Query 003648
Match_columns 805
No_of_seqs 255 out of 1018
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 03:23:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003648hhsearch_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 4E-135 9E-140 1101.7 47.7 649 147-803 2-656 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 5E-117 1E-121 1026.4 65.8 686 101-801 14-720 (725)
3 COG5647 Cullin, a subunit of E 100.0 6E-114 1E-118 957.2 60.2 687 98-798 14-763 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 5E-103 1E-107 814.3 51.6 657 102-802 10-722 (728)
5 PF00888 Cullin: Cullin family 100.0 8.8E-94 1.9E-98 847.7 60.2 576 108-706 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1.2E-83 2.5E-88 675.3 54.1 690 100-799 9-767 (777)
7 smart00182 CULLIN Cullin. 100.0 6.2E-34 1.3E-38 274.4 17.9 141 486-627 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 2.9E-25 6.4E-30 247.4 37.4 301 482-795 444-754 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.6 1.4E-16 3.1E-21 132.9 4.6 64 733-801 1-66 (68)
10 PF08539 HbrB: HbrB-like; Int 97.4 0.0023 5E-08 62.5 12.9 124 104-229 5-149 (158)
11 KOG2167 Cullins [Cell cycle co 96.9 0.0069 1.5E-07 68.9 11.0 310 104-438 110-456 (661)
12 TIGR01610 phage_O_Nterm phage 93.8 0.2 4.4E-06 44.7 6.8 66 633-706 20-93 (95)
13 PF09339 HTH_IclR: IclR helix- 93.2 0.13 2.9E-06 40.3 4.1 46 641-688 6-52 (52)
14 PF13412 HTH_24: Winged helix- 92.0 0.31 6.7E-06 37.4 4.8 46 637-684 2-47 (48)
15 PF12802 MarR_2: MarR family; 91.7 0.23 4.9E-06 40.1 3.9 51 636-688 3-55 (62)
16 PF02082 Rrf2: Transcriptional 91.7 0.5 1.1E-05 40.9 6.2 59 639-704 11-70 (83)
17 PF13463 HTH_27: Winged helix 89.7 0.5 1.1E-05 38.9 4.3 51 636-688 1-52 (68)
18 PF08220 HTH_DeoR: DeoR-like h 89.5 0.6 1.3E-05 37.4 4.4 46 640-687 2-47 (57)
19 PF01047 MarR: MarR family; I 89.2 0.3 6.6E-06 39.1 2.5 50 637-688 2-51 (59)
20 PF12840 HTH_20: Helix-turn-he 89.0 0.57 1.2E-05 38.0 4.0 51 637-689 9-59 (61)
21 TIGR02337 HpaR homoprotocatech 88.3 0.93 2E-05 41.9 5.5 52 635-688 25-76 (118)
22 PRK11512 DNA-binding transcrip 86.2 1.5 3.3E-05 42.1 5.8 52 635-688 37-88 (144)
23 PF01022 HTH_5: Bacterial regu 85.6 2 4.2E-05 32.9 5.0 43 640-685 4-46 (47)
24 smart00550 Zalpha Z-DNA-bindin 85.5 1.6 3.4E-05 36.4 4.7 48 639-688 7-56 (68)
25 TIGR01889 Staph_reg_Sar staphy 84.4 2.3 4.9E-05 38.9 5.8 52 635-688 22-77 (109)
26 smart00347 HTH_MARR helix_turn 83.7 2.1 4.5E-05 37.6 5.2 53 633-687 5-57 (101)
27 PF04492 Phage_rep_O: Bacterio 83.6 3.6 7.7E-05 37.1 6.5 61 636-706 30-98 (100)
28 smart00346 HTH_ICLR helix_turn 83.2 2.8 6.1E-05 36.5 5.7 46 641-688 8-54 (91)
29 smart00420 HTH_DEOR helix_turn 82.0 2.9 6.4E-05 32.0 4.8 46 641-688 3-48 (53)
30 PF04703 FaeA: FaeA-like prote 81.4 3 6.5E-05 34.1 4.7 56 643-702 5-61 (62)
31 PRK15090 DNA-binding transcrip 79.5 4.2 9.1E-05 43.2 6.5 46 641-688 17-62 (257)
32 PF01978 TrmB: Sugar-specific 79.0 2 4.3E-05 35.6 3.0 50 637-688 7-56 (68)
33 PHA00738 putative HTH transcri 77.6 5.3 0.00012 36.3 5.5 67 633-705 7-73 (108)
34 PRK10857 DNA-binding transcrip 77.3 7.3 0.00016 38.5 6.9 58 640-704 12-70 (164)
35 PF08279 HTH_11: HTH domain; 76.9 4.8 0.0001 31.6 4.6 33 645-677 8-40 (55)
36 PRK13777 transcriptional regul 76.7 5.4 0.00012 40.2 5.9 53 634-688 41-93 (185)
37 PRK03573 transcriptional regul 76.4 4.7 0.0001 38.6 5.3 53 634-688 27-80 (144)
38 PRK11920 rirA iron-responsive 76.0 8.3 0.00018 37.6 6.9 57 641-704 13-69 (153)
39 COG3355 Predicted transcriptio 75.6 6.9 0.00015 36.7 5.8 39 648-688 38-76 (126)
40 TIGR02010 IscR iron-sulfur clu 74.8 8.5 0.00018 36.6 6.5 44 641-686 13-57 (135)
41 TIGR03879 near_KaiC_dom probab 74.6 3.3 7.1E-05 35.0 3.1 42 643-686 23-64 (73)
42 cd00090 HTH_ARSR Arsenical Res 73.9 7.4 0.00016 31.8 5.3 48 637-687 6-53 (78)
43 PRK10141 DNA-binding transcrip 73.7 5.1 0.00011 37.3 4.5 56 642-703 20-75 (117)
44 smart00419 HTH_CRP helix_turn_ 73.4 8.1 0.00018 28.9 4.9 34 652-687 8-41 (48)
45 TIGR01884 cas_HTH CRISPR locus 73.3 5.4 0.00012 40.8 5.1 52 635-688 140-191 (203)
46 smart00345 HTH_GNTR helix_turn 72.5 7.3 0.00016 30.6 4.7 40 647-688 14-54 (60)
47 PF13601 HTH_34: Winged helix 72.3 3.1 6.8E-05 35.8 2.6 44 641-686 3-46 (80)
48 PRK10870 transcriptional repre 72.2 9.1 0.0002 38.2 6.3 51 636-688 53-105 (176)
49 KOG4552 Vitamin-D-receptor int 71.8 88 0.0019 31.7 12.6 114 332-464 24-142 (272)
50 PF05584 Sulfolobus_pRN: Sulfo 71.3 10 0.00023 31.9 5.3 41 643-686 10-50 (72)
51 TIGR00738 rrf2_super rrf2 fami 69.9 11 0.00024 35.3 6.1 46 640-687 12-58 (132)
52 PF08318 COG4: COG4 transport 69.7 1.1E+02 0.0024 33.7 14.8 160 343-509 7-213 (331)
53 PF05732 RepL: Firmicute plasm 69.6 6.3 0.00014 39.0 4.4 52 652-712 75-126 (165)
54 COG1414 IclR Transcriptional r 69.0 11 0.00023 39.9 6.3 46 641-688 7-53 (246)
55 PRK11569 transcriptional repre 68.5 10 0.00022 40.6 6.2 46 641-688 31-77 (274)
56 PRK10163 DNA-binding transcrip 68.3 11 0.00025 40.3 6.4 46 641-688 28-74 (271)
57 PRK09834 DNA-binding transcrip 67.3 11 0.00024 40.1 6.1 47 641-689 14-61 (263)
58 smart00418 HTH_ARSR helix_turn 67.2 11 0.00024 29.7 4.8 36 650-687 8-43 (66)
59 PF13404 HTH_AsnC-type: AsnC-t 67.1 9 0.0002 28.7 3.7 35 642-676 7-41 (42)
60 smart00344 HTH_ASNC helix_turn 65.9 11 0.00023 34.1 4.9 45 639-685 4-48 (108)
61 TIGR02431 pcaR_pcaU beta-ketoa 65.2 14 0.00031 38.9 6.3 44 641-686 12-56 (248)
62 PF09012 FeoC: FeoC like trans 64.9 6.2 0.00013 32.8 2.8 46 744-800 4-49 (69)
63 COG1959 Predicted transcriptio 64.8 17 0.00036 35.4 6.2 59 639-704 11-70 (150)
64 TIGR02944 suf_reg_Xantho FeS a 63.7 17 0.00037 34.1 6.0 44 642-687 13-58 (130)
65 PF10771 DUF2582: Protein of u 63.6 12 0.00026 30.9 4.2 45 641-685 11-56 (65)
66 PF13730 HTH_36: Helix-turn-he 63.2 16 0.00034 28.6 4.8 28 654-683 27-54 (55)
67 PF08221 HTH_9: RNA polymerase 62.9 9.9 0.00021 31.0 3.6 35 649-685 24-58 (62)
68 COG1846 MarR Transcriptional r 61.8 16 0.00035 33.0 5.4 51 636-688 20-70 (126)
69 cd00092 HTH_CRP helix_turn_hel 60.5 16 0.00034 29.5 4.5 36 651-688 24-59 (67)
70 PF01325 Fe_dep_repress: Iron 59.3 21 0.00046 28.9 4.9 44 643-688 13-56 (60)
71 PF08280 HTH_Mga: M protein tr 58.8 13 0.00028 29.9 3.6 38 640-677 7-44 (59)
72 PRK04172 pheS phenylalanyl-tRN 58.1 80 0.0017 37.0 11.4 50 635-686 3-52 (489)
73 PF08784 RPA_C: Replication pr 57.7 15 0.00033 32.9 4.3 43 635-677 44-90 (102)
74 PRK11014 transcriptional repre 56.7 32 0.0007 32.8 6.6 40 647-688 20-59 (141)
75 PF14394 DUF4423: Domain of un 56.7 28 0.00061 34.6 6.3 55 632-688 18-75 (171)
76 PF09763 Sec3_C: Exocyst compl 53.5 5.1E+02 0.011 31.8 20.7 52 375-426 646-701 (701)
77 cd07377 WHTH_GntR Winged helix 52.5 29 0.00064 27.6 4.8 39 648-688 20-59 (66)
78 PF02002 TFIIE_alpha: TFIIE al 52.0 11 0.00023 34.1 2.3 44 640-685 15-58 (105)
79 COG2345 Predicted transcriptio 51.9 22 0.00047 36.8 4.7 123 641-773 14-149 (218)
80 PRK10434 srlR DNA-bindng trans 51.5 20 0.00043 38.1 4.6 48 639-688 6-53 (256)
81 PF06784 UPF0240: Uncharacteri 50.5 27 0.00058 35.1 5.0 68 609-683 96-165 (179)
82 PRK11169 leucine-responsive tr 49.9 26 0.00056 34.5 4.8 49 636-686 12-60 (164)
83 PF08281 Sigma70_r4_2: Sigma-7 49.3 30 0.00066 26.8 4.3 24 651-674 25-48 (54)
84 PRK11179 DNA-binding transcrip 48.8 30 0.00065 33.6 5.1 48 636-685 7-54 (153)
85 PF04545 Sigma70_r4: Sigma-70, 48.5 41 0.0009 25.7 4.8 34 640-675 10-43 (50)
86 PRK13509 transcriptional repre 47.0 31 0.00067 36.5 5.2 50 639-690 6-55 (251)
87 COG4189 Predicted transcriptio 47.0 30 0.00066 35.7 4.7 49 637-687 22-70 (308)
88 COG4190 Predicted transcriptio 46.2 53 0.0011 31.0 5.7 63 642-706 68-133 (144)
89 TIGR02702 SufR_cyano iron-sulf 45.8 48 0.001 33.8 6.2 44 642-687 5-48 (203)
90 PF01726 LexA_DNA_bind: LexA D 45.7 28 0.00061 28.7 3.6 51 636-688 4-60 (65)
91 PRK06266 transcription initiat 44.9 31 0.00068 34.5 4.6 44 640-685 24-67 (178)
