|.+.+..||+.||.|+.-+.
T Consensus 243 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 243 LTDLSCSEYMEQVIVLLEQEEMRAKKYLHE-SSVEKVITLCQKVMIKAHKDKLHAVCHDLITNEENKDLRNMYRLLKPIQ 321 (728)
T ss_pred HhhccHHHHHHHHHHHhhHHHHHHHHhcCh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHh
Confidence 999999999999999999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred CCchHHHHHHHHHHHHHhHHHHHhhhhhhccCHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhcccccccc
Q psy14208 305 DGITPMLQDLEAHIVNAGLADMIASADIITQDSEKYVERLLELFNQFSKLVKDAFKDDPRFLTARDKAYKNVVNDTTVFK 384 (778)
Q Consensus 305 ~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~V~~ll~l~~~~~~l~~~~F~~~~~~~~~l~~af~~~lN~~~~~~ 384 (778)
-|+..+.+.|+.||.+.|.+..+.... .+-|..||+.++.+|.+|..++.-.|.+|..|..+++.|...++|....
T Consensus 322 ~gl~~mv~e~~~~v~~~gl~a~s~lt~--en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~ep-- 397 (728)
T KOG2284|consen 322 AGLSVMVKEFEEYVKKKGLEAVSRLTG--ENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEP-- 397 (728)
T ss_pred cCchHHHHHHHHHHHHHHHHHHhhhcc--ccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCC--
Confidence 999999999999999999987765432 2458999999999999999999999999999999999999999997521
Q ss_pred ccCCccccCCCCCCCCCchhHHHHHHhHHhhccCCCCCCCChHHHHHHHHhHHHhhhcccChhHHHHHHHHHHHHHHcCC
Q psy14208 385 LELPTKQCTGIKTLPESKCPELLANYCDMLLRKTPLSKRLTADEIESKLRNVLLVLKYVQNKDVFMRFHKAHLTRRLILD 464 (778)
Q Consensus 385 ~~~~~~~~~~~~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~LakRLL~~ 464 (778)
+.+-.++||.||+|||.+|+|+. +|+++.++|.+|+..+.+|+|++|||+|.++|.++||+||+.+
T Consensus 398 ------------g~sv~ka~e~la~y~d~llkks~--kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~ 463 (728)
T KOG2284|consen 398 ------------GQSVPKASERLARYTDGLLKKST--KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIAS 463 (728)
T ss_pred ------------CccccchHHHHHHHhhhHHhhhh--cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhh
Confidence 12346889999999999999984 8899999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccCCCCCCCceEEEeccCCCCCCCCCCccc
Q psy14208 465 TSADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGSKGSIGDSINIKILNAGAWARGSERVTV 543 (778)
Q Consensus 465 ~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~ 543 (778)
.|.|.|.|..||++|| .||+ +||+++- +.|++.|.+++.+|.+.+. ++
T Consensus 464 ~s~smd~ee~minklkqacgy--efts~~~--~td~~~s~~lnn~f~~~i~---------------------------nf 512 (728)
T KOG2284|consen 464 TSISMDAEELMINKLKQACGY--EFTSSWP--LTDPQLSTNLNNQFAQDIA---------------------------NF 512 (728)
T ss_pred cccccchHHHHHHHHHHHhCc--eecccCC--CCChhhccccchhHHHHHH---------------------------hc
Confidence 9999999999999999 9997 9999998 8999999999999986543 27
Q ss_pred cCChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCC
Q psy14208 544 SLPLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATEL 623 (778)
Q Consensus 544 ~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i 623 (778)
.+|.+|+..++.|+.||..+|+||+|+|++.++.|++++++-++.|.-.|++|||++||+||. .+.+++++|.+.+|+
T Consensus 513 ~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~--~~~i~~k~i~~~~~~ 590 (728)
T KOG2284|consen 513 HLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFER--RDAILVKDIGEEIGV 590 (728)
T ss_pred cchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcc--cccchHHhhhhhhCc
Confidence 899999999999999999999999999999999999999998899999999999999999999 589999999999999
Q ss_pred ChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccccccccccccceeeeec-cccccccchhhhhhh
Q psy14208 624 PDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFALVKMGKILKRGKINLI-GRLQLSTEKSKEEDN 702 (778)
Q Consensus 624 ~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~~~~~~k~~~~~ki~~~-~~~~~~~~~~~~~~~ 702 (778)
+.++|.+++.++.+. + +|..+. .++..+..|++|.+|++ | |.|..+. |+++..++.+.+.+.
T Consensus 591 ~~~~l~kti~tildv---~--~~~~d~-----~~~~a~s~~~lnm~~ts----k---r~kf~~~~p~~~k~~~~e~e~~~ 653 (728)
T KOG2284|consen 591 SGDYLLKTIRTILDV---T--LLTCDD-----QNLTADSLVRLNMSMTS----K---RMKFRLQAPQVNKAVEKEQEAVA 653 (728)
T ss_pred cHHHHHHHHHHHHhc---e--eecccc-----cccChhhhhhccccccc----c---ceeeEecchhhccccHHHHHHHH
Confidence 999999999999863 3 776543 46778889999999994 3 3444332 344555666777888
Q ss_pred HhHHHhhhhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 703 ESIVQLRILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 703 ~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
..|.+||++.++||||||||+||.+.|+.|+.||+.|.++||.|++++||+|||.||++-||+|...+ +.|.|+|
T Consensus 654 ~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 654 NTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 88999999999999999999999999999999999999999999999999999999999999998775 9999997
No 5
>KOG2167|consensus
Probab=100.00 E-value=2.7e-107 Score=866.65 Aligned_cols=651 Identities=29% Similarity=0.462 Sum_probs=592.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc-chHHHHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCCccccccc
Q psy14208 55 KIVDALKEDIMNFIRHAQQRVLAHE-EDQALLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISA 133 (778)
Q Consensus 55 ~LY~~l~~~i~~~l~~~~~~l~~~~-~~~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~ 133 (778)
.||+++++.+++|+.....++.... +...+|+.+.++|..|...+.+++.+|.||||.|+...++
T Consensus 1 ~ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp-------------- 66 (661)
T KOG2167|consen 1 VLYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNP-------------- 66 (661)
T ss_pred ChHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCC--------------
Confidence 3899999999999997655554322 3467999999999999999999999999999999987422
Q ss_pred cchhHHHHHHHhhhhhHHH----hhHHHHHHHHHHHHHHHhcCCcCChHhHHHHHHHHHhhcCCCCchhhhhHHhHHHHH
Q psy14208 134 EESTVRVLMLDSWNQSIFN----DIKQRLQDSAMKLVQSERNGEAFDSQLVIGVRESYVNLCSNPEDKLQIYREHFEKAY 209 (778)
Q Consensus 134 ~~~~i~~l~l~~f~~~v~~----~~~~~l~~~ll~~I~~~R~g~~id~~~i~~v~~~~~~l~~~~~~~~~~Y~~~FE~~~ 209 (778)
-+++++++++.+|+.+++. .+..++.++++.+|+++|.|+.+|+.++++++.|+..+ .+|.+.|++.|
T Consensus 67 ~v~siWem~l~LFR~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~--------~iY~esF~~~f 138 (661)
T KOG2167|consen 67 YVLSIWEMGLQLFRAHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL--------QIYKESFELTF 138 (661)
T ss_pred CcCCHHHhhHHHHHHHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH--------HhhhhhhHHHH
Confidence 2489999999999999887 47888999999999999999999999999999998765 47999999999
Q ss_pred HHHHHHHHHHHHHHHHHccChhHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHHHHH-hhHHHhccc
Q psy14208 210 IAATESFYTVKAAEFLQNNGVESYMKYADAKLHEEELRACKYLESSSSVQLLTDCCVTVLVSSFKNTILA-ECPKMIKMN 288 (778)
Q Consensus 210 L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~~t~~kl~~~l~~~LI~~~~~~l~~-~~~~ll~~~ 288 (778)
+..+.++|.+++.+..++..+++||.++++++.+|.+|+..|++. +|...+..++++.|+..|++.|+. ++..+++.+
T Consensus 139 ls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~-st~k~l~atV~~~LL~~hL~~IL~kgl~~lvDm~ 217 (661)
T KOG2167|consen 139 LSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDS-STKKPLIATVERCLLSRHLDLILTKGLDSLVDMR 217 (661)
T ss_pred HHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhccc-ccccchHHHHHHHHHHHHHHHHHhcchHHhhhhh
Confidence 999999999999999999999999999999999999999999999 787779999999999999999887 799999999
Q ss_pred hHHHHHHHHHhhhhhcCCchHHHHHHHHHHHHHhHHHHHhhhhhhccCHHHHHHHHHHHHHHHHHHHHHHhcCC--hHHH
Q psy14208 289 ETLKLELMMKLLDRIKDGITPMLQDLEAHIVNAGLADMIASADIITQDSEKYVERLLELFNQFSKLVKDAFKDD--PRFL 366 (778)
Q Consensus 289 ~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~V~~ll~l~~~~~~l~~~~F~~~--~~~~ 366 (778)
+..++.+||.+++++.+|...++..|++|+++-|..++... .-...+|+.+++++++.+-++..||..+ ..|.
T Consensus 218 q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de-----~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~ 292 (661)
T KOG2167|consen 218 QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDE-----EKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFL 292 (661)
T ss_pred hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCc-----hhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHH
Confidence 99999999999999998999999999999999998755211 1135799999999999999999999999 9999
Q ss_pred HHHHHHHHHhccccccccccCCccccCCCCCCCCCchhHHHHHHhHHhhccCCCCCCCChHHHHHHHHhHHHhhhcccCh
Q psy14208 367 TARDKAYKNVVNDTTVFKLELPTKQCTGIKTLPESKCPELLANYCDMLLRKTPLSKRLTADEIESKLRNVLLVLKYVQNK 446 (778)
Q Consensus 367 ~~l~~af~~~lN~~~~~~~~~~~~~~~~~~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~K 446 (778)
.++.+||+.|+|.. .+++||+||+|.|.+|+.| +++.++++++..++.++.+||||..|
T Consensus 293 ~~~~~afe~fink~-------------------~~rpAelIak~~dt~Lr~g--nk~~~d~~l~~~~d~i~~lfr~i~gk 351 (661)
T KOG2167|consen 293 NSMSKAFETFINKR-------------------RNRPAELIAKYVDTKLRAG--NKETSDEELEFVLDKILVLFRFIHGK 351 (661)
T ss_pred HHHHHHHHHHHhcc-------------------cCCHHHHHHHHHHHHHHhc--cccccchhHHHHHHHHHHHHHHHhcc
Confidence 99999999999963 3679999999999999987 57778899999999999999999999
Q ss_pred hHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccC-CCCCCCce
Q psy14208 447 DVFMRFHKAHLTRRLILDTSADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGS-KGSIGDSI 524 (778)
Q Consensus 447 d~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~-~~~~~~~~ 524 (778)
|+||.+|++.||+|||.++|+|.|+|++|+++|| +|| +.||+||+|||+|+..|++++..|+++...+ ....++ +
T Consensus 352 dvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecg--s~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~ 428 (661)
T KOG2167|consen 352 DVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECG--SAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-L 428 (661)
T ss_pred HHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcc--hHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-e
Confidence 9999999999999999999999999999999999 999 7999999999999999999999999985433 222233 8
Q ss_pred EEEeccCCCCCCCCCCccccCChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhh
Q psy14208 525 NIKILNAGAWARGSERVTVSLPLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAW 604 (778)
Q Consensus 525 ~v~VLt~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~F 604 (778)
.|.|||.|+||.++ +..+.||++|..+++.|+.||..+|.||+|+|++++|+|.+++.|+.|+.+|.+|++|++|||+|
T Consensus 429 ~v~vlt~~yWpty~-~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~f 507 (661)
T KOG2167|consen 429 TVNVLTMGYWPTYP-PMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMF 507 (661)
T ss_pred EEEeecccccCCCC-chhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhcc
Confidence 99999999999995 67999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccccccccccccceee
Q psy14208 605 NERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFALVKMGKILKRGKI 684 (778)
Q Consensus 605 N~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~~~~~~k~~~~~ki 684 (778)
|+ .+.+|++||.+.|+|.+.+|.|+|+||+ +||.| +|.+.|++ +++.+++.|.+|.+|+. | ..|+||
T Consensus 508 n~--~~~~s~~ei~~~t~i~d~el~rtlqsl~-cgr~r--vl~~~pkg---~~~~~~~~f~~n~~f~~----k-l~riki 574 (661)
T KOG2167|consen 508 NE--GEGLSYEEIKESTGIEDIELRRTLQSLA-CGRAR--VLQKVPKG---KEVEDGDKFIVNDKFTH----K-LYRIKI 574 (661)
T ss_pred CC--CCcccHHHHHHhccccHHHHHHHHHHHh-cccce--eeeeCCCC---CCCCCCCEEEechhhcc----h-hheehH
Confidence 98 4889999999999999999999999998 47877 99999864 56779999999999994 4 478898
Q ss_pred eeccccccccchhhhhhhHhHHHhhhhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccc
Q psy14208 685 NLIGRLQLSTEKSKEEDNESIVQLRILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYM 764 (778)
Q Consensus 685 ~~~~~~~~~~~~~~~~~~~~v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl 764 (778)
+.+.- .++..+++.+.++|.+||++.||||||||||+||+|+|+.|+.++.+||+ |+..+ ++|+|||+||+|||+
T Consensus 575 nqi~~--ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~ 649 (661)
T KOG2167|consen 575 NQIQM--KETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYL 649 (661)
T ss_pred hhhhH--HHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHh
Confidence 86621 23455678899999999999999999999999999999999999999997 98887 999999999999999
Q ss_pred ccCCCCCCceEecC
Q psy14208 765 RRDDDDINVFVYLA 778 (778)
Q Consensus 765 ~Rd~~d~~~y~Yia 778 (778)
+|| +| +.|.|||
T Consensus 650 erd-~n-~~y~yva 661 (661)
T KOG2167|consen 650 ERD-DN-NIYNYVA 661 (661)
T ss_pred ccc-cc-ccccccC
Confidence 999 44 9999998
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=2.2e-91 Score=820.65 Aligned_cols=585 Identities=31% Similarity=0.594 Sum_probs=520.6
Q ss_pred hhHHHHHHHHHHhcCCCChhHHHHHHHHHHhhcccCCCChhHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHH
Q psy14208 14 WPSMRPIVLKLLQQEPVSQNEWQNLFYAVHVVCLWDEKGPSKIVDALKEDIMNFIRHAQQRVLAHEEDQALLKAYIQEWS 93 (778)
Q Consensus 14 W~~L~~ai~~i~~~~~~~~~sy~~lY~~vY~lc~~~~~~~~~LY~~l~~~i~~~l~~~~~~l~~~~~~~~~L~~~~~~W~ 93 (778)
|+.|++||+.|+ .+.+++.+||++|++||++|.. ++|+.||+++++.+.+|+..+..++.+. +++.+|..|...|.
