Query 004654
Match_columns 739
No_of_seqs 254 out of 1020
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 02:56:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167 Cullins [Cell cycle co 100.0 2E-116 4E-121 947.3 40.0 589 147-736 2-608 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 4E-101 1E-105 884.4 55.8 630 101-736 14-670 (725)
3 COG5647 Cullin, a subunit of E 100.0 1.1E-96 2E-101 811.9 51.4 630 98-736 14-716 (773)
4 PF00888 Cullin: Cullin family 100.0 1.5E-95 3E-100 852.0 60.8 576 108-706 1-588 (588)
5 KOG2284 E3 ubiquitin ligase, C 100.0 1.1E-85 2.4E-90 679.3 45.9 596 102-736 10-671 (728)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1.4E-76 2.9E-81 617.1 49.0 613 101-718 10-687 (777)
7 smart00182 CULLIN Cullin. 100.0 2E-34 4.4E-39 274.8 17.9 141 486-627 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 5.4E-26 1.2E-30 251.0 46.9 220 482-706 444-665 (765)
9 PF08539 HbrB: HbrB-like; Int 97.8 0.00042 9.1E-09 66.9 12.7 130 104-237 5-155 (158)
10 KOG2167 Cullins [Cell cycle co 97.1 0.0028 6E-08 71.3 10.7 316 103-437 109-455 (661)
11 TIGR01610 phage_O_Nterm phage 93.7 0.2 4.3E-06 44.3 6.6 66 633-706 20-93 (95)
12 PF09339 HTH_IclR: IclR helix- 93.7 0.088 1.9E-06 40.9 3.8 46 641-688 6-52 (52)
13 PF02082 Rrf2: Transcriptional 92.7 0.29 6.3E-06 41.9 6.0 59 639-704 11-70 (83)
14 PF13412 HTH_24: Winged helix- 92.6 0.22 4.8E-06 37.8 4.6 46 637-684 2-47 (48)
15 PF08220 HTH_DeoR: DeoR-like h 92.4 0.19 4.2E-06 39.9 4.0 49 640-690 2-50 (57)
16 PF12802 MarR_2: MarR family; 92.2 0.17 3.7E-06 40.4 3.6 51 636-688 3-55 (62)
17 PF13463 HTH_27: Winged helix 90.2 0.4 8.7E-06 39.0 4.0 51 636-688 1-52 (68)
18 PF12840 HTH_20: Helix-turn-he 89.7 0.43 9.3E-06 38.3 3.7 52 637-690 9-60 (61)
19 PF01047 MarR: MarR family; I 89.6 0.25 5.3E-06 39.1 2.2 51 636-688 1-51 (59)
20 TIGR02337 HpaR homoprotocatech 89.1 0.75 1.6E-05 42.1 5.4 53 634-688 24-76 (118)
21 smart00550 Zalpha Z-DNA-bindin 87.3 1.7 3.6E-05 35.8 5.8 48 639-688 7-56 (68)
22 PRK11512 DNA-binding transcrip 86.3 1.4 3E-05 41.8 5.6 53 634-688 36-88 (144)
23 smart00346 HTH_ICLR helix_turn 86.2 1.8 4E-05 37.2 5.9 55 641-703 8-63 (91)
24 smart00347 HTH_MARR helix_turn 85.9 1.4 3E-05 38.3 5.0 54 633-688 5-58 (101)
25 PF04492 Phage_rep_O: Bacterio 85.7 2.4 5.1E-05 37.9 6.3 62 635-706 29-98 (100)
26 PF01022 HTH_5: Bacterial regu 85.0 2 4.4E-05 32.4 4.8 43 640-685 4-46 (47)
27 smart00420 HTH_DEOR helix_turn 84.3 2 4.3E-05 32.5 4.6 46 641-688 3-48 (53)
28 PF04703 FaeA: FaeA-like prote 83.9 1.9 4.2E-05 34.9 4.4 56 643-702 5-61 (62)
29 TIGR01889 Staph_reg_Sar staphy 83.9 2.4 5.1E-05 38.3 5.6 53 634-688 21-77 (109)
30 PRK10857 DNA-binding transcrip 82.0 4 8.7E-05 39.9 6.8 45 640-686 12-57 (164)
31 PRK15090 DNA-binding transcrip 81.9 3 6.5E-05 43.7 6.3 46 641-688 17-62 (257)
32 PRK11920 rirA iron-responsive 80.3 5 0.00011 38.7 6.7 46 641-688 13-58 (153)
33 TIGR02010 IscR iron-sulfur clu 80.0 4.7 0.0001 37.9 6.3 44 641-686 13-57 (135)
34 smart00345 HTH_GNTR helix_turn 79.8 3.3 7.1E-05 32.2 4.4 41 647-689 14-55 (60)
35 COG3355 Predicted transcriptio 79.2 4 8.8E-05 37.9 5.3 39 648-688 38-76 (126)
36 smart00419 HTH_CRP helix_turn_ 78.7 4.5 9.7E-05 30.0 4.7 33 652-686 8-40 (48)
37 cd00090 HTH_ARSR Arsenical Res 78.5 4.4 9.6E-05 32.7 5.1 49 637-688 6-54 (78)
38 PRK13777 transcriptional regul 78.3 4.4 9.6E-05 40.4 5.8 53 634-688 41-93 (185)
39 PF01978 TrmB: Sugar-specific 78.0 2 4.3E-05 35.1 2.7 50 637-688 7-56 (68)
40 PF08318 COG4: COG4 transport 77.9 65 0.0014 35.2 15.3 158 344-509 8-213 (331)
41 TIGR01884 cas_HTH CRISPR locus 77.8 3.3 7.3E-05 41.8 4.9 52 635-688 140-191 (203)
42 PF08279 HTH_11: HTH domain; 77.7 4.3 9.3E-05 31.5 4.5 33 645-677 8-40 (55)
43 PRK03573 transcriptional regul 77.5 4.1 8.9E-05 38.5 5.2 53 634-688 27-80 (144)
44 TIGR03879 near_KaiC_dom probab 77.1 2.7 5.9E-05 35.2 3.2 39 646-686 26-64 (73)
45 PF05732 RepL: Firmicute plasm 76.0 3.3 7.2E-05 40.5 4.1 53 652-713 75-127 (165)
46 TIGR00738 rrf2_super rrf2 fami 74.4 7.4 0.00016 36.1 5.9 46 640-687 12-58 (132)
47 PRK10870 transcriptional repre 73.1 8.1 0.00018 38.1 6.1 53 634-688 51-105 (176)
48 smart00418 HTH_ARSR helix_turn 72.8 6.7 0.00015 30.6 4.6 37 650-688 8-44 (66)
49 PF13601 HTH_34: Winged helix 72.6 2.8 6E-05 35.8 2.3 44 641-686 3-46 (80)
50 PRK11569 transcriptional repre 71.6 7.8 0.00017 41.1 6.0 45 642-688 32-77 (274)
51 PRK10163 DNA-binding transcrip 71.0 8.8 0.00019 40.6 6.2 56 641-704 28-84 (271)
52 PRK09834 DNA-binding transcrip 71.0 8 0.00017 40.7 5.9 46 642-689 15-61 (263)
53 smart00344 HTH_ASNC helix_turn 70.7 7.1 0.00015 34.8 4.7 46 639-686 4-49 (108)
54 PHA00738 putative HTH transcri 70.3 8.4 0.00018 34.7 4.8 67 633-705 7-73 (108)
55 COG1414 IclR Transcriptional r 70.1 9.6 0.00021 39.8 6.1 46 641-688 7-53 (246)
56 TIGR02944 suf_reg_Xantho FeS a 69.6 11 0.00023 35.1 5.8 43 643-687 14-58 (130)
57 PF05584 Sulfolobus_pRN: Sulfo 69.4 11 0.00025 31.3 5.1 46 638-687 6-51 (72)
58 TIGR02431 pcaR_pcaU beta-ketoa 69.2 10 0.00022 39.5 6.1 44 641-686 12-56 (248)
59 COG1959 Predicted transcriptio 69.0 12 0.00026 36.0 6.1 47 640-688 12-59 (150)
60 PF13404 HTH_AsnC-type: AsnC-t 68.9 7.5 0.00016 28.8 3.6 36 641-676 6-41 (42)
61 PF10771 DUF2582: Protein of u 68.7 8.5 0.00018 31.5 4.2 44 642-685 12-56 (65)
62 KOG4552 Vitamin-D-receptor int 67.8 1.1E+02 0.0024 30.8 12.2 115 331-464 23-142 (272)
63 PF13730 HTH_36: Helix-turn-he 66.9 12 0.00026 29.0 4.6 28 654-683 27-54 (55)
64 cd00092 HTH_CRP helix_turn_hel 66.6 9.8 0.00021 30.4 4.3 36 651-688 24-59 (67)
65 PRK10434 srlR DNA-bindng trans 65.0 8 0.00017 40.6 4.3 49 640-690 7-55 (256)
66 PRK11014 transcriptional repre 64.9 18 0.0004 34.1 6.4 40 647-688 20-59 (141)
67 PF08784 RPA_C: Replication pr 64.2 10 0.00022 33.7 4.3 44 635-678 44-91 (102)
68 COG1846 MarR Transcriptional r 64.1 13 0.00029 33.1 5.2 51 636-688 20-70 (126)
69 PRK10141 DNA-binding transcrip 63.5 8.1 0.00018 35.5 3.5 57 642-704 20-76 (117)
70 PF01325 Fe_dep_repress: Iron 61.2 17 0.00038 29.1 4.7 44 643-688 13-56 (60)
71 cd07377 WHTH_GntR Winged helix 60.6 17 0.00036 28.7 4.6 39 648-688 20-59 (66)
72 PF09763 Sec3_C: Exocyst compl 60.2 3.8E+02 0.0083 32.5 21.2 50 375-426 646-701 (701)
73 PF08280 HTH_Mga: M protein tr 59.4 12 0.00026 29.7 3.5 38 640-677 7-44 (59)
74 PF08281 Sigma70_r4_2: Sigma-7 57.9 18 0.00039 27.8 4.2 32 641-674 17-48 (54)
75 PF04545 Sigma70_r4: Sigma-70, 57.9 23 0.0005 26.8 4.7 34 640-675 10-43 (50)
76 PRK13509 transcriptional repre 57.7 16 0.00034 38.3 5.0 51 639-691 6-56 (251)
77 PF08221 HTH_9: RNA polymerase 56.9 13 0.00029 30.0 3.3 38 645-685 21-58 (62)
78 COG2345 Predicted transcriptio 56.6 16 0.00034 37.4 4.6 44 641-686 14-57 (218)
79 COG1349 GlpR Transcriptional r 56.1 14 0.00031 38.6 4.4 51 640-692 7-57 (253)
80 PF02002 TFIIE_alpha: TFIIE al 54.1 9 0.0002 34.2 2.1 43 641-685 16-58 (105)
81 PRK10906 DNA-binding transcrip 53.8 18 0.00038 38.0 4.6 50 640-691 7-56 (252)
82 COG4190 Predicted transcriptio 53.4 34 0.00074 31.9 5.7 63 642-706 68-133 (144)
83 PF01726 LexA_DNA_bind: LexA D 52.3 18 0.00039 29.5 3.4 51 637-689 5-61 (65)
84 PRK11179 DNA-binding transcrip 52.2 24 0.00052 33.8 4.9 49 636-686 7-55 (153)
85 PRK09802 DNA-binding transcrip 51.9 19 0.00041 38.1 4.5 51 638-690 17-67 (269)
86 COG4189 Predicted transcriptio 51.6 30 0.00066 35.4 5.5 64 637-702 22-92 (308)
87 PRK11169 leucine-responsive tr 51.2 23 0.0005 34.4 4.6 49 636-686 12-60 (164)
88 PRK10411 DNA-binding transcrip 50.1 25 0.00053 36.6 4.9 47 640-688 6-52 (240)
89 PRK00215 LexA repressor; Valid 49.4 34 0.00074 34.4 5.8 53 636-690 2-60 (205)
90 PRK06266 transcription initiat 48.7 24 0.00052 34.9 4.4 44 640-685 24-67 (178)
91 PF09012 FeoC: FeoC like trans 48.4 22 0.00049 29.1 3.5 39 646-686 8-46 (69)
92 TIGR02702 SufR_cyano iron-sulf 48.4 38 0.00082 34.1 5.9 44 642-687 5-48 (203)
93 TIGR00373 conserved hypothetic 47.4 30 0.00065 33.6 4.7 42 642-685 18-59 (158)
94 PF01853 MOZ_SAS: MOZ/SAS fami 45.8 19 0.00041 35.8 3.1 27 651-677 149-175 (188)
95 PF02796 HTH_7: Helix-turn-hel 45.2 29 0.00063 25.9 3.3 31 643-675 14-44 (45)
96 PRK04424 fatty acid biosynthes 44.2 21 0.00046 35.5 3.2 46 639-686 8-53 (185)
97 smart00421 HTH_LUXR helix_turn 42.3 51 0.0011 24.8 4.6 39 637-677 5-43 (58)
98 TIGR00498 lexA SOS regulatory 41.8 28 0.00061 34.8 3.8 51 636-688 4-60 (199)
99 PF14394 DUF4423: Domain of un 41.7 61 0.0013 31.9 6.0 55 632-688 18-75 (171)
100 COG1522 Lrp Transcriptional re 41.5 46 0.00099 31.5 5.0 49 636-686 6-54 (154)
101 KOG1488 Translational represso 41.2 2.9E+02 0.0062 32.0 11.9 41 293-337 457-497 (503)
102 cd06170 LuxR_C_like C-terminal 40.6 56 0.0012 24.6 4.6 38 638-677 3-40 (57)
103 PF00325 Crp: Bacterial regula 40.5 30 0.00066 24.1 2.5 26 652-677 2-27 (32)
104 PF01638 HxlR: HxlR-like helix 40.3 42 0.0009 29.0 4.1 44 641-687 8-52 (90)
105 PF06784 UPF0240: Uncharacteri 39.5 56 0.0012 32.4 5.3 70 609-685 96-167 (179)
106 PF03444 HrcA_DNA-bdg: Winged 38.8 77 0.0017 27.0 5.2 49 638-688 9-57 (78)
107 PF07393 Sec10: Exocyst comple 38.2 8.1E+02 0.018 29.7 27.0 98 127-227 192-302 (710)
108 PF00392 GntR: Bacterial regul 37.7 38 0.00083 27.1 3.2 39 649-689 20-59 (64)
109 PF10007 DUF2250: Uncharacteri 37.5 60 0.0013 28.5 4.6 53 634-688 3-55 (92)
110 PF07393 Sec10: Exocyst comple 36.7 8.5E+02 0.018 29.5 18.8 135 232-374 106-264 (710)
111 PRK11050 manganese transport r 36.6 73 0.0016 30.6 5.5 45 642-688 41-85 (152)
112 KOG2747 Histone acetyltransfer 36.5 41 0.00089 37.3 4.2 68 611-678 281-355 (396)
113 PRK04172 pheS phenylalanyl-tRN 36.1 57 0.0012 37.7 5.5 51 635-687 3-53 (489)
114 PLN03238 probable histone acet 35.9 54 0.0012 34.8 4.7 39 639-677 209-248 (290)
115 PRK10430 DNA-binding transcrip 34.8 66 0.0014 32.9 5.3 39 648-688 174-212 (239)
116 COG2512 Predicted membrane-ass 33.3 53 0.0011 34.6 4.2 53 638-692 196-248 (258)
117 PF11994 DUF3489: Protein of u 32.9 81 0.0018 26.4 4.3 47 637-683 9-55 (72)
118 TIGR02698 CopY_TcrY copper tra 32.9 1.1E+02 0.0023 28.7 5.8 51 636-688 2-56 (130)
119 PRK03902 manganese transport t 32.2 79 0.0017 29.7 5.0 43 643-687 13-55 (142)
120 PF13542 HTH_Tnp_ISL3: Helix-t 32.1 1E+02 0.0022 23.3 4.7 34 639-675 17-50 (52)
121 PRK06474 hypothetical protein; 31.9 1.2E+02 0.0026 30.0 6.3 53 634-688 7-61 (178)
122 PF13545 HTH_Crp_2: Crp-like h 31.9 79 0.0017 25.9 4.4 33 652-686 28-60 (76)
123 cd07153 Fur_like Ferric uptake 31.7 99 0.0021 27.7 5.3 57 642-703 5-67 (116)
124 PF01399 PCI: PCI domain; Int 30.8 68 0.0015 27.8 4.0 39 639-677 47-85 (105)
125 TIGR02844 spore_III_D sporulat 30.6 82 0.0018 26.9 4.2 34 640-674 8-41 (80)
126 cd06171 Sigma70_r4 Sigma70, re 30.6 1.1E+02 0.0025 22.2 4.8 39 637-676 12-50 (55)
127 PF09904 HTH_43: Winged helix- 30.1 1.1E+02 0.0025 26.6 4.9 40 643-685 13-52 (90)
128 PRK04214 rbn ribonuclease BN/u 29.8 1.3E+02 0.0027 34.0 6.8 40 647-688 305-344 (412)
129 PF10163 EnY2: Transcription f 29.7 2.1E+02 0.0045 24.6 6.7 55 105-159 29-85 (86)
130 PF09681 Phage_rep_org_N: N-te 29.6 74 0.0016 29.5 4.1 50 635-686 26-85 (121)
131 PF13384 HTH_23: Homeodomain-l 29.6 63 0.0014 24.2 3.1 33 643-677 10-42 (50)
132 PF07340 Herpes_IE1: Cytomegal 29.3 8.2E+02 0.018 27.1 19.7 258 135-424 70-352 (392)
133 PHA03103 double-strand RNA-bin 29.1 1.1E+02 0.0023 30.5 5.3 45 643-689 18-62 (183)
134 PLN00104 MYST -like histone ac 29.0 76 0.0016 36.0 4.7 31 647-677 369-399 (450)
135 PF12324 HTH_15: Helix-turn-he 28.9 1.3E+02 0.0028 25.6 4.9 38 640-677 26-63 (77)
136 PF00196 GerE: Bacterial regul 28.6 95 0.0021 24.2 4.1 39 637-677 5-43 (58)
137 PRK10681 DNA-binding transcrip 28.5 77 0.0017 33.1 4.6 39 639-677 8-46 (252)
138 TIGR02989 Sig-70_gvs1 RNA poly 28.4 88 0.0019 29.5 4.6 38 636-675 112-150 (159)
139 COG4742 Predicted transcriptio 28.3 90 0.002 32.8 4.9 42 643-687 18-59 (260)
140 COG1321 TroR Mn-dependent tran 27.6 1.1E+02 0.0023 29.7 4.9 45 643-689 15-59 (154)
141 PHA02943 hypothetical protein; 27.1 97 0.0021 29.8 4.4 54 643-703 16-69 (165)
142 smart00088 PINT motif in prote 27.0 1E+02 0.0023 26.0 4.4 34 649-684 21-54 (88)
143 smart00753 PAM PCI/PINT associ 27.0 1E+02 0.0023 26.0 4.4 34 649-684 21-54 (88)
144 COG1654 BirA Biotin operon rep 27.0 1.7E+02 0.0038 24.9 5.5 47 644-690 11-57 (79)
145 PRK12522 RNA polymerase sigma 26.9 87 0.0019 30.2 4.4 33 640-674 125-157 (173)
146 PRK12529 RNA polymerase sigma 26.9 91 0.002 30.4 4.6 37 636-674 128-165 (178)
147 PRK09642 RNA polymerase sigma 26.6 88 0.0019 29.6 4.3 37 636-674 107-144 (160)
148 TIGR02999 Sig-70_X6 RNA polyme 25.8 1E+02 0.0022 29.9 4.7 24 651-674 149-172 (183)
149 PRK12525 RNA polymerase sigma 25.8 99 0.0022 29.7 4.5 33 640-674 124-156 (168)
150 PF00165 HTH_AraC: Bacterial r 25.7 1E+02 0.0022 22.3 3.5 28 650-677 6-33 (42)
151 PF06163 DUF977: Bacterial pro 25.6 1.6E+02 0.0034 27.5 5.3 48 638-687 12-59 (127)
152 PRK14165 winged helix-turn-hel 25.5 1.2E+02 0.0025 31.2 5.0 43 643-687 12-54 (217)
153 COG1318 Predicted transcriptio 25.4 97 0.0021 30.4 4.1 51 606-677 36-86 (182)
154 smart00762 Cog4 COG4 transport 25.2 4.2E+02 0.0091 28.8 9.7 83 344-426 8-108 (324)
155 PF14947 HTH_45: Winged helix- 25.0 1.2E+02 0.0026 25.4 4.3 43 641-686 9-51 (77)
156 PF04182 B-block_TFIIIC: B-blo 24.7 1.1E+02 0.0023 25.6 3.9 49 638-688 2-52 (75)
157 smart00531 TFIIE Transcription 24.3 86 0.0019 29.9 3.7 30 649-678 12-41 (147)
158 PLN03239 histone acetyltransfe 24.1 1E+02 0.0022 33.7 4.5 40 638-677 266-309 (351)
159 PRK09647 RNA polymerase sigma 24.1 1.1E+02 0.0024 30.7 4.6 33 640-674 144-176 (203)
160 PF09105 SelB-wing_1: Elongati 23.9 1.5E+02 0.0033 22.5 4.0 44 650-701 15-59 (61)
161 TIGR01714 phage_rep_org_N phag 23.6 1E+02 0.0022 28.5 3.8 48 637-686 28-83 (119)
162 PRK08301 sporulation sigma fac 23.6 1.2E+02 0.0027 30.9 5.0 37 637-673 180-219 (234)
163 PRK09047 RNA polymerase factor 23.5 1.2E+02 0.0025 28.7 4.5 24 651-674 121-144 (161)
164 PF04967 HTH_10: HTH DNA bindi 23.4 1.1E+02 0.0024 23.9 3.4 30 646-675 17-46 (53)
165 PRK09333 30S ribosomal protein 23.4 98 0.0021 29.7 3.7 56 639-696 54-123 (150)