92 TIGR00373 conserved hypothetic 44.9 36 0.00077 33.4 4.9 43 641-685 17-59 (158)
93 PF09012 FeoC: FeoC like trans 44.5 30 0.00065 28.7 3.7 41 644-686 6-46 (69)
94 PRK00215 LexA repressor; Valid 44.3 47 0.001 33.8 5.9 52 636-689 2-59 (205)
95 COG1349 GlpR Transcriptional r 44.2 28 0.00062 36.9 4.4 49 640-690 7-55 (253)
96 COG1522 Lrp Transcriptional re 43.7 32 0.00069 33.0 4.3 48 637-686 7-54 (154)
97 PF01853 MOZ_SAS: MOZ/SAS fami 42.4 24 0.00053 35.5 3.3 26 652-677 150-175 (188)
98 PF01638 HxlR: HxlR-like helix 41.6 42 0.0009 29.4 4.4 45 640-687 7-52 (90)
99 PRK09802 DNA-binding transcrip 39.8 40 0.00086 36.1 4.7 49 638-688 17-65 (269)
100 PRK10906 DNA-binding transcrip 39.3 43 0.00092 35.5 4.8 49 639-689 6-54 (252)
101 PRK04424 fatty acid biosynthes 39.1 28 0.00061 35.0 3.2 46 639-686 8-53 (185)
102 PRK10411 DNA-binding transcrip 38.4 50 0.0011 34.7 5.1 46 640-687 6-51 (240)
103 TIGR00498 lexA SOS regulatory 37.4 38 0.00081 34.3 3.9 51 636-688 4-60 (199)
104 PF00325 Crp: Bacterial regula 37.4 44 0.00096 23.6 3.0 29 653-683 3-31 (32)
105 cd06170 LuxR_C_like C-terminal 36.4 74 0.0016 24.3 4.7 37 639-677 4-40 (57)
106 PF01726 LexA_DNA_bind: LexA D 35.5 81 0.0018 26.0 4.8 58 735-801 5-62 (65)
107 smart00421 HTH_LUXR helix_turn 35.5 78 0.0017 24.0 4.7 39 637-677 5-43 (58)
108 COG4742 Predicted transcriptio 35.2 61 0.0013 34.5 5.0 42 643-687 18-59 (260)
109 PF03444 HrcA_DNA-bdg: Winged 34.9 99 0.0021 26.6 5.3 49 638-688 9-57 (78)
110 PRK11050 manganese transport r 34.3 87 0.0019 30.4 5.7 44 642-687 41-84 (152)
111 KOG2747 Histone acetyltransfer 33.5 50 0.0011 37.0 4.3 67 611-677 281-354 (396)
112 PF10007 DUF2250: Uncharacteri 32.3 87 0.0019 27.8 4.7 53 634-688 3-55 (92)
113 PF02796 HTH_7: Helix-turn-hel 31.8 73 0.0016 23.9 3.7 30 643-674 14-43 (45)
114 PLN03238 probable histone acet 31.4 72 0.0016 34.3 4.8 39 639-677 209-248 (290)
115 smart00550 Zalpha Z-DNA-bindin 30.9 1.3E+02 0.0027 24.9 5.3 55 740-805 6-62 (68)
116 PRK03902 manganese transport t 30.4 92 0.002 29.6 5.1 43 642-686 12-54 (142)
117 PHA02943 hypothetical protein; 30.3 84 0.0018 30.5 4.6 43 643-688 16-58 (165)
118 TIGR02844 spore_III_D sporulat 30.1 84 0.0018 27.2 4.2 34 639-673 7-40 (80)
119 PF13542 HTH_Tnp_ISL3: Helix-t 29.8 1.2E+02 0.0026 23.1 4.8 35 639-675 16-50 (52)
120 PF13412 HTH_24: Winged helix- 29.8 1.2E+02 0.0027 22.7 4.8 45 741-796 4-48 (48)
121 PF04182 B-block_TFIIIC: B-blo 29.5 83 0.0018 26.6 4.1 49 638-688 2-52 (75)
122 PF10163 EnY2: Transcription f 29.3 2.1E+02 0.0046 24.9 6.7 55 105-159 29-85 (86)
123 PF11994 DUF3489: Protein of u 28.9 1.1E+02 0.0023 26.0 4.4 47 637-683 9-55 (72)
124 PF00392 GntR: Bacterial regul 28.8 70 0.0015 25.9 3.4 37 650-688 21-58 (64)
125 PRK06474 hypothetical protein; 28.6 1.5E+02 0.0033 29.6 6.5 52 635-688 8-61 (178)
126 COG2512 Predicted membrane-ass 28.5 75 0.0016 33.9 4.4 51 638-690 196-246 (258)
127 PF01399 PCI: PCI domain; Int 28.1 85 0.0018 27.5 4.2 39 639-677 47-85 (105)
128 cd06171 Sigma70_r4 Sigma70, re 26.5 1.4E+02 0.003 22.0 4.6 39 637-676 12-50 (55)
129 COG1321 TroR Mn-dependent tran 26.4 1.2E+02 0.0026 29.7 5.1 45 642-688 14-58 (154)
130 cd07153 Fur_like Ferric uptake 26.3 1.5E+02 0.0032 26.9 5.5 57 642-703 5-67 (116)
131 COG1654 BirA Biotin operon rep 26.2 1.9E+02 0.0042 24.9 5.7 34 644-677 11-44 (79)
132 PRK10681 DNA-binding transcrip 25.9 94 0.002 32.9 4.7 39 639-677 8-46 (252)
133 PF12324 HTH_15: Helix-turn-he 25.9 1.6E+02 0.0035 25.3 5.0 38 640-677 26-63 (77)
134 PF01047 MarR: MarR family; I 25.6 75 0.0016 24.9 3.0 49 742-801 5-53 (59)
135 PF08220 HTH_DeoR: DeoR-like h 25.6 98 0.0021 24.6 3.6 44 743-797 3-46 (57)
136 PLN00104 MYST -like histone ac 25.3 98 0.0021 35.5 4.8 38 640-677 361-399 (450)
137 PF09681 Phage_rep_org_N: N-te 25.3 81 0.0017 29.5 3.5 50 636-687 27-86 (121)
138 smart00753 PAM PCI/PINT associ 24.6 1.3E+02 0.0028 25.7 4.6 34 649-684 21-54 (88)
139 smart00088 PINT motif in prote 24.6 1.3E+02 0.0028 25.7 4.6 34 649-684 21-54 (88)
140 PF13384 HTH_23: Homeodomain-l 24.6 87 0.0019 23.7 3.1 33 643-677 10-42 (50)
141 TIGR02698 CopY_TcrY copper tra 24.6 1.9E+02 0.0041 27.3 6.0 50 636-687 2-55 (130)
142 smart00762 Cog4 COG4 transport 24.5 4.2E+02 0.0092 29.1 9.6 53 343-395 7-63 (324)
143 PRK10430 DNA-binding transcrip 24.5 1.2E+02 0.0026 31.3 5.1 37 648-686 174-210 (239)
144 PF09904 HTH_43: Winged helix- 24.2 1.7E+02 0.0037 25.8 5.0 40 643-685 13-52 (90)
145 PF09114 MotA_activ: Transcrip 24.1 1.1E+02 0.0024 26.9 3.7 46 641-688 19-66 (96)
146 PRK14165 winged helix-turn-hel 23.8 1.4E+02 0.003 31.0 5.3 43 643-687 12-54 (217)
147 PRK04214 rbn ribonuclease BN/u 23.6 1.9E+02 0.0042 32.9 7.0 39 647-687 305-343 (412)
148 TIGR02147 Fsuc_second hypothet 23.4 1.9E+02 0.004 31.1 6.3 37 652-690 137-175 (271)
149 TIGR01714 phage_rep_org_N phag 23.3 1.1E+02 0.0024 28.5 4.0 48 637-686 28-83 (119)
150 TIGR02989 Sig-70_gvs1 RNA poly 23.2 1.3E+02 0.0028 28.7 4.8 37 636-674 112-149 (159)
151 PF13545 HTH_Crp_2: Crp-like h 23.1 1.1E+02 0.0023 25.3 3.7 33 652-686 28-60 (76)
152 COG3682 Predicted transcriptio 22.8 1.4E+02 0.003 28.0 4.5 53 740-799 6-58 (123)
153 PF14947 HTH_45: Winged helix- 22.8 1.5E+02 0.0032 25.1 4.5 43 641-686 9-51 (77)
154 KOG1488 Translational represso 22.7 8.4E+02 0.018 28.7 11.7 30 305-337 468-497 (503)
155 PF00196 GerE: Bacterial regul 22.5 1.5E+02 0.0033 23.3 4.2 39 637-677 5-43 (58)
156 smart00531 TFIIE Transcription 21.9 1.1E+02 0.0023 29.6 3.8 30 649-678 12-41 (147)
157 PF06163 DUF977: Bacterial pro 21.9 2.1E+02 0.0046 26.9 5.5 48 638-687 12-59 (127)
158 PRK00135 scpB segregation and 21.3 4.7E+02 0.01 26.5 8.4 111 589-706 34-153 (188)
159 PLN03239 histone acetyltransfe 21.2 1.3E+02 0.0028 33.3 4.6 40 638-677 266-309 (351)
160 PF12108 SF3a60_bindingd: Spli 21.0 73 0.0016 21.8 1.7 14 487-500 3-16 (28)
161 PF11372 DUF3173: Domain of un 20.8 1.1E+02 0.0024 24.8 3.0 36 753-796 2-37 (59)
162 PRK12529 RNA polymerase sigma 20.8 1.4E+02 0.0031 29.3 4.6 37 636-674 128-165 (178)
163 PRK12522 RNA polymerase sigma 20.5 1.4E+02 0.003 29.1 4.5 32 641-674 126-157 (173)
164 PF02270 TFIIF_beta: Transcrip 20.5 1.4E+02 0.003 32.1 4.8 58 638-705 216-273 (275)
165 PRK09642 RNA polymerase sigma 20.5 1.4E+02 0.0031 28.5 4.5 24 651-674 121-144 (160)
166 PF12802 MarR_2: MarR family; 20.3 1.4E+02 0.003 23.5 3.6 48 742-800 7-56 (62)
167 PF10798 YmgB: Biofilm develop 20.0 2.5E+02 0.0054 23.0 4.9 53 738-792 4-56 (61)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4e-135 Score=1101.67 Aligned_cols=649 Identities=62% Similarity=0.960 Sum_probs=631.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhc-CCCcccHHHHHHHHHHH
Q 003648 147 LYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ-TPNVRSLWDMGLQLFRK 225 (805)
Q Consensus 147 LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~-~~~~~sI~~lgl~lFr~ 225 (805)
||++|++.|++|++..+.++...+.|.+.+|..+.++|+.|+.+|.+||+||.||||+|+.+ ++.++|||+||+.+||.
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 89999999999999988888777777789999999999999999999999999999999999 78899999999999999
Q ss_pred Hhcc--ccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHhhhccchhhhhHhHHHHHHHHHHHHHHHHHhcCChhh
Q 003648 226 YLSS--YSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (805)
Q Consensus 226 ~v~~--~~~i~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L~~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~ 303 (805)
+++. .+.+..++.++++..|+++|.|+++|+.+|++++.|+.++++|.+.|+..|++.+.++|.+++...+++..+++
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 67889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-chhHHHHH
Q 003648 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQ 382 (805)
Q Consensus 304 Yl~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~ 382 (805)
||++++.++.+|.+|+..|++.++.+.+..+++++|+..|++.|+..|+..+++..+..++.+||.|++++ ++...++.