T Consensus 1 W~~l~~~i~~i~-~~~~~~~~~~~lY~~vy~l~~~--~~~~~LY~~l~~~i~~~~~~~~~~l~~~-~~~~~l~~~~~~w~ 76 (588)
T PF00888_consen 1 WEILEEAIDQIF-KKSISKLSYMELYTCVYNLCDN--KYGEQLYDKLKEFISEYLKNIIESLLSS-SDEDLLEEYVQEWE 76 (588)
T ss_dssp HHHHHHHHHHHH-TT-GCCSHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHHHHHHHHHHCTT-TTCHHHHHHHHHHH
T ss_pred ChHHHHHHHHHH-cCCCChhHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHHHHHHhc-ChhHHHHHHHHHHH
Confidence 999999999999 4578999999999999999986 9999999999999999999988887765 57899999999999
Q ss_pred HHHHhhcccCcccccchhhhhccccccccccCCccccccccchhHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHhcCC
Q psy14208 94 KFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISAEESTVRVLMLDSWNQSIFNDIKQRLQDSAMKLVQSERNGE 173 (778)
Q Consensus 94 ~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~~~~~i~~l~l~~f~~~v~~~~~~~l~~~ll~~I~~~R~g~ 173 (778)
+|+.++.+|+++|+||||+|+.+ . +|++.|+.++++.++++++.+|.++|.|+
T Consensus 77 ~~~~~~~~i~~if~yLdr~yv~~-------------------~--------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~ 129 (588)
T PF00888_consen 77 KYKKAIKYISDIFSYLDRNYVKR-------------------N--------LFREQVFKPLKDKIINALLNLIKNEREGE 129 (588)
T ss_dssp HHHHHHHHHHHHTHHHHHTSTTT-------------------T--------HHHHHTTTSHHHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHhHhhhhh-------------------h--------hHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999775 2 99999999999999999999999999999
Q ss_pred cCChHhHHHHHHHHHhhcCCCCchhhhhHHhHHHHHHHHHHHHHHHHHHHHHHccChhHHHHHHHHHHHHHHHHHhhhcC
Q psy14208 174 AFDSQLVIGVRESYVNLCSNPEDKLQIYREHFEKAYIAATESFYTVKAAEFLQNNGVESYMKYADAKLHEEELRACKYLE 253 (778)
Q Consensus 174 ~id~~~i~~v~~~~~~l~~~~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~ 253 (778)
.+|..+++++++++++|+ +..+|.+.||++||+.|.+||+.++ ++..++.+|+.+|++++.+|.+||..||+
T Consensus 130 ~~~~~~l~~~~~~~~~l~-----~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~ 201 (588)
T PF00888_consen 130 KIDRSLLKNVIEMFVELG-----SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLH 201 (588)
T ss_dssp TSHHHHHHHHHHHHHHTT-----HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-
T ss_pred cccHHHHHHHHHHHhccc-----hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcc
Confidence 999999999999999997 4679999999999999999999999 77789999999999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHhhHHHhccchHHHHHHHHHhhhhhcCCchHHHHHHHHHHHHHhHHHHHhhhhhh
Q psy14208 254 SSSSVQLLTDCCVTVLVSSFKNTILAECPKMIKMNETLKLELMMKLLDRIKDGITPMLQDLEAHIVNAGLADMIASADII 333 (778)
Q Consensus 254 ~~~t~~kl~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~ 333 (778)
+ +|..++.+++.++||.+|.+.|.+++..|+.+++.++|++||+++++++++++.+++.|++||.+.|.+.+.... .
T Consensus 202 ~-~t~~ki~~~l~~~LI~~~~~~l~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~--~ 278 (588)
T PF00888_consen 202 P-STKEKIIKTLEEVLISDHLDELSSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFE--K 278 (588)
T ss_dssp G-GGHHHHHHHHHHHHTGGGHHHHHTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHC--C
T ss_pred h-hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcc--c
Confidence 9 899999999999999999999988999999999999999999999999999999999999999999998876543 1
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhccccccccccCCccccCCCCCCCCCchhHHHHHHhHH
Q psy14208 334 TQDSEKYVERLLELFNQFSKLVKDAFKDDPRFLTARDKAYKNVVNDTTVFKLELPTKQCTGIKTLPESKCPELLANYCDM 413 (778)
Q Consensus 334 ~~~~~~~V~~ll~l~~~~~~l~~~~F~~~~~~~~~l~~af~~~lN~~~~~~~~~~~~~~~~~~~~~~~~~~e~La~y~D~ 413 (778)
..+|..||+.+++++++|+.++.+||++++.|..++++||+.++|.+ ..++|++||+|||.
T Consensus 279 ~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~-------------------~~~~~e~La~y~d~ 339 (588)
T PF00888_consen 279 SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN-------------------NNKIPELLAKYCDS 339 (588)
T ss_dssp GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS-------------------TSHHHHHHHHHHHH
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC-------------------CcchHHHHHHHhhH
Confidence 35678999999999999999999999999999999999999999974 25799999999999
Q ss_pred hhccCCCCCCCChHHHHHHHHhHHHhhhcccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHH-HcCCChhhHHHH
Q psy14208 414 LLRKTPLSKRLTADEIESKLRNVLLVLKYVQNKDVFMRFHKAHLTRRLILDTSADSEKEENMVEWLR-DVGMPADYVNKL 492 (778)
Q Consensus 414 ~lk~~~~~~~~~~~e~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl 492 (778)
+|+++. ++.++++++..++.++.+|+|+++||+|+.+|+++||+|||.+++.+.+.|+.+|++|+ +|| .+||++|
T Consensus 340 ~l~~~~--~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g--~~~~~kl 415 (588)
T PF00888_consen 340 LLRKSN--KKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECG--SSYTSKL 415 (588)
T ss_dssp HHBSSC--CCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCC--CHHHHHH
T ss_pred hhhhcc--cccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccC--chhHHHH
Confidence 999985 55678889999999999999999999999999999999999999999999999999999 999 5999999
Q ss_pred HHHHHhHHHhHHHHHHHHHHhccCCCCC--CCceEEEeccCCCCCCCCCCccccCChHHHHHHHHHHHHHHhhCCCceeE
Q psy14208 493 ARMFQDIKVSQDLNYQFKQSYRGSKGSI--GDSINIKILNAGAWARGSERVTVSLPLELEDYIPEVEDFYKKKHSGRKLQ 570 (778)
Q Consensus 493 ~~Ml~D~~~S~~l~~~f~~~~~~~~~~~--~~~~~v~VLt~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~ 570 (778)
++|++|++.|++++++|++...+.+... +++|+|.||++|+||..+...++.+|++|+.+++.|++||+.+|+||+|+
T Consensus 416 ~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~ 495 (588)
T PF00888_consen 416 EVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLT 495 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEE
T ss_pred HHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 9999999999999999999887654332 67899999999999998644459999999999999999999999999999
Q ss_pred eccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 571 WYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 571 w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
|+|++|+|+|++++++++|+++||++||+||++||+ .+++|+++|++.||+++++++++|.+|+..+ +|...
T Consensus 496 w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~-----~l~~~- 567 (588)
T PF00888_consen 496 WLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFND--NDSLTVEEISEKTGISEEELKRALKSLVKSK-----ILILL- 567 (588)
T ss_dssp EEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGS--SSEEEHHHHHHHC---HHHHHHHHHCCCTTT-----TCSEE-
T ss_pred EecccCcEEEEEEecCCceeEEeeHHHHHHHHHHcc--CCCccHHHHHHHHCcCHHHHHHHHHHHHhCC-----cceee-
Confidence 999999999999999999999999999999999999 5899999999999999999999999999643 44422
Q ss_pred CCCCCCCCCCCCeEEEccccc
Q psy14208 651 EVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 651 ~~~~~~~~~~~~~f~lN~~F~ 671 (778)
..+.++++++++.|++|.+||
T Consensus 568 ~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 568 KEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp ETTTSSS--TT-EEEE-TT--
T ss_pred cCCccCCCCCCCEEEeCCCCC
Confidence 112457788999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.5e-32 Score=258.76 Aligned_cols=141 Identities=43% Similarity=0.771 Sum_probs=130.3
Q ss_pred cccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHhccCCCCC
Q psy14208 442 YVQNKDVFMRFHKAHLTRRLILDTSADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSYRGSKGSI 520 (778)
Q Consensus 442 ~l~~Kd~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~ 520 (778)
|+++||+|+.+|+++||+|||..++.+.+.|..||++|| +|| .+||++|++|++|++.|++++++|++...++....
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G--~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~~~~ 78 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECG--YEFTSKLERMFRDISLSKDLNQSFKDMLENNSNKP 78 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhC--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 789999999999999999999999999999999999999 999 59999999999999999999999998876533334
Q ss_pred CCceEEEeccCCCCCCCCCCccccCChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEe
Q psy14208 521 GDSINIKILNAGAWARGSERVTVSLPLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSN 584 (778)
Q Consensus 521 ~~~~~v~VLt~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~ 584 (778)
+++|+|.|||+++||..+...++.||++|+.+++.|++||..+|+||+|+|+|++|+|+|+++|
T Consensus 79 ~~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 79 IIDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CCceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 6789999999999999854378999999999999999999999999999999999999998753
No 8
>KOG2165|consensus
Probab=99.92 E-value=2.1e-23 Score=228.27 Aligned_cols=299 Identities=21% Similarity=0.301 Sum_probs=226.3
Q ss_pred HHHhhhcccChhHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhHHHHHHHHHHh-
Q psy14208 436 VLLVLKYVQNKDVFMRFHKAHLTRRLILDTSADSEKEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQDLNYQFKQSY- 513 (778)
Q Consensus 436 i~~lf~~l~~Kd~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~~l~~~f~~~~- 513 (778)
+-.+...+.+|+.|.+.||.+||.||+.....+.+.|..-++.|| .+|. .-.+.|++|++|+..|+++++.+++..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgE--t~lq~CevML~Dv~dS~~id~~i~~~~~ 519 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGE--TSLQGCEVMLNDVIDSRRIDQSIHNESE 519 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhccc--chHHHHHHHHHhhhhhhhhhhhhhhhhh
Confidence 345566678999999999999999999999999999999999999 9994 778899999999999999999999852
Q ss_pred --ccCCCCCCCceEEEeccCCCCCCCCCCccccCChHHHHHHHHHHHHHHhhCCCceeEeccCCceEEEEEEecCeeEEE
Q psy14208 514 --RGSKGSIGDSINIKILNAGAWARGSERVTVSLPLELEDYIPEVEDFYKKKHSGRKLQWYHHMSNGTITFSNEVGKYDL 591 (778)
Q Consensus 514 --~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l 591 (778)
++......+.+++.+|++.+||... ...+.+|..++..++.|.+-|.+...+|+|.|.+.+|.+++.+.+.+++.++
T Consensus 520 ~~r~~e~~~~~~i~~~IlS~~fWP~~~-~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~ 598 (765)
T KOG2165|consen 520 LSRGAEEVPDFGISATILSSLFWPPLC-DEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVL 598 (765)
T ss_pred hhcccccCCCCchhhhhhhhhcCCccc-cccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEE
Confidence 1122222467899999999999874 5789999999999999999999999999999999999999999999999999
Q ss_pred EecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccc
Q psy14208 592 DVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~ 671 (778)
+||+.||+|+++|.+. ++||++++++.+|||...+.+.|.-+.+.| +|+..|. +++..+|++++.=.
T Consensus 599 tVsp~qA~iI~~Fqek--~twt~eelse~l~ip~~~lrrrL~fWi~~G-----vL~e~~~------~s~tgt~T~iEse~ 665 (765)
T KOG2165|consen 599 TVSPEQAAIINLFQEK--NTWTLEELSESLGIPVPALRRRLSFWIQKG-----VLREEPI------ISDTGTLTVIESEM 665 (765)
T ss_pred eeCHHHHHHHHHhcCc--ccccHHHHHHHhCCCHHHHHHHHHHHHHcC-----eeecCCC------CCCCceeeeccccc
Confidence 9999999999999995 779999999999999999999999999643 8887652 25778999998543
Q ss_pred cccccccccceeeeeccccccccchhhhhh--hHhHHHhhh-h-hhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCC
Q psy14208 672 LVKMGKILKRGKINLIGRLQLSTEKSKEED--NESIVQLRI-L-RVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPS 747 (778)
Q Consensus 672 ~~~~~k~~~~~ki~~~~~~~~~~~~~~~~~--~~~v~~~R~-~-~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~ 747 (778)
. ..+ ..+..+.+.+.+..+. ...+++.+. . .-...||-.+-.-+.|+.+-+. +.|+ .|.|.
T Consensus 666 d--------~~q--~~~~~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIH----nmLk-mF~~~ 730 (765)
T KOG2165|consen 666 D--------FDQ--AEGTVLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIH----NMLK-MFVPP 730 (765)
T ss_pred c--------ccc--cCCCcccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHH----HHHe-eeecC
Confidence 1 011 0111122222222111 122222121 1 2234666666666888877444 4443 56665
Q ss_pred h-------hhHHHHHHHhhhhcccc
Q psy14208 748 K-------KMIKEQIEWLIEQKYMR 765 (778)
Q Consensus 748 ~-------~~iK~~Ie~LIereyl~ 765 (778)
. +.++--+..++.-|-|+
T Consensus 731 ~~~~~~TlqeL~~fLq~kV~e~kL~ 755 (765)
T KOG2165|consen 731 DGSAEITLQELQGFLQRKVREGKLE 755 (765)
T ss_pred CCCCcccHHHHHHHHHHHhhccceE
Confidence 4 34444444444444433
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=4.1e-20 Score=150.46 Aligned_cols=68 Identities=43% Similarity=0.653 Sum_probs=62.3
Q ss_pred HHHhhhhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCC
Q psy14208 705 IVQLRILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDIN 772 (778)
Q Consensus 705 v~~~R~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~ 772 (778)
|.++|...|+||||||||++|+++|++|+.+|.++++++|.|+..+||++||+||+||||+||++|+|
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 35789999999999999999999999999999999999999999999999999999999999999876
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=96.90 E-value=0.012 Score=56.13 Aligned_cols=148 Identities=24% Similarity=0.309 Sum_probs=99.8
Q ss_pred CCcHHhhhhHHHHHHHHHHhcCCCChhHHHHHHHHH---HhhcccCCCChhHHHHHHHHHHHHHHHHHHHHHhhccchHH
Q psy14208 7 TQTFEDKWPSMRPIVLKLLQQEPVSQNEWQNLFYAV---HVVCLWDEKGPSKIVDALKEDIMNFIRHAQQRVLAHEEDQA 83 (778)
Q Consensus 7 ~~~fe~~W~~L~~ai~~i~~~~~~~~~sy~~lY~~v---Y~lc~~~~~~~~~LY~~l~~~i~~~l~~~~~~l~~~~~~~~ 83 (778)
+...++.|..+..++-.+|++++.. .+-+++=..| -+.|+++ .....+-+.+.+.+..-+......+... +++.