166 PRK00118 putative DNA-binding 23.2 1.4E+02 0.003 26.9 4.5 25 651-675 32-56 (104)
167 PRK00135 scpB segregation and 22.5 2.5E+02 0.0054 28.1 6.7 111 589-706 34-153 (188)
168 PRK12537 RNA polymerase sigma 22.3 1.2E+02 0.0025 29.6 4.3 32 642-675 141-172 (182)
169 PRK04217 hypothetical protein; 22.2 1.5E+02 0.0032 27.1 4.5 39 636-675 43-81 (110)
170 PHA02591 hypothetical protein; 22.1 1E+02 0.0022 26.1 3.1 25 651-675 58-82 (83)
171 TIGR03209 P21_Cbot clostridium 22.1 83 0.0018 29.2 3.1 29 640-670 113-141 (142)
172 PF02270 TFIIF_beta: Transcrip 21.7 86 0.0019 33.3 3.4 40 638-677 216-255 (275)
173 PF03428 RP-C: Replication pro 21.5 1.2E+02 0.0025 30.2 4.0 38 653-692 71-111 (177)
174 PF12108 SF3a60_bindingd: Spli 21.3 72 0.0016 21.6 1.7 14 487-500 3-16 (28)
175 TIGR02835 spore_sigmaE RNA pol 21.2 1.4E+02 0.0031 30.6 4.8 35 640-674 184-220 (234)
176 TIGR00721 tfx DNA-binding prot 21.0 1.6E+02 0.0036 27.8 4.7 38 635-674 6-43 (137)
177 TIGR03001 Sig-70_gmx1 RNA poly 20.8 1.4E+02 0.0029 31.1 4.6 33 640-674 167-199 (244)
178 TIGR02983 SigE-fam_strep RNA p 20.8 1.2E+02 0.0027 28.6 4.1 39 637-676 112-150 (162)
179 PF07638 Sigma70_ECF: ECF sigm 20.5 1.4E+02 0.003 29.5 4.4 26 651-676 150-175 (185)
180 PF05186 Dpy-30: Dpy-30 motif; 20.4 1.5E+02 0.0032 22.0 3.4 29 430-458 10-38 (42)
181 PRK10046 dpiA two-component re 20.3 1.5E+02 0.0032 30.0 4.7 44 642-687 166-210 (225)
182 PRK13239 alkylmercury lyase; P 20.2 1.7E+02 0.0038 29.7 5.0 39 639-677 23-61 (206)
183 PRK09645 RNA polymerase sigma 20.1 1.5E+02 0.0032 28.5 4.5 35 637-673 120-155 (173)
184 PRK07037 extracytoplasmic-func 20.0 1.5E+02 0.0033 28.0 4.5 36 637-674 111-147 (163)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2e-116 Score=947.28 Aligned_cols=589 Identities=60% Similarity=0.946 Sum_probs=570.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc-ccccccHHHHHHHHHHH
Q 004654 147 LYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ-TPNVRSLWDMGLQLFRK 225 (739)
Q Consensus 147 LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~-~~~~~sI~~lgl~lFr~ 225 (739)
||++|++.|++|+++.+.++...+.|.+.+|..+.++|..|+.+|.+|++||.||||+|+.+ ++.+++||+||+.+||.
T Consensus 2 ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR~ 81 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFRA 81 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHHH
Confidence 89999999999999999888877777789999999999999999999999999999999999 78899999999999999
Q ss_pred Hhcc--chhhHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHhhhhccchhhhHHhHHHHHHHHHHHHHHHHHhcCChhh
Q 004654 226 YLSS--YSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (739)
Q Consensus 226 ~v~~--~~~l~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~ 303 (739)
+++. .+.+..++.++++..|+++|.|+++|+.+|++++.|+.++++|.+.|+..|++.+.++|++++...+++..+++
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~e 161 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPE 161 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHH
Confidence 9998 67899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCChHHHHHHHHhhccc-chHHHHHH
Q 004654 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQ 382 (739)
Q Consensus 304 Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~ 382 (739)
||++++.++.+|.+|+..|++.++.+.+..+|+++|+..|++.|+..|+..+++..++.++.+||.|++++ ++...++.
T Consensus 162 Yl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~q 241 (661)
T KOG2167|consen 162 YLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQ 241 (661)
T ss_pred HHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHH
Confidence 99999999999999999999998877899999999999999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHHhhhhhhcCcchhhHHHHHHHHHHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHhhcCCCcchHHHHHHHhHH
Q 004654 383 ALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDEK 460 (739)
Q Consensus 383 ~~~~yI~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~--~~f~~~l~~afe~~iN~~~~~~~e~LA~y~D~~ 460 (739)
.|..|+++.|..++.+++.++++|+.+++|+++.|-++..||..+ ..|.+++++||+.|+|.++++|||+||+|+|.+
T Consensus 242 q~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAelIak~~dt~ 321 (661)
T KOG2167|consen 242 QWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAELIAKYVDTK 321 (661)
T ss_pred HHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999988 999999999999999999999999999999999
Q ss_pred HhcCCCCCChHHHHhhhccceeeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHH
Q 004654 461 LRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFK 540 (739)
Q Consensus 461 lr~~~k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG~~~t~kle~M~~ 540 (739)
|+.|+|+.++++++..++.++.|||||.+||+||+||++.||+|||.++|+|.|+|+.|+.+||.+||..||+|||+||+
T Consensus 322 Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfk 401 (661)
T KOG2167|consen 322 LRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFK 401 (661)
T ss_pred HHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCCCCCcCChHHHHHHHHHHHHHhccCCCceEEeecCCce
Q 004654 541 DIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGH 620 (739)
Q Consensus 541 Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~ 620 (739)
||+.|++++..|+++...++..+.++ +.|.|||.|+||+|++.++.||++|..+++.|..||..+|+||+|+|+++||+
T Consensus 402 dme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~ 480 (661)
T KOG2167|consen 402 DMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGH 480 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcc
Confidence 99999999999999855434555556 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCceEEEEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEE
Q 004654 621 CVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFV 700 (739)
Q Consensus 621 ~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~ 700 (739)
|+|++.|+.|++||.||+||++|||+||+.+.+|++||.+.|+|.+.+|+|+|+||+||+.|+|.+.|+|+++.+||.|.
T Consensus 481 ~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~ 560 (661)
T KOG2167|consen 481 CVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFI 560 (661)
T ss_pred hhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCCceeEEecccccchhccc------------cccccceEEee
Q 004654 701 FNEGFTAPLYRIKVWASVMQQYCDT------------LSTLDCLICHL 736 (739)
Q Consensus 701 ~N~~F~~~~~rIki~~i~~k~~~e~------------~~~~d~~~~~~ 736 (739)
||.+|++|.+|||||+||+||+.|. -++|||||||+
T Consensus 561 ~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivri 608 (661)
T KOG2167|consen 561 VNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRI 608 (661)
T ss_pred echhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHH
Confidence 9999999999999999999998654 46779999985
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.4e-101 Score=884.39 Aligned_cols=630 Identities=35% Similarity=0.606 Sum_probs=582.3
Q ss_pred CchHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhccCch----hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 004654 101 TNFEEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMG----GNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (739)
Q Consensus 101 ~~~~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~----~~LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~ 176 (739)
..+.+++|.+|..+++.+..+.....+++++|+++|++|.+++| ++||+++++.+.+|+.+.+.......++ ..+
T Consensus 14 w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~-~~~ 92 (725)
T KOG2166|consen 14 WSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHD-EYM 92 (725)
T ss_pred HHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCc-HHH
Confidence 47778999999999986664445667999999999999999999 9999999999999999998877766655 689
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccHHHHH-HHHHHHHhccchhhHHHHHHHHHHHHHHHhcCCcCC
Q 004654 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMG-LQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVD 255 (739)
Q Consensus 177 L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lg-l~lFr~~v~~~~~l~~~l~~~ll~lI~~eR~g~~id 255 (739)
|+.+.+.|.+|+.++.+++++|.||||+||.+..+..++++++ +.+|+..+... ++.++++++++.+|..+|.|+.||
T Consensus 93 l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~in 171 (725)
T KOG2166|consen 93 LRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQID 171 (725)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhccccccc
Confidence 9999999999999999999999999999999873456777776 99999998865 699999999999999999999999
Q ss_pred hHHHHHHHHHhhhhc-----cchhhhHHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHhhhcCcCcHHH
Q 004654 256 RTLLNHLLKMFTALG-----IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKP 330 (739)
Q Consensus 256 ~~llk~ii~ml~~L~-----~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~~ 330 (739)
+..|+++++|+..|| +|.+.||++|++.|+.||..++++|+...++.+|+..++.++.+|.+|+..|++..+..+
T Consensus 172 ~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~ 251 (725)
T KOG2166|consen 172 RELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPK 251 (725)
T ss_pred HHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccch
Confidence 999999999999986 999999999999999999999999999889999999999999999999999988777777
Q ss_pred HHHHHHHHHHHHHHHHHH---HHHHHhhhccCChHHHHHHHHhhccc-chHHHHHHHHHHHHHHhhhhhhcCc-----ch
Q 004654 331 LIATAERQLLERHISAIL---DKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE-----EK 401 (739)
Q Consensus 331 l~~~l~~~LI~~~~~~ll---~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~~-----~~ 401 (739)
+...++..++..|.+.++ .+|+..|+.+++.++|.+||+|++|+ +|++.++..+..|++..|..++... .+
T Consensus 252 ~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~ 331 (725)
T KOG2166|consen 252 LVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATN 331 (725)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccc
Confidence 777788877777777665 58999999999999999999999999 9999999999999999998777532 45
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcCCCcchHHHHHHHhHHHhcCCCCCChHHHHhhhccce
Q 004654 402 DKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVL 481 (739)
Q Consensus 402 ~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~afe~~iN~~~~~~~e~LA~y~D~~lr~~~k~~s~~e~e~~l~~i~ 481 (739)
++.+|+.++++++++..++..||+++..|.++++.||+.|+|.+...++|+||+|||.++|+|.++.+|++++..+++++
T Consensus 332 ~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~ 411 (725)
T KOG2166|consen 332 PVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVV 411 (725)
T ss_pred hHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcce
Confidence 68999999999999999999999999999999999999999998854569999999999999999999999999999999
Q ss_pred eeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 004654 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTK 561 (739)
Q Consensus 482 ~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~ 561 (739)
.+|+|+.+||+|+.||+++||||||+++|.|+|+|+.||++|+++||.+||+||++||+|+..|++++..|+++ .+ ..
T Consensus 412 ~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~-~~-~~ 489 (725)
T KOG2166|consen 412 KLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY-AN-YS 489 (725)
T ss_pred eeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh-hc-hh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999976 22 22
Q ss_pred CCCCcceEEEEeecCCCCCCCCCCCcCChHHHHHHHHHHHHHhccCCCceEEeecCCceEEEEEEecCceEEEEEcHHHH
Q 004654 562 LPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQT 641 (739)
Q Consensus 562 ~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa 641 (739)
...+++|.|.|||+|+||.++..++.||++|..+++.|..||.++|+||+|.|+|+||.|+|.++|.+++++|+||++||
T Consensus 490 ~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm 569 (725)
T KOG2166|consen 490 ANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQM 569 (725)
T ss_pred ccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHH
Confidence 33579999999999999999988899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEEecccccch
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVWASVMQQ 721 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~~~~~rIki~~i~~k~ 721 (739)
||||+||+.+.+|+++|.++|+|+.++|.+.|+||+|.|.+|+.+ |.+++ +++|.|.+|.+|+++..||+|+++..++
T Consensus 570 ~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e 647 (725)
T KOG2166|consen 570 AVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDE 647 (725)
T ss_pred HHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCchh
Confidence 999999999999999999999999999999999999989888888 88888 9999999999999999999999888775
Q ss_pred h--------ccccccccceEEee
Q 004654 722 Y--------CDTLSTLDCLICHL 736 (739)
Q Consensus 722 ~--------~e~~~~~d~~~~~~ 736 (739)
+ .++-..+||||||+
T Consensus 648 ~~~~~~~ve~dRk~~i~AaIVRI 670 (725)
T KOG2166|consen 648 RKKVVEDVDKDRKYAIDAAIVRI 670 (725)
T ss_pred HHHHHhhhhhHHHHHHHHHHHHH
Confidence 4 34455569999985
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-96 Score=811.88 Aligned_cols=630 Identities=34% Similarity=0.545 Sum_probs=562.4
Q ss_pred CCCCchHHHHHHHHHHHHHHHH---hcCCCCCcHHHHHHHHHhhhccC----------------chhHHHHHHHHHHHHH
Q 004654 98 TLPTNFEEDTWAKLKLAIKAIF---LKQPTSCDLEKLYQAVNDLCLHK----------------MGGNLYQRIEKECEEH 158 (739)
Q Consensus 98 ~~~~~~~e~~W~~L~~aI~~I~---~~~~~~~s~e~LY~~Vy~lC~~k----------------~~~~LY~~L~~~i~~~ 158 (739)
.++++.++.+|..++.||..|+ ......++++++|+.+|+.|..+ +|+.+|++|....+++
T Consensus 14 ~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~ 93 (773)
T COG5647 14 TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNY 93 (773)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHH
Confidence 3566667999999999999999 44556689999999999999876 4778999999988888
Q ss_pred HHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc--cc--ccccHHHHHHHHHHHHhccchhhH
Q 004654 159 ISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ--TP--NVRSLWDMGLQLFRKYLSSYSEVE 234 (739)
Q Consensus 159 l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~--~~--~~~sI~~lgl~lFr~~v~~~~~l~ 234 (739)
+...-..... ...+.||..++++|.+|+.++.++.++|.||||.|++. .+ ....+..+++..|+-.+|. .+.