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 99999999999999999999999977899999999999999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHHhhhhhccCchhhHHHHHHHHHHHHHHHHHHHHhccCC--HHhHHHHHhHHHHHhhcCCCCchHHHHHHHHHH
Q 003648 383 ALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDEK 460 (805)
Q Consensus 383 ~~~~yI~~~g~~iv~~~~~~~~~V~~ll~l~~~~~~ii~~~F~~~--~~f~~~l~~af~~~iN~~~~k~~e~Laky~D~~ 460 (805)
.|.+|+++.|..+|.+++.++++|+.+++|+++.|-++..||-.+ ..|.+++++||+.|+|.+.++|||+||+|+|.+
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 HhcCCCCCChHHHHhhhccceeeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 003648 461 LRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFK 540 (805)
Q Consensus 461 Lk~~~k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG~~~t~kle~M~~ 540 (805)
||.|+|+.+|++++..++.++.|||||.+|||||+||+++||+|||.++|+|.|+|++||.+||.+||..||+||||||+
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 003648 541 DIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGH 620 (805)
Q Consensus 541 Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~ 620 (805)
||+.|++++..|+++...+...+.++ +.|+|||.|+||+|++.++.||++|..+++.|..||..+|+||+|+|+++||+
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 99999999999999855545555566 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCceEEEEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEE
Q 003648 621 CVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFV 700 (805)
Q Consensus 621 ~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~ 700 (805)
|++++.|+.|++||+||+||++|||+||+++.+|++||.+.|+|.+.+|.|+|+||+||+.++|.++|+|+++.+||.|.
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 EecCCCCCceeEEecccccccchhhhhhhhHhHHhhhHHHHHHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHh
Q 003648 701 FNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIY 780 (805)
Q Consensus 701 ~N~~F~~~~~riki~~i~~ket~~e~~~~~~~v~~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~ 780 (805)
+|..|+++.+|||||+|++||+.+|++.|.|+|.+||+++||||||||||+||+|+|+.|++|+++||+||+.| |+
T Consensus 561 ~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlkfpv~~-d~--- 636 (661)
T KOG2167|consen 561 VNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLKFPVKP-DL--- 636 (661)
T ss_pred echhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcCCCCCh-hH---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred hhhhHHHHHHhhhcccccccCCC
Q 003648 781 LKHNKISHIQSQSYWTMPQITNI 803 (805)
Q Consensus 781 ~~k~~ie~Li~~eyl~~~~~~~~ 803 (805)
|++||+||+|||++||-+ ||
T Consensus 637 --kkriesli~rey~erd~n-~~ 656 (661)
T KOG2167|consen 637 --KKRIESLIDREYLERDDN-NI 656 (661)
T ss_pred --HHHHHHHHhHHHhccccc-cc
Confidence 999999999999999965 55
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=5.4e-117 Score=1026.42 Aligned_cols=686 Identities=35% Similarity=0.602 Sum_probs=637.2
Q ss_pred CchHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhccCch----hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 003648 101 TNFEEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMG----GNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (805)
Q Consensus 101 ~~~~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~----e~LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~ 176 (805)
..+.+++|..|..|++.+..+-....+|+++|+++|++|.+++| ++||+++++.+.+|+.+.+......+++ +.+
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 36778999999999986654445667999999999999999999 9999999999999999999887776665 789
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhcCCCcccHHHHH-HHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcCC
Q 003648 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMG-LQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVD 255 (805)
Q Consensus 177 L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lg-l~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g~~id 255 (805)
|..+...|.+|+.++.+++++|.||||+||.+.....++++++ +.+||..+... ++..+++++++.+|..+|.|+.||
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 9999999999999999999999999999999873466777776 99999998865 699999999999999999999999
Q ss_pred hHHHHHHHHHHhhhc-----cchhhhhHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHhhhccCcCcHHH
Q 003648 256 RTLLNHLLKMFTALG-----IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKP 330 (805)
Q Consensus 256 ~~llk~ii~ml~~L~-----~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yl~~~t~~~ 330 (805)
+.+|+++++|+..|| +|.+.||++|++.|+.||..++.+|+...++.+|+.+++.++.+|..|+..|++..+..+
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 999999999999999999999999999889999999999999999999998888777777
Q ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHhhccCCHHHHHHHHHHhccc-chhHHHHHHHHHHHHHhhhhhccCc-----hh
Q 003648 331 LIATAERQLLERHISAIL---DKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE-----EK 401 (805)
Q Consensus 331 l~~~l~~~LI~~~~~~ll---~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~~-----~~ 401 (805)
+...++..++..|++.++ .+||..|+++++.++|.+||+|++|+ +|++.++..++.|++..|..++... .+
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 777777777777766665 58999999999999999999999999 9999999999999999998777532 45
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhccCCHHhHHHHHhHHHHHhhcCCCCchHHHHHHHHHHHhcCCCCCChHHHHhhhccce
Q 003648 402 DKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVL 481 (805)
Q Consensus 402 ~~~~V~~ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~~~k~~e~Laky~D~~Lk~~~k~~~~~e~e~~l~~i~ 481 (805)
++.+|+.+++++++|..++..||+++..|..+++.||..|+|.+...++|+||+|||.+||+|.++.++++++..+++++
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 67999999999999999999999999999999999999999998844469999999999999999999999999999999
Q ss_pred eeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 003648 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTK 561 (805)
Q Consensus 482 ~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~ 561 (805)
.+|+|+.+||+|+.+|+++||||||+++|.|+|+|+.||.+|+++||.+||.||++||+|+..|++++..|.++. + ..
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 KLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYA-N-YS 489 (725)
T ss_pred eeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhh-c-hh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999762 1 22
Q ss_pred CCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHccCCCceeEeecCCceEEEEEEecCceEEEEEcHHHH
Q 003648 562 LPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQT 641 (805)
Q Consensus 562 ~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa 641 (805)
...+++|.|.|||+|+||.+++.++.||++|..+++.|..||.++|+||+|.|+|+||.|+|.++|.+++|+|+||++||
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 HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEEeccccccc
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKE 721 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~riki~~i~~ke 721 (805)
+|||+||+.+.+|+++|.++|+++.+++.+.|+||+|.|.+++.+ |.|++ .+++.|.+|.+|+++..|++++.+..+
T Consensus 570 ~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~- 646 (725)
T KOG2166|consen 570 AVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD- 646 (725)
T ss_pred HHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch-
Confidence 999999999999999999999999999999999999988777777 88888 899999999999999999999987655
Q ss_pred chhhhhhhhHhHHhhhHHHHHHHHHHhhccCCCCChHHHHHHHHHhcC--CCCChhhHHHhhhhhHHHHHHhhhcccccc
Q 003648 722 TVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQVL--PPVLQFELFIYLKHNKISHIQSQSYWTMPQ 799 (805)
Q Consensus 722 t~~e~~~~~~~v~~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~--F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~ 799 (805)
|.+.+.+.|++||+++|+||||||||+||.|.|++|+.||++|++ |.|+|..| |++||.||+||||+||.
T Consensus 647 ---e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~I-----Kk~Ie~LIEkeYleR~~ 718 (725)
T KOG2166|consen 647 ---ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMI-----KKRIEDLIEREYLERDE 718 (725)
T ss_pred ---hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHH-----HHHHHHHHHHHHHhccC
Confidence 677889999999999999999999999999999999999999998 99999999 99999999999999984
Q ss_pred cC
Q 003648 800 IT 801 (805)
Q Consensus 800 ~~ 801 (805)
..
T Consensus 719 ~~ 720 (725)
T KOG2166|consen 719 NP 720 (725)
T ss_pred CC
Confidence 33
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.6e-114 Score=957.17 Aligned_cols=687 Identities=34% Similarity=0.545 Sum_probs=624.3
Q ss_pred CCCCchHHHHHHHHHHHHHHHH---hcCCCCCcHHHHHHHHHhhhccC----------------chhHHHHHHHHHHHHH
Q 003648 98 TLPTNFEEDTWAKLKLAIKAIF---LKQPTSCDLEKLYQAVNDLCLHK----------------MGGNLYQRIEKECEEH 158 (805)
Q Consensus 98 ~~~~~~~e~~W~~L~~aI~~I~---~~~~~~~s~e~LY~~Vy~lC~~k----------------~~e~LY~~L~~~i~~~ 158 (805)
+++++.++.+|..++.||+.|+ ......++|+++|+.+|+.|.++ +++.||++|....+++
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 4566666899999999999999 44566789999999999999976 4778999999998888
Q ss_pred HHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh--cCC--CcccHHHHHHHHHHHHhccccchH
Q 003648 159 ISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVK--QTP--NVRSLWDMGLQLFRKYLSSYSEVE 234 (805)
Q Consensus 159 l~~~~~~l~~~~~~~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~--~~~--~~~sI~~lgl~lFr~~v~~~~~i~ 234 (805)
+...-.. ... ...+.||..++.+|++|+.++.++.++|.||||.|++ +.+ .+..+..+++..|+..+|. .+.
T Consensus 94 i~~~~~~-~s~-~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~--~i~ 169 (773)
T COG5647 94 IEEYNRG-RSQ-ENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFR--LIV 169 (773)
T ss_pred HHHhccc-ccc-hhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHH--hhh
Confidence 8876544 111 2247999999999999999999999999999999999 222 2567788999999998885 899
Q ss_pred HHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHhhh-----------ccchhhhhHhHHHHHHHHHHHHHHHHHhcCChhh
Q 003648 235 HKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTAL-----------GIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (805)
Q Consensus 235 ~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~~L-----------~~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~ 303 (805)
+.+++.+|..+++.|.|+.+|+..+..++.|+..+ .+|...|||.||+.|.+||..++.+.+..+++.+
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 HHHHHHHHHHHHHHHhhhccCcCcHHHHHHHHHHHHHHHHHHHHHH--HHHHHhhccCCHHHHHHHHHHhccc-chhHHH
Q 003648 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILD--KGFTMLMDGHRTEDLQRMYSLFSRV-NALESL 380 (805)
Q Consensus 304 Yl~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~~LI~~~~~~ll~--~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l 380 (805)
||.+++.++++|..++..|++.++.++|..+++++||.+|.+.+.. +|+..+++..+.+.|..||++++++ .++..|
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 3899999999999999999999999 789999
Q ss_pred HHHHHHHHHHhhh--hh-----cc----------CchhhHHHHHHHHHHHHHHHHHHHHhccCCHHhHHHHHhHHHHHhh
Q 003648 381 RQALAMYIRRTGH--GI-----VM----------DEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLIN 443 (805)
Q Consensus 381 ~~~~~~yI~~~g~--~i-----v~----------~~~~~~~~V~~ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN 443 (805)
+..|.+||++.|. .+ +. ++..+..+|+.++.+++.+..++...|.+|..+..++++||+.|+|
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 11 11 1223578999999999999999999999999999999999999999
Q ss_pred cCC---CCchHHHHHHHHHHHhcCCCCCChHHHHhhhccceeeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 003648 444 LRQ---NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMI 520 (805)
Q Consensus 444 ~~~---~k~~e~Laky~D~~Lk~~~k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i 520 (805)
.+. ..++|+||+|+|.+||++.+......++..+..++.||||+.+||+||++|+++||||||+|+|+|.++|..||
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 36999999999999999987666667888899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHH
Q 003648 521 SKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIF 599 (805)
Q Consensus 521 ~kLk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F 599 (805)
++||+.||.+||+|||+||+||.+|.++...|++...+ ....+|+.|.||+..+||..|. ..++||++|.+.++.|
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 99999999999999999999999999999999875532 2256899999999999997664 6899999999999999
Q ss_pred HHHHHccCCCceeEeecCCceEEEEEEecCceEEEE---EcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003648 600 KEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELA---VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (805)
Q Consensus 600 ~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~---vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL 676 (805)
++||.+||+||+|.|.++||+|+|+++|+.+++.+. ++++|++|+++||+++++|+++|.+.|+|+.++++++|+||
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 999999999999999999999999999998865554 56789999999999999999999999999999999999999
Q ss_pred hcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEEecccccccchhhhhhhhHhHHhhhHHHHHHHHHHhhccCCCCC
Q 003648 677 ACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLS 756 (805)
Q Consensus 677 ~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~riki~~i~~ket~~e~~~~~~~v~~dR~~~I~AaIVRIMK~rK~l~ 756 (805)
+|.|..+|.+ +++.+++++.|.+|.+|+++..|||++.+...+..+++..++++|.+||+..+|||||||||+||+|.