T Consensus 2 ~~~~~~~W~~~~~~vl~lF~g~~l~-~~iEdlN~lv~~~i~~~~~~-~~~~~~~~dl~elL~tg~~~L~~~l~~~-~~~~ 78 (158)
T PF08539_consen 2 NMSSDDAWNSLCAKVLPLFQGERLR-LPIEDLNELVRFHIKLCIQS-FPPSYFLEDLEELLTTGMYILENQLNEV-PDNR 78 (158)
T ss_pred CCchhhhHHHHHHHHHHHHcCCCCC-cCHHHHHHHHHHHHHHhhcc-cchHHHHHHHHHHHHHHHHHHHHHHhhc-chhH
Confidence 3467899999999999999988655 5555555444 4556652 3345566667777776666555555443 5788
Q ss_pred HHHHHHHHHHHH-HHhhcccCcccccchhhhhcccccc-ccccC--CccccccccchhHHHHHHHhhhhhHHHhhHHHHH
Q psy14208 84 LLKAYIQEWSKF-LAQCSYLPTPFRQLETSLVNKSVST-SLTNN--NNKQKISAEESTVRVLMLDSWNQSIFNDIKQRLQ 159 (778)
Q Consensus 84 ~L~~~~~~W~~y-~~~~~~l~~vf~YLdr~yv~~~~~~-~~~~~--~~~~~~~~~~~~i~~l~l~~f~~~v~~~~~~~l~ 159 (778)
+|..+...|.-| ....-++..+|..|++.+-...... +.... -|+. ..+..+|+.++|..||+.|.-+..+++.
T Consensus 79 ~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~--~~~~l~Vr~l~L~~FRD~IvLP~y~~l~ 156 (158)
T PF08539_consen 79 LLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNK--AGSELDVRRLLLIAFRDSIVLPYYQRLK 156 (158)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhcccccc--CCCCCcHHHHHHHHHHHHhhhcchHhhh
Confidence 999999999986 4556778889999997765442110 00000 0110 0133789999999999999888777664
No 11
>KOG2167|consensus
Probab=94.19 E-value=2.4 Score=48.00 Aligned_cols=199 Identities=8% Similarity=0.034 Sum_probs=118.3
Q ss_pred hhhHHHHHHHHHHhcCC---CChhHHHHHHHHHHhhcccCCCChhHHHHHHHHHHHHHHHHHHHHHh---hc--c-chHH
Q psy14208 13 KWPSMRPIVLKLLQQEP---VSQNEWQNLFYAVHVVCLWDEKGPSKIVDALKEDIMNFIRHAQQRVL---AH--E-EDQA 83 (778)
Q Consensus 13 ~W~~L~~ai~~i~~~~~---~~~~sy~~lY~~vY~lc~~~~~~~~~LY~~l~~~i~~~l~~~~~~l~---~~--~-~~~~ 83 (778)
-|..|++++.-|...+- .-...|-.+++.+|+-|.....+...+-+.++.....+......-+. .. . ....
T Consensus 113 drslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~at 192 (661)
T KOG2167|consen 113 DRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIAT 192 (661)
T ss_pred hHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHH
Confidence 46777777776554321 12244566678999999986556666666666665555544222111 10 0 1246
Q ss_pred HHHHHHHHHHHHHHhhcccCcccccchhhhhccccccccccCCccccccccchhHHHHHHHhhh--hhHHHhhHHHHHHH
Q psy14208 84 LLKAYIQEWSKFLAQCSYLPTPFRQLETSLVNKSVSTSLTNNNNKQKISAEESTVRVLMLDSWN--QSIFNDIKQRLQDS 161 (778)
Q Consensus 84 ~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~~~~~~~~~~~~~~~~~~~~i~~l~l~~f~--~~v~~~~~~~l~~~ 161 (778)
+.+.+...|-+..... ++++-+|-.=+.. ....+.++-..+. ..+.....+-+++.
T Consensus 193 V~~~LL~~hL~~IL~k----gl~~lvDm~q~~d------------------~~rly~L~~r~~~g~l~l~qq~sdylk~~ 250 (661)
T KOG2167|consen 193 VERCLLSRHLDLILTK----GLDSLVDMRQTSD------------------LTRLYMLFSRVQGGQLSLLQQWSDYLKKP 250 (661)
T ss_pred HHHHHHHHHHHHHHhc----chHHhhhhhhccc------------------hHhHHHHHHHHhcchHHHHHHHHHHHhcc
Confidence 7778888888663322 3344444331111 1333444434331 12233567777777
Q ss_pred HHHHHHHHhcCCcCChH--hHHHHHHHHHhhcCCCCchhhhhHHhHHHHHHHHHHHHHHHHHHHHHHccChhHHHHHHHH
Q psy14208 162 AMKLVQSERNGEAFDSQ--LVIGVRESYVNLCSNPEDKLQIYREHFEKAYIAATESFYTVKAAEFLQNNGVESYMKYADA 239 (778)
Q Consensus 162 ll~~I~~~R~g~~id~~--~i~~v~~~~~~l~~~~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~ 239 (778)
...+|..++.++.-..+ ..+.-+++++..+ ++...- .+|+..++.+|..+++ ...+.+.+|+.+...
T Consensus 251 G~KlV~de~kDk~mVqELL~FK~k~Dii~~~s--------F~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~d 319 (661)
T KOG2167|consen 251 GFKLVIDEEKDKDMVQELLDFKKKVDIIVDES--------FLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVD 319 (661)
T ss_pred cceeccCchhhHHHHHHHHHHHHHhhHHHHHH--------HHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHH
Confidence 88888888877653322 3566666665532 343333 8999999999999998 567789999998877
Q ss_pred HHHHH
Q psy14208 240 KLHEE 244 (778)
Q Consensus 240 ~l~eE 244 (778)
.+-.+
T Consensus 320 t~Lr~ 324 (661)
T KOG2167|consen 320 TKLRA 324 (661)
T ss_pred HHHHh
Confidence 65555
No 12
>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=92.33 E-value=0.21 Score=38.14 Aligned_cols=46 Identities=24% Similarity=0.242 Sum_probs=37.0
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
+.||.+|.+. ...+|+.||++.+|+|...+.+.|..|...| ++.++
T Consensus 6 l~iL~~l~~~-~~~~t~~eia~~~gl~~stv~r~L~tL~~~g-----~v~~d 51 (52)
T PF09339_consen 6 LRILEALAES-GGPLTLSEIARALGLPKSTVHRLLQTLVEEG-----YVERD 51 (52)
T ss_dssp HHHHHCHHCT-BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTT-----SEEEC
T ss_pred HHHHHHHHcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCc-----CeecC
Confidence 4578888875 3569999999999999999999999999643 67654
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=89.69 E-value=1.3 Score=37.50 Aligned_cols=61 Identities=11% Similarity=0.109 Sum_probs=41.5
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEcccc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEF 670 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F 670 (778)
+++.+.+..+.. ...+|.++|++.+++|...+.+.|+.|... +++...++ .++-|.++.+-
T Consensus 11 l~~l~~la~~~~-~~~~s~~eiA~~~~i~~~~l~kil~~L~~~-----Gli~s~~G--------~~GGy~L~~~~ 71 (83)
T PF02082_consen 11 LRILLYLARHPD-GKPVSSKEIAERLGISPSYLRKILQKLKKA-----GLIESSRG--------RGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHCTTT-SC-BEHHHHHHHHTS-HHHHHHHHHHHHHT-----TSEEEETS--------TTSEEEESS-C
T ss_pred HHHHHHHHhCCC-CCCCCHHHHHHHHCcCHHHHHHHHHHHhhC-----CeeEecCC--------CCCceeecCCH
Confidence 445555554442 234999999999999999999999999853 37765432 45678777653
No 14
>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=89.32 E-value=1.1 Score=39.12 Aligned_cols=67 Identities=18% Similarity=0.182 Sum_probs=50.4
Q ss_pred EEecHHHHHHHHhhcC------CCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeE
Q psy14208 591 LDVTTFQMAVLFAWNE------RPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSF 664 (778)
Q Consensus 591 l~~s~~Q~~ILl~FN~------~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f 664 (778)
..++.-|+.+|+..-. .....+|-.||++.+|++.+.+.+.|..|... ++|.... ....|
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~-----GlI~r~~---------~~~~~ 86 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR-----RIIFRQG---------MMGIV 86 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC-----CCeeeec---------CCcee
Confidence 4467788888875531 01478999999999999999999999999853 2776543 23689
Q ss_pred EEccccc
Q psy14208 665 WINQEFA 671 (778)
Q Consensus 665 ~lN~~F~ 671 (778)
++|.++.
T Consensus 87 ~~n~~~~ 93 (95)
T TIGR01610 87 GVNTPLS 93 (95)
T ss_pred ecCCCcc
Confidence 9998764
No 15
>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=86.93 E-value=1.3 Score=34.92 Aligned_cols=53 Identities=19% Similarity=0.191 Sum_probs=41.8
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+|.-|+.||..+...+.+.+|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~-----Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK-----GLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT-----TSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-----CCEEEeC
Confidence 4678889998777743334999999999999999999999999853 2777654
No 16
>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=85.83 E-value=1.7 Score=32.37 Aligned_cols=42 Identities=19% Similarity=0.132 Sum_probs=33.3
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
+..+.-||....+ ++.+|..+|++.+|++...+.++|..|..
T Consensus 2 ~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4456677877777 46799999999999999999999999985
No 17
>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=85.60 E-value=1.5 Score=40.71 Aligned_cols=60 Identities=13% Similarity=0.189 Sum_probs=45.5
Q ss_pred hhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 714 QEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 714 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
+..|++++-..+.++..+++.. +.....++...+...|..|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 4457777777778877766644 444566788899999999999999999854 45788865
No 18
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=82.88 E-value=2.2 Score=38.76 Aligned_cols=62 Identities=19% Similarity=0.197 Sum_probs=52.8
Q ss_pred hhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 712 RVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 712 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
..++.|++||=.++..+.+|++.++.+ .+.++...|+.-|.-|..||.|.|.-+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 467889999999999999988877754 578899999999999999999999865 56888854
No 19
>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=80.69 E-value=3.8 Score=32.78 Aligned_cols=51 Identities=16% Similarity=0.073 Sum_probs=38.1
Q ss_pred ecHHHHHHHHhhc-CCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWN-ERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN-~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+|..|..||.... . ++.++..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 1 lt~~q~~vL~~l~~~--~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g-----lv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHS--DGPMTQSDLAERLGISKSTVSRIIKKLEEKG-----LVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT-----SEEEEE
T ss_pred CCHHHHHHHHHHHcc--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEecC
Confidence 3567889998888 4 4789999999999999999999999998632 776554
No 20
>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=79.00 E-value=2.5 Score=32.90 Aligned_cols=50 Identities=14% Similarity=0.079 Sum_probs=40.4
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
|..|+.+|....+ ++++|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 2 t~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L~~~-----g~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRLEKK-----GLIERER 51 (59)
T ss_dssp THHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHHHHT-----TSEEEEE
T ss_pred CHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHHHHC-----CCEEecc
Confidence 6678888887776 367999999999999999999999999853 2777654
No 21
>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=76.58 E-value=1.8 Score=39.20 Aligned_cols=60 Identities=15% Similarity=0.222 Sum_probs=44.5
Q ss_pred hhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 714 QEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 714 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
+..|++++=..+.++..|++. .+.....+....|...+..|.+||||.|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~----~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHE----ALPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH----HHCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHH----HHHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 455677777777787776554 4445567788999999999999999999865 46888865
No 22
>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=76.56 E-value=1.4 Score=35.84 Aligned_cols=45 Identities=33% Similarity=0.426 Sum_probs=34.5
Q ss_pred hhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 717 IIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 717 IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
|-.+|+.++.++.+||- .+|..+++.+..-|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa--------~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELA--------REFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHH--------HHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHH--------HHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 45678888888887664 3578899999999999999999998654
No 23
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=76.40 E-value=7.8 Score=37.47 Aligned_cols=47 Identities=9% Similarity=0.003 Sum_probs=36.6
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
.+++.+.|+.. ...+|.++|++.+++|...+.+.|..|...| ++...
T Consensus 12 ~~l~~lA~~~~-~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aG-----Lv~s~ 58 (164)
T PRK10857 12 TAMLDVALNSE-AGPVPLADISERQGISLSYLEQLFSRLRKNG-----LVSSV 58 (164)
T ss_pred HHHHHHHhCCC-CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEeC
Confidence 44555567653 3579999999999999999999999998543 77743
No 24
>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=75.77 E-value=4.6 Score=31.44 Aligned_cols=40 Identities=23% Similarity=0.213 Sum_probs=34.2
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
|..|+.+.++ .+.+|+++|++.+|++...+.+-|..|...
T Consensus 2 ~~~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 2 QQQILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred HHHHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3456777777 478999999999999999999999999863
No 25
>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=75.58 E-value=8 Score=28.63 Aligned_cols=39 Identities=18% Similarity=0.187 Sum_probs=31.1
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
..-||.++-+ ++.++.||++.+|++...+.++|..|...
T Consensus 4 R~~Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 4 RLRILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 3456666655 57999999999999999999999999754
No 26
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=75.51 E-value=9.6 Score=33.53 Aligned_cols=62 Identities=21% Similarity=0.421 Sum_probs=46.2
Q ss_pred ecHHHHHHHHh-------hcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEE
Q psy14208 593 VTTFQMAVLFA-------WNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFW 665 (778)
Q Consensus 593 ~s~~Q~~ILl~-------FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~ 665 (778)
+|.-|.-|+++ ||.. .+.+|..++++.||++...+.+++..|+.. + +|... +..+.