T Consensus 94 i~~~~~~~s~--~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~--~i~ 169 (773)
T COG5647 94 IEEYNRGRSQ--ENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFR--LIV 169 (773)
T ss_pred HHHhcccccc--hhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHH--hhh
Confidence 8876544221 22479999999999999999999999999999999992 22 1456778889999988885 899
Q ss_pred HHHHHHHHHHHHHHhcCCcCChHHHHHHHHHhhhh-----------ccchhhhHHhHHHHHHHHHHHHHHHHHhcCChhh
Q 004654 235 HKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTAL-----------GIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (739)
Q Consensus 235 ~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L-----------~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~ 303 (739)
+.+++.+|..+++.|.|+.+|+..+..++.|+..+ .+|.+.|||.||+.|.+||..++++.+..+++.+
T Consensus 170 ~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~e 249 (773)
T COG5647 170 DSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTE 249 (773)
T ss_pred HHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHH
Confidence 99999999999999999999999999999999998 5899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHHHHHHHHHHHHHH--HHHHhhhccCChHHHHHHHHhhccc-chHHHH
Q 004654 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILD--KGFTMLMDGHRTEDLQRMYSLFSRV-NALESL 380 (739)
Q Consensus 304 Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~~LI~~~~~~ll~--~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l 380 (739)
||.+|+.++++|..++..|++.++.++|..+++++||..|.+.+.. +|+..+++..+.+.|+.||++++++ .++..|
T Consensus 250 yL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl 329 (773)
T COG5647 250 YLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPL 329 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhH
Confidence 9999999999999999999999999999999999999999999985 4899999999999999999999999 789999
Q ss_pred HHHHHHHHHHhhh--hhhc---------------CcchhhHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 004654 381 RQALAMYIRRTGH--GIVM---------------DEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLIN 443 (739)
Q Consensus 381 ~~~~~~yI~~~g~--~iv~---------------~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~afe~~iN 443 (739)
++.|..||+..|. .+.. ++..+..+|+.++.+++.+..++.+.|.+|..+.+++++||+.|+|
T Consensus 330 ~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin 409 (773)
T COG5647 330 QEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFIN 409 (773)
T ss_pred HHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhc
Confidence 9999999999991 1111 1223578999999999999999999999999999999999999999
Q ss_pred cCC---CcchHHHHHHHhHHHhcCCCCCChHHHHhhhccceeeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHH
Q 004654 444 LRQ---NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMI 520 (739)
Q Consensus 444 ~~~---~~~~e~LA~y~D~~lr~~~k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i 520 (739)
.+. ..++|+||+|+|.+||++.+......++..+..++.||+|+.+||+||++|+++||||||+++|+|.++|..||
T Consensus 410 ~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mi 489 (773)
T COG5647 410 GNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMI 489 (773)
T ss_pred cccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHH
Confidence 843 36999999999999999887655667888899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCchhHhHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCC-CCCcCChHHHHHHHHH
Q 004654 521 SKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIF 599 (739)
Q Consensus 521 ~~Lk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F 599 (739)
++||+.||.+||+|||+||+||.+|.++...|++...+ ....+|+.|.||++.+||..|. ..+.||++|.+.++.|
T Consensus 490 s~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f 566 (773)
T COG5647 490 SMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGF 566 (773)
T ss_pred HHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHH
Confidence 99999999999999999999999999999999875432 2246899999999999996654 6899999999999999
Q ss_pred HHHHhccCCCceEEeecCCceEEEEEEecCceEEEEE---cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhh
Q 004654 600 KEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAV---SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (739)
Q Consensus 600 ~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~v---s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL 676 (739)
++||.+||+||+|.|.++||+|+|+++|+.|++.+.+ +.+|+.|+++||+++.+|+++|.+.|+|+.++++++|+||
T Consensus 567 ~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl 646 (773)
T COG5647 567 KKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSL 646 (773)
T ss_pred HHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHH
Confidence 9999999999999999999999999999988765554 5788889999999999999999999999999999999999
Q ss_pred hcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEEecccccchhcc------------ccccccceEEee
Q 004654 677 ACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVWASVMQQYCD------------TLSTLDCLICHL 736 (739)
Q Consensus 677 ~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~~~~~rIki~~i~~k~~~e------------~~~~~d~~~~~~ 736 (739)
+|.|..+|.+. ++.+++++.|.+|.+|++++.|||||.+..++... +--..+|+|||+
T Consensus 647 ~~ak~~~l~~~--~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRI 716 (773)
T COG5647 647 SCAKLVVLLKD--DKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRI 716 (773)
T ss_pred Hhhheeeeccc--cccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHH
Confidence 97776666654 89999999999999999999999999987654433 222337777774
No 4
>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=1.5e-95 Score=851.96 Aligned_cols=576 Identities=43% Similarity=0.716 Sum_probs=525.5
Q ss_pred HHHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhccCchhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHH
Q 004654 108 WAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDL 187 (739)
Q Consensus 108 W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~~~LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~ 187 (739)
|..|++||+.|+.+.....+|+++|+.||++|..++|++||+++++.+.+|+..++..+.+..+ ..+|..|..+|.+|
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~--~~~l~~~~~~w~~~ 78 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSD--EDLLEEYVQEWEKY 78 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTT--CHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcCh--hHHHHHHHHHHHHH
Confidence 9999999999999889999999999999999999999999999999999999998888776533 59999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHhh
Q 004654 188 CDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFT 267 (739)
Q Consensus 188 ~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lgl~lFr~~v~~~~~l~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~ 267 (739)
+.++.+|+++|+||||.|+.++ +|++.|+. .+.++++++++.+|.++|.|+.+|+.+++.+++|+.
T Consensus 79 ~~~~~~i~~if~yLdr~yv~~~------------~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~ 144 (588)
T PF00888_consen 79 KKAIKYISDIFSYLDRNYVKRN------------LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFV 144 (588)
T ss_dssp HHHHHHHHHHTHHHHHTSTTTT------------HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHhhhhhh------------hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence 9999999999999999999774 99999997 599999999999999999999999999999999999
Q ss_pred hhc---cchhhhHHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHHHHHHHHH
Q 004654 268 ALG---IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHI 344 (739)
Q Consensus 268 ~L~---~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~~LI~~~~ 344 (739)
++| +|.+.||++|++.|.+||+.++ +.+.++.+||.+|+.++.+|.+||..|+++++.+++.++++++||..|.
T Consensus 145 ~l~~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~ 221 (588)
T PF00888_consen 145 ELGSLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHL 221 (588)
T ss_dssp HTTHTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGH
T ss_pred ccchHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHH
Confidence 775 8999999999999999999999 6777999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhccCChHHHHHHHHhhccc-chHHHHHHHHHHHHHHhhhhhhcCc---chhhHHHHHHHHHHHHHHHHH
Q 004654 345 SAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIW 420 (739)
Q Consensus 345 ~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~~---~~~~~~V~~Ll~l~~~~~~ii 420 (739)
+.| .+|+..|+++++.++|++||+|++++ ++++.+++.|++||.+.|..++... ..+.++|+.+++++++++.++
T Consensus 222 ~~l-~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 222 DEL-SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp HHH-HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred HHH-HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 988 78999999999999999999999998 9999999999999999999998753 467899999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHHHHhhcCCCcchHHHHHHHhHHHhcCCCCCChHHHHhhhccceeeeeeccChHHHHHHHHHH
Q 004654 421 EQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKD 500 (739)
Q Consensus 421 ~~~F~~~~~f~~~l~~afe~~iN~~~~~~~e~LA~y~D~~lr~~~k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~ 500 (739)
.+||++++.|..++++||+.++|.+..+++|+||+|||.+++++.++.++++++..++.++.||+|+++||+|+.+|+++
T Consensus 301 ~~~F~~~~~f~~~l~~af~~~~n~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~ 380 (588)
T PF00888_consen 301 QECFDNDSEFKKALDEAFEEFLNKNNNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKL 380 (588)
T ss_dssp HHTTTT-HHHHHHHHHHHHHHHHCSTSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHH
T ss_pred HHhccccHHHHHHHHHhHHHHHHcCCcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHH
Confidence 99999999999999999999999996689999999999999999888888999999999999999999999999999999
Q ss_pred HHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CcceEEEEeecCCC
Q 004654 501 LAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPS--GIEMSVHVLTTGYW 578 (739)
Q Consensus 501 LakRLL~~~s~s~d~E~~~i~~Lk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~--~~~~~v~VLt~~~W 578 (739)
||+|||.+++.+.+.|+.||++|+.+||.+||++|++|++|++.|++++++|++.... .+... +++|++.||++++|
T Consensus 381 L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~-~~~~~~~~~~~~~~vls~~~W 459 (588)
T PF00888_consen 381 LAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQ-NNIQLIPPFDFNVKVLSKGYW 459 (588)
T ss_dssp HHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TT-SS--CCEEEEEEEETTTS
T ss_pred HHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhh-ccccccCCCceEEEEecCCCC
Confidence 9999999999999999999999999999999999999999999999999999987654 22222 79999999999999
Q ss_pred CCCCCCC-CcCChHHHHHHHHHHHHHhccCCCceEEeecCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCCCHHH
Q 004654 579 PTYPPMD-VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQD 657 (739)
Q Consensus 579 P~~~~~~-~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~~~ls~~e 657 (739)
|.++... +.||++|+.+++.|++||+.+|+||+|+|.+.+|+|+|+++|++|++++.||++||+||++||+++++|++|
T Consensus 460 p~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~e 539 (588)
T PF00888_consen 460 PKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEE 539 (588)
T ss_dssp -S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHH
T ss_pred CCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHH
Confidence 9999876 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCHHHHHHHhhhhhcCCcceee--eCCCCCCCCCCCeEEEecCCC
Q 004654 658 IKDATGIEDKELRRTLQSLACGKVRVLQ--KLPKGRDVEDDDSFVFNEGFT 706 (739)
Q Consensus 658 I~~~t~i~~~~l~~~L~sL~~~k~~iL~--k~p~~~~v~~~d~f~~N~~F~ 706 (739)
|++.||+++++|+++|.+|+ +.++|. +.|++++++++|.|+||.+|+
T Consensus 540 i~~~~~~~~~~l~~~L~~l~--~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 540 ISEKTGISEEELKRALKSLV--KSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHC---HHHHHHHHHCCC--TTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHCcCHHHHHHHHHHHH--hCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999 555554 889999999999999999996
No 5
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-85 Score=679.28 Aligned_cols=596 Identities=24% Similarity=0.470 Sum_probs=545.8
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCC-CcHHHHHHHHHhhhcc---CchhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHH
Q 004654 102 NFEEDTWAKLKLAIKAIFLKQPTS-CDLEKLYQAVNDLCLH---KMGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFL 177 (739)
Q Consensus 102 ~~~e~~W~~L~~aI~~I~~~~~~~-~s~e~LY~~Vy~lC~~---k~~~~LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~L 177 (739)
+| +++|.+|...|.+|.+-++.. ..|..-|..||.+|.. ..|+.||...+.++++|+...+..+...++ +.+|
T Consensus 10 ~f-d~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~p--~~~l 86 (728)
T KOG2284|consen 10 EF-DKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVDP--DLLL 86 (728)
T ss_pred eH-HHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCCH--HHHH
Confidence 44 899999999999999988765 5899999999999986 479999999999999999988777665443 4799
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccc-----------------ccccHHHHHHHHHHHHhccchhhHHHHHHH
Q 004654 178 SLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-----------------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTG 240 (739)
Q Consensus 178 ~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~-----------------~~~sI~~lgl~lFr~~v~~~~~l~~~l~~~ 240 (739)
..|.+.|+.|..+..++..+|.||+..|+++++ .+..|..+|+.+||+.++. .+...++..
T Consensus 87 ~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~--~i~~~lv~~ 164 (728)
T KOG2284|consen 87 QEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVK--TILPQLVKL 164 (728)
T ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHH--HHHHHHHHH
Confidence 999999999999999999999999999998863 3456778899999999885 799999999
Q ss_pred HHHHHHHHhcCCcCC-hHHHHHHHHHhhhh----------------------ccchhhhHHhHHHHHHHHHHHHHHHHHh
Q 004654 241 LLRMIERERLGEAVD-RTLLNHLLKMFTAL----------------------GIYSESFEKPFLECTSEFYAAEGMKYMQ 297 (739)
Q Consensus 241 ll~lI~~eR~g~~id-~~llk~ii~ml~~L----------------------~~Y~~~FE~~~L~~t~~yY~~~~~~~l~ 297 (739)
+|..|.++|.|+.++ ...+..+|..|+.+ .+|++.||.|||.+|.+||+++++.+++
T Consensus 165 ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~ 244 (728)
T KOG2284|consen 165 LLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQKMLT 244 (728)
T ss_pred HHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHHHHh
Confidence 999999999999887 56788888888654 2799999999999999999999999999
Q ss_pred cCChhhHHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCChHHHHHHHHhhccc-ch
Q 004654 298 QSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NA 376 (739)
Q Consensus 298 ~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~ 376 (739)
+.+|++|+.+|..++++|+-||.+||++++..+++..|++.+|..|.+.+ .-.+..++.+.+..||+.||.|+..+ .|
T Consensus 245 ~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l-ha~ch~~i~~e~~~d~~nmy~ll~~i~~g 323 (728)
T KOG2284|consen 245 DLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL-HAVCHDLITNEENKDLRNMYRLLKPIQAG 323 (728)
T ss_pred hccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhhhhhhHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999976 56799999999999999999999999 89
Q ss_pred HHHHHHHHHHHHHHhhhhhhcCc---chhhHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcCC-----Cc
Q 004654 377 LESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ-----NR 448 (739)
Q Consensus 377 l~~l~~~~~~yI~~~g~~iv~~~---~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~afe~~iN~~~-----~~ 448 (739)
+..+.+.|.+||++.|...++.. .-+..||+.+|..|.+|..++...|.+|..|..+++.|+..++|.+. .+
T Consensus 324 l~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~k 403 (728)
T KOG2284|consen 324 LSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPK 403 (728)
T ss_pred chHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccc
Confidence 99999999999999999988653 33679999999999999999999999999999999999999999754 37
Q ss_pred chHHHHHHHhHHHhcCCCCCChHHHHhhhccceeeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhC
Q 004654 449 PAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG 528 (739)
Q Consensus 449 ~~e~LA~y~D~~lr~~~k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG 528 (739)
.+|.||+|||.+|+++.||+++.++|.+|+..+.+|+||+|||+|.+||.++||+||+.+.|.|.|+|..||++||+.||
T Consensus 404 a~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacg 483 (728)
T KOG2284|consen 404 ASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACG 483 (728)
T ss_pred hHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhHhHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCCCCCcCChHHHHHHHHHHHHHhccCC
Q 004654 529 SQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYS 608 (739)
Q Consensus 529 ~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~ 608 (739)
.+||+++- +.|+..|.+++++|.+.+.+ +.||.+|+..++.|+.||..+|+
T Consensus 484 yefts~~~--~td~~~s~~lnn~f~~~i~n---------------------------f~~pq~l~~~iq~fe~fyt~~~~ 534 (728)
T KOG2284|consen 484 YEFTSSWP--LTDPQLSTNLNNQFAQDIAN---------------------------FHLPQILQPVIQEFEKFYTGKHN 534 (728)
T ss_pred ceecccCC--CCChhhccccchhHHHHHHh---------------------------ccchHHHHHHHHHHHHHhccccC
Confidence 99999998 99999999999999886542 78999999999999999999999
Q ss_pred CceEEeecCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
||||+|.+.+++++++.++-++.|.-.|.++||++||+||..+.+++.||.+.+|+++++|.+++.++. .+++|.-..
T Consensus 535 grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~til--dv~~~~~d~ 612 (728)
T KOG2284|consen 535 GRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCDD 612 (728)
T ss_pred CceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHH--hceeecccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999 889888644
Q ss_pred CCCCCCCCCeEEEecCCCCCceeEEecccccchh-------------ccccccccceEEee
Q 004654 689 KGRDVEDDDSFVFNEGFTAPLYRIKVWASVMQQY-------------CDTLSTLDCLICHL 736 (739)
Q Consensus 689 ~~~~v~~~d~f~~N~~F~~~~~rIki~~i~~k~~-------------~e~~~~~d~~~~~~ 736 (739)
.++..+..|++|.+|++++.|.||.+.++... .++-.-|.|||||+
T Consensus 613 --~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivri 671 (728)
T KOG2284|consen 613 --QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRI 671 (728)
T ss_pred --cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence 47778889999999999999999977553322 22333457888875
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-76 Score=617.13 Aligned_cols=613 Identities=26% Similarity=0.438 Sum_probs=549.9
Q ss_pred CchHHHHHHHHHHHHHHHHhcCCC-CCcHHHHHHHHHhhhccC--chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHH
Q 004654 101 TNFEEDTWAKLKLAIKAIFLKQPT-SCDLEKLYQAVNDLCLHK--MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFL 177 (739)
Q Consensus 101 ~~~~e~~W~~L~~aI~~I~~~~~~-~~s~e~LY~~Vy~lC~~k--~~~~LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~L 177 (739)
.+-+|+.|...++.+.+++..... ...|++||.+|+.+|.+. ...++|+.|+..+.+++...........+| ..+|
T Consensus 10 r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d-~aLL 88 (777)
T KOG2285|consen 10 RDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTD-GALL 88 (777)
T ss_pred hhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccc-cHHH
Confidence 344589999999999999977654 358999999999999985 678999999999999999877766655554 6899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccc-------ccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhc
Q 004654 178 SLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERL 250 (739)
Q Consensus 178 ~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~-------~~~sI~~lgl~lFr~~v~~~~~l~~~l~~~ll~lI~~eR~ 250 (739)
..|...|..|..+..++.--|.-|+.+-.-..+ .-.+|..+.+.-|.+++|. .++.++....+.++..+|.
T Consensus 89 ~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER~ 166 (777)
T KOG2285|consen 89 IGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAERD 166 (777)
T ss_pred HHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999998554322 2357999999999999997 7999999999999999999
Q ss_pred CCcCChHHHHHHHHHhhhhc--------cchhhhHHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHhhh
Q 004654 251 GEAVDRTLLNHLLKMFTALG--------IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLY 322 (739)
Q Consensus 251 g~~id~~llk~ii~ml~~L~--------~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~y 322 (739)
|+.+|.+++-.+-..++.|. +|.+.||..||++|.+||+..+..+++++++-+|+++++..++||+.|+.+|
T Consensus 167 G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRY 246 (777)
T KOG2285|consen 167 GNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRY 246 (777)
T ss_pred cchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHh
Confidence 99999999999999998874 9999999999999999999999999999999999999999999999999999
Q ss_pred cCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCChHHHHHHHHhhccc-chHHHHHHHHHHHHHHhhhhhhcC-
Q 004654 323 LDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMD- 398 (739)
Q Consensus 323 L~~--~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~- 398 (739)
|.. .+..+++.++...||..|.+.|+. .+..|+...+++-|.+||+|+.|+ .|++.+...+..||...|..-+-.