T Consensus 647 ~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~ 724 (773)
T COG5647 647 SCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLK 724 (773)
T ss_pred Hhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 9666555554 48899999999999999999999999998777666788889999999999999999999999999999
Q ss_pred hHHHHHHHHHhcC--CCCChhhHHHhhhhhHHHHHHhhhccccc
Q 003648 757 HTLLITELFQQVL--PPVLQFELFIYLKHNKISHIQSQSYWTMP 798 (805)
Q Consensus 757 h~~Li~ev~~~l~--F~~~~~~i~~~~~k~~ie~Li~~eyl~~~ 798 (805)
|++|++||+.|.+ |.|+|+++ |++||.|||+|||+|.
T Consensus 725 H~~Lv~e~i~q~~~Rf~p~vsmv-----Kr~Ie~LiEKeYLeR~ 763 (773)
T COG5647 725 HGDLVKEVIAQHKSRFEPKVSMV-----KRAIETLIEKEYLERQ 763 (773)
T ss_pred HHHHHHHHHHHhhccCCCCHHHH-----HHHHHHHHHHHHHHhc
Confidence 9999999999998 99999999 9999999999999983
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.9e-103 Score=814.34 Aligned_cols=657 Identities=26% Similarity=0.468 Sum_probs=610.5
Q ss_pred chHHHHHHHHHHHHHHHHhcCCCC-CcHHHHHHHHHhhhccC---chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHH
Q 003648 102 NFEEDTWAKLKLAIKAIFLKQPTS-CDLEKLYQAVNDLCLHK---MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFL 177 (805)
Q Consensus 102 ~~~e~~W~~L~~aI~~I~~~~~~~-~s~e~LY~~Vy~lC~~k---~~e~LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~L 177 (805)
+| +++|.+|...|.+|..-++.. ..|..-|..||.+|..- .||+||...+.++++|++..+..+...++ +.+|
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 899999999999999988865 58999999999999864 79999999999999999987776665433 5699
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhHhhcCC-----------------CcccHHHHHHHHHHHHhccccchHHHHHHH
Q 003648 178 SLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-----------------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTG 240 (805)
Q Consensus 178 ~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~-----------------~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ 240 (805)
..|.+.|+.|..+..++..+|.||+..|+++++ ++..|..+++.+||+.++. .+...|+.-
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 999999999999999999999999999999864 3457888999999999875 799999999
Q ss_pred HHHHHHHHhcCCcCC-hHHHHHHHHHHhhh----------------------ccchhhhhHhHHHHHHHHHHHHHHHHHh
Q 003648 241 LLRMIERERLGEAVD-RTLLNHLLKMFTAL----------------------GIYSESFEKPFLECTSEFYAAEGMKYMQ 297 (805)
Q Consensus 241 ll~lI~~eR~g~~id-~~llk~ii~ml~~L----------------------~~Y~~~FE~~fL~~t~~yY~~~~~~~l~ 297 (805)
+|..|.++|.|+..+ ...+..+|..|+.+ .+|++.||.|||.+|.+||+.+++.+++
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 56788888888754 2799999999999999999999999999
Q ss_pred cCChhhHHHHHHHHHHHHHHHhhhccCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-ch
Q 003648 298 QSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NA 376 (805)
Q Consensus 298 ~~~~~~Yl~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~ 376 (805)
+.+|++|+.+|..++++|+-||..||++++..+++..|++.+|..|.+.+ .-.+..++.+++..||+.||.|+..+ -|
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 66799999999999999999999999 89
Q ss_pred hHHHHHHHHHHHHHhhhhhccCch---hhHHHHHHHHHHHHHHHHHHHHhccCCHHhHHHHHhHHHHHhhcCC-----CC
Q 003648 377 LESLRQALAMYIRRTGHGIVMDEE---KDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ-----NR 448 (805)
Q Consensus 377 l~~l~~~~~~yI~~~g~~iv~~~~---~~~~~V~~ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~~-----~k 448 (805)
+..+...|.+||++.|...++... -+..||+.+|.+|.+|..++...|.+|..|..+++.|+..++|.+. .+
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 999999999999999998886532 3678999999999999999999999999999999999999999764 37
Q ss_pred chHHHHHHHHHHHhcCCCCCChHHHHhhhccceeeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhC
Q 003648 449 PAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG 528 (805)
Q Consensus 449 ~~e~Laky~D~~Lk~~~k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG 528 (805)
.+|.||+|||.+||++.|++++.++|.+|+..+.+|+||+|||+|.+||.+.||+||+.+.|.|.|+|..||.+||+.||
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 003648 529 SQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYS 608 (805)
Q Consensus 529 ~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~ 608 (805)
.+||+++- +.|+..|.+++++|.+.+.+ +.+|.+|+...+.|+.||..+|+
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 99999999 99999999999999876543 78999999999999999999999
Q ss_pred CceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
||+|+|.+.++++++++++-++.|.-.|.+|||++||+||..+.+++.+|.+.||+++++|.+++.++. ..++|....
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 888887643
Q ss_pred CCCCCCCCCeEEEecCCCCCceeEEeccccc-ccchhhhhhhhHhHHhhhHHHHHHHHHHhhccCCCCChHHHHHHHHHh
Q 003648 689 KGRDVEDDDSFVFNEGFTAPLYRIKVNAIQM-KETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQ 767 (805)
Q Consensus 689 ~~~~i~~~d~f~~N~~F~~~~~riki~~i~~-ket~~e~~~~~~~v~~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~ 767 (805)
.++..+..|++|.+|++++.+.++...++ |.+++|.+.+...|.+||++.++||||||||+||.+.|+.|++||++|
T Consensus 613 --~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~q 690 (728)
T KOG2284|consen 613 --QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQ 690 (728)
T ss_pred --cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHh
Confidence 46778889999999999999999976543 567788889999999999999999999999999999999999999999
Q ss_pred cC--CCCChhhHHHhhhhhHHHHHHhhhcccccccCC
Q 003648 768 VL--PPVLQFELFIYLKHNKISHIQSQSYWTMPQITN 802 (805)
Q Consensus 768 l~--F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~~~ 802 (805)
.+ |.|+.+.| |++||.||++.||+|.+-+|
T Consensus 691 t~~rf~p~v~~i-----kk~ie~li~k~yi~rt~~~d 722 (728)
T KOG2284|consen 691 TKGRFSPDVPFI-----KKSIEDLIEKMYIQRTDQND 722 (728)
T ss_pred hcccCCCCchHH-----HHHHHHHHHHHHHhhccccc
Confidence 98 99999999 99999999999999988654
No 5
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=8.8e-94 Score=847.68 Aligned_cols=576 Identities=43% Similarity=0.716 Sum_probs=525.2
Q ss_pred HHHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhccCchhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHH
Q 003648 108 WAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDL 187 (805)
Q Consensus 108 W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~L~~~~~~W~~~ 187 (805)
|..|++||+.|+.+.....+|+++|+.||++|..++|+.||+++++.+.+|+..++..+.+..+ ..+|..|..+|.+|
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 9999999999999999999999999999999999999999999999999999998888776533 68999999999999
Q ss_pred HHHHHHHHHHHHHhhhhHhhcCCCcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHh
Q 003648 188 CDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFT 267 (805)
Q Consensus 188 ~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g~~id~~llk~ii~ml~ 267 (805)
+.++.+|+++|+||||.|+.++ +||+.|+. .+.++++++++.+|.++|.|+.+|+.+++.+++|+.
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 9999999999999999999875 99999986 599999999999999999999999999999999999
Q ss_pred hhc---cchhhhhHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHhhhccCcCcHHHHHHHHHHHHHHHHH
Q 003648 268 ALG---IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHI 344 (805)
Q Consensus 268 ~L~---~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~~LI~~~~ 344 (805)
++| +|.+.||++||+.|.+||+.++ +.+.++.+||.+|+.++++|.+||..|++++|..++.++++++||..|.
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 765 8999999999999999999999 6777999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHhccc-chhHHHHHHHHHHHHHhhhhhccCc---hhhHHHHHHHHHHHHHHHHHH
Q 003648 345 SAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIW 420 (805)
Q Consensus 345 ~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~~---~~~~~~V~~ll~l~~~~~~ii 420 (805)
+.| .+|+..|+++++.++|++||+|++++ ++++.++..|++||.+.|..++... ..+..+|+.+++++++++.++
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 HHhccCCHHhHHHHHhHHHHHhhcCCCCchHHHHHHHHHHHhcCCCCCChHHHHhhhccceeeeeeecchHHHHHHHHHH
Q 003648 421 EQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKD 500 (805)
Q Consensus 421 ~~~F~~~~~f~~~l~~af~~~iN~~~~k~~e~Laky~D~~Lk~~~k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~ 500 (805)
.+||++++.|..++++||+.++|....+++++||+|||.+|+++.++.++++++..++.++.||+|+++||+|+.+|+++
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 HHHHHhCCCCCCHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CccEEEEEeecCCC
Q 003648 501 LAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPS--GIEMSVHVLTTGYW 578 (805)
Q Consensus 501 LakRLL~~~s~s~d~E~~~i~kLk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~--~~~~~v~VLt~~~W 578 (805)
||+|||.+++.+.+.|+.||++|+.+||.+||++|++|++|++.|++++++|++.... .+... +++|+|.||++|+|
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 9999999999999999999999999999999999999999999999999999988765 22222 79999999999999
Q ss_pred CCCCCCC-ccCChHHHHHHHHHHHHHHccCCCceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhhcCCCCCCHHH
Q 003648 579 PTYPPMD-VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDAQKLSFQD 657 (805)
Q Consensus 579 P~~~~~~-~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~~~lt~~e 657 (805)
|.++... +.||++|+.+++.|++||+.+|+||+|+|.|.+|+|+|+++|++++++++||++||+||++||+.+++|++|
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 003648 658 IKDATGIEDKELRRTLQSLACGKVRVLQ--KLPKGRDVEDDDSFVFNEGFT 706 (805)
Q Consensus 658 I~~~t~i~~~~l~~~L~sL~~~k~~iL~--k~~~~~~i~~~d~f~~N~~F~ 706 (805)
|++.||+++++++++|.+|+ +.++|. +.+++++++++|.|++|.+|+
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 789999999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-83 Score=675.25 Aligned_cols=690 Identities=26% Similarity=0.424 Sum_probs=612.2
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCC-CCcHHHHHHHHHhhhccC--chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 003648 100 PTNFEEDTWAKLKLAIKAIFLKQPT-SCDLEKLYQAVNDLCLHK--MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (805)
Q Consensus 100 ~~~~~e~~W~~L~~aI~~I~~~~~~-~~s~e~LY~~Vy~lC~~k--~~e~LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~ 176 (805)
+.+-+++.|...++.+-+++..... ...|..||.+|+.+|.+. ...++|+.|+..+.+++...........+| ..+
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d-~aL 87 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTD-GAL 87 (777)
T ss_pred chhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccc-cHH
Confidence 3345689999999999998876554 458999999999999975 678999999999999999887777665555 789
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhcCC-------CcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHh
Q 003648 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERER 249 (805)
Q Consensus 177 L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~-------~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR 249 (805)
|..|...|.+|..+..++.--|.-||.+-.-..+ +-.+|..+-+.-|-+++|. .++.++....+.++..+|
T Consensus 88 L~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER 165 (777)
T KOG2285|consen 88 LIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAER 165 (777)
T ss_pred HHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999988554322 2357999999999999997 799999999999999999
Q ss_pred cCCcCChHHHHHHHHHHhhhc--------cchhhhhHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHhhh
Q 003648 250 LGEAVDRTLLNHLLKMFTALG--------IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLL 321 (805)
Q Consensus 250 ~g~~id~~llk~ii~ml~~L~--------~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~ 321 (805)
.|+.+|.+++-.+-..++.|. +|.+.||..||++|.+||+..+..++++.++-+|+++++..+++|+.|..+
T Consensus 166 ~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkR 245 (777)
T KOG2285|consen 166 DGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKR 245 (777)
T ss_pred ccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHH
Confidence 999999999988888988774 999999999999999999999999999999999999999999999999999
Q ss_pred ccCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhccc-chhHHHHHHHHHHHHHhhhhhccC
Q 003648 322 YLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMD 398 (805)
Q Consensus 322 yl~~--~t~~~l~~~l~~~LI~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~-~~l~~l~~~~~~yI~~~g~~iv~~ 398 (805)
||.. .+..+++.++.+.|+.+|.+.|+. .+..|+...+++-|++||+|+.|+ .|++.+..-+..||...|..-+-.