T Consensus 30 ls~rq~ki~~ai~RkTyG~nKk-~d~Is~sq~~e~tg~~~~~V~~al~~Li~~---~--vI~~~-----------g~~~G 92 (100)
T PF04492_consen 30 LSGRQLKILLAIIRKTYGWNKK-MDRISNSQIAEMTGLSRDHVSKALNELIRR---G--VIIRD-----------GKRIG 92 (100)
T ss_pred ccHHHHHHHHHHHHHccCCCCc-cceeeHHHHHHHHCcCHHHHHHHHHHHHHC---C--CEEeC-----------CcEEe
Confidence 45556666664 6764 688999999999999999999999999852 3 88653 34666
Q ss_pred Eccccc
Q psy14208 666 INQEFA 671 (778)
Q Consensus 666 lN~~F~ 671 (778)
+|.+.+
T Consensus 93 ~N~~i~ 98 (100)
T PF04492_consen 93 VNKNIS 98 (100)
T ss_pred eecccc
Confidence 666543
No 27
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=74.58 E-value=6.6 Score=33.43 Aligned_cols=58 Identities=19% Similarity=0.208 Sum_probs=42.2
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEcccc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEF 670 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F 670 (778)
..||..+... .+.+|..+|++.+|++...+.+.|..|...+ +|...+ .++.|.+...+
T Consensus 8 ~~Il~~l~~~-~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g-----~l~~~~---------~~~~y~l~~~~ 65 (91)
T smart00346 8 LAVLRALAEE-PGGLTLAELAERLGLSKSTAHRLLNTLQELG-----YVEQDG---------QNGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHhC-CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC-----CeeecC---------CCCceeecHHH
Confidence 3466666652 2579999999999999999999999998632 776543 23456665544
No 28
>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=72.91 E-value=11 Score=35.17 Aligned_cols=46 Identities=9% Similarity=0.035 Sum_probs=35.1
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeec
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLY 648 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~ 648 (778)
.+++.|.++.. ...+|.++|++.+++|...+.+.|..|...| ++..
T Consensus 12 ~~l~~La~~~~-~~~~s~~~ia~~~~ip~~~l~kil~~L~~~g-----lv~s 57 (135)
T TIGR02010 12 TAMLDLALNAE-TGPVTLADISERQGISLSYLEQLFAKLRKAG-----LVKS 57 (135)
T ss_pred HHHHHHHhCCC-CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC-----ceEE
Confidence 34444555542 3469999999999999999999999998543 7764
No 29
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=72.56 E-value=9.5 Score=30.88 Aligned_cols=43 Identities=21% Similarity=0.187 Sum_probs=34.0
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
..--||.++.+.+...+|..+|++.+|++...+.++|..|...
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3445777777642224999999999999999999999999853
No 30
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=71.30 E-value=8.5 Score=40.16 Aligned_cols=47 Identities=13% Similarity=0.143 Sum_probs=38.9
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
-+.||.+|.. ...+|+.||++.+|+|...+.+.|..|+..+ .|.+.+
T Consensus 16 ~l~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G-----~l~~~~ 62 (257)
T PRK15090 16 VFGILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLG-----YVAQEG 62 (257)
T ss_pred HHHHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEEcC
Confidence 3567888887 3579999999999999999999999999643 777654
No 31
>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=70.54 E-value=10 Score=29.83 Aligned_cols=44 Identities=9% Similarity=0.046 Sum_probs=34.7
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
++.-.-||.++.. .+++|+.+|++.+|++...+.++|..|...|
T Consensus 9 ~p~R~~Il~~L~~--~~~~t~~ela~~l~~~~~t~s~hL~~L~~aG 52 (61)
T PF12840_consen 9 DPTRLRILRLLAS--NGPMTVSELAEELGISQSTVSYHLKKLEEAG 52 (61)
T ss_dssp SHHHHHHHHHHHH--CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHhc--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 3455667777733 3789999999999999999999999998643
No 32
>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=70.52 E-value=7.6 Score=35.11 Aligned_cols=51 Identities=20% Similarity=0.143 Sum_probs=42.6
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
++..|..||..+.. ++.+|..+|++.+|++...+.+.+..|... +++.+.+
T Consensus 26 lt~~q~~iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~Le~~-----GlI~r~~ 76 (118)
T TIGR02337 26 LTEQQWRILRILAE--QGSMEFTQLANQACILRPSLTGILARLERD-----GLVTRLK 76 (118)
T ss_pred CCHHHHHHHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHHHHC-----CCEEecc
Confidence 47889999988876 467999999999999999999999999853 3777654
No 33
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=69.67 E-value=14 Score=35.33 Aligned_cols=46 Identities=17% Similarity=0.060 Sum_probs=34.8
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+++.|..+. .+.+|..+|++..++|...|.+.|..|... +++....
T Consensus 13 ~L~~LA~~~--~~~~s~~eIA~~~~is~~~L~kIl~~L~~a-----Glv~S~r 58 (153)
T PRK11920 13 MLMYCAAND--GKLSRIPEIARAYGVSELFLFKILQPLVEA-----GLVETVR 58 (153)
T ss_pred HHHHHHhCC--CCcCcHHHHHHHHCcCHHHHHHHHHHHHHC-----CCEEeec
Confidence 334444454 356899999999999999999999999853 3777543
No 34
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=68.71 E-value=10 Score=39.90 Aligned_cols=59 Identities=19% Similarity=0.124 Sum_probs=44.8
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEcccc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEF 670 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F 670 (778)
-..||.+|... ...+|+.||++.+|+|...+.+.|.+|+..+ .|.+.+ .++.|.+...+
T Consensus 27 ~l~IL~~~~~~-~~~~tl~eIa~~lglpkStv~RlL~tL~~~G-----~l~~~~---------~~~~Y~lG~~l 85 (271)
T PRK10163 27 GIAILQYLEKS-GGSSSVSDISLNLDLPLSTTFRLLKVLQAAD-----FVYQDS---------QLGWWHIGLGV 85 (271)
T ss_pred HHHHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEEcC---------CCCeEEecHHH
Confidence 45688899764 3579999999999999999999999999643 777653 23456655443
No 35
>PRK11569 transcriptional repressor IclR; Provisional
Probab=68.58 E-value=9.7 Score=40.21 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=39.5
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
-..||.+|.+. ...+|+.||++.+|+|...+.+.|.+|+..+ .|.+.+
T Consensus 30 al~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G-----~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQG-----FVRQVG 77 (274)
T ss_pred HHHHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEEcC
Confidence 45578889874 4679999999999999999999999999643 777654
No 36
>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=68.29 E-value=10 Score=28.88 Aligned_cols=29 Identities=14% Similarity=0.255 Sum_probs=25.2
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
+.+|.++|++.+|++...+.+.|..|-..
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 56999999999999999999999999653
No 37
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=68.13 E-value=11 Score=34.87 Aligned_cols=47 Identities=19% Similarity=0.132 Sum_probs=36.0
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeec
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLY 648 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~ 648 (778)
-..+|..+...+.+.+|+.+|++.+|+|...+.+.|..|...| ++..
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~G-----li~~ 57 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAG-----IVTS 57 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCC-----cEEe
Confidence 3445555544324679999999999999999999999998643 7764
No 38
>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=67.60 E-value=6 Score=31.84 Aligned_cols=49 Identities=14% Similarity=0.058 Sum_probs=36.7
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
|-.++-|+..+-. .+..|..+|++.+|++...+.+.|..|...| ++.+.
T Consensus 7 s~~E~~vy~~Ll~--~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G-----lV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLK--NGPATAEEIAEELGISRSTVYRALKSLEEKG-----LVERE 55 (68)
T ss_dssp HHHHHHHHHHHHH--HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT-----SEEEE
T ss_pred CHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEEE
Confidence 3445555544433 3789999999999999999999999999633 66654
No 39
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=66.54 E-value=12 Score=35.17 Aligned_cols=51 Identities=20% Similarity=0.029 Sum_probs=41.9
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+|..|+.||..... .+++|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 38 lt~~q~~vL~~l~~--~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~-----GlI~R~~ 88 (144)
T PRK11512 38 ITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCK-----GWVERLP 88 (144)
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEecc
Confidence 57789988876654 367999999999999999999999999852 3777654
No 40
>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=65.81 E-value=8.9 Score=37.10 Aligned_cols=46 Identities=15% Similarity=0.255 Sum_probs=38.9
Q ss_pred ccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEcccccc
Q psy14208 612 LSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFAL 672 (778)
Q Consensus 612 ~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~~ 672 (778)
+|.++|++.+|++...+.+++..|... ++|.+. ..+.|.||++|..
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~-----~iI~k~----------~~G~Y~iNP~~~~ 121 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK-----NIIKKI----------RNGAYMINPNFFF 121 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC-----CcEEEc----------cCCeEEECcHHhe
Confidence 788999999999999999999999852 388765 2458999999875
No 41
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=65.74 E-value=13 Score=38.61 Aligned_cols=47 Identities=26% Similarity=0.263 Sum_probs=39.0
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+.||.+|... ...+++.||++.+|+|...+.+.|..|...| ++.+++
T Consensus 7 l~iL~~l~~~-~~~l~l~ela~~~glpksT~~RlL~tL~~~G-----~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEG-PGGLSLAELAERLGLPKSTVHRLLQTLVELG-----YVEQDP 53 (246)
T ss_pred HHHHHHHHhC-CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC-----CEEEcC
Confidence 4578888874 3448899999999999999999999999643 888765
No 42
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=65.54 E-value=6.7 Score=32.93 Aligned_cols=39 Identities=23% Similarity=0.194 Sum_probs=29.8
Q ss_pred HHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 599 AVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 599 ~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
.||.+.+. .+++++.+|.+.+|+++..|.++|..|...|
T Consensus 4 ~Il~~L~~--~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~G 42 (80)
T PF13601_consen 4 AILALLYA--NEEATFSELKEELGLTDGNLSKHLKKLEEAG 42 (80)
T ss_dssp HHHHHHHH--HSEEEHHHHHHHTT--HHHHHHHHHHHHHTT
T ss_pred HHHHHHhh--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence 45544444 3689999999999999999999999998643
No 43
>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=65.33 E-value=6.8 Score=31.55 Aligned_cols=56 Identities=14% Similarity=0.196 Sum_probs=40.1
Q ss_pred hhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEec
Q psy14208 714 QEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYL 777 (778)
Q Consensus 714 ~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yi 777 (778)
++.|-+.|-.++.++..+|...+ ..+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 34444444466777777655433 257788999999999999999999876666554
No 44
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=63.51 E-value=12 Score=34.36 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=31.6
Q ss_pred CCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 609 LDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 609 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
++.+|+++|++.++.+...+.++|++|..+| ++.+.
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~G-----lV~Re 75 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAG-----LVERE 75 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcC-----Ceeee
Confidence 4789999999999999999999999999754 66654
No 45
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=62.23 E-value=21 Score=33.98 Aligned_cols=60 Identities=8% Similarity=0.044 Sum_probs=42.6
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQE 669 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~ 669 (778)
+.+.+.|.-+.. ....|.++|++..|+|...|.+.|..|...| ++...++ .++-|.++.+
T Consensus 11 l~~L~~LA~~~~-~~~~s~~~IA~~~~is~~~L~kil~~L~kaG-----lV~S~rG--------~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPG-GGPVSSAEIAERQGISPSYLEKILSKLRKAG-----LVKSVRG--------KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCC-CCcccHHHHHHHhCcCHHHHHHHHHHHHHcC-----CEEeecC--------CCCCccCCCC
Confidence 455555666652 2268899999999999999999999998533 7765442 3455666654
No 46
>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=62.16 E-value=17 Score=37.60 Aligned_cols=45 Identities=29% Similarity=0.358 Sum_probs=37.7
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeec
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLY 648 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~ 648 (778)
..||.+|... ...+|+.||++.+|+|...+.+.|.+|...| .|.+
T Consensus 12 l~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G-----~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELG-----YVTS 56 (248)
T ss_pred HHHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEe
Confidence 4578889864 4679999999999999999999999999643 6764
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=61.68 E-value=20 Score=32.90 Aligned_cols=48 Identities=13% Similarity=0.096 Sum_probs=35.4
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
+++.+.+.-++. ...+|.++|++.+++|...+.+.|..|...+ +|...
T Consensus 11 l~~l~~la~~~~-~~~~s~~eia~~~~i~~~~v~~il~~L~~~g-----li~~~ 58 (132)
T TIGR00738 11 LRALLDLALNPD-EGPVSVKEIAERQGISRSYLEKILRTLRRAG-----LVESV 58 (132)
T ss_pred HHHHHHHHhCCC-CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC-----cEEec
Confidence 344444544431 2479999999999999999999999998543 77643
No 48
>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=60.52 E-value=22 Score=31.68 Aligned_cols=54 Identities=11% Similarity=0.193 Sum_probs=41.7
Q ss_pred EecHHHHHHHHhhc--CCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 592 DVTTFQMAVLFAWN--ERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN--~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.+|..|..||.... ..+.+.+|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k-----g~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK-----GYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEeccC
Confidence 34777888886554 221367999999999999999999999999853 3777654
No 49
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=59.83 E-value=18 Score=29.27 Aligned_cols=54 Identities=17% Similarity=0.190 Sum_probs=41.2
Q ss_pred hhhhhhhhhccCCC--CChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCce
Q psy14208 713 VQEAIIKILKMRKR--ISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVF 774 (778)
Q Consensus 713 i~A~IVRiMK~~k~--l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y 774 (778)
.+..|...||.++. ++-.+|-.++ ..+...+.+.+..|.++||+.++++.+..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 44567888898876 8877655433 256778999999999999999988765554
No 50
>PRK10870 transcriptional repressor MprA; Provisional
Probab=58.51 E-value=25 Score=34.44 Aligned_cols=53 Identities=11% Similarity=-0.006 Sum_probs=42.0
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+|..|..||......++.++|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~k-----GlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR-----GWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEecC
Confidence 4667888887776432467999999999999999999999999852 3777654
No 51
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=57.86 E-value=16 Score=31.29 Aligned_cols=52 Identities=23% Similarity=0.145 Sum_probs=42.1
Q ss_pred EEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 591 LDVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 591 l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
..++..+..||...... +.+|..+|++.++++...+.+.|..|...+ ++.+.
T Consensus 6 ~~l~~~~~~il~~l~~~--~~~~~~~la~~~~~s~~~i~~~l~~L~~~g-----~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEE--GPLSVSELAKRLGVSPSTVTRVLDRLEKKG-----LIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHc--CCcCHHHHHHHHCCCchhHHHHHHHHHHCC-----CeEec
Confidence 34677888888888763 579999999999999999999999998632 66643
No 52
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=57.05 E-value=21 Score=37.38 Aligned_cols=47 Identities=26% Similarity=0.089 Sum_probs=38.1
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+.||.+|.+. ...+|..||++.+|++...+.+.|..|...+ +|.+.+
T Consensus 14 l~iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g-----~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEG-----YVRRSA 60 (263)
T ss_pred HHHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC-----CEEEec
Confidence 4577788663 3459999999999999999999999998642 787654
No 53
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=55.04 E-value=28 Score=25.24 Aligned_cols=33 Identities=18% Similarity=0.106 Sum_probs=28.1
Q ss_pred cccHHHHHHHcCCChHHHHHHHHHhhcccccccceeec
Q psy14208 611 RLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLY 648 (778)
Q Consensus 611 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~ 648 (778)
.+|..+|++.+|++...+.+.|..|... +++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~-----g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKE-----GLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEE
Confidence 4789999999999999999999999853 26664
No 54
>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=54.00 E-value=4.8e+02 Score=31.62 Aligned_cols=140 Identities=14% Similarity=0.212 Sum_probs=74.4
Q ss_pred HHHHHHHHHHHHHHHHHHccChhHHHHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHH--HHHHHHHHHHHHhhHHHhc
Q psy14208 209 YIAATESFYTVKAAEFLQNNGVESYMKYADAKLHEEELRACKYLESSSSVQLLTDCCVT--VLVSSFKNTILAECPKMIK 286 (778)
Q Consensus 209 ~L~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~~t~~kl~~~l~~--~LI~~~~~~l~~~~~~ll~ 286 (778)
.++...-||...+..-. ...+..+...|....+++.+..-..+-. ...++|.+.++. .|+..... +++....