T Consensus 247 LE~~~~s~~~lme~~VnaLv~sf~~tIlA-EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~a 325 (777)
T KOG2285|consen 247 LEMNSPSSGKLMEKAVNALVESFEDTILA-ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNA 325 (777)
T ss_pred hccCCCcHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhh
Confidence 874 788999999999999999999985 589999999999999999999999 999999999999999999764422
Q ss_pred c----chhhHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhcC--------------------CCcchHHHH
Q 004654 399 E----EKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLR--------------------QNRPAELIA 454 (739)
Q Consensus 399 ~----~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~afe~~iN~~--------------------~~~~~e~LA 454 (739)
. ..+..+|++||.++++|..++.++|.+|+.|..+-+.||..++|+. .+++||+||
T Consensus 326 aE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLA 405 (777)
T KOG2285|consen 326 AENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLA 405 (777)
T ss_pred hhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHH
Confidence 1 2245799999999999999999999999999999999999999962 157899999
Q ss_pred HHHhHHHhcCC--CCCChHHHHhhhccceeeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhC--Cc
Q 004654 455 KFLDEKLRAGN--KGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG--SQ 530 (739)
Q Consensus 455 ~y~D~~lr~~~--k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG--~~ 530 (739)
.|||.+||+.. |..+.+|++.+|.+|+-+++|+++||+|..|++.+|.+||+.+.|++.+.|..|++.|+ ||| .+
T Consensus 406 NYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaD 484 (777)
T KOG2285|consen 406 NYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPAD 484 (777)
T ss_pred HHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHH
Confidence 99999999964 66788999999999999999999999999999999999999999999999999999999 888 57
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCC-CCCcCChHHHHHHHHHHHHHhccCCC
Q 004654 531 FTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSG 609 (739)
Q Consensus 531 ~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~fY~~k~~~ 609 (739)
|++||..||+||+.|++++.+|+..+...+.....-.+++.||+.|.|..... ..+.||.+|+..+-.-++||+++|+|
T Consensus 485 yVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsg 564 (777)
T KOG2285|consen 485 YVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSG 564 (777)
T ss_pred HHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCc
Confidence 99999999999999999999999977653332333568899999999998754 57999999999999999999999999
Q ss_pred ceEEeecCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCC--CCCCHHHHHHHhCCCHHHHHHHhhhhhc-CC--ccee
Q 004654 610 RRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLAC-GK--VRVL 684 (739)
Q Consensus 610 RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~--~~ls~~eI~~~t~i~~~~l~~~L~sL~~-~k--~~iL 684 (739)
|||+|.|+++.++|++.-+-|.|.|.|++|||+||.+||+. +.+|++.+.-+|.+|+.+|+|+|-||+. || .+||
T Consensus 565 rkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiL 644 (777)
T KOG2285|consen 565 RKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQIL 644 (777)
T ss_pred cchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhhee
Confidence 99999999999999987666899999999999999999984 7899999999999999999999999987 65 6788
Q ss_pred eeCCCC----CCCCCCCeEEEecCCCC-----CceeEEecccc
Q 004654 685 QKLPKG----RDVEDDDSFVFNEGFTA-----PLYRIKVWASV 718 (739)
Q Consensus 685 ~k~p~~----~~v~~~d~f~~N~~F~~-----~~~rIki~~i~ 718 (739)
..+|+. +++.++..|.+|.+|.- ...|-|||.|.
T Consensus 645 L~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIG 687 (777)
T KOG2285|consen 645 LCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIG 687 (777)
T ss_pred eecCcccCCcccccccceEEeechhhhhhccchhhcccceeee
Confidence 888853 78899999999999963 45677777654
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2e-34 Score=274.75 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=133.0
Q ss_pred eccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHHHHHHHHHHHHHHhhhccCCCCC
Q 004654 486 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 565 (739)
Q Consensus 486 ~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~ 565 (739)
||++||+|+.+|+++||+|||.+++++.|.|+.||++||.+||.+||++|++||+|++.|++++++|++.+.. +....+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~-~~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLEN-NSNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999987654 223457
Q ss_pred cceEEEEeecCCCCCCCC-CCCcCChHHHHHHHHHHHHHhccCCCceEEeecCCceEEEEEEe
Q 004654 566 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 627 (739)
Q Consensus 566 ~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f 627 (739)
++|+|.|||.++||..+. .++.||++|+.+++.|++||..+|+||+|+|.|+||+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999988 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=5.4e-26 Score=251.01 Aligned_cols=220 Identities=25% Similarity=0.358 Sum_probs=201.5
Q ss_pred eeeeeccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHHHHHHHHHHHHHH--hhhc
Q 004654 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQS--SQAR 559 (739)
Q Consensus 482 ~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~~Lk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~--~~~~ 559 (739)
.|...+.+|+-|.+.||..||.|||....++.+.|..-++.||-.+|..-.+.|++|++|+..|+++++.++.. ...+
T Consensus 444 mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~ 523 (765)
T KOG2165|consen 444 MLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRG 523 (765)
T ss_pred HHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhcc
Confidence 45555699999999999999999999999999999999999999999999999999999999999999999874 2211
Q ss_pred cCCCCCcceEEEEeecCCCCCCCCCCCcCChHHHHHHHHHHHHHhccCCCceEEeecCCceEEEEEEecCceEEEEEcHH
Q 004654 560 TKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLF 639 (739)
Q Consensus 560 ~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~ 639 (739)
......+.+++.+|++.+||......+.||..++..++.|.+-|..-..+|+|.|.+++|.|+|++.|.+++.+++||+.
T Consensus 524 ~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~ 603 (765)
T KOG2165|consen 524 AEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPE 603 (765)
T ss_pred cccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHH
Confidence 11222578899999999999998889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~ 706 (739)
||+|+++|.+.++||++|+++.+|||..-|+|.|..|+ +.+||..+|.. +++.+|++++.=.
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~~---s~tgt~T~iEse~ 665 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPII---SDTGTLTVIESEM 665 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCCC---CCCceeeeccccc
Confidence 99999999999999999999999999999999999999 99999998753 7788999999443
No 9
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.76 E-value=0.00042 Score=66.90 Aligned_cols=130 Identities=16% Similarity=0.226 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHh---hhccCch-hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHH
Q 004654 104 EEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVND---LCLHKMG-GNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSL 179 (739)
Q Consensus 104 ~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~---lC~~k~~-~~LY~~L~~~i~~~l~~~~~~l~~~~~d~~~~L~~ 179 (739)
.++.|..+..++..+|+++....+.|+|-+.|.- .|.++.. ..+-+.+++.+..-+......+.... +..+|..
T Consensus 5 ~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~~--~~~~l~r 82 (158)
T PF08539_consen 5 SDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEVP--DNRLLKR 82 (158)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhcc--hhHHHHH
Confidence 4789999999999999999999999999998865 4555542 23334444444444333333343322 3689999
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHhhhhhhhcc----------------cccccHHHHHHHHHHHHhccchhhHHHH
Q 004654 180 VERCWQDLCDQML-MIRGIALYLDRTYVKQT----------------PNVRSLWDMGLQLFRKYLSSYSEVEHKT 237 (739)
Q Consensus 180 ~~~~W~~~~~~~~-~i~~iF~YLDR~yv~~~----------------~~~~sI~~lgl~lFr~~v~~~~~l~~~l 237 (739)
+...|.-|...+. ++..||..|++.+-... ....+|..++|..||+.|+- +..+++
T Consensus 83 L~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL--P~y~~l 155 (158)
T PF08539_consen 83 LVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL--PYYQRL 155 (158)
T ss_pred HHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh--cchHhh
Confidence 9999999777655 89999999996543221 23578999999999999985 444443
No 10
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.11 E-value=0.0028 Score=71.30 Aligned_cols=316 Identities=11% Similarity=0.028 Sum_probs=175.0
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCC----CcHHHHHHHHHhhhccCc--hhHHHHHHHHHHHHHHHHHHHhhhcC---C--C
Q 004654 103 FEEDTWAKLKLAIKAIFLKQPTS----CDLEKLYQAVNDLCLHKM--GGNLYQRIEKECEEHISAAIRSLVGQ---S--P 171 (739)
Q Consensus 103 ~~e~~W~~L~~aI~~I~~~~~~~----~s~e~LY~~Vy~lC~~k~--~~~LY~~L~~~i~~~l~~~~~~l~~~---~--~ 171 (739)
+....|..|++++..|..-.... ..|-++.+.+|+-|..+. ...+.+-++..+..+..+...-+... + +
T Consensus 109 geAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~ 188 (661)
T KOG2167|consen 109 GEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKP 188 (661)
T ss_pred cchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccc
Confidence 34567888999998888765433 345678899999998873 34456666666665555532222211 1 2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhcC
Q 004654 172 DLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLG 251 (739)
Q Consensus 172 d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lgl~lFr~~v~~~~~l~~~l~~~ll~lI~~eR~g 251 (739)
....+.+.+...|-+.-.. .+++.-+|-. +.++....|+++-..+-...-.-+...+-+.+....+|..++.+
T Consensus 189 l~atV~~~LL~~hL~~IL~----kgl~~lvDm~---q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kD 261 (661)
T KOG2167|consen 189 LIATVERCLLSRHLDLILT----KGLDSLVDMR---QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKD 261 (661)
T ss_pred hHHHHHHHHHHHHHHHHHh----cchHHhhhhh---hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhh
Confidence 2456777788777655333 3455555654 22335667776665553222112355666777777888888877
Q ss_pred CcCC--hHHHHHHHHHhhhhccchhhhHHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHH--HHHHh-------
Q 004654 252 EAVD--RTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEE--HERCL------- 320 (739)
Q Consensus 252 ~~id--~~llk~ii~ml~~L~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE--~~r~~------- 320 (739)
+... .-..|..++|......+...- .+|+..++++|..+++ .....+.+||.+.....-.+ .+-+.
T Consensus 262 k~mVqELL~FK~k~Dii~~~sF~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~ 338 (661)
T KOG2167|consen 262 KDMVQELLDFKKKVDIIVDESFLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRAGNKETSDEELEFVL 338 (661)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHhccccccchhHHHHH
Confidence 7532 334678888887776554434 8899999999999998 36667889998776644333 11111
Q ss_pred -------hhcCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCChHHHHHHHHhhcccchHHHHHHHHHHHHHHh
Q 004654 321 -------LYLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYIRRT 391 (739)
Q Consensus 321 -------~yL~~--~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~~yI~~~ 391 (739)
+|+.. -...-....+.+.|+..|...+ +.|+.-|.+-+.....+..|+|.+.....+...+..+.|....
T Consensus 339 d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsv-dae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~ 417 (661)
T KOG2167|consen 339 DKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASV-DAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSK 417 (661)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhh-cchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 11110 0001111222233333332221 3444444444566778889999887754444444444444433
Q ss_pred hhhhhcCcchhhHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q 004654 392 GHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDA 437 (739)
Q Consensus 392 g~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~a 437 (739)
|..-- . ...|+.++--....|-.||..+..+-..+++-
T Consensus 418 ~~~~~-~-------~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~ 455 (661)
T KOG2167|consen 418 GANNR-L-------EGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDC 455 (661)
T ss_pred Hhhcc-C-------cCCceEEEeecccccCCCCchhccCCHHHHHH
Confidence 32210 0 01112222223456666776655444444433
No 11
>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=93.71 E-value=0.2 Score=44.27 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=54.7
Q ss_pred EEEEcHHHHHHHHHhc--------CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 004654 633 ELAVSLFQTVVLMLFN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (739)
Q Consensus 633 ~l~vs~~Qa~ILllFN--------~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~ 704 (739)
...++.-|+.+|+..- ..+.+|-.||++.+|++.+.+.+.|..|. +.+++.+.. ....|.+|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 4567888888888554 46789999999999999999999999999 999998643 2477999987
Q ss_pred CC
Q 004654 705 FT 706 (739)
Q Consensus 705 F~ 706 (739)
.+
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
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=93.69 E-value=0.088 Score=40.88 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=39.2
Q ss_pred HHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 641 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 641 a~ILllFN~~~-~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.||-.|.+.+ .+|+.||++.+|++...+.|.|+.|. ..+.+.++|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecCc
Confidence 35788888875 58999999999999999999999999 888888754
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=92.71 E-value=0.29 Score=41.93 Aligned_cols=59 Identities=17% Similarity=0.289 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 004654 639 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (739)
Q Consensus 639 ~Qa~ILllFN~~~-~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~ 704 (739)
+++.+.+..+..+ .+|.+||++.++++...+.+.|+.|. +.+++...+ .++.-|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCC
Confidence 3444555444443 49999999999999999999999999 889887654 24566776654
No 14
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=92.64 E-value=0.22 Score=37.78 Aligned_cols=46 Identities=15% Similarity=0.333 Sum_probs=37.5
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCccee
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (739)
+..+.-||....+++.+|..||++.+|++...+.++|+.|. +.+++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~--~~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE--EKGLI 47 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCcCc
Confidence 45677788888888899999999999999999999999998 65554
No 15
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=92.37 E-value=0.19 Score=39.89 Aligned_cols=49 Identities=24% Similarity=0.501 Sum_probs=42.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
|..|+-..++.+.+|++||++.+|+++..+++-|..|. +.+++.+.-+|
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~~GG 50 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRTHGG 50 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEcCE
Confidence 45577778889999999999999999999999999999 88888876544
No 16
>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=92.19 E-value=0.17 Score=40.40 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=44.6
Q ss_pred EcHHHHHHHHHhcCCCC--CCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~--ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
++.-|+.||......+. +|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 57789999988877766 9999999999999999999999999 888888865
No 17
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=90.21 E-value=0.4 Score=38.98 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=40.6
Q ss_pred EcHHHHHHHHHhc-CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN-~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
++.-|..||.... ..+.++..+|++.++++...+-+.|+.|. ..+++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~--~~glv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLE--EKGLVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEecC
Confidence 4667899998888 77899999999999999999999999999 888887754
No 18
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=89.71 E-value=0.43 Score=38.29 Aligned_cols=52 Identities=13% Similarity=0.289 Sum_probs=42.8
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
++.-.-||.++...+++|+.||++.+|++...+.++|.-|. +.+++.....|
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~~~g 60 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVEREG 60 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEEET
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEeccC
Confidence 34556678777777899999999999999999999999999 88888765443
No 19
>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=89.62 E-value=0.25 Score=39.14 Aligned_cols=51 Identities=14% Similarity=0.289 Sum_probs=45.1
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+|.-|+.+|....+.+.++..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 367899999888888889999999999999999999999999 888888755
No 20
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=89.06 E-value=0.75 Score=42.05 Aligned_cols=53 Identities=15% Similarity=0.240 Sum_probs=48.2
Q ss_pred EEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
..++..|+.||.....++.+|..+|++.+|++...+-+.+..|. +.+++.+.+
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 35688899999988888899999999999999999999999999 889999865
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=87.27 E-value=1.7 Score=35.83 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCCCC--CCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 639 FQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 639 ~Qa~ILllFN~~~~--ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
..-.||.++.+.+. ++..||++.+|++...+.++|..|. +.+.+.+.+
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 34457777777755 9999999999999999999999999 778887743
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=86.34 E-value=1.4 Score=41.82 Aligned_cols=53 Identities=23% Similarity=0.253 Sum_probs=47.7
Q ss_pred EEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.++..|+.||......+.+|..||++.++++...+-+.+..|. +.+++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 45788899999877667789999999999999999999999999 999999876
No 23
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.24 E-value=1.8 Score=37.21 Aligned_cols=55 Identities=13% Similarity=0.308 Sum_probs=43.8
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 004654 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (739)
Q Consensus 641 a~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~ 703 (739)
..||..+... +.+|..||++.+|++...+.+.|..|. +.++|.+.+. +..|.+..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~~------~~~y~l~~ 63 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDGQ------NGRYRLGP 63 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecCC------CCceeecH
Confidence 3466667666 689999999999999999999999999 8899987542 34565544
No 24
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=85.93 E-value=1.4 Score=38.32 Aligned_cols=54 Identities=24% Similarity=0.437 Sum_probs=48.2
Q ss_pred EEEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 633 ~l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
++.++..+..||.+....+.++..+|++.++++...+.+.|..|. +.+++.+..
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~~ 58 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRLP 58 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEecC
Confidence 456788899999888888889999999999999999999999999 888888753
No 25
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=85.72 E-value=2.4 Score=37.88 Aligned_cols=62 Identities=21% Similarity=0.364 Sum_probs=48.0
Q ss_pred EEcHHHHHHHHH-------hcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 004654 635 AVSLFQTVVLML-------FNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (739)
Q Consensus 635 ~vs~~Qa~ILll-------FN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~ 706 (739)
.++.-|.-|++. ||.. +.+|..+|++.||++...+.+.+..|+ +.+||.+ ++..+-+|.+.+
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~--------~g~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIR--------DGKRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe--------CCcEEeeecccc
Confidence 445556666554 4543 689999999999999999999999999 9999976 346677776543
No 26
>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=84.96 E-value=2 Score=32.45 Aligned_cols=43 Identities=14% Similarity=0.398 Sum_probs=34.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
..-||.+.-+ ++.++.||++.+|++...+.++|..|. +.+++.
T Consensus 4 R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 4456666655 689999999999999999999999998 777664
No 27
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=84.27 E-value=2 Score=32.52 Aligned_cols=46 Identities=22% Similarity=0.460 Sum_probs=37.8
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
-.|+..+.+...++..+|++.++++...+.+.|..|. +.+++.+.+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~--~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLE--EQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 3456566666789999999999999999999999998 777776644
No 28
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=83.88 E-value=1.9 Score=34.88 Aligned_cols=56 Identities=23% Similarity=0.326 Sum_probs=40.6
Q ss_pred HHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEe
Q 004654 643 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFN 702 (739)
Q Consensus 643 ILllFN~-~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N 702 (739)
||-.++. +.+++..||++.+|++....++.|..|. +.+.+.+.|.++... ..+.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~~--~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGKS--TYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSSS---EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCcc--eeeeec
Confidence 4555666 6789999999999999999999999999 888778766544332 245554
No 29
>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=83.88 E-value=2.4 Score=38.30 Aligned_cols=53 Identities=23% Similarity=0.339 Sum_probs=46.2
Q ss_pred EEEcHHHHHHHHHhc----CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFN----DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN----~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.+|..|..||.... ..+.++..+|++.++++...+-+.+..|. +.+.+.+.+
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 356888888886655 45789999999999999999999999999 999999876
No 30
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=81.99 E-value=4 Score=39.86 Aligned_cols=45 Identities=18% Similarity=0.284 Sum_probs=37.9
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 640 Qa~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
.+++.+.|+.. ..+|.++|++.+|+|...|.+.|+.|. +.+++..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 34455567654 589999999999999999999999999 8998885
No 31
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=81.92 E-value=3 Score=43.74 Aligned_cols=46 Identities=9% Similarity=0.209 Sum_probs=41.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.||.+|.....+|+.||++.+|++...+.|.|+.|. ..+.|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 3478889887789999999999999999999999999 899998864
No 32
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=80.27 E-value=5 Score=38.69 Aligned_cols=46 Identities=20% Similarity=0.285 Sum_probs=37.6
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+++.|..+..+.+|..+|++..|+|...|.+.|+.|. +.+++....