T Consensus 246 YLE~~~~s~~~lme~~VnaLv~sf~~tIlA-EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~ 324 (777)
T KOG2285|consen 246 YLEMNSPSSGKLMEKAVNALVESFEDTILA-ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRN 324 (777)
T ss_pred hhccCCCcHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHh
Confidence 9864 788999999999999999999985 689999999999999999999999 999999999999999999754321
Q ss_pred -----chhhHHHHHHHHHHHHHHHHHHHHhccCCHHhHHHHHhHHHHHhhcC--------------------CCCchHHH
Q 003648 399 -----EEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLR--------------------QNRPAELI 453 (805)
Q Consensus 399 -----~~~~~~~V~~ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~--------------------~~k~~e~L 453 (805)
..+...+|+.||.++++|..++.++|..|+.|..+-+.||+.++|.. .+++||+|
T Consensus 325 aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELL 404 (777)
T KOG2285|consen 325 AAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELL 404 (777)
T ss_pred hhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHH
Confidence 12345799999999999999999999999999999999999999963 15789999
Q ss_pred HHHHHHHHhcCC--CCCChHHHHhhhccceeeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhC--C
Q 003648 454 AKFLDEKLRAGN--KGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG--S 529 (805)
Q Consensus 454 aky~D~~Lk~~~--k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG--~ 529 (805)
|.|||.+||+.. |..+.+|++.+|.+++-+++|+++||+|..|++.+|.+||+.+.|++.+.|..|+..|+ ||| .
T Consensus 405 ANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPa 483 (777)
T KOG2285|consen 405 ANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPA 483 (777)
T ss_pred HHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcH
Confidence 999999999963 66788999999999999999999999999999999999999999999999999999999 788 5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHccCC
Q 003648 530 QFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYS 608 (805)
Q Consensus 530 ~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~fY~~k~~ 608 (805)
+|.+||-.||+||+.|++++.+|+..+...+.....-.+++.||+.|.|-.... ..+.||.+|+..+-.-+.||+++|+
T Consensus 484 DyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hs 563 (777)
T KOG2285|consen 484 DYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHS 563 (777)
T ss_pred HHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccC
Confidence 799999999999999999999999987653332223458899999999987754 5799999999999999999999999
Q ss_pred CceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHhHhhc-CC--cce
Q 003648 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLAC-GK--VRV 683 (805)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~--~~lt~~eI~~~t~i~~~~l~~~L~sL~~-~k--~~i 683 (805)
||+|+|.|++++++|++.-+-|.|.|.|++|||+||.+||+. +.+|++.+.-+|.+|+.+|+|+|-||+. || ..|
T Consensus 564 grkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~Qi 643 (777)
T KOG2285|consen 564 GRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQI 643 (777)
T ss_pred ccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhhe
Confidence 999999999999999887666899999999999999999985 7899999999999999999999999987 65 578
Q ss_pred eeeCCCC----CCCCCCCeEEEecCCCC-----CceeEEeccccc-c-cchhhhhhhhHhHHhhhHHHHHHHHHHhhccC
Q 003648 684 LQKLPKG----RDVEDDDSFVFNEGFTA-----PLYRIKVNAIQM-K-ETVEENTSTTERVFQDRQYQVDAAIVRIMKTR 752 (805)
Q Consensus 684 L~k~~~~----~~i~~~d~f~~N~~F~~-----~~~riki~~i~~-k-et~~e~~~~~~~v~~dR~~~I~AaIVRIMK~r 752 (805)
|..+|+. +++.++..|.+|.+|.- ...|-|+|-|.. . .+....++.++.+.+-|-...|-+||+|||.|
T Consensus 644 LL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~R 723 (777)
T KOG2285|consen 644 LLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTR 723 (777)
T ss_pred eeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHH
Confidence 8877743 78888999999999963 224556655421 1 12333345567889999999999999999999
Q ss_pred CCCChHHHHHHHHHhcC--CCCChhhHHHhhhhhHHHHHHhhhcccccc
Q 003648 753 KVLSHTLLITELFQQVL--PPVLQFELFIYLKHNKISHIQSQSYWTMPQ 799 (805)
Q Consensus 753 K~l~h~~Li~ev~~~l~--F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~ 799 (805)
|+++..+|-.|+++.|+ |-|+...| |.+||-|||..|+.||-
T Consensus 724 K~~~nAqLq~ELveILKnmFlP~kKmI-----KEQieWLIEnKYmrRd~ 767 (777)
T KOG2285|consen 724 KTYTNAQLQMELVEILKNMFLPNKKMI-----KEQIEWLIENKYMRRDA 767 (777)
T ss_pred HHhhHHHHHHHHHHHHHHccCCcHHHH-----HHHHHHHHhhhhhccch
Confidence 99999999999999999 99999988 99999999999999984
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=6.2e-34 Score=274.35 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=132.9
Q ss_pred eecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCC
Q 003648 486 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 565 (805)
Q Consensus 486 ~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~~~~~~~~~~ 565 (805)
|+++||+|+.+|+++||+|||.+++++.|.|+.||++||.+||.+||++|++||+|++.|++++.+|++.+.+ .....+
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 7899999999999999999999999999999999999999999999999999999999999999999987754 223356
Q ss_pred ccEEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHccCCCceeEeecCCceEEEEEEe
Q 003648 566 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 627 (805)
Q Consensus 566 ~~~~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f 627 (805)
++|+|.|||.++||.++. .++.||++|+.+++.|++||..+|+||+|+|.|+||+|+|+++|
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 899999999999999987 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=2.9e-25 Score=247.42 Aligned_cols=301 Identities=21% Similarity=0.274 Sum_probs=231.0
Q ss_pred eeeeeecchHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHh--hhc
Q 003648 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSS--QAR 559 (805)
Q Consensus 482 ~lf~~l~~KD~Fe~~Y~k~LakRLL~~~s~s~d~E~~~i~kLk~~cG~~~t~kle~M~~Di~~S~~l~~~f~~~~--~~~ 559 (805)
.|...+.+|+-|.+.||..||.|||....++.+.|..-++.||-.+|.+-.+.|++|++|+..|+++++.+++.. ...
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 344455999999999999999999999999999999999999999999999999999999999999999998742 110
Q ss_pred cCCCCCccEEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHccCCCceeEeecCCceEEEEEEecCceEEEEEcHH
Q 003648 560 TKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLF 639 (805)
Q Consensus 560 ~~~~~~~~~~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~ 639 (805)
......+.+++.||++.+||......+.||.+++..++.|.+-|.+...+|+|.|.+++|.|+|+++|.+.+.+++||+.
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 11112578899999999999988888999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeEE-ecccc
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIK-VNAIQ 718 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~rik-i~~i~ 718 (805)
||+|+++|.+.++||++++++.+|||...++|.|..|+ +.++|.++|. +++..+|++++.=.+. .+ -+.+.
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~---~q~~~~~~ 675 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDF---DQAEGTVL 675 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeeccccccc---cccCCCcc
Confidence 99999999999999999999999999999999999999 9999998873 2677899999853222 22 11121
Q ss_pred cccchhhhhhhh--HhHHhhhH--HHHHHHHHHhhccCCCCChHHHHHHHHHhcC-CCCCh--hhHHHhhhhhHHHHHHh
Q 003648 719 MKETVEENTSTT--ERVFQDRQ--YQVDAAIVRIMKTRKVLSHTLLITELFQQVL-PPVLQ--FELFIYLKHNKISHIQS 791 (805)
Q Consensus 719 ~ket~~e~~~~~--~~v~~dR~--~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~-F~~~~--~~i~~~~~k~~ie~Li~ 791 (805)
+ |..+|..+.+ ..+.+-+. ..-...||-.+-.-..|..+-+- +.|+ |-|.+ .++.-+..+-.+..+|.
T Consensus 676 ~-e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIH----nmLkmF~~~~~~~~~TlqeL~~fLq~kV~ 750 (765)
T KOG2165|consen 676 L-EAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIH----NMLKMFVPPDGSAEITLQELQGFLQRKVR 750 (765)
T ss_pred c-ccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHH----HHHeeeecCCCCCcccHHHHHHHHHHHhh
Confidence 1 2222221111 12222111 12233566555444677665544 5667 75443 23323333555555555
Q ss_pred hhcc
Q 003648 792 QSYW 795 (805)
Q Consensus 792 ~eyl 795 (805)
-|-|
T Consensus 751 e~kL 754 (765)
T KOG2165|consen 751 EGKL 754 (765)
T ss_pred ccce
Confidence 4444
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.64 E-value=1.4e-16 Score=132.91 Aligned_cols=64 Identities=38% Similarity=0.533 Sum_probs=57.7
Q ss_pred HHhhhHHHHHHHHHHhhccCCCCChHHHHHHHHHhcC--CCCChhhHHHhhhhhHHHHHHhhhcccccccC
Q 003648 733 VFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQVL--PPVLQFELFIYLKHNKISHIQSQSYWTMPQIT 801 (805)
Q Consensus 733 v~~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~--F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~~ 801 (805)
|.++|.+.|+||||||||++|+|+|++|+.+|.++++ |+|++.+| |++||.||++|||+||...
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~i-----k~~Ie~LIekeyi~Rd~~d 66 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDI-----KKRIESLIEKEYIERDEDD 66 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHH-----HHHHHHHHHTTSEEEESSE
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHH-----HHHHHHHHHhhhhhcCCCC
Confidence 4689999999999999999999999999999999996 99999999 9999999999999999753
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.43 E-value=0.0023 Score=62.45 Aligned_cols=124 Identities=15% Similarity=0.212 Sum_probs=89.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHhh---hccCch-hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHH
Q 003648 104 EEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDL---CLHKMG-GNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSL 179 (805)
Q Consensus 104 ~e~~W~~L~~aI~~I~~~~~~~~s~e~LY~~Vy~l---C~~k~~-e~LY~~L~~~i~~~l~~~~~~l~~~~~~~~~~L~~ 179 (805)
.++.|..+..++-.+|+++....+.|++-+.|.-. |.++.. ..+-+.+++.+..-+......+.... ++.+|..
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 47899999999999999999889999988888654 555442 23444445555444444333443322 3689999
Q ss_pred HHHHHHHHHHH-HHHHHHHHHHhhhhHhhcC----------------CCcccHHHHHHHHHHHHhcc
Q 003648 180 VERCWQDLCDQ-MLMIRGIALYLDRTYVKQT----------------PNVRSLWDMGLQLFRKYLSS 229 (805)
Q Consensus 180 ~~~~W~~~~~~-~~~i~~iF~YLDR~yv~~~----------------~~~~sI~~lgl~lFr~~v~~ 229 (805)
+...|.-|... +-++..||+.|++.+-... ....+|..++|..||+.|+-
T Consensus 83 L~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL 149 (158)
T PF08539_consen 83 LVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL 149 (158)
T ss_pred HHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh
Confidence 99999996555 5679999999996543221 23579999999999999985
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=96.85 E-value=0.0069 Score=68.88 Aligned_cols=310 Identities=11% Similarity=0.042 Sum_probs=174.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCC----cHHHHHHHHHhhhccCc--hhHHHHHHHHHHHHHHHHHHHhhhc---CC--Cc
Q 003648 104 EEDTWAKLKLAIKAIFLKQPTSC----DLEKLYQAVNDLCLHKM--GGNLYQRIEKECEEHISAAIRSLVG---QS--PD 172 (805)
Q Consensus 104 ~e~~W~~L~~aI~~I~~~~~~~~----s~e~LY~~Vy~lC~~k~--~e~LY~~L~~~i~~~l~~~~~~l~~---~~--~~ 172 (805)
....|..|++++.-|.......- .|-++.+.+|+-|..+. ...+.+.++-.+..+..+...-+.. .+ ..