T Consensus 552 ~leN~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~-r~~~kL~~F~~gve~l~~~~~~---~ei~~~~- 625 (701)
T PF09763_consen 552 LLENYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLR-RPFGKLLDFFEGVEALLQTVSP---EEISYQA- 625 (701)
T ss_pred HHHHHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHhccCc---hhcccch-
Confidence 34555555555555222 2567778888888888888765444333 456666664421 12211000 0111110
Q ss_pred cchHHHHHHHHHhh--hhhcCCchHHHHHHHHHHHHHhHH------HHHhhhhhhccCHHHHHHHHHHHHHHHHHHHHHH
Q psy14208 287 MNETLKLELMMKLL--DRIKDGITPMLQDLEAHIVNAGLA------DMIASADIITQDSEKYVERLLELFNQFSKLVKDA 358 (778)
Q Consensus 287 ~~~~~~L~~ly~l~--~~~~~~~~~l~~~~~~~i~~~g~~------~~~~~~~~~~~~~~~~V~~ll~l~~~~~~l~~~~ 358 (778)
......|+.+-.-+ +.+..|++.|.+.+.+|+...+.. .+.. .+ ..+-+..+..|.++..++..|
T Consensus 626 ~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~-----vW--~~~q~~~i~~~~~l~~li~~~ 698 (701)
T PF09763_consen 626 AYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQV-----VW--SAMQEEFIRQYERLETLIQKC 698 (701)
T ss_pred hccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHH-----HH--HHHHHHHHHHHHHHHHHHHHh
Confidence 11234555555542 235567777777777777221110 1110 01 224566889999999999999
Q ss_pred hcC
Q psy14208 359 FKD 361 (778)
Q Consensus 359 F~~ 361 (778)
+.|
T Consensus 699 Y~g 701 (701)
T PF09763_consen 699 YPG 701 (701)
T ss_pred CCC
Confidence 864
No 55
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=53.91 E-value=24 Score=32.99 Aligned_cols=53 Identities=21% Similarity=0.137 Sum_probs=42.1
Q ss_pred EecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 592 DVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.+|..|..||...... .+.+|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 28 glt~~q~~vL~~l~~~-~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~-----GlV~r~~ 80 (144)
T PRK03573 28 ELTQTHWVTLHNIHQL-PPEQSQIQLAKAIGIEQPSLVRTLDQLEEK-----GLISRQT 80 (144)
T ss_pred CCCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHC-----CCEeeec
Confidence 3577898888877642 246899999999999999999999999853 3777654
No 56
>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=53.79 E-value=16 Score=30.09 Aligned_cols=29 Identities=7% Similarity=-0.045 Sum_probs=25.0
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
+.+|+.||++.+|++...++..+..+...
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~ 59 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKA 59 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCccc
Confidence 46899999999999999999988876543
No 57
>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=52.19 E-value=20 Score=25.96 Aligned_cols=35 Identities=26% Similarity=0.325 Sum_probs=24.4
Q ss_pred HHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHh
Q psy14208 599 AVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSL 635 (778)
Q Consensus 599 ~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL 635 (778)
.||-.+.. +...|+.+|++.+|++...+.+.+.-|
T Consensus 7 ~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQE--DGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 34444444 367999999999999999998877654
No 58
>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=51.83 E-value=25 Score=31.50 Aligned_cols=58 Identities=17% Similarity=0.101 Sum_probs=43.2
Q ss_pred hhhhhhcc-CCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEe
Q psy14208 716 AIIKILKM-RKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVY 776 (778)
Q Consensus 716 ~IVRiMK~-~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Y 776 (778)
+|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.....|
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 35555655 56799999998887642 457889999999999999999986554444444
No 59
>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=51.08 E-value=18 Score=28.69 Aligned_cols=54 Identities=19% Similarity=0.193 Sum_probs=34.2
Q ss_pred hhhhhhhhc-cCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc--CCCCCCceE
Q psy14208 714 QEAIIKILK-MRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR--DDDDINVFV 775 (778)
Q Consensus 714 ~A~IVRiMK-~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R--d~~d~~~y~ 775 (778)
+..|.+.+. ..+.++..+|... +..+...+-+.|+.|+++|||++ ++.|+....
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~--------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~ 61 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER--------LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKR 61 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEE
T ss_pred HHHHHHHHHccCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeE
Confidence 445666666 6667776655433 44677889999999999999965 455555333
No 60
>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=50.93 E-value=27 Score=30.66 Aligned_cols=48 Identities=15% Similarity=0.145 Sum_probs=38.3
Q ss_pred EecHHHHHHHHhhcC-C-CCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 592 DVTTFQMAVLFAWNE-R-PLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN~-~-~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
.++..|-.||-.+.. . ..+.+++++|++.++++..+++.+|.-|+.-|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 578899999988876 1 14679999999999999999999999998644
No 61
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=49.99 E-value=34 Score=33.82 Aligned_cols=52 Identities=13% Similarity=0.033 Sum_probs=42.6
Q ss_pred EecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 592 DVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.+|..|..||..... ++++|..+|++.++++...+.+.+..|... +++.+.+
T Consensus 42 gLt~~q~~iL~~L~~--~~~itq~eLa~~l~l~~sTvtr~l~rLE~k-----GlI~R~~ 93 (185)
T PRK13777 42 DLNINEHHILWIAYH--LKGASISEIAKFGVMHVSTAFNFSKKLEER-----GYLTFSK 93 (185)
T ss_pred CCCHHHHHHHHHHHh--CCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-----CCEEecC
Confidence 357789999988877 468999999999999999999999999852 3777654
No 62
>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=49.99 E-value=23 Score=27.71 Aligned_cols=38 Identities=11% Similarity=0.172 Sum_probs=28.1
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
|.-+|-++-+ .+.+|+++|++.+|++...++.-+.-|-
T Consensus 7 q~~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLK--NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4444544433 2689999999999999999998887774
No 63
>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=49.82 E-value=27 Score=26.41 Aligned_cols=24 Identities=13% Similarity=0.340 Sum_probs=17.5
Q ss_pred CcccHHHHHHHcCCChHHHHHHHH
Q psy14208 610 DRLSFENLLLATELPDPELRRTLW 633 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~ 633 (778)
+++|++||++.+|++...+...+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999887764
No 64
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.74 E-value=28 Score=26.76 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=32.7
Q ss_pred hhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCC
Q psy14208 717 IIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDI 771 (778)
Q Consensus 717 IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~ 771 (778)
|++.+. .+.++..++...+ ..+...+.+.|+.|.++|++.+..+.+
T Consensus 2 il~~l~-~~~~~~~~i~~~l--------~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 2 ILKLLA-EGELCVCELAEIL--------GLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHHhh-cCCccHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 344555 6667777554332 356788999999999999999876543
No 65
>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=47.83 E-value=14 Score=28.69 Aligned_cols=46 Identities=24% Similarity=0.383 Sum_probs=38.6
Q ss_pred hhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 715 EAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 715 A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
..|+..++.++.++..+|.+ .|..|...|.+=+..|-++|.|.|.-
T Consensus 3 ~~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 35778889999999887764 36789999999999999999999864
No 66
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=47.23 E-value=40 Score=30.57 Aligned_cols=36 Identities=25% Similarity=0.273 Sum_probs=30.7
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
+++++.+|++.+|++...+.++|.-|..+| ++....
T Consensus 29 ~~~~v~ela~~l~lsqstvS~HL~~L~~AG-----LV~~~r 64 (117)
T PRK10141 29 GELCVCDLCTALDQSQPKISRHLALLRESG-----LLLDRK 64 (117)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCC-----ceEEEE
Confidence 579999999999999999999999998643 776543
No 67
>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=46.85 E-value=36 Score=27.01 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=27.5
Q ss_pred HHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 600 VLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 600 ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
+-.+++. +..|+.+|...|++|.+.++.+|..|.++
T Consensus 19 ~~~Ll~~---G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh 54 (62)
T PF08221_consen 19 GEVLLSR---GRLTLREIVRRTGLSPKQVKKALVVLIQH 54 (62)
T ss_dssp HHHHHHC----SEEHHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred HHHHHHc---CCcCHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 3345554 68999999999999999999999999864
No 68
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=46.15 E-value=32 Score=33.78 Aligned_cols=65 Identities=14% Similarity=0.036 Sum_probs=49.1
Q ss_pred ceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 567 RKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 567 R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
|.-.|.+.+|..+++ ..+.|+ ||+.||.-|+.-....-..||.+.|++..+++.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~-~vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPE-KVPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCcc-cCCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 344577788887775 334565 68899988876554434679999999999999999998887665
No 69
>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=45.87 E-value=34 Score=34.24 Aligned_cols=52 Identities=13% Similarity=0.054 Sum_probs=42.9
Q ss_pred EecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 592 DVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 592 ~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.++.-|..||..+.+ ++.++..+|++.+|++...+.++|..|... +++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~--~g~~s~~eia~~l~is~stv~r~L~~Le~~-----GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKA--EGEKSVKNIAKKLGKSLSTISRHLRELEKK-----GLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-----CCEEEEc
Confidence 457788899988876 367899999999999999999999999853 2777653
No 70
>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=45.15 E-value=52 Score=26.95 Aligned_cols=40 Identities=23% Similarity=0.159 Sum_probs=30.9
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
+..|. ||+..-. ...|+++|.+.||++...|...|.-|..
T Consensus 5 t~~~~-IL~~ls~---~c~TLeeL~ekTgi~k~~LlV~LsrL~k 44 (72)
T PF05584_consen 5 TVTQK-ILIILSK---RCCTLEELEEKTGISKNTLLVYLSRLAK 44 (72)
T ss_pred hHHHH-HHHHHHh---ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34443 3444433 3789999999999999999999999985
No 71
>PHA00738 putative HTH transcription regulator
Probab=44.85 E-value=60 Score=28.85 Aligned_cols=65 Identities=15% Similarity=-0.057 Sum_probs=45.0
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~ 671 (778)
..+.=-.||.++.+ .+.+++.+|++.++|+.+.+-++|.-|-.+| ++.....+ ....|++|.+..
T Consensus 10 ~dptRr~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLKvLreAG-----LV~srK~G-------r~vyY~Ln~~~~ 74 (108)
T PHA00738 10 AKILRRKILELIAE--NYILSASLISHTLLLSYTTVLRHLKILNEQG-----YIELYKEG-------RTLYAKIRENSK 74 (108)
T ss_pred CCHHHHHHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHHHHHHCC-----ceEEEEEC-------CEEEEEECCCcc
Confidence 33333345544444 2569999999999999999999999998654 77654321 234678887654
No 72
>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=44.47 E-value=51 Score=26.50 Aligned_cols=40 Identities=28% Similarity=0.090 Sum_probs=32.5
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
..|--++|+ ...+|+.+|++.|++++.++..++--|+.-+
T Consensus 11 G~Vw~~L~~--~~~~s~~el~k~~~l~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 11 GKVWQLLNE--NGEWSVSELKKATGLSDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHHHCC--SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTT
T ss_pred HHHHHHHhh--CCCcCHHHHHHHhCcCHHHHHHHHHHHhccC
Confidence 345567787 4789999999999999999999999998533
No 73
>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=44.31 E-value=38 Score=27.16 Aligned_cols=55 Identities=20% Similarity=0.285 Sum_probs=37.0
Q ss_pred hhhhhhhhhhhhhccCC-CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCC
Q psy14208 709 RILRVQEAIIKILKMRK-RISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDD 770 (778)
Q Consensus 709 R~~~i~A~IVRiMK~~k-~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d 770 (778)
|+..|=.+|...++..+ .-+..|| .+.+- +. |+.-+...++.|.++|||+|++.-
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEI----a~~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREI----AEALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHH----HHHHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHH----HHHhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 55556666777666655 4455544 44442 43 688899999999999999999764
No 74
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=44.16 E-value=75 Score=29.68 Aligned_cols=36 Identities=6% Similarity=-0.035 Sum_probs=30.7
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
..+|..+|++.+|+|...+.+.|..|... +++...+
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L~~~-----Glv~s~~ 59 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQLSRA-----GYVTAVR 59 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHhC-----CEEEEec
Confidence 56899999999999999999999999853 3777654
No 75
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=44.04 E-value=39 Score=24.87 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=30.7
Q ss_pred HHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 599 AVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 599 ~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
.|+..++. +..+|..+|++.++++...+.+.|..|..
T Consensus 4 ~il~~l~~--~~~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 4 QILELLAQ--QGKVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45555555 35699999999999999999999999975
No 76
>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=43.30 E-value=57 Score=25.57 Aligned_cols=35 Identities=17% Similarity=0.047 Sum_probs=29.8
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
..+|..+|++.+|++...+.+.|..|... +++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~-----g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE-----GLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEec
Confidence 56999999999999999999999999853 277654
No 77
>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=42.97 E-value=15 Score=36.30 Aligned_cols=58 Identities=19% Similarity=0.249 Sum_probs=39.9
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
+-...|...|.+|.+..++|-. .|..+++++-.+|..|...|-|.---+|++.|+||+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 4445568889999998887642 477888999999999999999998888999999984
No 78
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=42.72 E-value=32 Score=34.76 Aligned_cols=41 Identities=22% Similarity=0.167 Sum_probs=33.6
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
+|-+ .||.+.+. .+++|.+||++.+||+...++++|..|..