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r 58 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR 58 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec
Confidence 3344555556678999999999999999999999999 888887543
No 33
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=80.04 E-value=4.7 Score=37.90 Aligned_cols=44 Identities=18% Similarity=0.328 Sum_probs=36.5
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 641 a~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
+++.|.++.. ..+|.++|++.+++|...+.+.|+.|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 4444555544 479999999999999999999999999 8888874
No 34
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=79.78 E-value=3.3 Score=32.25 Aligned_cols=41 Identities=22% Similarity=0.395 Sum_probs=34.9
Q ss_pred hcCCCCC-CHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCC
Q 004654 647 FNDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 647 FN~~~~l-s~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
+...+.+ |..+|++.+|++...+.+.|..|. +.+++...++
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~~ 55 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRPG 55 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEecC
Confidence 4445567 999999999999999999999999 8888877553
No 35
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=79.22 E-value=4 Score=37.85 Aligned_cols=39 Identities=13% Similarity=0.286 Sum_probs=35.8
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 648 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 648 N~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.++++|+++|++.++.+...+.+.|+.|+ ..+++.++.
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeeee
Confidence 367899999999999999999999999999 899998864
No 36
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=78.68 E-value=4.5 Score=30.04 Aligned_cols=33 Identities=27% Similarity=0.475 Sum_probs=30.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 652 ~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
.++..||++.+|++...+.+.|..|. +.+++.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 58899999999999999999999999 8888876
No 37
>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=78.45 E-value=4.4 Score=32.69 Aligned_cols=49 Identities=14% Similarity=0.314 Sum_probs=40.8
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|. ..+++...+
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~~~ 54 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLE--EAGLVESRR 54 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEEEE
Confidence 455777887776666 9999999999999999999999998 777777644
No 38
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=78.28 E-value=4.4 Score=40.39 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=48.5
Q ss_pred EEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.++..|..||......+.+|..+|++.++++...+-+.|..|. +.+++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEecC
Confidence 56788899999999888999999999999999999999999999 889999865
No 39
>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=78.00 E-value=2 Score=35.14 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=41.0
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
|-.++-|+...-..+..|..||++.+|++...+.+.|..|. +.+++.+.+
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~--~~GlV~~~~ 56 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE--EKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH--HTTSEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 44556666555467789999999999999999999999999 888887754
No 40
>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=77.92 E-value=65 Score=35.20 Aligned_cols=158 Identities=15% Similarity=0.233 Sum_probs=91.9
Q ss_pred HHHHHHHHHHhhhccCChHHHHHHHHhhccc----chHHHHHHHHHHHHHHhhhhhhcCc-------chhhHHHHHHHHH
Q 004654 344 ISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLLEF 412 (739)
Q Consensus 344 ~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yI~~~g~~iv~~~-------~~~~~~V~~Ll~l 412 (739)
+..++.+.|..-.+.++.+.+.+.++||-.+ .|++....-+++.|.......+... ..+.-++..|..+
T Consensus 8 L~~~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~L 87 (331)
T PF08318_consen 8 LCEIFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKL 87 (331)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHH
Confidence 3445556788888899999999999999876 4677776666666666666555432 2233566666667
Q ss_pred HHHHHHH-------HHHhcCCCHHHHHHHH-------H----HHHHHhhcCC-CcchHHHHHHHhHHHhcC---------
Q 004654 413 KASLDTI-------WEQSFSKNEAFCNTIK-------D----AFEYLINLRQ-NRPAELIAKFLDEKLRAG--------- 464 (739)
Q Consensus 413 ~~~~~~i-------i~~~F~~~~~f~~~l~-------~----afe~~iN~~~-~~~~e~LA~y~D~~lr~~--------- 464 (739)
++..-.+ |..+|+.... ...+. . -+..|...+. .+...-+..|-...+.++
T Consensus 88 Fe~ia~ii~~h~~lI~~~yG~~~~-~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~ 166 (331)
T PF08318_consen 88 FEHIATIIEQHQPLIEKYYGPGYM-VYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSS 166 (331)
T ss_pred HHHHHHHHHHccHHHHHHcCCcHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccc
Confidence 6665444 5678875542 12111 1 2333333332 111223333433333220
Q ss_pred ---------CCCCChHHHHhhhccceeeeeeccChHHHHHHHHHHHHHHhcCCC
Q 004654 465 ---------NKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 509 (739)
Q Consensus 465 ---------~k~~s~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~ 509 (739)
..+.+.-+++..|+.+..+..... .|.++++.|.-...
T Consensus 167 ~~~~~~~~~~~~~d~reld~lL~Eis~i~~~w~-------lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 167 RAASSSQSEDEGIDPRELDALLNEISLILQRWS-------LYCRFISRKWNEFS 213 (331)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhccc
Confidence 011233567778887777765544 89999999987743
No 41
>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=77.79 E-value=3.3 Score=41.79 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=47.4
Q ss_pred EEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 635 ~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.++.-|..||..+.+++.++..||++.+|++...+.++|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 5688899999999887889999999999999999999999999 889998865
No 42
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=77.68 E-value=4.3 Score=31.49 Aligned_cols=33 Identities=15% Similarity=0.538 Sum_probs=28.1
Q ss_pred HHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 645 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 645 llFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
++.+..+.+|.++|++.+|++...+.+.|..|-
T Consensus 8 ~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 8 LLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344666679999999999999999999999997
No 43
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=77.46 E-value=4.1 Score=38.51 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=46.5
Q ss_pred EEEcHHHHHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.++..|..||...... +.+|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeec
Confidence 46788899998877654 578999999999999999999999999 999999876
No 44
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=77.13 E-value=2.7 Score=35.16 Aligned_cols=39 Identities=21% Similarity=0.271 Sum_probs=31.4
Q ss_pred HhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 646 LFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 646 lFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
++...+.+|+.||++.+|++...++..+..+. +.++|.+
T Consensus 26 L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~~ 64 (73)
T TIGR03879 26 LAREEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLVK 64 (73)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHHH
Confidence 33444679999999999999999999998877 6666654
No 45
>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=76.04 E-value=3.3 Score=40.48 Aligned_cols=53 Identities=19% Similarity=0.358 Sum_probs=44.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEE
Q 004654 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIK 713 (739)
Q Consensus 652 ~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~~~~~rIk 713 (739)
-+|..+|++.+|++...+.+++..|. +.++|.+.. ...|.+|++|--+-.+.+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~~~~ 127 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGDRDK 127 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCcHHH
Confidence 47899999999999999999999999 899999843 458999999865544444
No 46
>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=74.40 E-value=7.4 Score=36.11 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=36.6
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 640 Qa~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
++++.+.-++. ..+|.++|++.+|+|...+.+.|..|. +.+++...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 44444444433 389999999999999999999999999 88888753
No 47
>PRK10870 transcriptional repressor MprA; Provisional
Probab=73.08 E-value=8.1 Score=38.13 Aligned_cols=53 Identities=11% Similarity=0.145 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHHhcC--CCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~--~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+.++..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 3467778888877654 4579999999999999999999999999 999999876
No 48
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=72.82 E-value=6.7 Score=30.57 Aligned_cols=37 Identities=11% Similarity=0.287 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 650 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 650 ~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.+..|..+|++.+|++...+.+.|..|. +.+++....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeeee
Confidence 5679999999999999999999999999 788887644
No 49
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=72.59 E-value=2.8 Score=35.77 Aligned_cols=44 Identities=20% Similarity=0.458 Sum_probs=34.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
..||...+..+.+++.+|.+.+|+++..|-++|..|. +.+.+..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le--~~GyV~~ 46 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLE--EAGYVEV 46 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEE
Confidence 3456556667789999999999999999999999999 6666554
No 50
>PRK11569 transcriptional repressor IclR; Provisional
Probab=71.59 E-value=7.8 Score=41.08 Aligned_cols=45 Identities=9% Similarity=0.315 Sum_probs=40.0
Q ss_pred HHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 642 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 642 ~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.||.+|.+. ..+++.||++.+|++...+.|.|.+|. ..+.|.+.+
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 477889875 579999999999999999999999999 999998754
No 51
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=71.04 E-value=8.8 Score=40.61 Aligned_cols=56 Identities=14% Similarity=0.100 Sum_probs=45.3
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 004654 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (739)
Q Consensus 641 a~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~ 704 (739)
..||.+|... ..+|+.||++.+|++...+-|.|.+|. ..+.|.+.+ .+..|.+-..
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~------~~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDS------QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC------CCCeEEecHH
Confidence 3478899775 479999999999999999999999999 899998854 3445655433
No 52
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=70.97 E-value=8 Score=40.70 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=40.4
Q ss_pred HHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCC
Q 004654 642 VVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 642 ~ILllFN~~~-~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
.||.+|.+.+ .+|..||++.+|++...+.|.|..|. ..+.|.+.+.
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~~ 61 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSAS 61 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecC
Confidence 4778887655 59999999999999999999999999 9999988653
No 53
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=70.74 E-value=7.1 Score=34.81 Aligned_cols=46 Identities=11% Similarity=0.314 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
..-.||..+..+..+|+.+|++.+|++...+.+.++.|. +.+++.+
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeec
Confidence 345677778777899999999999999999999999999 7777763
No 54
>PHA00738 putative HTH transcription regulator
Probab=70.26 E-value=8.4 Score=34.68 Aligned_cols=67 Identities=18% Similarity=0.202 Sum_probs=52.2
Q ss_pred EEEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCC
Q 004654 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 705 (739)
Q Consensus 633 ~l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F 705 (739)
++...+.=-.||.+..+++.+++.+|++.++|+...+-++|.-|- ..+|+.....|+.+ .|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~v----yY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRTL----YAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCEE----EEEECCCc
Confidence 455555555677666677789999999999999999999999998 89999987765432 46666654
No 55
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=70.06 E-value=9.6 Score=39.79 Aligned_cols=46 Identities=22% Similarity=0.446 Sum_probs=40.8
Q ss_pred HHHHHHhcCCCC-CCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 641 TVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 641 a~ILllFN~~~~-ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
..||.+|..... +++.||++.+|+|...+.|.|..|. ..+.+.+.+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 357888987654 7899999999999999999999999 999999865
No 56
>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=69.56 E-value=11 Score=35.06 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=35.7
Q ss_pred HHHHhcC--CCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 643 VLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 643 ILllFN~--~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
+|..+.. .+.+|..||++.+|++...+.+.|+.|. +.+++...
T Consensus 14 ~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 14 VLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred HHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 4444433 3579999999999999999999999999 88988754
No 57
>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=69.37 E-value=11 Score=31.32 Aligned_cols=46 Identities=22% Similarity=0.426 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
..|. ||+..... ..|++||.+.||++.+.|...|.-|+ +.+++.+.
T Consensus 6 ~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred HHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 3344 33344333 89999999999999999999999999 88888763
No 58
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=69.15 E-value=10 Score=39.47 Aligned_cols=44 Identities=25% Similarity=0.446 Sum_probs=38.8
Q ss_pred HHHHHHhcC-CCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 641 TVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 641 a~ILllFN~-~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
..||.+|.. ...+|+.||++.+|+|...+.|.|..|. ..+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~--~~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV--ELGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 347888986 4589999999999999999999999999 8888876
No 59
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=68.99 E-value=12 Score=35.99 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCC-CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 640 QTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 640 Qa~ILllFN~~~-~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.+.+.|.-+..+ ..|.++|++..|+|...|.+.|..|. |.+++...+
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r 59 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR 59 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec
Confidence 444445444444 68899999999999999999999999 999888644
No 60
>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=68.93 E-value=7.5 Score=28.81 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=27.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhh
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL 676 (739)
-.||-...+....++.+|++.+|++...+.+-++.|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 346666666789999999999999999999887755
No 61
>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=68.69 E-value=8.5 Score=31.50 Aligned_cols=44 Identities=32% Similarity=0.430 Sum_probs=35.5
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhc-CCcceee
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC-GKVRVLQ 685 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~-~k~~iL~ 685 (739)
.|--+.++...+|+.+|+..||+++.++...|--|+. +|+.+-.
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~ 56 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEE 56 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEE
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEe
Confidence 3556778888999999999999999999999999995 4455443
No 62
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=67.83 E-value=1.1e+02 Score=30.75 Aligned_cols=115 Identities=18% Similarity=0.338 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----HHhhhccCChHHHHHHHHhhcccchHHHHHHHHHHHHHHhhhhhhcCcchhhHHH
Q 004654 331 LIATAERQLLERHISAILDKG----FTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYIRRTGHGIVMDEEKDKDMV 406 (739)
Q Consensus 331 l~~~l~~~LI~~~~~~ll~~g----l~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~~yI~~~g~~iv~~~~~~~~~V 406 (739)
|.+.+.+.||...-+.+++.| +-.|+.. +-++++.|..|.-.-...+.+.+.++.+|.++-. .|
T Consensus 23 i~kelie~l~~~~~qk~l~~gE~v~il~Ll~~-kd~ef~~llkla~eq~k~e~~m~~Lea~VEkrD~-----------~I 90 (272)
T KOG4552|consen 23 IVKELIETLINRDKQKMLKNGETVNILKLLDS-KDDEFKTLLKLAPEQQKREQLMRTLEAHVEKRDE-----------VI 90 (272)
T ss_pred HHHHHHHHHHhhhHHHHHhcchHHHHHHHHHh-ccHHHHHHHHHhHhHHHHHHHHHHHHHHHHHhHH-----------HH
Confidence 333344444444444555432 3334433 3355665555544445566666777777666533 34
Q ss_pred HHHHHHHHHHHHHH-HHhcCCCHHHHHHHHHHHHHHhhcCCCcchHHHHHHHhHHHhcC
Q 004654 407 SSLLEFKASLDTIW-EQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAG 464 (739)
Q Consensus 407 ~~Ll~l~~~~~~ii-~~~F~~~~~f~~~l~~afe~~iN~~~~~~~e~LA~y~D~~lr~~ 464 (739)
+.|-.--+..+.++ ..||+-+..+ +.|++| +.++ -.+|.|-||.+.+=+.+
T Consensus 91 QqLqk~LK~aE~iLtta~fqA~qKL-ksi~~A-----~krp-vsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 91 QQLQKNLKSAEVILTTACFQANQKL-KSIKEA-----EKRP-VSSEELIKYAHRISKHN 142 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-----hcCC-CCHHHHHHHHHHhhhcc
Confidence 55444334444444 3577766654 345554 5555 46799999999986643
No 63
>PF13730 HTH_36: Helix-turn-helix domain
Probab=66.92 E-value=12 Score=28.97 Aligned_cols=28 Identities=14% Similarity=0.385 Sum_probs=25.3
Q ss_pred CHHHHHHHhCCCHHHHHHHhhhhhcCCcce
Q 004654 654 SFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (739)
Q Consensus 654 s~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (739)
|.+.|++.+|++...+.+++..|. +.++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~--~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE--EKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH--HCcC
Confidence 899999999999999999999998 5544
No 64
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=66.57 E-value=9.8 Score=30.41 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
..+|..||++.+|++...+.+.|+.|. +.+++.+.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 479999999999999999999999999 888888754
No 65
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=65.01 E-value=8 Score=40.63 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
|..|+-+.++++.+++.||++.+|++...++|-|..|. +.++|.+..+|
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~Gg 55 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTYGG 55 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEECC
Confidence 66788889999999999999999999999999999999 88888775544
No 66
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=64.85 E-value=18 Score=34.14 Aligned_cols=40 Identities=8% Similarity=0.325 Sum_probs=35.0
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 647 FN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+..+..+|..+|++.+|+|...+++.|+.|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 4445578999999999999999999999999 889888765
No 67
>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=64.22 E-value=10 Score=33.65 Aligned_cols=44 Identities=23% Similarity=0.422 Sum_probs=37.5
Q ss_pred EEcHHHHHHHHHhcC----CCCCCHHHHHHHhCCCHHHHHHHhhhhhc
Q 004654 635 AVSLFQTVVLMLFND----AQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (739)
Q Consensus 635 ~vs~~Qa~ILllFN~----~~~ls~~eI~~~t~i~~~~l~~~L~sL~~ 678 (739)
.++..|-.||-.+.+ .+.+++++|++.+++++.+++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 678999999998887 35899999999999999999999999983
No 68
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=64.11 E-value=13 Score=33.15 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=45.6
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
++..|..||......+..+..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 788899999888887777669999999999999999999999 889888866
No 69
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.50 E-value=8.1 Score=35.53 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=45.1
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~ 704 (739)
.||.+.-+.++.++.||++.+|++...+-++|.-|. +.+++.....|+. -.|.+|.+
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr~----~~Y~l~~~ 76 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGKW----VHYRLSPH 76 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcCE----EEEEECch
Confidence 355444445679999999999999999999999999 8999998776543 34777764
No 70
>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=61.25 E-value=17 Score=29.05 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=36.6
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
|..+-.+...++..+|++.+|++...+...|..|. +.+++..+|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 33444477899999999999999999999999999 888888765
No 71
>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=60.59 E-value=17 Score=28.75 Aligned_cols=39 Identities=18% Similarity=0.440 Sum_probs=32.1
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 648 NDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 648 N~~~~l-s~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.....+ |..+|++.+|++...+.+.|..|. +.++|...+
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~~ 59 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELE--AEGLVERRP 59 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 334444 499999999999999999999999 888887644
No 72
>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=60.21 E-value=3.8e+02 Score=32.45 Aligned_cols=50 Identities=12% Similarity=0.217 Sum_probs=30.6
Q ss_pred chHHHHHHHHHHHHHHhhhh------hhcCcchhhHHHHHHHHHHHHHHHHHHHhcCC
Q 004654 375 NALESLRQALAMYIRRTGHG------IVMDEEKDKDMVSSLLEFKASLDTIWEQSFSK 426 (739)
Q Consensus 375 ~~l~~l~~~~~~yI~~~g~~------iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~ 426 (739)
.+++.|.+.+.+|+..-+.. ++..-- ..+-+..+..|.++..++..|+.+
T Consensus 646 k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW--~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 646 KGIEALYKRVEKHFSRDADDPSFEEDLLQVVW--SAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHcCCccccccchhhHHHHHH--HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 56677776666666221110 000000 256677888999999999999864
No 73
>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=59.36 E-value=12 Score=29.75 Aligned_cols=38 Identities=13% Similarity=0.348 Sum_probs=29.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
|.-+|-++-+.+.++++||++.+|++...++.-+.-|-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44555444447899999999999999999998877665
No 74
>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=57.94 E-value=18 Score=27.78 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=21.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
.++++.|- +.+|++||++.+|++...++..|.