T Consensus 110 eAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l 189 (661)
T KOG2167|consen 110 EAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPL 189 (661)
T ss_pred chhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccch
Confidence 45678888888888776554433 45578899999999873 3445566666555555543222211 11 12
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhcCCCcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCC
Q 003648 173 LVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGE 252 (805)
Q Consensus 173 ~~~~L~~~~~~W~~~~~~~~~i~~iF~YLDR~yv~~~~~~~sI~~lgl~lFr~~v~~~~~i~~~l~~~ll~lI~~eR~g~ 252 (805)
...+.+.+...|-+.-.. .++++-+|-.=+ ++...+|.++-..+-...-.-+...+-+.+....+|..++.++
T Consensus 190 ~atV~~~LL~~hL~~IL~----kgl~~lvDm~q~---~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk 262 (661)
T KOG2167|consen 190 IATVERCLLSRHLDLILT----KGLDSLVDMRQT---SDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDK 262 (661)
T ss_pred HHHHHHHHHHHHHHHHHh----cchHHhhhhhhc---cchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhH
Confidence 456777888888665333 344555665422 2345677766666532221123556667777777777777777
Q ss_pred cCCh--HHHHHHHHHHhhhccchhhhhHhHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHhhhccCcCcHHH
Q 003648 253 AVDR--TLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKP 330 (805)
Q Consensus 253 ~id~--~llk~ii~ml~~L~~Y~~~FE~~fL~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~yl~~~t~~~ 330 (805)
.... -..|..++|......+...- .+|+..++++|..+++. +...+.+|+.+....+-.+-+. ..+-+.
T Consensus 263 ~mVqELL~FK~k~Dii~~~sF~~~v~-e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~gnk------~~~d~~ 333 (661)
T KOG2167|consen 263 DMVQELLDFKKKVDIIVDESFLKYVA-EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRAGNK------ETSDEE 333 (661)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHhhH-HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHhccc------cccchh
Confidence 6333 34578888887776555444 88999999999999994 6667899998876654433100 111222
Q ss_pred HHHHHHHHH------------------------HHHHHHHHHHHHHHHhhccCCHHHHHHHHHHhcccchhHHHHHHHHH
Q 003648 331 LIATAERQL------------------------LERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAM 386 (805)
Q Consensus 331 l~~~l~~~L------------------------I~~~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~~ 386 (805)
|-.++.+++ +..|... ++.|+.-|.+-+...+.+..|+|.+..+..+...+..+.
T Consensus 334 l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs-vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~ 412 (661)
T KOG2167|consen 334 LEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS-VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRA 412 (661)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh-hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHH
Confidence 333333333 3333222 134444344445566788899998877544444444444
Q ss_pred HHHHhhhhhccCchhhHHHHHHHHHHHHHHHHHHHHhccCCHHhHHHHHhHH
Q 003648 387 YIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAF 438 (805)
Q Consensus 387 yI~~~g~~iv~~~~~~~~~V~~ll~l~~~~~~ii~~~F~~~~~f~~~l~~af 438 (805)
|....|..-- . ...|+.++--....|-.||+.+..+-..+++.+
T Consensus 413 f~~~~~~~~~-~-------~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~~ 456 (661)
T KOG2167|consen 413 FKQSKGANNR-L-------EGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDCQ 456 (661)
T ss_pred HHHHHHhhcc-C-------cCCceEEEeecccccCCCCchhccCCHHHHHHH
Confidence 4433232110 0 011222222234456666666554444444433
No 12
>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=93.76 E-value=0.2 Score=44.73 Aligned_cols=66 Identities=17% Similarity=0.184 Sum_probs=53.9
Q ss_pred EEEEcHHHHHHHHhhc--------CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003648 633 ELAVSLFQTVVLMLFN--------DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (805)
Q Consensus 633 ~l~vs~~Qa~ILllFn--------~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (805)
...++.-|+.+|+..- ....+|-.||++.+|++...+.+.|..|. +.+++.+.. ....|.+|.+
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 3456778888888655 45689999999999999999999999999 889998642 2368999988
Q ss_pred CC
Q 003648 705 FT 706 (805)
Q Consensus 705 F~ 706 (805)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
No 13
>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=93.21 E-value=0.13 Score=40.31 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=39.0
Q ss_pred HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~~-~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+.||-.|.+.+ .+|+.||++.+|++...+.+.|+.|. ..+++.++|
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 45788888775 58999999999999999999999999 888888754
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=92.04 E-value=0.31 Score=37.37 Aligned_cols=46 Identities=15% Similarity=0.333 Sum_probs=37.5
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (805)
+..+.-||....+++.+|..||++.+|++...+.+.|+.|. +.+++
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 44577788888888899999999999999999999999998 66654
No 15
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.73 E-value=0.23 Score=40.14 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=44.1
Q ss_pred EcHHHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn~~~~--lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++.-|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 46788999988877766 9999999999999999999999999 888888764
No 16
>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=91.68 E-value=0.5 Score=40.94 Aligned_cols=59 Identities=19% Similarity=0.330 Sum_probs=42.8
Q ss_pred HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003648 639 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (805)
Q Consensus 639 ~Qa~ILllFn~~~-~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (805)
+++++.+..+..+ .+|.++|++.+++++..+.+.++.|. +.+++...+ | .+.-|.++.+
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-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 3445555444444 49999999999999999999999999 889887543 2 4567877775
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=89.75 E-value=0.5 Score=38.87 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=40.3
Q ss_pred EcHHHHHHHHhhc-CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFN-DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn-~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++..|..||.... ..+.++..+|++.++++...+.+.|+.|. ..+++.+.+
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 3567889998888 77899999999999999999999999999 888887653
No 18
>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=89.47 E-value=0.6 Score=37.45 Aligned_cols=46 Identities=24% Similarity=0.502 Sum_probs=40.6
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
|..|+-+.++.+.+|++||++.+|+++..+++-|..|. +.+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 45677788888999999999999999999999999999 77777764
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=89.20 E-value=0.3 Score=39.06 Aligned_cols=50 Identities=14% Similarity=0.282 Sum_probs=44.3
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
|..|..||....+.+.++..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 67799999888888889999999999999999999999999 888887754
No 20
>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=88.97 E-value=0.57 Score=37.99 Aligned_cols=51 Identities=12% Similarity=0.251 Sum_probs=41.8
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCC
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~ 689 (805)
++.-..||.++...+++|+.+|++.+|++...+.++|.-|. +.+++.....
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~~~ 59 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVERE 59 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEecc
Confidence 34556678777677899999999999999999999999999 8888876543
No 21
>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=88.29 E-value=0.93 Score=41.93 Aligned_cols=52 Identities=15% Similarity=0.257 Sum_probs=47.0
Q ss_pred EEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.++..|..||..+...+.+|..+|++.+|++...+.+.+..|. +.+++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 4578899999988888899999999999999999999999999 889998764
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=86.18 E-value=1.5 Score=42.13 Aligned_cols=52 Identities=21% Similarity=0.233 Sum_probs=46.5
Q ss_pred EEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.++..|+.||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 4677899999877667789999999999999999999999999 999998865
No 23
>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=85.64 E-value=2 Score=32.88 Aligned_cols=43 Identities=14% Similarity=0.398 Sum_probs=35.2
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
..-||.++-+ ++.++.||++.+|++...+.++|..|. +.+++.
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 4456666666 689999999999999999999999998 777764
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=85.45 E-value=1.6 Score=36.41 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=40.3
Q ss_pred HHHHHHHhhcCCCC--CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 639 FQTVVLMLFNDAQK--LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 639 ~Qa~ILllFn~~~~--lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.+
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 34567777777765 9999999999999999999999999 788887643
No 25
>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=84.42 E-value=2.3 Score=38.88 Aligned_cols=52 Identities=23% Similarity=0.333 Sum_probs=45.2
Q ss_pred EEcHHHHHHHHhhc----CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 635 AVSLFQTVVLMLFN----DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 635 ~vs~~Qa~ILllFn----~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|. +.+.+.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 46778888887665 55789999999999999999999999999 999998865
No 26
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=83.75 E-value=2.1 Score=37.64 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=46.9
Q ss_pred EEEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 633 ~l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+..++..+..||.+....+.++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 455778899999888888889999999999999999999999999 88888764
No 27
>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=83.57 E-value=3.6 Score=37.15 Aligned_cols=61 Identities=20% Similarity=0.324 Sum_probs=46.6
Q ss_pred EcHHHHHHHHh-------hcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 003648 636 VSLFQTVVLML-------FNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (805)
Q Consensus 636 vs~~Qa~ILll-------Fn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~ 706 (805)
++.-|.-|++. ||.. +.+|..++++.||++...+.+++..|+ +.+||... +..+-+|.+.+
T Consensus 30 ls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 30 LSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred ccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 44455555544 4543 589999999999999999999999999 99999763 45677776653
No 28
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=83.21 E-value=2.8 Score=36.49 Aligned_cols=46 Identities=15% Similarity=0.306 Sum_probs=39.2
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..||-.+... +.+|..||++.+|++...+.+.|..|. +.++|.+.+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 3466667665 689999999999999999999999999 889998753
No 29
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=82.03 E-value=2.9 Score=31.95 Aligned_cols=46 Identities=22% Similarity=0.460 Sum_probs=37.5
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
-.|+..+.+...++..+|++.++++...+.+.|..|. +.+++.+..
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 3456556666789999999999999999999999998 777776543
No 30
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=81.44 E-value=3 Score=34.12 Aligned_cols=56 Identities=23% Similarity=0.326 Sum_probs=40.3
Q ss_pred HHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEe
Q 003648 643 VLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFN 702 (805)
Q Consensus 643 ILllFn~-~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N 702 (805)
||-.++. +..++..||++.+|++...+++.|..|. +.+.+.+.|.++... ..+.+|
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 4555566 6789999999999999999999999999 888888766544322 245555
No 31
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=79.52 E-value=4.2 Score=43.16 Aligned_cols=46 Identities=9% Similarity=0.209 Sum_probs=41.3
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..||-+|.....+|+.||++.+|++...+.|.|.+|. ..+.|.+.+
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 4478888887789999999999999999999999999 889998764
No 32
>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=79.00 E-value=2 Score=35.56 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=41.1
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
|-.++-|+..+-..+..|..||++.+|++...+.+.|..|. +.+++.+.+
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 44566666555566789999999999999999999999999 888887643
No 33
>PHA00738 putative HTH transcription regulator
Probab=77.62 E-value=5.3 Score=36.26 Aligned_cols=67 Identities=18% Similarity=0.202 Sum_probs=52.8
Q ss_pred EEEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCC
Q 003648 633 ELAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 705 (805)
Q Consensus 633 ~l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F 705 (805)
++...+.=-.||.++.+++.+++.+|++.++|+...+-++|.-|. ..+|+.....|+.+ .|++|.+-
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 444555555677666777789999999999999999999999999 89999887666433 57777764
No 34
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.27 E-value=7.3 Score=38.50 Aligned_cols=58 Identities=16% Similarity=0.324 Sum_probs=43.3
Q ss_pred HHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003648 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (805)
Q Consensus 640 Qa~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (805)
.+++.+.|+.. ..+|.++|++.+|+|...+.+.|+.|. +.+++.... | .++-|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~r-G----~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVR-G----PGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC-C----CCCCeeccCC
Confidence 34455556654 579999999999999999999999999 999887531 1 2334666554
No 35
>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=76.87 E-value=4.8 Score=31.58 Aligned_cols=33 Identities=15% Similarity=0.538 Sum_probs=27.9
Q ss_pred HhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 645 MLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 645 llFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
++.+..+.+|.++|++.+|++...+.+.|..|.
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 36
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=76.69 E-value=5.4 Score=40.21 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=47.4
Q ss_pred EEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 634 l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+.++..|..||......+.+|..+|++.++++...+.+.|..|. +-+++.+.+
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 44677899999999888899999999999999999999999999 889998764
No 37
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=76.45 E-value=4.7 Score=38.56 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=45.7
Q ss_pred EEEcHHHHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 634 LAVSLFQTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 634 l~vs~~Qa~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+.++..|..||...... +.+|..+|++.+|++...+.+.+..|. +.+++.+.+
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 44677898898877654 568999999999999999999999999 999998865
No 38
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=76.00 E-value=8.3 Score=37.62 Aligned_cols=57 Identities=18% Similarity=0.279 Sum_probs=41.9
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (805)
+++.|..+..+.+|..+|++..|++...|.+.|+.|. +.+++.... | .+.-|.++..