T Consensus 11 ~tr~-~il~lL~~--~g~~sa~elA~~Lgis~~avR~HL~~Le~ 51 (218)
T COG2345 11 STRE-RILELLKK--SGPVSADELAEELGISPMAVRRHLDDLEA 51 (218)
T ss_pred cHHH-HHHHHHhc--cCCccHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 4444 45555665 47899999999999999999999999985
No 79
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=42.44 E-value=24 Score=28.05 Aligned_cols=39 Identities=21% Similarity=-0.020 Sum_probs=29.4
Q ss_pred HHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 600 VLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 600 ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
||-.++.. +.+++..||++.+|++.......|..|...|
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 34444442 3679999999999999999999999998654
No 80
>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=42.27 E-value=35 Score=25.09 Aligned_cols=45 Identities=22% Similarity=0.326 Sum_probs=34.0
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccc
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMR 765 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~ 765 (778)
.+-.|+..+.....++..+|-..+ ..+...+.+.|..|.++|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 345577788888889988766544 367889999999999999985
No 81
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=42.20 E-value=30 Score=33.21 Aligned_cols=51 Identities=12% Similarity=0.221 Sum_probs=38.1
Q ss_pred hCCCceeEeccCCceEEEEEEecCeeEEEEecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 563 KHSGRKLQWYHHMSNGTITFSNEVGKYDLDVTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 563 k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
+++.+.|+|.++| ...|.++-. +. -..|+++|++.+|..+.+++++|..=.
T Consensus 36 ~~~~~~lTWvdSL-------------------avAAga~ar-ek---ag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 36 KDPYERLTWVDSL-------------------AVAAGALAR-EK---AGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred hCcccccchhhHH-------------------HHHHHHHHH-HH---ccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 4588999998876 112333333 55 468999999999999999999887544
No 82
>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=39.22 E-value=1.8e+02 Score=31.67 Aligned_cols=88 Identities=15% Similarity=0.224 Sum_probs=53.8
Q ss_pred HHHHhhHHHhccchHHHHHHHHHhhhhh---cCCchHHHHHHHHHHHHHhHHHHHhhhhhh--ccCHHHHHHHHHHHHHH
Q psy14208 276 TILAECPKMIKMNETLKLELMMKLLDRI---KDGITPMLQDLEAHIVNAGLADMIASADII--TQDSEKYVERLLELFNQ 350 (778)
Q Consensus 276 ~l~~~~~~ll~~~~~~~L~~ly~l~~~~---~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~--~~~~~~~V~~ll~l~~~ 350 (778)
.+...|..-.+.+|.+.+.+.|+||.-+ +.|++....-+.+.|.....+.+....... ...+.-|+..|..+++.
T Consensus 11 ~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~ 90 (331)
T PF08318_consen 11 IFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEH 90 (331)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHH
Confidence 3445677788899999999999998865 346666666666666655554444332111 22344455555555555
Q ss_pred HH-------HHHHHHhcCCh
Q psy14208 351 FS-------KLVKDAFKDDP 363 (778)
Q Consensus 351 ~~-------~l~~~~F~~~~ 363 (778)
.. .+|..+|+...
T Consensus 91 ia~ii~~h~~lI~~~yG~~~ 110 (331)
T PF08318_consen 91 IATIIEQHQPLIEKYYGPGY 110 (331)
T ss_pred HHHHHHHccHHHHHHcCCcH
Confidence 44 45566887654
No 83
>KOG2905|consensus
Probab=38.62 E-value=41 Score=34.15 Aligned_cols=58 Identities=14% Similarity=0.250 Sum_probs=44.5
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~ 671 (778)
+-..++-+|.. +..||+.+|.+.|+-|+..|+.+|..+| ++.+.++ -..+|.+-++|.
T Consensus 187 vld~lFk~FEk--~~ywtlK~Lv~~t~QP~~fLKEiL~~ic--------v~NkKg~--------~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEK--YQYWTLKDLVEITKQPEAFLKEILKDIC--------VLNKKGP--------YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhc--CccccHHHHHHHhcCHHHHHHHHHHHHH--------HHhccCc--------ccCceecCHHHh
Confidence 33445567777 5889999999999999999999999998 5554432 235788888776
No 84
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=38.19 E-value=55 Score=28.75 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=32.8
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
.-.||.++.. +..+|+.+|++.+|++...+.+.+..|..
T Consensus 5 D~~il~~L~~--~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 5 DRKILEELQK--DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3456666666 36799999999999999999999999985
No 85
>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=37.38 E-value=43 Score=26.99 Aligned_cols=32 Identities=16% Similarity=0.101 Sum_probs=25.8
Q ss_pred CCcccHHHHHHHcCCChHHHHHHHHHhhcccc
Q psy14208 609 LDRLSFENLLLATELPDPELRRTLWSLVAFPK 640 (778)
Q Consensus 609 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k 640 (778)
.+.+|+++|+..++++.+.+...|.-|...|+
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~ 43 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQLIRKGY 43 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTS
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCc
Confidence 36799999999999999999999999997443
No 86
>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=37.28 E-value=68 Score=25.31 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=34.1
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
+..+..|+..+.+. + ++..+|++.+|++...+.+.|..|..
T Consensus 6 ~~~~~~il~~l~~~--~-~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 6 DPTRLRILRLLLEG--P-LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred ChHHHHHHHHHHHC--C-cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 34577778776662 4 99999999999999999999999975
No 87
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.17 E-value=45 Score=29.32 Aligned_cols=46 Identities=22% Similarity=0.316 Sum_probs=38.1
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR 766 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R 766 (778)
+|-.|++.+.....++..+|-..+ ..+...+.++|..|.++|+|+|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeec
Confidence 456788889888889988766444 4688999999999999999985
No 88
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.53 E-value=71 Score=24.15 Aligned_cols=37 Identities=22% Similarity=0.145 Sum_probs=30.1
Q ss_pred CCcc-cHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 609 LDRL-SFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 609 ~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.+.+ |..+|++.+|++...+.++|..|... ++|...+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~-----g~i~~~~ 54 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE-----GLVQRRP 54 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEEec
Confidence 3557 89999999999999999999999853 2666543
No 89
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=36.44 E-value=80 Score=24.00 Aligned_cols=28 Identities=18% Similarity=0.119 Sum_probs=25.9
Q ss_pred CcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 610 DRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 610 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
+.+|..+|++.+|++...+.+.|..|..
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5689999999999999999999999985
No 90
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=36.22 E-value=55 Score=24.05 Aligned_cols=45 Identities=22% Similarity=0.290 Sum_probs=33.2
Q ss_pred hhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 717 IIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 717 IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 4455555566777766544 35688899999999999999998653
No 91
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=35.44 E-value=50 Score=33.20 Aligned_cols=55 Identities=13% Similarity=0.183 Sum_probs=43.5
Q ss_pred HHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccc
Q psy14208 599 AVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 599 ~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~ 671 (778)
.++-+|.+ .+.||++.|++.+|-|+..|+.+|.+.+ +|.+.++ -...|++-++|+
T Consensus 199 ~lFK~Fe~--Y~yWtlKgL~e~~~QPea~lkEild~ia--------vLnKkgp--------ya~kY~LrPEYK 253 (297)
T COG5090 199 MLFKAFEK--YPYWTLKGLAEFCGQPEAFLKEILDDIA--------VLNKKGP--------YANKYELRPEYK 253 (297)
T ss_pred HHHHHhhc--CCchhhhhHHHHhcChHHHHHHHHHHHH--------hhhccCc--------ccceeecCHHHH
Confidence 34568887 6899999999999999999999999987 5665431 234788888887
No 92
>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=35.30 E-value=95 Score=26.42 Aligned_cols=55 Identities=15% Similarity=0.324 Sum_probs=32.1
Q ss_pred Hhhh-hHHHHHHHHHHhcCCCChhHHHHHHHHHHhhcccCCCChhHHHHHHHHHHHHH
Q psy14208 11 EDKW-PSMRPIVLKLLQQEPVSQNEWQNLFYAVHVVCLWDEKGPSKIVDALKEDIMNF 67 (778)
Q Consensus 11 e~~W-~~L~~ai~~i~~~~~~~~~sy~~lY~~vY~lc~~~~~~~~~LY~~l~~~i~~~ 67 (778)
+.|| ..++..+..++...+..+.+|.+++..|--.+.. .-++.+...+-..|..|
T Consensus 29 e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~--~VP~~vk~ell~~Ir~~ 84 (86)
T PF10163_consen 29 ECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARA--MVPDEVKKELLQRIRAF 84 (86)
T ss_dssp HTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHH--CS-HHHHHHHHHHHHHH
T ss_pred HCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHH
Confidence 4577 5566666666665456677788888877776665 33444444444444443
No 93
>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=35.16 E-value=90 Score=23.99 Aligned_cols=31 Identities=13% Similarity=0.208 Sum_probs=25.1
Q ss_pred hhcCCCCCcccHHHHHHHcCCChHHHHHHHHHh
Q psy14208 603 AWNERPLDRLSFENLLLATELPDPELRRTLWSL 635 (778)
Q Consensus 603 ~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL 635 (778)
.|+. ....|.++|++.+||+...+..+|..-
T Consensus 17 Yfd~--PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 17 YFDV--PRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCC--CCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4554 357999999999999999988887644
No 94
>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=35.15 E-value=79 Score=23.46 Aligned_cols=35 Identities=14% Similarity=0.246 Sum_probs=25.0
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHh
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSL 635 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL 635 (778)
+.+|-+.|- +.+|++||++.+|++...+.+.+..-
T Consensus 10 r~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 10 REVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 344455663 46899999999999999888766543
No 95
>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=35.03 E-value=72 Score=27.22 Aligned_cols=44 Identities=16% Similarity=0.131 Sum_probs=34.9
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHc-CCChHHHHHHHHHhhcccccccceeecc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLAT-ELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t-~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
+.||..... +...|.||.+.+ |++...|.+.|.-|...| ++.+.
T Consensus 8 ~~IL~~l~~---g~~rf~el~~~l~~is~~~L~~~L~~L~~~G-----Lv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ---GPMRFSELQRRLPGISPKVLSQRLKELEEAG-----LVERR 52 (90)
T ss_dssp HHHHHHHTT---SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTT-----SEEEE
T ss_pred HHHHHHHHh---CCCcHHHHHHhcchhHHHHHHHHHHHHHHcc-----hhhcc
Confidence 466666665 578999999999 999999999999998643 77764
No 96
>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=34.95 E-value=40 Score=27.10 Aligned_cols=55 Identities=18% Similarity=0.270 Sum_probs=32.8
Q ss_pred hhhhhhhhhccCC-CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 713 VQEAIIKILKMRK-RISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 713 i~A~IVRiMK~~k-~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
.=|.||..||.+. .++.+||..++. +..+ ++.++.|-+-+=|+-|++ .+.|.|.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 3477899999984 688887776653 4343 234456667888988874 47999976
No 97
>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=34.79 E-value=23 Score=27.51 Aligned_cols=48 Identities=19% Similarity=0.263 Sum_probs=31.9
Q ss_pred hhhhhhhhccCCC--CChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 714 QEAIIKILKMRKR--ISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 714 ~A~IVRiMK~~k~--l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
+..|...+..... ++..+|...+ ..+...+.+.|..|+++|||+|..+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l--------~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERL--------GISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 3444555555554 6666554333 3577889999999999999999754
No 98
>PF13730 HTH_36: Helix-turn-helix domain
Probab=34.77 E-value=1.1e+02 Score=22.98 Aligned_cols=25 Identities=20% Similarity=0.177 Sum_probs=23.6
Q ss_pred cHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 613 SFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 613 t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999975
No 99
>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=32.83 E-value=38 Score=29.83 Aligned_cols=39 Identities=26% Similarity=0.269 Sum_probs=27.8
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
.+.|+.++.. ++.++-++|++.+|++..++.+.|..|..
T Consensus 15 ~~~Il~~L~~--~~~l~de~la~~~~l~~~~vRkiL~~L~~ 53 (105)
T PF02002_consen 15 AVRILDALLR--KGELTDEDLAKKLGLKPKEVRKILYKLYE 53 (105)
T ss_dssp THHHHHHHHH--H--B-HHHHHHTT-S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHH--cCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4456655554 36799999999999999999999999985
No 100
>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=32.76 E-value=28 Score=26.82 Aligned_cols=46 Identities=20% Similarity=0.281 Sum_probs=31.8
Q ss_pred hhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 715 EAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 715 A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
..+..++-..+.++..+|-.. +..+...+.+.|..|.++|||+|..
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~--------~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEK--------LGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHH--------HCCChhHHHHHHHHHHHCCCEEecc
Confidence 344555555666666654432 3367899999999999999999854
No 101
>PF04001 Vhr1: Transcription factor Vhr1; InterPro: IPR007147 This is a family of proteins of unknown function found in yeast.
Probab=32.42 E-value=1.9e+02 Score=24.45 Aligned_cols=52 Identities=23% Similarity=0.390 Sum_probs=35.7
Q ss_pred HHHHHHHHHH-------cCCCCCCh-H-HHHHHHHHHH-HcCCChhhHHHHHHHHHhHHHhH
Q psy14208 452 FHKAHLTRRL-------ILDTSADS-E-KEENMVEWLR-DVGMPADYVNKLARMFQDIKVSQ 503 (778)
Q Consensus 452 ~Y~~~LakRL-------L~~~s~s~-~-~E~~~i~~Lk-~~G~~~~~t~kl~~Ml~D~~~S~ 503 (778)
..+++-++|| |..+.+|. | .=+.+-..|+ ++|+|++++...+....---+|-
T Consensus 23 ~WK~FSsRRLELId~~~Ls~~KASEQd~~I~~iA~iLR~Ef~Yp~~~~~~FeKLV~aavQSV 84 (95)
T PF04001_consen 23 KWKRFSSRRLELIDKFDLSSRKASEQDDNIRQIAEILRTEFGYPESYSSEFEKLVTAAVQSV 84 (95)
T ss_pred HHHHHHHHHHHHHHHcCcccchhhhhHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHH
Confidence 5677777886 23333332 2 2366777899 99999999988888877666554
No 102
>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=32.29 E-value=1.2e+02 Score=26.55 Aligned_cols=53 Identities=9% Similarity=0.169 Sum_probs=44.2
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR 766 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R 766 (778)
++-+|..++. .+.++=-+|.+++.+.....+.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 5566677776 5678889999998877655678899999999999999999998
No 103
>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=32.13 E-value=54 Score=27.16 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=20.9
Q ss_pred hhhhhhhhhhccCC--CCChHHHHHHHH
Q psy14208 712 RVQEAIIKILKMRK--RISNAQLQTELV 737 (778)
Q Consensus 712 ~i~A~IVRiMK~~k--~l~~~~L~~~v~ 737 (778)
..=|.||..||+|. .++.+|+..++.
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHh
Confidence 44578999999986 689998887774
No 104
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=31.68 E-value=66 Score=23.49 Aligned_cols=30 Identities=13% Similarity=0.123 Sum_probs=21.0
Q ss_pred HHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHH
Q psy14208 600 VLFAWNERPLDRLSFENLLLATELPDPELRRTLW 633 (778)
Q Consensus 600 ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~ 633 (778)
|+-++.+ ++|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~----G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAE----GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHT----T--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHh
Confidence 4445554 38999999999999999988763
No 105
>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=31.54 E-value=63 Score=34.14 Aligned_cols=59 Identities=14% Similarity=0.206 Sum_probs=33.1
Q ss_pred HHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccccc
Q psy14208 595 TFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQEFA 671 (778)
Q Consensus 595 ~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~F~ 671 (778)
-+--.|+-+|.. +..||+++|.+.|+-|+..|+.+|..++ ++.+.++ -...|.|=++|.