T Consensus 17 ~i~~l~~~--~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 17 EIFLLRYF--QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHHT--S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHH--HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 33444443 459999999999999999888765
No 75
>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=57.91 E-value=23 Score=26.80 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
+.+|-+.| .+.+|++||++.+|++...+.+.+..
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 44555667 55799999999999999988876644
No 76
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=57.69 E-value=16 Score=38.25 Aligned_cols=51 Identities=20% Similarity=0.344 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCC
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGR 691 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~ 691 (739)
-|..|+-.+++++.+++.||++.+|++...++|-|..|. +.+++.+..+|.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gga 56 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCCc
Confidence 356688889999999999999999999999999999998 777777765554
No 77
>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=56.91 E-value=13 Score=29.97 Aligned_cols=38 Identities=24% Similarity=0.506 Sum_probs=29.5
Q ss_pred HHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 645 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 645 llFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
.+++ .+.+|+.+|...|+++.+.++..|-.|+ +.+++.
T Consensus 21 ~Ll~-~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v~ 58 (62)
T PF08221_consen 21 VLLS-RGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLVQ 58 (62)
T ss_dssp HHHH-C-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSEE
T ss_pred HHHH-cCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCee
Confidence 3443 4589999999999999999999999999 777664
No 78
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=56.63 E-value=16 Score=37.36 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=37.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
..||.+.+..+++|.+||++.+||+..-++++|+.|. .-+++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le--~~Glv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLE--AEGLVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHH--hCcceee
Confidence 3467777888899999999999999999999999999 6555543
No 79
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=56.12 E-value=14 Score=38.63 Aligned_cols=51 Identities=22% Similarity=0.436 Sum_probs=44.9
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRD 692 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~ 692 (739)
|-.|+-+.++++.++++||++.+|+++..++|=|..|. +.++|.+..+|..
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGGa~ 57 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGGAV 57 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCCEe
Confidence 55688888899999999999999999999999999999 8888888665543
No 80
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=54.09 E-value=9 Score=34.24 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=30.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
+.|+..+..++.++-++|++.+|++..++++.|..|. ..+++.
T Consensus 16 ~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~--~~~lv~ 58 (105)
T PF02002_consen 16 VRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLY--EDGLVS 58 (105)
T ss_dssp HHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHH--HHSS-E
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeE
Confidence 4566556556789999999999999999999999999 666653
No 81
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=53.75 E-value=18 Score=37.98 Aligned_cols=50 Identities=16% Similarity=0.315 Sum_probs=43.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGR 691 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~ 691 (739)
|..|+-+.++.+.+++.||++.++++...++|-|..|. +.++|.+.-+|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~GGa 56 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHGGA 56 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCE
Confidence 55677777888999999999999999999999999999 888888876654
No 82
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=53.39 E-value=34 Score=31.91 Aligned_cols=63 Identities=22% Similarity=0.347 Sum_probs=52.7
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCC---CCeEEEecCCC
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVED---DDSFVFNEGFT 706 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~---~d~f~~N~~F~ 706 (739)
-.|-+..+.+..|+.|+++.+|=+.+.+-|+|..|+ ..+|+..+.+|+...+ =|.|.++-.|.
T Consensus 68 eLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 68 ELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 356677788999999999999999999999999999 9999998877765444 36677887776
No 83
>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=52.32 E-value=18 Score=29.53 Aligned_cols=51 Identities=20% Similarity=0.356 Sum_probs=37.0
Q ss_pred cHHHHHHHHHhcC-----CCCCCHHHHHHHhCCC-HHHHHHHhhhhhcCCcceeeeCCC
Q 004654 637 SLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 637 s~~Qa~ILllFN~-----~~~ls~~eI~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
+.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.|.
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~~ 61 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDPG 61 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGCC
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCCC
Confidence 4456666654432 2367999999999996 999999999999 8888888764
No 84
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=52.19 E-value=24 Score=33.82 Aligned_cols=49 Identities=4% Similarity=0.249 Sum_probs=42.4
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
++..--.||..+..+...|+.+|++.+|+++..+.+-++.|. ..+++.+
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~--~~GvI~~ 55 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK--QAGIITG 55 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeee
Confidence 455667788888888999999999999999999999999999 6777653
No 85
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=51.85 E-value=19 Score=38.11 Aligned_cols=51 Identities=14% Similarity=0.208 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
--|..|+.+.+..+.+++.||++.+|++...++|-|.-|. +.+++.+..+|
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~GG 67 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEeCC
Confidence 4577888899999899999999999999999999999998 66777765544
No 86
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=51.63 E-value=30 Score=35.35 Aligned_cols=64 Identities=20% Similarity=0.400 Sum_probs=50.8
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC----CCCC---CCCCCeEEEe
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP----KGRD---VEDDDSFVFN 702 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p----~~~~---v~~~d~f~~N 702 (739)
|..-..||-+......+.+.||++.+|+|...+-.+++.|. +.+++..+. +|.+ +...|...+|
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~t~karkG~QKiC~s~~~ei~i~ 92 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTETVKARKGSQKICISTTDEIEIN 92 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeeeeeccccCceeEeEeecceEEEe
Confidence 45555688888888999999999999999999999999999 999988643 2221 4556666666
No 87
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=51.19 E-value=23 Score=34.43 Aligned_cols=49 Identities=10% Similarity=0.199 Sum_probs=42.6
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
+.-.-.-||-...++..+|+.+|++.+|++...+.+-++.|. +.+++..
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~~ 60 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQG 60 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEE
Confidence 345566788888899999999999999999999999999999 7777763
No 88
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=50.11 E-value=25 Score=36.60 Aligned_cols=47 Identities=15% Similarity=0.281 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
|..|+..+++++.++.+||++.+|+++..++|-|.-|. ..+.|.+..
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~--~~~~l~r~~ 52 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQ--TQGKILRNH 52 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 55678888888899999999999999999999999997 445555543
No 89
>PRK00215 LexA repressor; Validated
Probab=49.37 E-value=34 Score=34.36 Aligned_cols=53 Identities=21% Similarity=0.317 Sum_probs=42.8
Q ss_pred EcHHHHHHHHHhcC-----CCCCCHHHHHHHhCC-CHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 636 vs~~Qa~ILllFN~-----~~~ls~~eI~~~t~i-~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
++.-|..||....+ ...+|+.||++.+|+ +...+.+.|+.|. +.+.+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~~ 60 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPGR 60 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCCC
Confidence 35668888865542 347899999999999 9999999999999 88888876643
No 90
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.68 E-value=24 Score=34.93 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
...||...-.++.+|-++|++.+||+...++++|..|. ..+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~--e~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLY--DARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeE
Confidence 34466555566789999999999999999999999999 777776
No 91
>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=48.40 E-value=22 Score=29.08 Aligned_cols=39 Identities=15% Similarity=0.363 Sum_probs=29.2
Q ss_pred HhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 646 LFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 646 lFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
...+...+|++||+..++++.+.+...|.-|+ +.+-+.+
T Consensus 8 ~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~--~kG~I~~ 46 (69)
T PF09012_consen 8 YLRERGRVSLAELAREFGISPEAVEAMLEQLI--RKGYIRK 46 (69)
T ss_dssp HHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH--CCTSCEE
T ss_pred HHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEE
Confidence 34456789999999999999999999999999 5444443
No 92
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=48.38 E-value=38 Score=34.12 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=36.8
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
.||......+.+|..||++.+|++...+.++|..|. +.+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 345444445679999999999999999999999999 88888775
No 93
>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=47.40 E-value=30 Score=33.57 Aligned_cols=42 Identities=21% Similarity=0.300 Sum_probs=34.6
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
.|+...=.+..+|-+||++.+||+..++++.|..|. ..+++.
T Consensus 18 ~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~--e~~Lv~ 59 (158)
T TIGR00373 18 LVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALY--DAGLAD 59 (158)
T ss_pred HHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCce
Confidence 345433345589999999999999999999999999 777774
No 94
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=45.83 E-value=19 Score=35.84 Aligned_cols=27 Identities=37% Similarity=0.613 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
..+|+++|++.|||..+++..+|+.|-
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 379999999999999999999999885
No 95
>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=45.19 E-value=29 Score=25.89 Aligned_cols=31 Identities=19% Similarity=0.414 Sum_probs=22.2
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
|+-++.++ +|+.+|++.+|++...+.|.|..
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHhc
Confidence 44455554 99999999999999999988753
No 96
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=44.16 E-value=21 Score=35.51 Aligned_cols=46 Identities=11% Similarity=0.177 Sum_probs=39.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
-|..|+.+.+.++.+++++|++.+|++...++|=|..|. ..++|.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~--~~g~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG--IPELRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh--cchHHHH
Confidence 466788888999999999999999999999999999998 5555443
No 97
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.34 E-value=51 Score=24.78 Aligned_cols=39 Identities=23% Similarity=0.398 Sum_probs=29.3
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
+.-|.-|+.++. ..++..+|++.+|++...+.+.+..+.
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 358999999999999999998887654
No 98
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=41.77 E-value=28 Score=34.78 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=42.3
Q ss_pred EcHHHHHHHHHhcC-----CCCCCHHHHHHHhCCC-HHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN~-----~~~ls~~eI~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 46778888866553 2358999999999998 999999999999 889888764
No 99
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=41.68 E-value=61 Score=31.85 Aligned_cols=55 Identities=20% Similarity=0.154 Sum_probs=42.7
Q ss_pred EEEEEcHHHHHHHHHhcCCCCC-CHHHHHHHh--CCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 632 KELAVSLFQTVVLMLFNDAQKL-SFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 632 ~~l~vs~~Qa~ILllFN~~~~l-s~~eI~~~t--~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+++.-+-+..+|+-+..-.+.- +.++|+..+ +|+.++++..|..|. +.++|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 3344455556666665544433 899999999 999999999999999 999999854
No 100
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=41.47 E-value=46 Score=31.50 Aligned_cols=49 Identities=14% Similarity=0.341 Sum_probs=42.2
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
+.-.-.-||-...++...++.+|++.+|++...+.+.+..|. +.+|+.+
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 344556688888888889999999999999999999999999 8888775
No 101
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=41.24 E-value=2.9e+02 Score=32.02 Aligned_cols=41 Identities=20% Similarity=0.235 Sum_probs=25.0
Q ss_pred HHHHhcCChhhHHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHH
Q 004654 293 MKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAER 337 (739)
Q Consensus 293 ~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~ 337 (739)
+.+++.++. +=++.+..++.....+.++| +..++|+..|++
T Consensus 457 Qkmi~~~~~-~q~~~i~~rI~~h~~~Lrk~---syGKhIia~lek 497 (503)
T KOG1488|consen 457 QKMIDICGP-EQRELIKSRVKPHASRLRKF---SYGKHIIAKLEK 497 (503)
T ss_pred HHHHHhcCH-HHHHHHHHHHHHHHHHHccC---ccHHHHHHHHHH
Confidence 344444433 33666777777777777775 456677776655
No 102
>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=40.61 E-value=56 Score=24.64 Aligned_cols=38 Identities=24% Similarity=0.369 Sum_probs=27.7
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
.-|.-++.++- +.+|..+|++.+|++...+...+..+.
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 34444554442 458999999999999998888876654
No 103
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=40.52 E-value=30 Score=24.11 Aligned_cols=26 Identities=31% Similarity=0.489 Sum_probs=21.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 652 KLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 652 ~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
.+|-+||++.+|+..+.+-|.|..|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999999887
No 104
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=40.35 E-value=42 Score=29.02 Aligned_cols=44 Identities=18% Similarity=0.379 Sum_probs=37.0
Q ss_pred HHHHHHhcCCCCCCHHHHHHHh-CCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 641 TVVLMLFNDAQKLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
+.||..... +...|.||.+.+ |++...|.+.|..|. ..+++.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 456665555 689999999999 999999999999999 88888874
No 105
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=39.48 E-value=56 Score=32.39 Aligned_cols=70 Identities=19% Similarity=0.285 Sum_probs=54.0
Q ss_pred CceEEeecCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCC--CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~--~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
.|.-.|.+.+|.++++ +.+.|+ |++.||.-||.-... ..||.+.|++..+|+.++++..|..+. -+.|.+
T Consensus 96 ~r~~~~~~~fg~~ep~-~vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~--~F~v~i 167 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPE-KVPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK--PFEVKI 167 (179)
T ss_pred CCCCcccccccccCcc-cCCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC--CceeeC
Confidence 3445688889998886 345565 577899988765443 479999999999999999999999997 455543
No 106
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.77 E-value=77 Score=26.95 Aligned_cols=49 Identities=12% Similarity=0.361 Sum_probs=40.9
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.++++|=+.-.....+.-.+|++.++++...++..+..|- ..++|.+.|
T Consensus 9 IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 9 ILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 3555565666667899999999999999999999999998 899997654
No 107
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=38.17 E-value=8.1e+02 Score=29.73 Aligned_cols=98 Identities=15% Similarity=0.267 Sum_probs=51.7
Q ss_pred cHHHHHHHHHhhhccC----------chhHHHHHHHHHHHHHHHHHHHhhhcCCC--cHHHHHHHHHHHHHHHHHHHHHH
Q 004654 127 DLEKLYQAVNDLCLHK----------MGGNLYQRIEKECEEHISAAIRSLVGQSP--DLVVFLSLVERCWQDLCDQMLMI 194 (739)
Q Consensus 127 s~e~LY~~Vy~lC~~k----------~~~~LY~~L~~~i~~~l~~~~~~l~~~~~--d~~~~L~~~~~~W~~~~~~~~~i 194 (739)
+++.+|..+-..|... ...-+..-++..+.+.|...+..+..... +...||+.+...+..-. .++
T Consensus 192 ~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~~a~~~s~~~YLr~l~~~y~~t~---~lv 268 (710)
T PF07393_consen 192 SLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLEEASSISTLAYLRTLHGLYSQTK---KLV 268 (710)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHH---HHH
Confidence 4677888888777654 23335666666666666666666654332 34678887776654433 333
Q ss_pred HHHHHHhhhhhhhc-ccccccHHHHHHHHHHHHh
Q 004654 195 RGIALYLDRTYVKQ-TPNVRSLWDMGLQLFRKYL 227 (739)
Q Consensus 195 ~~iF~YLDR~yv~~-~~~~~sI~~lgl~lFr~~v 227 (739)
.++=.++...-... ......+..+--.+|..++
T Consensus 269 ~~L~~~~~~~~~~~~~~~~~~l~~~~~~lF~~~l 302 (710)
T PF07393_consen 269 DDLKEFFSGENPDPDSSDSAFLDQLVESLFEPYL 302 (710)
T ss_pred HHHHHhhcccCCCccchHHHHHHHHHHHHHHHHc
Confidence 33333322111000 0012345556666776666
No 108
>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=37.72 E-value=38 Score=27.11 Aligned_cols=39 Identities=18% Similarity=0.419 Sum_probs=32.5
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCC
Q 004654 649 DAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 649 ~~~~l-s~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
.++.+ |..+|++..|++-..++++|.-|. ..+++...|+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~--~~g~i~~~~~ 59 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLE--AEGLIERRPG 59 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEETT
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHH--HCCcEEEECC
Confidence 34678 999999999999999999999999 8888887653
No 109
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=37.53 E-value=60 Score=28.52 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+..+....-||..+...+.=.-.-|+..|+++.+++...|..|. ..++|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 44566778899888888777778899999999999999999999 999998865
No 110
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=36.71 E-value=8.5e+02 Score=29.55 Aligned_cols=135 Identities=15% Similarity=0.172 Sum_probs=75.5
Q ss_pred hhHHHHHHHHHHHHHHH-hcCCcCChHHHHHHHHHhhhhccchhhhHHhHHHHHHHHHHHHH----------HHH--Hh-
Q 004654 232 EVEHKTVTGLLRMIERE-RLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEG----------MKY--MQ- 297 (739)
Q Consensus 232 ~l~~~l~~~ll~lI~~e-R~g~~id~~llk~ii~ml~~L~~Y~~~FE~~~L~~t~~yY~~~~----------~~~--l~- 297 (739)
...+.+-+.+|+..+.. |.+ |...++.+...|..++-+.. .-..|++...-|+.... ..| +.