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecCC
Confidence 3344444555678999999999999999999999999 999887543 2 2334555553
No 39
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=75.63 E-value=6.9 Score=36.72 Aligned_cols=39 Identities=13% Similarity=0.286 Sum_probs=35.4
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 648 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 648 n~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+.++.+|+++|++.++.+...+.++|+.|. ..+++.++.
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 899998753
No 40
>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=74.78 E-value=8.5 Score=36.58 Aligned_cols=44 Identities=18% Similarity=0.328 Sum_probs=36.2
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 641 a~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+++.|.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
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 3444555544 479999999999999999999999999 8998864
No 41
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=74.60 E-value=3.3 Score=35.03 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=32.1
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+..++...+.+|+.||++.+|++...++..+..+. +.++|.+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~~ 64 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLVK 64 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHHH
Confidence 33333444679999999999999999999988776 6666543
No 42
>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=73.92 E-value=7.4 Score=31.76 Aligned_cols=48 Identities=15% Similarity=0.327 Sum_probs=40.0
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|. ..+++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLE--EAGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEEE
Confidence 345777887777766 9999999999999999999999998 67777653
No 43
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=73.72 E-value=5.1 Score=37.26 Aligned_cols=56 Identities=16% Similarity=0.260 Sum_probs=43.8
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~ 703 (805)
.||.+.-+.++.++.||++.+|++...+-++|.-|. +.+++.....|+. -.|.+|.
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr~----~~Y~l~~ 75 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGKW----VHYRLSP 75 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcCE----EEEEECc
Confidence 455544445679999999999999999999999999 8999987765532 2466665
No 44
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.37 E-value=8.1 Score=28.93 Aligned_cols=34 Identities=26% Similarity=0.433 Sum_probs=30.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 652 ~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.++..+|++.+|++...+.+.|..|. +.+++.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 47899999999999999999999999 88888763
No 45
>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=73.28 E-value=5.4 Score=40.77 Aligned_cols=52 Identities=19% Similarity=0.222 Sum_probs=46.7
Q ss_pred EEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.++.-|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.+
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 4677899999999887889999999999999999999999999 889998764
No 46
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=72.50 E-value=7.3 Score=30.57 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=34.0
Q ss_pred hcCCCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 647 FNDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 647 Fn~~~~l-t~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+...+.+ |..+|++.+|++...+.+.|..|. +.+++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 4445567 899999999999999999999999 788887654
No 47
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=72.28 E-value=3.1 Score=35.83 Aligned_cols=44 Identities=20% Similarity=0.458 Sum_probs=34.9
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
..||...+..+.+++.+|.+.+|+++..|.++|..|. +.+.+..
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 4566666667789999999999999999999999999 7666653
No 48
>PRK10870 transcriptional repressor MprA; Provisional
Probab=72.17 E-value=9.1 Score=38.22 Aligned_cols=51 Identities=12% Similarity=0.158 Sum_probs=44.0
Q ss_pred EcHHHHHHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn~--~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 56678888877754 4579999999999999999999999999 899998865
No 49
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=71.82 E-value=88 Score=31.68 Aligned_cols=114 Identities=18% Similarity=0.340 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH----HHHhhccCCHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhhhhccCchhhHHHHH
Q 003648 332 IATAERQLLERHISAILDKG----FTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYIRRTGHGIVMDEEKDKDMVS 407 (805)
Q Consensus 332 ~~~l~~~LI~~~~~~ll~~g----l~~ll~~~~~~~L~~ly~Ll~~~~~l~~l~~~~~~yI~~~g~~iv~~~~~~~~~V~ 407 (805)
.+.+.+.||...-+.+++.| +-.||.. +.++++.|..|--.-...+.+.+.++.+|.++. ..|+
T Consensus 24 ~kelie~l~~~~~qk~l~~gE~v~il~Ll~~-kd~ef~~llkla~eq~k~e~~m~~Lea~VEkrD-----------~~IQ 91 (272)
T KOG4552|consen 24 VKELIETLINRDKQKMLKNGETVNILKLLDS-KDDEFKTLLKLAPEQQKREQLMRTLEAHVEKRD-----------EVIQ 91 (272)
T ss_pred HHHHHHHHHhhhHHHHHhcchHHHHHHHHHh-ccHHHHHHHHHhHhHHHHHHHHHHHHHHHHHhH-----------HHHH
Confidence 33344444444444455332 3333433 234555555544433455566666666665543 4466
Q ss_pred HHHHHHHHHHHHHH-HhccCCHHhHHHHHhHHHHHhhcCCCCchHHHHHHHHHHHhcC
Q 003648 408 SLLEFKASLDTIWE-QSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAG 464 (805)
Q Consensus 408 ~ll~l~~~~~~ii~-~~F~~~~~f~~~l~~af~~~iN~~~~k~~e~Laky~D~~Lk~~ 464 (805)
.|-.-.+..+.++. -||+-+..+ +.|++| ++++ -.+|.|-||.|.+-+..
T Consensus 92 qLqk~LK~aE~iLtta~fqA~qKL-ksi~~A-----~krp-vsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 92 QLQKNLKSAEVILTTACFQANQKL-KSIKEA-----EKRP-VSSEELIKYAHRISKHN 142 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-----hcCC-CCHHHHHHHHHHhhhcc
Confidence 66555555555544 477766554 345555 5555 46899999999986653
No 50
>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=71.28 E-value=10 Score=31.87 Aligned_cols=41 Identities=22% Similarity=0.476 Sum_probs=34.8
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
||+..... ..|++||.+.||++.+.|...|.-|. +-+++.+
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 44444444 89999999999999999999999999 8888875
No 51
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=69.87 E-value=11 Score=35.32 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=36.5
Q ss_pred HHHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 640 QTVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 640 Qa~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
++++.+.-++. ..+|.++|++.+|++...+.+.|..|. +.+++...
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 88888653
No 52
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=69.66 E-value=1.1e+02 Score=33.72 Aligned_cols=160 Identities=13% Similarity=0.236 Sum_probs=91.6
Q ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHhccc----chhHHHHHHHHHHHHHhhhhhccCc-------hhhHHHHHHHHH
Q 003648 343 HISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLLE 411 (805)
Q Consensus 343 ~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yI~~~g~~iv~~~-------~~~~~~V~~ll~ 411 (805)
++..++.+.|..-...++.+.+.+.++||-.+ .|++....-+...|.....+.+... ..+--|+..|..
T Consensus 7 ~L~~~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~ 86 (331)
T PF08318_consen 7 SLCEIFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTK 86 (331)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHH
Confidence 34455667788888999999999999999776 4677776666666666665555432 123346666666
Q ss_pred HHHHHHH-------HHHHhccCCHHh--HHHHHh--------HHHHHhhcCC-CCchHHHHHHHHHHHhc----------
Q 003648 412 FKASLDT-------IWEQSFSKNEAF--CNTIKD--------AFEYLINLRQ-NRPAELIAKFLDEKLRA---------- 463 (805)
Q Consensus 412 l~~~~~~-------ii~~~F~~~~~f--~~~l~~--------af~~~iN~~~-~k~~e~Laky~D~~Lk~---------- 463 (805)
+++..-. +|..+||..... ...+.. -+..|...+. .+...-+..|-...+.+
T Consensus 87 LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~ 166 (331)
T PF08318_consen 87 LFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSS 166 (331)
T ss_pred HHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccc
Confidence 6666544 456788754411 111111 2223333321 11112233333333322
Q ss_pred --------CCCCCChHHHHhhhccceeeeeeecchHHHHHHHHHHHHHHHhCCC
Q 003648 464 --------GNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 509 (805)
Q Consensus 464 --------~~k~~~~~e~e~~l~~i~~lf~~l~~KD~Fe~~Y~k~LakRLL~~~ 509 (805)
+....+.-+++..|+++..+.... ..|.++++.|.-...
T Consensus 167 ~~~~~~~~~~~~~d~reld~lL~Eis~i~~~w-------~lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 167 RAASSSQSEDEGIDPRELDALLNEISLILQRW-------SLYCRFISRKWNEFS 213 (331)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhccc
Confidence 001123356788888877776443 389999999987743
No 53
>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=69.57 E-value=6.3 Score=39.00 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=43.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCCCCceeE
Q 003648 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRI 712 (805)
Q Consensus 652 ~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~~~~~ri 712 (805)
-+|..+|++.+|++...+.+++..|. +.++|.+.. ...|.+|++|--+-.+.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~~~ 126 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGDRD 126 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCcHH
Confidence 47899999999999999999999999 889998753 35899999986554443
No 54
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=68.97 E-value=11 Score=39.86 Aligned_cols=46 Identities=22% Similarity=0.446 Sum_probs=40.6
Q ss_pred HHHHHhhcCCCC-CCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDAQK-LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~~~-lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..||.+|..... +++.||++.+|+|...+.|.|..|. ..+.+.+.+
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 457888887654 7899999999999999999999999 999999876
No 55
>PRK11569 transcriptional repressor IclR; Provisional
Probab=68.52 E-value=10 Score=40.63 Aligned_cols=46 Identities=9% Similarity=0.299 Sum_probs=40.3
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..||-+|.+. ..+++.||++.+|++...+.|.|.+|. ..+.|.+.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 3477888875 579999999999999999999999999 899998754
No 56
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=68.33 E-value=11 Score=40.26 Aligned_cols=46 Identities=15% Similarity=0.117 Sum_probs=40.5
Q ss_pred HHHHHhhcCC-CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDA-QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~-~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..||-+|... ..+|+.||++.+|++...+.|.|.+|. ..+.|.+.+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~ 74 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDS 74 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 4488889765 479999999999999999999999999 889998764
No 57
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=67.28 E-value=11 Score=40.12 Aligned_cols=47 Identities=19% Similarity=0.304 Sum_probs=40.5
Q ss_pred HHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCC
Q 003648 641 TVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (805)
Q Consensus 641 a~ILllFn~~~-~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~ 689 (805)
+.||.+|.+.+ .+|..||++.+|++...+.|.|..|. ..++|.+.+.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~~ 61 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSAS 61 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecC
Confidence 34778887654 59999999999999999999999999 8999988653
No 58
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=67.18 E-value=11 Score=29.66 Aligned_cols=36 Identities=11% Similarity=0.303 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 650 AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 650 ~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.+..|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 5678999999999999999999999999 77887654
No 59
>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=67.11 E-value=9 Score=28.68 Aligned_cols=35 Identities=20% Similarity=0.546 Sum_probs=26.8
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL 676 (805)
.||-.+......++.+|++.+|+++..+.+-++-|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46666666688999999999999999999887765
No 60
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=65.89 E-value=11 Score=34.06 Aligned_cols=45 Identities=11% Similarity=0.329 Sum_probs=39.1
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
..-.||..+..+...|+.+|++.+|++...+.+.+..|. +.+++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCee
Confidence 345677778777889999999999999999999999999 777776
No 61
>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=65.19 E-value=14 Score=38.86 Aligned_cols=44 Identities=25% Similarity=0.446 Sum_probs=38.7
Q ss_pred HHHHHhhcC-CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 641 TVVLMLFND-AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 641 a~ILllFn~-~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
..||-+|.. ...+|+.||++.+|++...+.|.|.+|. ..+.|.+
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 4579999999999999999999999999 8888876
No 62
>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=64.88 E-value=6.2 Score=32.82 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=35.9
Q ss_pred HHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhccccccc
Q 003648 744 AIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQI 800 (805)
Q Consensus 744 aIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~ 800 (805)
.|-.+|+.++.++.++|-.+ |..+++.+ +..|+.|+.+|||+.-..