T Consensus 216 eL~d~lF~~Fe~--~~ywslK~L~~~t~QP~~yLKeiL~eIa--------~~~k~g~--------~~~~w~LKpeyk 274 (275)
T PF02270_consen 216 ELLDLLFKLFEK--HQYWSLKDLRQRTQQPEAYLKEILEEIA--------VLNKRGP--------HKNMWELKPEYK 274 (275)
T ss_dssp HHHHHHHHHHHH---S-B-HHHHHHH--S-HHHHHHHHHHH----------EE--TT-----------EE----SS-
T ss_pred HHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHH--------HHhccCC--------cCCcEecchHHc
Confidence 345566778988 5789999999999999999999999998 5665432 235677666653
No 106
>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=31.34 E-value=1e+02 Score=24.18 Aligned_cols=37 Identities=11% Similarity=0.118 Sum_probs=30.2
Q ss_pred CCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 609 LDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 609 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
.+.++..+|++.+|++...+...+.-|...| ++...|
T Consensus 20 ~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~G-----lV~~~~ 56 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVSPPTVTEMLKRLAEKG-----LVEYEP 56 (60)
T ss_dssp TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTT-----SEEEET
T ss_pred CCCccHHHHHHHHCCChHHHHHHHHHHHHCC-----CEEecC
Confidence 4789999999999999999999999998532 676554
No 107
>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=30.52 E-value=36 Score=34.74 Aligned_cols=37 Identities=16% Similarity=0.334 Sum_probs=30.6
Q ss_pred HHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 738 DILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 738 ~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
.+|..+|..+...+.++|+.|++.|+|.|..+ +++|+
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 34555799999999999999999999999865 56664
No 108
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=30.26 E-value=56 Score=33.57 Aligned_cols=55 Identities=13% Similarity=0.351 Sum_probs=39.6
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
|...|...++....|.-+ .+|...|..+...+.++|+.|++.|+|.|-.. +++|+
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 333343356666566544 44555799999999999999999999999765 55654
No 109
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.38 E-value=44 Score=25.35 Aligned_cols=29 Identities=14% Similarity=0.208 Sum_probs=24.6
Q ss_pred hcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 741 KNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 741 ~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
..+|..+...+.+.+..|.+.|+|.+.++
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34567899999999999999999988754
No 110
>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=29.07 E-value=80 Score=25.31 Aligned_cols=52 Identities=19% Similarity=0.023 Sum_probs=34.7
Q ss_pred cHHHHHHHHhhcC---CCCCcccHHHHHHHcCCC-hHHHHHHHHHhhcccccccceeeccc
Q psy14208 594 TTFQMAVLFAWNE---RPLDRLSFENLLLATELP-DPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 594 s~~Q~~ILl~FN~---~~~~~~t~~ei~~~t~i~-~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
|.-|.-||...-+ ...-.-|+.||++.+|+. ...+..+|..|... +.|.+.|
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k-----G~I~r~~ 60 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK-----GYIRRDP 60 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT-----TSEEEGC
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-----cCccCCC
Confidence 5556666654322 112356999999999996 89999999999853 2777765
No 111
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.99 E-value=1.2e+02 Score=22.48 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=29.2
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
|.-+.-|+.++- .+++..+|++.+|++...+.+.+..+.
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 444555555553 347999999999999999998887664
No 112
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=28.80 E-value=1e+02 Score=27.12 Aligned_cols=51 Identities=22% Similarity=0.158 Sum_probs=39.7
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
++..|..||...... +..+..+|++.++++...+.+.+..|... +++.+.+
T Consensus 20 lt~~q~~~L~~l~~~--~~~~~~~la~~l~i~~~~vt~~l~~Le~~-----glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEA--GGITVKELAERLGLDRSTVTRLLKRLEDK-----GLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHh--CCCcHHHHHHHHCCCHHHHHHHHHHHHHC-----CCeeecC
Confidence 578898988877663 44444899999999999999999999853 2666553
No 113
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=27.74 E-value=56 Score=27.83 Aligned_cols=39 Identities=10% Similarity=0.086 Sum_probs=33.9
Q ss_pred HhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEecC
Q psy14208 740 LKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVYLA 778 (778)
Q Consensus 740 l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Yia 778 (778)
+..++......-+++|..|-++|-|+.-..++..-+|.|
T Consensus 47 lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 47 LASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 345678899999999999999999988888888899976
No 114
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=27.66 E-value=43 Score=34.40 Aligned_cols=37 Identities=22% Similarity=0.225 Sum_probs=30.1
Q ss_pred HHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 738 DILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 738 ~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
.+|...|..+...+.++|+.|++.|+|.|... +++|+
T Consensus 37 ~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 37 NELCTQYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 34445688999999999999999999999865 56664
No 115
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=27.22 E-value=1.1e+02 Score=25.85 Aligned_cols=48 Identities=19% Similarity=0.220 Sum_probs=35.6
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
.+..|...+...+.++..+|... +.++...+.+.|..|.++|+|.+..
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 34556677777777887766544 2356788999999999999998654
No 116
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=27.20 E-value=1.2e+02 Score=31.93 Aligned_cols=40 Identities=25% Similarity=0.274 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
....|+-.+.+. ...+|+++|+..|||..+++..+|++|-
T Consensus 209 W~~~il~~L~~~-~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 209 WTRVLLEQLRDV-KGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHhc-CCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 444555444332 3679999999999999999999999874
No 117
>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=27.07 E-value=1.2e+02 Score=24.89 Aligned_cols=51 Identities=10% Similarity=0.044 Sum_probs=40.3
Q ss_pred HHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 595 TFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 595 ~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
..|.++|...-.....+++-.+|...+|++...+-..+..|... +++++.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~-----gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKK-----GLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHC-----CCEEEEE
Confidence 46778887776544577899999999999999999999999853 2777654
No 118
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=26.98 E-value=77 Score=30.64 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=31.7
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
|..-+|.+|. +++|.+||++.||++...+-..|.-|...
T Consensus 30 ~iYgilyls~---~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 30 QIYGILYLSR---KPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHhhhheecC---CCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 4444667776 78999999999999999988888888753
No 119
>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=26.97 E-value=95 Score=23.33 Aligned_cols=44 Identities=20% Similarity=0.381 Sum_probs=30.3
Q ss_pred hhhhhccCC-CCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 717 IIKILKMRK-RISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 717 IVRiMK~~k-~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
|.+.+...+ .++..||...+ . .+...+-+-+..|.+.||++||+
T Consensus 8 iL~~l~~~~~~~t~~eia~~~----g----l~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARAL----G----LPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHH----T----S-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHcCCCCCCHHHHHHHH----C----cCHHHHHHHHHHHHHCcCeecCc
Confidence 344444443 46777665443 2 45678999999999999999985
No 120
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.69 E-value=1.1e+02 Score=22.05 Aligned_cols=39 Identities=15% Similarity=0.211 Sum_probs=27.4
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHh
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSL 635 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL 635 (778)
+..+-.++.++-- +.+|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~~---~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRFG---EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4444444444321 35899999999999999998877654
No 121
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=26.55 E-value=1.4e+02 Score=26.90 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHhcCCc-CChHhHHHHHHHHHhhcCCCCchhhhhHHh
Q psy14208 156 QRLQDSAMKLVQSERNGEA-FDSQLVIGVRESYVNLCSNPEDKLQIYREH 204 (778)
Q Consensus 156 ~~l~~~ll~~I~~~R~g~~-id~~~i~~v~~~~~~l~~~~~~~~~~Y~~~ 204 (778)
+++.+.|-+++...|.... ...--+.++..||++|| +.+|+-.
T Consensus 3 ~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELG------LRVYeaQ 46 (118)
T PRK13713 3 NEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELG------LRVYEAQ 46 (118)
T ss_pred hHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHh------HHHHHHH
Confidence 4556667777888886544 22234668888999998 6677643
No 122
>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=26.13 E-value=45 Score=26.35 Aligned_cols=30 Identities=17% Similarity=0.285 Sum_probs=24.8
Q ss_pred HhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 740 LKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 740 l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
+..+|..+...+.+++..|.+.|+|.+.+.
T Consensus 30 la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 30 LAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 334678899999999999999999998764
No 123
>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=26.10 E-value=1.4e+02 Score=22.07 Aligned_cols=38 Identities=8% Similarity=0.095 Sum_probs=27.4
Q ss_pred HHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 595 TFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 595 ~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
..|.-++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 3 ~~e~~i~~~~~----~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 3 PREREVLRLLA----EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444444442 347999999999999999888877654
No 124
>PRK00215 LexA repressor; Validated
Probab=26.04 E-value=1.1e+02 Score=30.60 Aligned_cols=53 Identities=15% Similarity=-0.014 Sum_probs=39.8
Q ss_pred ecHHHHHHHHhhcC---CCCCcccHHHHHHHcCC-ChHHHHHHHHHhhcccccccceeeccc
Q psy14208 593 VTTFQMAVLFAWNE---RPLDRLSFENLLLATEL-PDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~---~~~~~~t~~ei~~~t~i-~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
++.-|..||..+.+ ......|+.||++.+|+ +...+.+.|..|...+ ++.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g-----~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKG-----FIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCC-----CEEeCC
Confidence 35668888866642 11346899999999999 9999999999998532 676654
No 125
>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=25.85 E-value=70 Score=31.51 Aligned_cols=26 Identities=19% Similarity=0.236 Sum_probs=22.8
Q ss_pred cccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 611 RLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 611 ~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
.+|+++|++.|||..+++..+|+.|-
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 69999999999999999999999884
No 126
>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=25.70 E-value=60 Score=28.82 Aligned_cols=46 Identities=17% Similarity=0.346 Sum_probs=32.2
Q ss_pred cCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc--CCCCC-CceEe
Q psy14208 723 MRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR--DDDDI-NVFVY 776 (778)
Q Consensus 723 ~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R--d~~d~-~~y~Y 776 (778)
..+.++..+|...+ ..+..-+-+.|+.|.++|||.| ++.|+ .++.|
T Consensus 40 ~~~~~t~~eL~~~l--------~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~ 88 (109)
T TIGR01889 40 NEGKLTLKEIIKEI--------LIKQSALVKIIKKLSKKGYLSKERSEDDERKVIIS 88 (109)
T ss_pred cCCcCcHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEE
Confidence 44567777665433 3567889999999999999996 55553 34443
No 127
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.45 E-value=52 Score=24.90 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=18.3
Q ss_pred CCCChhhHHHHHHHhhhhccc
Q psy14208 744 FLPSKKMIKEQIEWLIEQKYM 764 (778)
Q Consensus 744 F~p~~~~iK~~Ie~LIereyl 764 (778)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 346789999999999999987
No 128
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=25.03 E-value=99 Score=32.22 Aligned_cols=41 Identities=22% Similarity=0.143 Sum_probs=35.8
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
-|..|+-+.+. ++.+++.||++.+|++...++|-|..|...
T Consensus 6 R~~~Il~~L~~--~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 6 RQAAILEYLQK--QGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHH--cCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 36678888887 478999999999999999999999999853
No 129
>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=24.94 E-value=51 Score=33.65 Aligned_cols=36 Identities=22% Similarity=0.388 Sum_probs=29.7
Q ss_pred HHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 739 ILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 739 ~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
+|..+|..+...+.++|+.|.+.|+|.|... +++|+
T Consensus 37 eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 3445688999999999999999999999765 55654
No 130
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.93 E-value=1.2e+02 Score=27.81 Aligned_cols=52 Identities=17% Similarity=0.253 Sum_probs=44.5
Q ss_pred hhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 710 ILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 710 ~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
+..|.+-||-..+.++.++..||...+ -.+...+++.+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~T--------GasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAKT--------GASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 456889999999999999999888654 3678889999999999999988764
No 131
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=24.87 E-value=48 Score=29.74 Aligned_cols=30 Identities=10% Similarity=0.490 Sum_probs=21.2
Q ss_pred CcHHhhhhHHHHHHHHHHhcCCCChhHHHHH
Q psy14208 8 QTFEDKWPSMRPIVLKLLQQEPVSQNEWQNL 38 (778)
Q Consensus 8 ~~fe~~W~~L~~ai~~i~~~~~~~~~sy~~l 38 (778)
.|+++.|+.|.++|+.+++..++. ..|+.|
T Consensus 46 ~dL~~nWeVlaEpIQTvmRr~g~~-~pYE~L 75 (115)
T PF08328_consen 46 EDLDENWEVLAEPIQTVMRRYGIP-NPYEKL 75 (115)
T ss_dssp HHHCT-GGGGHHHHHHHHHHTT-S-SHHHHH
T ss_pred HHHHHCHHHHHHHHHHHHHHcCCC-CHHHHH
Confidence 478999999999999999865433 344444
No 132
>KOG2747|consensus
Probab=24.80 E-value=89 Score=34.43 Aligned_cols=69 Identities=14% Similarity=0.146 Sum_probs=40.4
Q ss_pred eeEeccCCceEEEEEEecCeeE-EEE----ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 568 KLQWYHHMSNGTITFSNEVGKY-DLD----VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 568 ~L~w~~~l~~~~i~~~~~~~~~-~l~----~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
-+.+.+.||..|=++-.+.+.. +|= -+-.-..||-++-......+|+++|++.|||..+++..+|++|-
T Consensus 281 LIdFSYeLSr~E~~~GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhhcccCcCCCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 4566777776665443221110 000 02223333333333212349999999999999999999999884
No 133
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=24.74 E-value=1.1e+02 Score=29.37 Aligned_cols=44 Identities=14% Similarity=0.019 Sum_probs=36.0
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
.-.-.-||-++.. +..+|+.+|++.+|++...+.+.++.|...|
T Consensus 13 D~~D~~IL~~Lq~--d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQK--DGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHHhcc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3445567777766 4789999999999999999999999998643
No 134
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=24.58 E-value=1.3e+02 Score=31.37 Aligned_cols=42 Identities=10% Similarity=0.133 Sum_probs=33.4
Q ss_pred HHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 600 VLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 600 ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
||++.-+ ++.|++||...++++...+..+|.-|... +++.+.