T Consensus 106 ~~~e~fE~~LL~eFe~ay~~~---d~~~M~~~A~vL~~fngg~~-~i~~fi~k~~~f~~~~~~~~~~~~~~~~~~~~l~d 181 (710)
T PF07393_consen 106 KYCEIFENALLREFEIAYREG---DYERMKEFAKVLLEFNGGSS-CIDFFINKHEFFIDEDQLDESNGFEDEEIWEKLSD 181 (710)
T ss_pred HHHHHHHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCcH-HHHHHHHhChhhhhhhhhccccccchhHHHHhccC
Confidence 45566667777776543 333 57789999999999875542 33335554444441100 111 11
Q ss_pred --------cCChhhHHHHHHHHHHHHHHHHhhhcCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCChHHHHHH
Q 004654 298 --------QSDVPDYLKHVEIRLHEEHERCLLYLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRM 367 (739)
Q Consensus 298 --------~~~~~~Yl~~v~~~l~eE~~r~~~yL~~--~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~l 367 (739)
...+.+++..+...+++|...+..-++. .....+++.+-..-|.+++..+|. .-.......-|+.+
T Consensus 182 ~~~~~~~~~~~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~----~a~~~s~~~YLr~l 257 (710)
T PF07393_consen 182 PDSHPPINEESLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLE----EASSISTLAYLRTL 257 (710)
T ss_pred cccccccchHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHH----hhccCCHHHHHHHH
Confidence 1135678999999999999999887653 223344444444444455554442 11112223346666
Q ss_pred HHhhccc
Q 004654 368 YSLFSRV 374 (739)
Q Consensus 368 y~Ll~~~ 374 (739)
+.++..+
T Consensus 258 ~~~y~~t 264 (710)
T PF07393_consen 258 HGLYSQT 264 (710)
T ss_pred HHHHHHH
Confidence 6666554
No 111
>PRK11050 manganese transport regulator MntR; Provisional
Probab=36.55 E-value=73 Score=30.56 Aligned_cols=45 Identities=18% Similarity=0.314 Sum_probs=37.9
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
.|+.++...+.++..+|++.++++...+.+.|..|. +.+++.+.+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le--~~GlI~r~~ 85 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLA--RDGLVEMRP 85 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 345566677889999999999999999999999999 667777654
No 112
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=36.51 E-value=41 Score=37.28 Aligned_cols=68 Identities=26% Similarity=0.348 Sum_probs=42.9
Q ss_pred eEEeecCCceEEEEEEecCceE-EEE----EcHHHHHHHHHhcC-CC-CCCHHHHHHHhCCCHHHHHHHhhhhhc
Q 004654 611 RLMWQNSLGHCVLKAEFPKGKK-ELA----VSLFQTVVLMLFND-AQ-KLSFQDIKDATGIEDKELRRTLQSLAC 678 (739)
Q Consensus 611 kL~W~~~lg~~~l~~~f~~~~~-~l~----vs~~Qa~ILllFN~-~~-~ls~~eI~~~t~i~~~~l~~~L~sL~~ 678 (739)
=+.+.+.||..|=++--|.+.. +|- -+-+-..||-++-. .+ .+|+++|++.|||..+++.-+|++|-+
T Consensus 281 LIdFSYeLSr~E~~~GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m 355 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNM 355 (396)
T ss_pred hhhhhhhhhcccCcCCCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhCC
Confidence 3567777887776553332211 110 12333344433333 32 399999999999999999999999964
No 113
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=36.12 E-value=57 Score=37.72 Aligned_cols=51 Identities=10% Similarity=0.219 Sum_probs=45.3
Q ss_pred EEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 635 ~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
.++..|..||......+.++..+|++.+|++...+.+.+.+|. +.+++..+
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le--~kGlV~~~ 53 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLE--EKGLVKVE 53 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHH--hCCCEEEE
Confidence 4688999999999888899999999999999999999999999 66666653
No 114
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=35.89 E-value=54 Score=34.82 Aligned_cols=39 Identities=33% Similarity=0.472 Sum_probs=31.0
Q ss_pred HHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 639 FQTVVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 639 ~Qa~ILllF-N~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
+...|+-.+ +....+|+++|++.|||..+++..+|++|-
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 444455443 445789999999999999999999999885
No 115
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=34.76 E-value=66 Score=32.86 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=34.0
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 648 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 648 N~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+....+|.++|++.+++++..++.++..|+ +.++|...+
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~--~~~~~~~~~ 212 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLV--NCHILFTSI 212 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHH--hCCEEEEEe
Confidence 335789999999999999999999999999 888885543
No 116
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=33.30 E-value=53 Score=34.61 Aligned_cols=53 Identities=19% Similarity=0.354 Sum_probs=45.0
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCC
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRD 692 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~ 692 (739)
.-|.++-+.-+.++.++-+||..++|+|...+-|+|+.|. |.++..+...|++
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~K~G~~ 248 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKEKKGRT 248 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEEEeCCe
Confidence 4566666777778889999999999999999999999999 9999888765543
No 117
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=32.93 E-value=81 Score=26.38 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=39.0
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcce
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (739)
.+=|+.|+-++..-+.-|+++|++.||-....++-.|..+.-.|.++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl 55 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGL 55 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCc
Confidence 44589999999888999999999999999999999998886323333
No 118
>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=32.89 E-value=1.1e+02 Score=28.67 Aligned_cols=51 Identities=16% Similarity=0.086 Sum_probs=40.8
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHh----CCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t----~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+|..+..|+..+=+.+..|..||.+.+ ++....+...|.-|. +.+++.+..
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~~k 56 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTTEK 56 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceeeec
Confidence 466778888766567789999977765 788999999999999 888887643
No 119
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=32.17 E-value=79 Score=29.74 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=36.3
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
|..+.+..+..++.+|++.++++...+.+.|..|. +.+++.+.
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~~ 55 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIYE 55 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEEe
Confidence 44455667788999999999999999999999999 77887753
No 120
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=32.06 E-value=1e+02 Score=23.28 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
-|+++-++.+ . .|+.+|+..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~-~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRE-S--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhh-c--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 3444444443 2 79999999999999999998865
No 121
>PRK06474 hypothetical protein; Provisional
Probab=31.90 E-value=1.2e+02 Score=30.00 Aligned_cols=53 Identities=11% Similarity=0.199 Sum_probs=41.4
Q ss_pred EEEcHHHHHHHHHhcCCC-CCCHHHHHHHh-CCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 634 LAVSLFQTVVLMLFNDAQ-KLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 634 l~vs~~Qa~ILllFN~~~-~ls~~eI~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+-.++.-..||-.+-..+ .+|..||.+.+ +++...+-++|.-|. +.+++...+
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 334556666775554444 49999999999 799999999999999 888888644
No 122
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=31.87 E-value=79 Score=25.86 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=30.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 652 ~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
.+|-++|++.+|++...+.+.|.-|. +.+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 48999999999999999999999999 8888875
No 123
>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=31.70 E-value=99 Score=27.72 Aligned_cols=57 Identities=18% Similarity=0.325 Sum_probs=41.3
Q ss_pred HHHHHhcC-CCCCCHHHHHHHh-----CCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 004654 642 VVLMLFND-AQKLSFQDIKDAT-----GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (739)
Q Consensus 642 ~ILllFN~-~~~ls~~eI~~~t-----~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~ 703 (739)
.||-.+.+ ...+|.+||.+.+ +++...+-|+|..|. ..+++.+...+. ....|..|.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~--~~Gli~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLE--EAGLVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHH--hCCCEEEEEeCC---CceEEEeCC
Confidence 35544444 4679999999998 689999999999999 888888743211 124566664
No 124
>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=30.84 E-value=68 Score=27.76 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=31.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
...++.-++.....+++++|++.++++.+++...+..++
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I 85 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLI 85 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHH
Confidence 334444555577899999999999999999999999998
No 125
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=30.62 E-value=82 Score=26.94 Aligned_cols=34 Identities=6% Similarity=0.165 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
|+.|+-...+ ..+|+.+|++.+|++...+.+.|.
T Consensus 8 ~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 8 VLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 5677777788 899999999999999999999885
No 126
>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=30.58 E-value=1.1e+02 Score=22.22 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=27.9
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhh
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL 676 (739)
+..|..++.++- .+.++..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444444432 245899999999999999998887654
No 127
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=30.09 E-value=1.1e+02 Score=26.65 Aligned_cols=40 Identities=15% Similarity=0.414 Sum_probs=26.3
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceee
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (739)
+..+..+.+. ++..|.+.||||.-.++.+|.+|. ...|-+
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~--~~~I~~ 52 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALP--ELGIEC 52 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGG--GGT-EE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhh--cCCeEE
Confidence 3344555556 999999999999999999999998 544433
No 128
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=29.76 E-value=1.3e+02 Score=34.04 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=35.9
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 647 FN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
+...+.+|.+||++.++++...+++.|..|. +.+++.+..
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~~~ 344 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRRGE 344 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEecC
Confidence 5667799999999999999999999999999 999998643
No 129
>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=29.65 E-value=2.1e+02 Score=24.64 Aligned_cols=55 Identities=9% Similarity=0.198 Sum_probs=39.4
Q ss_pred HHHHH-HHHHHHHHHHhc-CCCCCcHHHHHHHHHhhhccCchhHHHHHHHHHHHHHH
Q 004654 105 EDTWA-KLKLAIKAIFLK-QPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHI 159 (739)
Q Consensus 105 e~~W~-~L~~aI~~I~~~-~~~~~s~e~LY~~Vy~lC~~k~~~~LY~~L~~~i~~~l 159 (739)
+.+|. .++..+..+... ....+++++|+..|.-.++....+.+...+-..+.+++
T Consensus 29 e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 29 ECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 56776 677777777665 45578999999999988888777777766666666654
No 130
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=29.62 E-value=74 Score=29.45 Aligned_cols=50 Identities=10% Similarity=0.133 Sum_probs=39.9
Q ss_pred EEcHHHHHHHHH--hc--------CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 635 AVSLFQTVVLML--FN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 635 ~vs~~Qa~ILll--FN--------~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
.+-.++-.+++. -| ..-+.+.++|+..++-+.+.++.+|..|. +.+++..
T Consensus 26 ~~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~ 85 (121)
T PF09681_consen 26 YTVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEI 85 (121)
T ss_pred eHHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 344555555555 33 44589999999999999999999999999 9998876
No 131
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.60 E-value=63 Score=24.22 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=22.0
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
++.++.+ .+|..+|++.+|++...+.+-+.-+.
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4445544 79999999999999999998887765
No 132
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=29.33 E-value=8.2e+02 Score=27.13 Aligned_cols=258 Identities=13% Similarity=0.204 Sum_probs=128.7
Q ss_pred HHhhhccCchhHHHHHHHHHHHHHHHHHHHhhhcC-----CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcc
Q 004654 135 VNDLCLHKMGGNLYQRIEKECEEHISAAIRSLVGQ-----SPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQT 209 (739)
Q Consensus 135 Vy~lC~~k~~~~LY~~L~~~i~~~l~~~~~~l~~~-----~~d~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~ 209 (739)
|-+-|-..-|..+.+.|...+.-.|......+... ......|-..+...|.-...++.+|..+--.++
T Consensus 70 i~~e~~~~p~~~~~q~lv~QiKlrv~~~r~~~k~~~l~qy~~~r~~~~~~F~~i~~~l~n~~~lL~k~~epf~------- 142 (392)
T PF07340_consen 70 IINECDDNPGKDVLQELVKQIKLRVARNRTEIKEQMLKQYNQIRMVFIGKFNDIQGGLQNAIDLLNKVMEPFE------- 142 (392)
T ss_pred HHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc-------
Confidence 34446666666655555555544444433332211 111257888999999999999998887633332
Q ss_pred cccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHH-----hcCCcC------------C---hHHHHHHHHHhhhh
Q 004654 210 PNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERE-----RLGEAV------------D---RTLLNHLLKMFTAL 269 (739)
Q Consensus 210 ~~~~sI~~lgl~lFr~~v~~~~~l~~~l~~~ll~lI~~e-----R~g~~i------------d---~~llk~ii~ml~~L 269 (739)
....|..++..+|-++++. |..+++...++-++.+.. +-+..+ + ..-+|.+..+...+
T Consensus 143 -dmK~I~~t~~~~~~nY~vp-p~~~ekwm~clK~l~d~av~~s~kle~alk~Kv~~kkddL~~k~~Yt~~Ky~e~~mk~~ 220 (392)
T PF07340_consen 143 -DMKCILQTMNDMYENYVVP-PDKQEKWMACLKELADVAVNASKKLEKALKEKVQQKKDDLKRKCTYTCLKYIEMFMKNL 220 (392)
T ss_pred -ccccHHHHHHHHccCCcCC-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHccC
Confidence 2456777777777777763 445666666655554321 001100 0 01122222222222
Q ss_pred ccchhhhHHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHhhhcCcCcHHHHHHHHHHHHHHHHHHHHHH
Q 004654 270 GIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILD 349 (739)
Q Consensus 270 ~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~~l~~~l~~~LI~~~~~~ll~ 349 (739)
+.=+ -..-.+++..|.+...+- ....+..|-..+-..|++|.+-+..-++ .-...++.
T Consensus 221 ~~PK---ttn~~sQA~~fL~nlp~~--d~d~v~~~g~~iik~LD~Eq~~Vl~~id-----------------~~f~~ll~ 278 (392)
T PF07340_consen 221 CMPK---TTNGQSQAKAFLRNLPQC--DPDEVNEYGQKIIKTLDKEQKEVLFHID-----------------NVFMDLLT 278 (392)
T ss_pred CCCC---CcccHHHHHHHHhccccC--CHHHHHHHHHHHHHHhhhhHHHHHHHHH-----------------HHHHHHHH
Confidence 2100 001122333333332210 0011334444555555555543321111 10122444
Q ss_pred HHHHhhhccCChHHHHHHHHhhcccchHHHHHHHHHHHHHHhhhhhhcCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 004654 350 KGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSF 424 (739)
Q Consensus 350 ~gl~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~~yI~~~g~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F 424 (739)
++...+..+.+...=..|++.+..+..+..+.+.+.-||..+...++....+ ...=+-+-.+..|+..|+.++|
T Consensus 279 ~~~~~~~~E~k~~~D~~mm~my~~Itq~s~~~~vL~~fIleET~~ii~~~~~-~t~deiv~~M~~Ki~~I~~e~~ 352 (392)
T PF07340_consen 279 TCVKAMYKEGKVKNDECMMSMYAPITQLSEFVNVLSAFILEETVVIIAKNPN-ITKDEIVKIMKPKIRAIVNEMF 352 (392)
T ss_pred HHHHHHHHhcccchHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-CChHHHHHHHHHHHHHHHHHHH
Confidence 5555565555444444566666666778899999999999887766642111 1111222345566666766665
No 133
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=29.09 E-value=1.1e+02 Score=30.49 Aligned_cols=45 Identities=13% Similarity=0.154 Sum_probs=38.2
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
++.-.+.++..|..+|+..+||+..++.|+|-+|. +.+.+...|.
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~~~ 62 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMSDS 62 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecCCC
Confidence 55666778899999999999999999999999999 7777766543
No 134
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=28.98 E-value=76 Score=35.99 Aligned_cols=31 Identities=29% Similarity=0.452 Sum_probs=27.4
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 647 FN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
.+....+|+++|++.|||..+++..+|++|-
T Consensus 369 ~~~~~~~si~~is~~T~i~~~Dii~tL~~l~ 399 (450)
T PLN00104 369 KKHKGNISIKELSDMTAIKAEDIVSTLQSLN 399 (450)
T ss_pred HhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 3445689999999999999999999999985
No 135
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=28.88 E-value=1.3e+02 Score=25.60 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
.-.+|-+.-...++|..+|+..+|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 33456667778899999999999999999999998875
No 136
>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=28.60 E-value=95 Score=24.20 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=31.0
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
|.-+.-||.++..+ .+..||++..|++...++.++..+.
T Consensus 5 T~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHH
Confidence 45566777777654 8999999999999999999998876
No 137
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=28.50 E-value=77 Score=33.11 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=36.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
=|..|+-+.+.++.+++.||++.+|+++..++|=|..|.
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 467889999999999999999999999999999999887
No 138
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=28.45 E-value=88 Score=29.49 Aligned_cols=38 Identities=16% Similarity=0.268 Sum_probs=28.5
Q ss_pred EcHHHHHHHHH-hcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 636 VSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 636 vs~~Qa~ILll-FN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
+|.-|..|+.+ |- +.++++||++.+||+...++..+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45556666655 43 5699999999999999988877543
No 139
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=28.33 E-value=90 Score=32.84 Aligned_cols=42 Identities=12% Similarity=0.319 Sum_probs=35.7
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
||++.-+ ++.|++||...++++...+..+|.-|. +.+++.++
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 4555544 789999999999999999999999999 88888874
No 140
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=27.61 E-value=1.1e+02 Score=29.67 Aligned_cols=45 Identities=13% Similarity=0.255 Sum_probs=38.4
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~ 689 (739)
|..++.+.......+|++.++++...+...|+-|. +.+++...|.
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~y 59 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEPY 59 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEecC
Confidence 44555577789999999999999999999999999 8888887664
No 141
>PHA02943 hypothetical protein; Provisional
Probab=27.12 E-value=97 Score=29.79 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=39.5
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~ 703 (739)
||-.+ ..+..|..||++.+|++..+.+-+|.-|. +-+.+.+..-| .-..+.+|+
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~~G----~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVEIG----RAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEeec----ceEEEEECh
Confidence 34444 56678899999999999999999999998 77777665433 233455554
No 142
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=27.03 E-value=1e+02 Score=26.02 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=29.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCccee
Q 004654 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (739)
Q Consensus 649 ~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (739)
....+++++|++.++++.+++.+.+..++ ..+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l 54 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCe
Confidence 35789999999999999999999999998 44444
No 143
>smart00753 PAM PCI/PINT associated module.
Probab=27.03 E-value=1e+02 Score=26.02 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=29.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCccee
Q 004654 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (739)
Q Consensus 649 ~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (739)
....+++++|++.++++.+++.+.+..++ ..+.|
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i--~~~~l 54 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAI--RDGEI 54 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHH--HCCCe
Confidence 35789999999999999999999999998 44444
No 144
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=26.99 E-value=1.7e+02 Score=24.89 Aligned_cols=47 Identities=21% Similarity=0.270 Sum_probs=35.7
Q ss_pred HHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCCCC
Q 004654 644 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (739)
Q Consensus 644 LllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~ 690 (739)
++.-++.+.+|=++|++.+|++...+-++++.|-.-.+.|.....+|
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kG 57 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKG 57 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCc
Confidence 34455667899999999999999999999999983335566544334
No 145
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=87 Score=30.20 Aligned_cols=33 Identities=15% Similarity=0.430 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.+++|.+-+ .++++||++.+|++...++..|.
T Consensus 125 r~i~~l~~~~--~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 125 KTVLVLYYYE--QYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHH
Confidence 3444454433 58999999999999988877654
No 146
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.93 E-value=91 Score=30.36 Aligned_cols=37 Identities=11% Similarity=0.149 Sum_probs=27.2
Q ss_pred EcHHHHHHHHH-hcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 636 VSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 636 vs~~Qa~ILll-FN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
++.-|-.|+.+ +- +++|++||++.+|++...++..|.
T Consensus 128 Lp~~~R~v~~L~~~--~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMATL--DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45545555544 43 569999999999999998887664
No 147
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.62 E-value=88 Score=29.63 Aligned_cols=37 Identities=24% Similarity=0.189 Sum_probs=25.7
Q ss_pred EcHHHHH-HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 636 VSLFQTV-VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 636 vs~~Qa~-ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
++.-|-. +.|.+- +.+|++||++.+|++...++..|.
T Consensus 107 Lp~~~r~v~~l~~~--~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 107 LPENYRDVVLAHYL--EEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CCHHHHHHHHHHHH--hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3443333 334443 459999999999999998876654
No 148
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=25.84 E-value=1e+02 Score=29.92 Aligned_cols=24 Identities=17% Similarity=0.415 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.+|++||++.+|++...++..|.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 459999999999999998887764
No 149
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.79 E-value=99 Score=29.70 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.++.|.+- +.+|++||++.+|++...++..|.