T Consensus 18 lLllL~e---gPkti~EI~~~l~vs~~ai~pqiKkL~~~-----~LV~~~ 59 (260)
T COG4742 18 LLLLLKE---GPKTIEEIKNELNVSSSAILPQIKKLKDK-----GLVVQE 59 (260)
T ss_pred HHHHHHh---CCCCHHHHHHHhCCCcHHHHHHHHHHhhC-----CCEEec
Confidence 4555554 67899999999999999999999999753 266654
No 135
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.95 E-value=1.2e+02 Score=28.62 Aligned_cols=45 Identities=11% Similarity=0.085 Sum_probs=36.1
Q ss_pred ecHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 593 VTTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 593 ~s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
+...--.||.++.. +...|+.+|++.+|++...+.+.+..|...|
T Consensus 7 lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 7 IDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34455566766665 4679999999999999999999999998643
No 136
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=23.64 E-value=1.3e+02 Score=25.19 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=34.2
Q ss_pred hhhhhccC-CCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCC
Q psy14208 717 IIKILKMR-KRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDD 769 (778)
Q Consensus 717 IVRiMK~~-k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~ 769 (778)
|...+... +.++..+|..++ ..+...+.+.+..|.+.|||.+++.
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 34444444 678888777665 3577889999999999999999754
No 137
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=23.60 E-value=2.4e+02 Score=26.28 Aligned_cols=56 Identities=13% Similarity=0.092 Sum_probs=46.0
Q ss_pred hhhhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccC
Q psy14208 710 ILRVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRD 767 (778)
Q Consensus 710 ~~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd 767 (778)
..-+.-+|..++..+ +.=-+|..++.+.-.+.|.|+...|=..+..|-++|+|+..
T Consensus 41 ~~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~ 96 (135)
T PRK09416 41 EEDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSS 96 (135)
T ss_pred cccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEe
Confidence 445777888888765 78889998887764456899999999999999999999874
No 138
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.54 E-value=96 Score=30.42 Aligned_cols=40 Identities=20% Similarity=0.178 Sum_probs=32.1
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhcc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVAF 638 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 638 (778)
...||.++-. ++.+|-++|++.+||+...+.++|..|...
T Consensus 24 ~~~Vl~~L~~--~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~ 63 (178)
T PRK06266 24 GFEVLKALIK--KGEVTDEEIAEQTGIKLNTVRKILYKLYDA 63 (178)
T ss_pred HhHHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3445554444 367999999999999999999999999863
No 139
>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=22.94 E-value=1.3e+02 Score=23.02 Aligned_cols=40 Identities=10% Similarity=0.138 Sum_probs=31.7
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
|.-+..||.++-. +.+..+|++.+|++...+..++..+..
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 4556777777764 579999999999999999999988863
No 140
>PRK14999 histidine utilization repressor; Provisional
Probab=22.71 E-value=58 Score=33.49 Aligned_cols=48 Identities=19% Similarity=0.290 Sum_probs=35.0
Q ss_pred hhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 720 ILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 720 iMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
..+....|.-+ .+|..+|..+...+.++|+.|.+.|+|.|..+ +++|+
T Consensus 29 ~~~~G~~LPsE-------~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSE-------AELVAQYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 44555555333 33344688999999999999999999999765 56664
No 141
>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=22.51 E-value=1.5e+02 Score=26.47 Aligned_cols=62 Identities=15% Similarity=0.083 Sum_probs=44.3
Q ss_pred hhhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceEe
Q psy14208 712 RVQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFVY 776 (778)
Q Consensus 712 ~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~Y 776 (778)
.+|+.|.+- ....-..-..++.+|..++. .+ ++...+--||+.||+.|.|+-.++-..+-+|
T Consensus 48 ~yD~~Il~~-~~~~~~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQ-APDEFQKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhc-CCccccHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 466777761 12233566788999998864 34 5668899999999999999988765555444
No 142
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.44 E-value=1.8e+02 Score=21.52 Aligned_cols=35 Identities=17% Similarity=0.167 Sum_probs=25.6
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHH
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWS 634 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~s 634 (778)
+.+.|+.+.-+ ..|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~----~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRE----SRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhh----cCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34445544432 269999999999999999987754
No 143
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=22.19 E-value=1e+02 Score=21.92 Aligned_cols=28 Identities=11% Similarity=0.170 Sum_probs=20.4
Q ss_pred CCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 609 LDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 609 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
...+|+++|++..|++..-+.+......
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 3569999999999999999988776554
No 144
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.85 E-value=72 Score=29.72 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=21.8
Q ss_pred CCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 743 MFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 743 ~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34467788999999999999999854
No 145
>PF14164 YqzH: YqzH-like protein
Probab=21.76 E-value=3.9e+02 Score=21.45 Aligned_cols=39 Identities=15% Similarity=0.373 Sum_probs=25.4
Q ss_pred CCChhHHHHHHHHHHhhcccCCCChhHHHHHHHHHHHHHHH
Q psy14208 29 PVSQNEWQNLFYAVHVVCLWDEKGPSKIVDALKEDIMNFIR 69 (778)
Q Consensus 29 ~~~~~sy~~lY~~vY~lc~~~~~~~~~LY~~l~~~i~~~l~ 69 (778)
+++..+|+.|+..|-..-.. ...+.||+.+.+.+-.|+.
T Consensus 25 pls~~E~~~L~~~i~~~~~~--~~~~Dl~eiVeDvVY~yiT 63 (64)
T PF14164_consen 25 PLSDEEWEELCKHIQERKNE--EPDEDLHEIVEDVVYDYIT 63 (64)
T ss_pred CCCHHHHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHhc
Confidence 67777888887765443332 4456788877777766654
No 146
>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=21.73 E-value=1.6e+02 Score=25.22 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=27.4
Q ss_pred CCcccHHHHHHHcCCChHHHHHHHHHhhccc
Q psy14208 609 LDRLSFENLLLATELPDPELRRTLWSLVAFP 639 (778)
Q Consensus 609 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~~ 639 (778)
...+++++|++.++++..++...+..++..+
T Consensus 58 y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~ 88 (105)
T PF01399_consen 58 YSSISISEIAKALQLSEEEVESILIDLISNG 88 (105)
T ss_dssp -SEEEHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred hcccchHHHHHHhccchHHHHHHHHHHHHCC
Confidence 5789999999999999999999999998644
No 147
>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=21.66 E-value=1.7e+02 Score=28.26 Aligned_cols=60 Identities=20% Similarity=0.243 Sum_probs=44.2
Q ss_pred HHHHHHhhcCCCCCcccHHHHHHHc--CCChHHHHHHHHHhhcccccccceeecccCCCCCCCCCCCCeEEEccc
Q psy14208 597 QMAVLFAWNERPLDRLSFENLLLAT--ELPDPELRRTLWSLVAFPKIKRQILLYSEEVQSPKDFTEHTSFWINQE 669 (778)
Q Consensus 597 Q~~ILl~FN~~~~~~~t~~ei~~~t--~i~~~~l~~~L~sL~~~~k~k~~iL~~~~~~~~~~~~~~~~~f~lN~~ 669 (778)
...|+-.|... +.+.|..+|...+ +++...+.++|..|+..| + |..+. +....+|..|.+
T Consensus 3 e~~Il~y~~~q-NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g--~--i~~K~--------~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQ-NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEG--K--IVEKE--------YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHc-CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCC--C--eeeee--------ecceEEEeeCcc
Confidence 45788888775 6789999999877 589999999999999744 3 55543 223456777654
No 148
>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=21.48 E-value=1.8e+02 Score=22.31 Aligned_cols=33 Identities=18% Similarity=0.069 Sum_probs=27.3
Q ss_pred ccHHHHHHHcCCChHHHHHHHHHhhcccccccceeecc
Q psy14208 612 LSFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYS 649 (778)
Q Consensus 612 ~t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~ 649 (778)
.|..+|++.+|++...+.++|..|... ++|...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~-----G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAE-----GLVERR 58 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC-----CCEEec
Confidence 349999999999999999999999853 276544
No 149
>PRK04217 hypothetical protein; Provisional
Probab=21.46 E-value=1.4e+02 Score=26.79 Aligned_cols=40 Identities=18% Similarity=0.013 Sum_probs=27.8
Q ss_pred cHHHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhh
Q psy14208 594 TTFQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLV 636 (778)
Q Consensus 594 s~~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 636 (778)
+.-|..++.+... +.+|+++|++.+|++...+.+.|....
T Consensus 44 t~eereai~l~~~---eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 44 TYEEFEALRLVDY---EGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred CHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4444444433332 458999999999999998888776543
No 150
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=21.26 E-value=98 Score=29.06 Aligned_cols=46 Identities=26% Similarity=0.394 Sum_probs=0.0
Q ss_pred hhhhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhccccc
Q psy14208 713 VQEAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRR 766 (778)
Q Consensus 713 i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~R 766 (778)
+|..|.+++....+++..+|-..+= .++..+.+||+.|.++|.|++
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceee
No 151
>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=21.23 E-value=80 Score=24.43 Aligned_cols=29 Identities=17% Similarity=0.213 Sum_probs=24.2
Q ss_pred HhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 740 LKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 740 l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
+..+|..+...+.+.+..|.++|||.+.+
T Consensus 31 la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 31 LAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 33456678899999999999999998875
No 152
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=21.22 E-value=1.5e+02 Score=26.51 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=31.9
Q ss_pred hhhhhhhccCCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 715 EAIIKILKMRKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 715 A~IVRiMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
..|...+.....++..+|-..+ ..+...+-+.|+.|.++|||+|..
T Consensus 31 ~~iL~~l~~~~~~t~~ela~~~--------~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 31 WRILRILAEQGSMEFTQLANQA--------CILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHcCCcCHHHHHHHh--------CCCchhHHHHHHHHHHCCCEEecc
Confidence 3445555566777776555332 245567899999999999999844
No 153
>PRK09462 fur ferric uptake regulator; Provisional
Probab=20.98 E-value=1.7e+02 Score=27.56 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=39.1
Q ss_pred hhhhhhcc--CCCCChHHHHHHHHHHHhcCCCCChhhHHHHHHHhhhhcccccCC
Q psy14208 716 AIIKILKM--RKRISNAQLQTELVDILKNMFLPSKKMIKEQIEWLIEQKYMRRDD 768 (778)
Q Consensus 716 ~IVRiMK~--~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~ 768 (778)
+|.+++.. .+-++.++|...+.+.. ..++...|=+.|+.|.+.|.|.+-.
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 45566654 36899999998887643 4567889999999999999998754
No 154
>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=20.94 E-value=1.1e+02 Score=27.11 Aligned_cols=55 Identities=16% Similarity=0.259 Sum_probs=31.2
Q ss_pred hhhhhhhhhhhccCCCCChHHHHHHHHHHHhc-CCCCChhhHHHHHHHhhhhccccc
Q psy14208 711 LRVQEAIIKILKMRKRISNAQLQTELVDILKN-MFLPSKKMIKEQIEWLIEQKYMRR 766 (778)
Q Consensus 711 ~~i~A~IVRiMK~~k~l~~~~L~~~v~~~l~~-~F~p~~~~iK~~Ie~LIereyl~R 766 (778)
..+.--|+.+.-.++.-. -++.++..+..++ -|.|+...|=+++..|++.||++|
T Consensus 17 aFlKlYiitm~e~~r~Yg-~q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 17 AFLKLYIITMVEQERGYG-LQLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHHHTT-EBC-TCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhhhhcccchH-HHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 345555666665555111 1233333344433 399999999999999999999955
No 155
>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=20.87 E-value=1.5e+02 Score=23.30 Aligned_cols=37 Identities=24% Similarity=0.148 Sum_probs=29.5
Q ss_pred CCcc-cHHHHHHHcCCChHHHHHHHHHhhcccccccceeeccc
Q psy14208 609 LDRL-SFENLLLATELPDPELRRTLWSLVAFPKIKRQILLYSE 650 (778)
Q Consensus 609 ~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~~k~k~~iL~~~~ 650 (778)
++.+ |..+|++..|++-..+.++|.-|...+ ++...|
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g-----~i~~~~ 58 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEG-----LIERRP 58 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTT-----SEEEET
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCC-----cEEEEC
Confidence 4678 999999999999999999999998633 777654
No 156
>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=20.69 E-value=1.6e+02 Score=28.15 Aligned_cols=38 Identities=24% Similarity=0.307 Sum_probs=30.5
Q ss_pred HHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 598 MAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 598 ~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
..|+.++=. ++.+|-++|+..+||+..++.+.|..|..
T Consensus 17 v~Vl~aL~~--~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e 54 (158)
T TIGR00373 17 GLVLFSLGI--KGEFTDEEISLELGIKLNEVRKALYALYD 54 (158)
T ss_pred HHHHHHHhc--cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344543333 35799999999999999999999999986
No 157
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=20.19 E-value=1.6e+02 Score=30.60 Aligned_cols=40 Identities=15% Similarity=0.141 Sum_probs=35.1
Q ss_pred HHHHHHHhhcCCCCCcccHHHHHHHcCCChHHHHHHHHHhhc
Q psy14208 596 FQMAVLFAWNERPLDRLSFENLLLATELPDPELRRTLWSLVA 637 (778)
Q Consensus 596 ~Q~~ILl~FN~~~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 637 (778)
-|..|+..+++ ++.+++.||++.+|++...+.|-|..|..
T Consensus 6 R~~~Il~~l~~--~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 6 RHQILLELLAQ--LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred HHHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35668888887 47899999999999999999999999975
No 158
>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=20.13 E-value=74 Score=27.55 Aligned_cols=27 Identities=37% Similarity=0.594 Sum_probs=20.2
Q ss_pred HhcCCCCChhhHHHHHHHhhhhcccccC
Q psy14208 740 LKNMFLPSKKMIKEQIEWLIEQKYMRRD 767 (778)
Q Consensus 740 l~~~F~p~~~~iK~~Ie~LIereyl~Rd 767 (778)
+++.| |...-+.+-||.||.-|||.|+
T Consensus 34 iKk~f-~~qk~~D~fie~li~~GYI~re 60 (93)
T PF08820_consen 34 IKKDF-PKQKRLDIFIEALIKLGYIERE 60 (93)
T ss_pred HHHhh-ccccchhHHHHHHHHcCCeEec
Confidence 44445 3445577889999999999994
No 159
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=20.08 E-value=71 Score=32.80 Aligned_cols=37 Identities=22% Similarity=0.345 Sum_probs=30.4
Q ss_pred HHHhcCCCCChhhHHHHHHHhhhhcccccCCCCCCceE
Q psy14208 738 DILKNMFLPSKKMIKEQIEWLIEQKYMRRDDDDINVFV 775 (778)
Q Consensus 738 ~~l~~~F~p~~~~iK~~Ie~LIereyl~Rd~~d~~~y~ 775 (778)
..|..+|..|...+.++|..|.+.|+|.|-.+ +++|+
T Consensus 35 ~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 35 RELAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 34555799999999999999999999999764 56664
Done!