T Consensus 124 r~v~~L~~~--eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 124 RAAFLMSQL--EGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 444444443 469999999999999988776653
No 150
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=25.67 E-value=1e+02 Score=22.31 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 650 AQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 650 ~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
...+++++|++..|++..-+.+..+...
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 4579999999999999999999887654
No 151
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.57 E-value=1.6e+02 Score=27.50 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
.+.+-|+-+--+++.+|+.|+...||++-..+++.+.-|+ -.+-|...
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLV--a~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELV--ARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCCeEeC
Confidence 3566778888888999999999999999999999999998 54445443
No 152
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=25.48 E-value=1.2e+02 Score=31.18 Aligned_cols=43 Identities=23% Similarity=0.324 Sum_probs=35.7
Q ss_pred HHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 643 ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
.+-.-++...+|..||++.++++...+.+.|..|. +.+++.+.
T Consensus 12 llg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~ 54 (217)
T PRK14165 12 LLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRT 54 (217)
T ss_pred HHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 34444555679999999999999999999999999 77777764
No 153
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=25.36 E-value=97 Score=30.36 Aligned_cols=51 Identities=22% Similarity=0.366 Sum_probs=37.9
Q ss_pred cCCCceEEeecCCceEEEEEEecCceEEEEEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 606 KYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 606 k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
+++.++|+|.++|.- -|.++-. +.-..|+++|++.+|.++.+++++|+.=.
T Consensus 36 ~~~~~~lTWvdSLav-------------------AAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 36 KDPYERLTWVDSLAV-------------------AAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred hCcccccchhhHHHH-------------------HHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 457899999886532 1222322 34479999999999999999999998655
No 154
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=25.19 E-value=4.2e+02 Score=28.83 Aligned_cols=83 Identities=13% Similarity=0.286 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhhhccCChHHHHHHHHhhccc----chHHHHHHHHHHHHHHhhhhhhcCcc-------hhhHHHHHHHHH
Q 004654 344 ISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDEE-------KDKDMVSSLLEF 412 (739)
Q Consensus 344 ~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yI~~~g~~iv~~~~-------~~~~~V~~Ll~l 412 (739)
+..++.+.|..-+++++...+.+.++||-.+ .|++....-+++.|......+..... .+--++..|..+
T Consensus 8 L~~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~~~~~~~~~a~~lt~L 87 (324)
T smart00762 8 LTELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASDDTRAAVFYADTLTHL 87 (324)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccccccccchHHHHHHHH
Confidence 3445556788888899999999999999876 46666666666666555544443211 122466666666
Q ss_pred HHHHHH-------HHHHhcCC
Q 004654 413 KASLDT-------IWEQSFSK 426 (739)
Q Consensus 413 ~~~~~~-------ii~~~F~~ 426 (739)
++.+-. +|..+|+.
T Consensus 88 fe~ia~ii~~h~~~I~~~yG~ 108 (324)
T smart00762 88 FENVATIIEQHQPVIEKYYGP 108 (324)
T ss_pred HHHHHHHHHhccHHHHHHcCc
Confidence 655544 45566663
No 155
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=24.97 E-value=1.2e+02 Score=25.38 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=31.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 641 a~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
+-||.... .+..++.+|+..+|++...+.+.|..|. +.+++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~--~~gLI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELE--EKGLIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHH--HTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCcCeeC
Confidence 34555554 6678999999999999999999999999 7777754
No 156
>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=24.74 E-value=1.1e+02 Score=25.59 Aligned_cols=49 Identities=18% Similarity=0.249 Sum_probs=41.5
Q ss_pred HHHHHHHHHhcCC--CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeCC
Q 004654 638 LFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (739)
Q Consensus 638 ~~Qa~ILllFN~~--~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~p 688 (739)
..|.++|...-.. .+++-.||...+|++...+-..++.|. +.+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 4677888777653 578999999999999999999999999 888888755
No 157
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.35 E-value=86 Score=29.90 Aligned_cols=30 Identities=27% Similarity=0.348 Sum_probs=27.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHhhhhhc
Q 004654 649 DAQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (739)
Q Consensus 649 ~~~~ls~~eI~~~t~i~~~~l~~~L~sL~~ 678 (739)
.++.+|-++|++.+||+..++++.|..|.-
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 345799999999999999999999999983
No 158
>PLN03239 histone acetyltransferase; Provisional
Probab=24.10 E-value=1e+02 Score=33.72 Aligned_cols=40 Identities=23% Similarity=0.387 Sum_probs=30.4
Q ss_pred HHHHHHHHHh-cCC---CCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 638 LFQTVVLMLF-NDA---QKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 638 ~~Qa~ILllF-N~~---~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
-+...|+-.+ +.. ..+|+++|+..|||..+++..+|+.|-
T Consensus 266 YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~ 309 (351)
T PLN03239 266 YWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLG 309 (351)
T ss_pred HHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 3444555433 322 469999999999999999999999985
No 159
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=24.07 E-value=1.1e+02 Score=30.70 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
|.+++|.| .+.++++||++.+|++...++..|.
T Consensus 144 r~v~~L~~--~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 144 RAAVVLCD--IEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34444554 3469999999999999887776654
No 160
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=23.90 E-value=1.5e+02 Score=22.54 Aligned_cols=44 Identities=27% Similarity=0.505 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHhhhhhc-CCcceeeeCCCCCCCCCCCeEEE
Q 004654 650 AQKLSFQDIKDATGIEDKELRRTLQSLAC-GKVRVLQKLPKGRDVEDDDSFVF 701 (739)
Q Consensus 650 ~~~ls~~eI~~~t~i~~~~l~~~L~sL~~-~k~~iL~k~p~~~~v~~~d~f~~ 701 (739)
.+.+..+|-+..-.++.++.++.|+|++. |.+-+|.- ++|.|.+
T Consensus 15 regldwqeaatraslsleetrkllqsmaaagqvtllrv--------endlyai 59 (61)
T PF09105_consen 15 REGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRV--------ENDLYAI 59 (61)
T ss_dssp TT-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEEE--------TTEEEEE
T ss_pred HccCcHHHHHHHhhccHHHHHHHHHHHHhcCceEEEEe--------cccceec
Confidence 46789999999999999999999999997 56677764 4666655
No 161
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=23.61 E-value=1e+02 Score=28.50 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=38.8
Q ss_pred cHHHHHHHHHhcCC--------CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeee
Q 004654 637 SLFQTVVLMLFNDA--------QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (739)
Q Consensus 637 s~~Qa~ILllFN~~--------~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (739)
..+.-..|+..|.. -+.+.++|+..++-+.+.++.+|.-|. +.+++..
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~ 83 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEK 83 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 34555555555543 479999999999999999999999999 9988876
No 162
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.59 E-value=1.2e+02 Score=30.89 Aligned_cols=37 Identities=19% Similarity=0.265 Sum_probs=26.5
Q ss_pred cHHHHHH-HHHh--cCCCCCCHHHHHHHhCCCHHHHHHHh
Q 004654 637 SLFQTVV-LMLF--NDAQKLSFQDIKDATGIEDKELRRTL 673 (739)
Q Consensus 637 s~~Qa~I-LllF--N~~~~ls~~eI~~~t~i~~~~l~~~L 673 (739)
+.-|-.| .|.| +..+.+|++||++.+|++...++..+
T Consensus 180 p~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~ 219 (234)
T PRK08301 180 SDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3333344 4444 34578999999999999999887665
No 163
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.46 E-value=1.2e+02 Score=28.68 Aligned_cols=24 Identities=8% Similarity=0.263 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.+|++||++.+|++...++..|.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999988876653
No 164
>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=23.41 E-value=1.1e+02 Score=23.93 Aligned_cols=30 Identities=13% Similarity=0.485 Sum_probs=24.3
Q ss_pred HhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 646 LFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 646 lFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
.|+.--..|.+||++.+||+...+-.+|..
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 355455899999999999999888777764
No 165
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=23.36 E-value=98 Score=29.75 Aligned_cols=56 Identities=21% Similarity=0.281 Sum_probs=46.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCC-------CHHH-------HHHHhhhhhcCCcceeeeCCCCCCCCCC
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGI-------EDKE-------LRRTLQSLACGKVRVLQKLPKGRDVEDD 696 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i-------~~~~-------l~~~L~sL~~~k~~iL~k~p~~~~v~~~ 696 (739)
=.|+||-..-....+.+..++..+|. |... ++..|+.|- +.+++.+.|+|+-+++.
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE--~~glVek~~~GR~lT~~ 123 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLE--KAGLVEKTKKGRVITPK 123 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHH--HCCCeeeCCCCCEeCHH
Confidence 35778877766779999999999999 5555 999999999 99999999988777643
No 166
>PRK00118 putative DNA-binding protein; Validated
Probab=23.22 E-value=1.4e+02 Score=26.92 Aligned_cols=25 Identities=8% Similarity=0.276 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
+..|+.||++.+|++...+.+.+..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3699999999999999888877653
No 167
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.47 E-value=2.5e+02 Score=28.07 Aligned_cols=111 Identities=16% Similarity=0.161 Sum_probs=60.1
Q ss_pred ChHHHHHHHHHHHHHhccCCCceEEeecCCceEEEEEE--ec-------CceEEEEEcHHHHHHHHHhcCCCCCCHHHHH
Q 004654 589 PHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAE--FP-------KGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 659 (739)
Q Consensus 589 P~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~--f~-------~~~~~l~vs~~Qa~ILllFN~~~~ls~~eI~ 659 (739)
|.++..+++....-|.....| +.-...=|.-.+..+ +. .....-..|...+-+|-..--+.++|-.||.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~~g--i~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDDRG--LKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCCCC--EEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 357899999999999866433 333222222222221 10 0111122333333344333334689999999
Q ss_pred HHhCCCHHHHHHHhhhhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 004654 660 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (739)
Q Consensus 660 ~~t~i~~~~l~~~L~sL~~~k~~iL~k~p~~~~v~~~d~f~~N~~F~ 706 (739)
+.+|++. ..++..|. ..+++..............|.++..|-
T Consensus 112 ~irGv~~---~~ii~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNS---DGALQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCH---HHHHHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999986 45566666 555555322111122445677777773
No 168
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.26 E-value=1.2e+02 Score=29.63 Aligned_cols=32 Identities=13% Similarity=0.209 Sum_probs=24.0
Q ss_pred HHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 642 ~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
++++.| .+.+|++||++.+|++...++..+..
T Consensus 141 i~~l~~--~~~~s~~eIA~~lgis~~tV~~~l~r 172 (182)
T PRK12537 141 CILHAY--VDGCSHAEIAQRLGAPLGTVKAWIKR 172 (182)
T ss_pred HHHHHH--HcCCCHHHHHHHHCCChhhHHHHHHH
Confidence 344544 34699999999999999888766543
No 169
>PRK04217 hypothetical protein; Provisional
Probab=22.22 E-value=1.5e+02 Score=27.06 Aligned_cols=39 Identities=21% Similarity=0.268 Sum_probs=26.4
Q ss_pred EcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 636 vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
++.-|..++.+. ..+.+|++||++.+|++...+.+.|..
T Consensus 43 Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 43 MTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444343322 224589999999999999888877653
No 170
>PHA02591 hypothetical protein; Provisional
Probab=22.15 E-value=1e+02 Score=26.11 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQS 675 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~s 675 (739)
..+|.++|++.+|++.+.+++.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3699999999999999999988875
No 171
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=22.08 E-value=83 Score=29.22 Aligned_cols=29 Identities=17% Similarity=0.283 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHH
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELR 670 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~ 670 (739)
+.++.|.+- +.+|++||++.+|++...++
T Consensus 113 r~v~~l~~~--~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 113 KKIIYMKFF--EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCcCHHhhc
Confidence 344444443 35899999999999987764
No 172
>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=21.66 E-value=86 Score=33.30 Aligned_cols=40 Identities=23% Similarity=0.383 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 638 ~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
-+--.|.-+|.++..|++.+|.+.|+-|+..|+.+|..++
T Consensus 216 eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa 255 (275)
T PF02270_consen 216 ELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA 255 (275)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445577899999999999999999999999999999987
No 173
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.53 E-value=1.2e+02 Score=30.16 Aligned_cols=38 Identities=24% Similarity=0.504 Sum_probs=32.1
Q ss_pred CCHHHHHHHh-CCCHHHHHHHhhhhhcCCcceeeeC--CCCCC
Q 004654 653 LSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL--PKGRD 692 (739)
Q Consensus 653 ls~~eI~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~--p~~~~ 692 (739)
-|-.+|++.+ ||++..|+++|..|+ ..+++.+. |.||-
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~Lv--eaGLI~rrDS~NgkR 111 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLV--EAGLIVRRDSPNGKR 111 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHH--HCCCeeeccCCCCCc
Confidence 4567899999 999999999999999 99999874 55543
No 174
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=21.31 E-value=72 Score=21.62 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=8.5
Q ss_pred ccChHHHHHHHHHH
Q 004654 487 IQGKDVFEAFYKKD 500 (739)
Q Consensus 487 l~~KD~Fe~~Y~k~ 500 (739)
+.+.|.|..||.++
T Consensus 3 is~~d~f~eFY~rl 16 (28)
T PF12108_consen 3 ISGGDPFSEFYERL 16 (28)
T ss_dssp --S--HHHHHHHHH
T ss_pred CCCCChHHHHHHHH
Confidence 45789999999865
No 175
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=21.17 E-value=1.4e+02 Score=30.59 Aligned_cols=35 Identities=14% Similarity=0.296 Sum_probs=25.8
Q ss_pred HHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLF--NDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllF--N~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.++.|.| ++.+++|++||++.+|++...++..+.
T Consensus 184 R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 184 KKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred HHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33444444 334689999999999999998877653
No 176
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=20.99 E-value=1.6e+02 Score=27.83 Aligned_cols=38 Identities=18% Similarity=0.091 Sum_probs=30.2
Q ss_pred EEcHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 635 ~vs~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
.++.-|..|+.++ ...+|.+||++.+|++...+.+.+.
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ 43 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEK 43 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3567788888886 4679999999999999887775443
No 177
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=20.85 E-value=1.4e+02 Score=31.15 Aligned_cols=33 Identities=15% Similarity=0.235 Sum_probs=24.7
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 640 Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.+++|.+- +.+|++||++.+|++...++..|.
T Consensus 167 R~v~~L~~~--eg~S~~EIA~~Lgis~~TVk~rl~ 199 (244)
T TIGR03001 167 RHLLRLHFV--DGLSMDRIGAMYQVHRSTVSRWVA 199 (244)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 444555544 459999999999999988776653
No 178
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=20.76 E-value=1.2e+02 Score=28.61 Aligned_cols=39 Identities=23% Similarity=0.240 Sum_probs=27.6
Q ss_pred cHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhh
Q 004654 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (739)
Q Consensus 637 s~~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL 676 (739)
+.-|-.|+.++- .+.+|++||++.+|++...++..+.--
T Consensus 112 ~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 112 PARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred CHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 444555553332 347999999999999998888776543
No 179
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.46 E-value=1.4e+02 Score=29.51 Aligned_cols=26 Identities=31% Similarity=0.602 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHhhhh
Q 004654 651 QKLSFQDIKDATGIEDKELRRTLQSL 676 (739)
Q Consensus 651 ~~ls~~eI~~~t~i~~~~l~~~L~sL 676 (739)
+++|++||++.+|+++..+++.|...
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999988754
No 180
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=20.45 E-value=1.5e+02 Score=22.03 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhhcCCCcchHHHHHHHh
Q 004654 430 FCNTIKDAFEYLINLRQNRPAELIAKFLD 458 (739)
Q Consensus 430 f~~~l~~afe~~iN~~~~~~~e~LA~y~D 458 (739)
+...+.+|+.+....++..+.++||.|+-
T Consensus 10 v~p~L~~gL~~l~~~rP~DPi~~La~~Ll 38 (42)
T PF05186_consen 10 VGPVLTEGLAELAKERPEDPIEFLAEYLL 38 (42)
T ss_dssp THHHHHHHHHHHHHH--SSHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCChHHHHHHHHH
Confidence 45567788888888888889999999974
No 181
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.34 E-value=1.5e+02 Score=29.97 Aligned_cols=44 Identities=20% Similarity=0.232 Sum_probs=35.4
Q ss_pred HHHHHhcCC-CCCCHHHHHHHhCCCHHHHHHHhhhhhcCCcceeeeC
Q 004654 642 VVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (739)
Q Consensus 642 ~ILllFN~~-~~ls~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (739)
-||-++-+. ...|.+||++.++|+...+++++..|. ..+.+...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~--~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCA--SRHLIIAE 210 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHH--hCCeEEEE
Confidence 456556543 268999999999999999999999999 77766653
No 182
>PRK13239 alkylmercury lyase; Provisional
Probab=20.18 E-value=1.7e+02 Score=29.67 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHhhhhh
Q 004654 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (739)
Q Consensus 639 ~Qa~ILllFN~~~~ls~~eI~~~t~i~~~~l~~~L~sL~ 677 (739)
+...||-++-++...|.++|++.+|.+.+++++.|+.|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 444566667788999999999999999999999999986
No 183
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.08 E-value=1.5e+02 Score=28.46 Aligned_cols=35 Identities=23% Similarity=0.282 Sum_probs=24.2
Q ss_pred cHHHHHHHHH-hcCCCCCCHHHHHHHhCCCHHHHHHHh
Q 004654 637 SLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTL 673 (739)
Q Consensus 637 s~~Qa~ILll-FN~~~~ls~~eI~~~t~i~~~~l~~~L 673 (739)
+.-|-.|+.+ +- +.+|++||++.+|++...++..|
T Consensus 120 ~~~~r~vl~L~~~--~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 120 SPEHRAVLVRSYY--RGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHH
Confidence 3334444433 32 46999999999999998886554
No 184
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.00 E-value=1.5e+02 Score=28.01 Aligned_cols=36 Identities=11% Similarity=0.080 Sum_probs=24.9
Q ss_pred cHHHHHHH-HHhcCCCCCCHHHHHHHhCCCHHHHHHHhh
Q 004654 637 SLFQTVVL-MLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (739)
Q Consensus 637 s~~Qa~IL-llFN~~~~ls~~eI~~~t~i~~~~l~~~L~ 674 (739)
+.-|-.|+ +.|- +.+|++||++.+|++...++..+.
T Consensus 111 ~~~~r~v~~l~~~--~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 111 PARTRYAFEMYRL--HGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34344444 3342 368999999999999988776643
Done!