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~------~~~s~~~v-----e~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELARE------FGISPEAV-----EAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHH------TT--HHHH-----HHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCcCHHHH-----HHHHHHHHHCCcEEEecC
Confidence 35678999999999988744 68889988 999999999999987543
No 63
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=64.84 E-value=17 Score=35.38 Aligned_cols=59 Identities=15% Similarity=0.325 Sum_probs=44.0
Q ss_pred HHHHHHHhhcCCC-CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecC
Q 003648 639 FQTVVLMLFNDAQ-KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 704 (805)
Q Consensus 639 ~Qa~ILllFn~~~-~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~ 704 (805)
+.+.+.|.-+..+ ..|.++|++..|+++..|.+.|..|. |.+++...+ | .+.-|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-G----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-G----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-C----CCCCccCCCC
Confidence 3444555555554 68899999999999999999999999 999987543 1 3455777664
No 64
>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=63.65 E-value=17 Score=34.11 Aligned_cols=44 Identities=20% Similarity=0.363 Sum_probs=36.1
Q ss_pred HHHHhhcC--CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 642 VVLMLFND--AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 642 ~ILllFn~--~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.+|+.+.. .+.+|..||++.+|++...+.+.|..|. +.+++...
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 34545543 3579999999999999999999999999 88998653
No 65
>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=63.62 E-value=12 Score=30.93 Aligned_cols=45 Identities=31% Similarity=0.412 Sum_probs=35.7
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhc-CCcceee
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLAC-GKVRVLQ 685 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~-~k~~iL~ 685 (805)
..|--+.++...+|+.+|+..||+++.++..+|--|+. +|..+-.
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~ 56 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEE 56 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEE
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEe
Confidence 34566778888999999999999999999999999995 3444443
No 66
>PF13730 HTH_36: Helix-turn-helix domain
Probab=63.18 E-value=16 Score=28.57 Aligned_cols=28 Identities=14% Similarity=0.385 Sum_probs=25.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003648 654 SFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (805)
Q Consensus 654 t~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (805)
|.+.|++.+|++...+.++|..|. +.++
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 5554
No 67
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=62.92 E-value=9.9 Score=31.04 Aligned_cols=35 Identities=23% Similarity=0.473 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 649 ~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
..+.+|+.+|.+.|+++.+.++..|-.|+ +.+++.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCee
Confidence 34689999999999999999999999999 777764
No 68
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=61.76 E-value=16 Score=33.01 Aligned_cols=51 Identities=18% Similarity=0.373 Sum_probs=44.8
Q ss_pred EcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++..|..||......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 678899999888877766669999999999999999999999 888888764
No 69
>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=60.49 E-value=16 Score=29.54 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 651 QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 651 ~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..+|..+|++.+|++...+.+.|..|. +.+++...+
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 888888653
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=59.26 E-value=21 Score=28.88 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=36.3
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
|..+-.+.+.++..+|++.+|++...+...+..|. +.+++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577899999999999999999999999999 888887765
No 71
>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=58.79 E-value=13 Score=29.90 Aligned_cols=38 Identities=13% Similarity=0.348 Sum_probs=29.5
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
|.-+|-++-+.+.+++.+|++.+|++...++.-+.-|-
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 45555444447789999999999999999998887775
No 72
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=58.12 E-value=80 Score=36.96 Aligned_cols=50 Identities=10% Similarity=0.242 Sum_probs=44.8
Q ss_pred EEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 635 AVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
.++..|..||......+.++..+|++.+|++...+.+.+.+|. +.+++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le--~kGlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLE--EKGLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHH--hCCCEEE
Confidence 4678899999999888899999999999999999999999999 6677764
No 73
>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=57.71 E-value=15 Score=32.88 Aligned_cols=43 Identities=23% Similarity=0.446 Sum_probs=37.0
Q ss_pred EEcHHHHHHHHhhcC----CCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 635 AVSLFQTVVLMLFND----AQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~----~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
.++..|-.||-.+.+ .+.+++++|++.+++++.+++.+|..|+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~ 90 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLS 90 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH
Confidence 578899999988887 3579999999999999999999999999
No 74
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=56.74 E-value=32 Score=32.83 Aligned_cols=40 Identities=8% Similarity=0.325 Sum_probs=34.4
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 647 Fn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+..+..++..+|++.+|++...+++.|+.|. +.+++...+
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 3344578999999999999999999999999 889887654
No 75
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=56.70 E-value=28 Score=34.64 Aligned_cols=55 Identities=20% Similarity=0.147 Sum_probs=42.7
Q ss_pred EEEEEcHHHHHHHHhhcCCCC-CCHHHHHHHh--CCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 632 KELAVSLFQTVVLMLFNDAQK-LSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 632 ~~l~vs~~Qa~ILllFn~~~~-lt~~eI~~~t--~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+++--+-+..+|+-+..-.+. -+.++|++.+ +|+.++++.+|..|. +.++|.+..
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 344445556666666554443 3899999999 999999999999999 999999864
No 76
>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=53.48 E-value=5.1e+02 Score=31.80 Aligned_cols=52 Identities=12% Similarity=0.173 Sum_probs=31.2
Q ss_pred chhHHHHHHHHHHHHHhhhhh-ccC-chh--hHHHHHHHHHHHHHHHHHHHHhccC
Q 003648 375 NALESLRQALAMYIRRTGHGI-VMD-EEK--DKDMVSSLLEFKASLDTIWEQSFSK 426 (805)
Q Consensus 375 ~~l~~l~~~~~~yI~~~g~~i-v~~-~~~--~~~~V~~ll~l~~~~~~ii~~~F~~ 426 (805)
.+++.|.+.+.+|+...+..- ... -.. =..+-+..+..|.++..++..|+.+
T Consensus 646 k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 646 KGIEALYKRVEKHFSRDADDPSFEEDLLQVVWSAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHcCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 566777777776662221100 000 000 0256777899999999999999864
No 77
>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=52.46 E-value=29 Score=27.60 Aligned_cols=39 Identities=18% Similarity=0.440 Sum_probs=31.7
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 648 NDAQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 648 n~~~~l-t~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.....+ |..+|++.+|++...+.+.|..|. +.++|...+
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~~ 59 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELE--AEGLVERRP 59 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 333444 499999999999999999999999 888887543
No 78
>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=51.98 E-value=11 Score=34.13 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=31.2
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
.+.|+..+..++.++-++|++.+|++..++++.|..|. ..+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~--~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLY--EDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHH--HHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeE
Confidence 34566666666789999999999999999999999999 666663
No 79
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=51.94 E-value=22 Score=36.75 Aligned_cols=123 Identities=15% Similarity=0.217 Sum_probs=73.0
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC--C--CCCCCCCCCeEEEec----CCCCCceeE
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL--P--KGRDVEDDDSFVFNE----GFTAPLYRI 712 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~--~--~~~~i~~~d~f~~N~----~F~~~~~ri 712 (805)
..||.+.+..+..|..||++.+||+...++++|+.|. .-+++... + .|+ +.-.|.+-. .|.+..-.+
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le--~~Glv~~~~~~~g~GR---P~~~y~Lt~~g~~~f~~~y~~l 88 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLE--AEGLVEVERQQGGRGR---PAKLYRLTEKGREQFPKRYGEL 88 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHH--hCcceeeeeccCCCCC---CceeeeecccchhhcchhhHHH
Confidence 4577777888899999999999999999999999999 65555432 1 122 333444322 121111000
Q ss_pred Eecccccccchhh--hhhhhHhHHhhhHHHHHHHHHHhhccCCCCChHHHHHHHHHhc---CCCCC
Q 003648 713 KVNAIQMKETVEE--NTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQV---LPPVL 773 (805)
Q Consensus 713 ki~~i~~ket~~e--~~~~~~~v~~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l---~F~~~ 773 (805)
-+..+ ...++ ..+....+.+.|...+-|..--.|.- ..+.++.+..+.+.+ .|.|.
T Consensus 89 ~~~~l---~~l~~~~G~~~l~~~l~~r~~~~~~~~~~~~~~--~~~~ee~~e~Lv~l~~~~gy~~e 149 (218)
T COG2345 89 ALALL---DALEETGGEEALNAFLEKRAQAIGAQYRPAMGG--DADLEEKVERLVELLSDLGYMPE 149 (218)
T ss_pred HHHHH---HHHHHhccHHHHHHHHHHHHHHHHHHHhhcCCC--CCCHHHHHHHHHHHHHhCCcccc
Confidence 00000 00111 11233556788888888888888876 566666665554444 46655
No 80
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=51.53 E-value=20 Score=38.12 Aligned_cols=48 Identities=15% Similarity=0.190 Sum_probs=42.8
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
=|..||-+.++.+.+++.||++.+|+++..++|-|..|. +.++|.+.-
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~~ 53 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEEE
Confidence 367788889999999999999999999999999999999 888887753
No 81
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=50.49 E-value=27 Score=35.06 Aligned_cols=68 Identities=19% Similarity=0.313 Sum_probs=52.4
Q ss_pred CceeEeecCCceEEEEEEecCceEEEEEcHHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003648 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (805)
Q Consensus 609 ~RkL~W~~~lg~~~l~~~f~~~~~~l~vs~~Qa~ILllFn~~--~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (805)
.|.-.|.+..|.++++ +.+.|. |++.||+-||.-... ..||.+.|++..+|+.+++...|..+. -+.|
T Consensus 96 ~r~~~~~~~fg~~ep~-~vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~--~F~v 165 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPE-KVPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK--PFEV 165 (179)
T ss_pred CCCCcccccccccCcc-cCCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC--Ccee
Confidence 3445588889988885 356676 567899888765443 479999999999999999999998887 4444
No 82
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=49.88 E-value=26 Score=34.48 Aligned_cols=49 Identities=10% Similarity=0.199 Sum_probs=42.5
Q ss_pred EcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+.-.-.-||-.+.++..+|+.+|++.+|++...+.+.++.|. +.+++..
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 344566788888898999999999999999999999999999 7787763
No 83
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=49.34 E-value=30 Score=26.80 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 651 QKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 651 ~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
+.+|++||++.+|+++..++..+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 358999999999999998887764
No 84
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=48.84 E-value=30 Score=33.56 Aligned_cols=48 Identities=4% Similarity=0.262 Sum_probs=41.9
Q ss_pred EcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 636 VSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
++..--.||-.+..+...|+.+|++.+|+++..+.+.++.|. ..+++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~--~~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK--QAGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCee
Confidence 455666788888888899999999999999999999999999 777775
No 85
>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=48.51 E-value=41 Score=25.69 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=24.8
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhH
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~s 675 (805)
+.+|-+.| ...+|++||++.+|++...+.+....
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 34445666 45689999999999999888776543
No 86
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=47.02 E-value=31 Score=36.50 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=43.3
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (805)
-|..|+-.+++++.+++.||++.+|+++..++|-|..|. +.+++.+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~gg 55 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecCC
Confidence 356788889999999999999999999999999999998 77888775444
No 87
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=47.01 E-value=30 Score=35.71 Aligned_cols=49 Identities=18% Similarity=0.368 Sum_probs=42.6
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
|..-..||-+....+.+.+.||++.+|+|...+..+++.|. +.+++..+
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeee
Confidence 44445688888888899999999999999999999999999 99998754
No 88
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=46.15 E-value=53 Score=31.02 Aligned_cols=63 Identities=22% Similarity=0.347 Sum_probs=49.7
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCC---CCeEEEecCCC
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVED---DDSFVFNEGFT 706 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~---~d~f~~N~~F~ 706 (805)
-.|-+..+.+..|+.|+++.+|=+.+.+-++|..|. ..+|+..+.+|+...+ -+.|.++-.|.
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 355667788899999999999999999999999999 9999987666654433 24566666664
No 89
>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=45.81 E-value=48 Score=33.77 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=37.0
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
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 455545455679999999999999999999999999 88888765
No 90
>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=45.71 E-value=28 Score=28.70 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=36.7
Q ss_pred EcHHHHHHHHhhcC-----CCCCCHHHHHHHhCCC-HHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn~-----~~~lt~~eI~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++.-|.-||...-+ .-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.|
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCC
Confidence 34556666654433 2356999999999996 999999999999 888888765
No 91
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.92 E-value=31 Score=34.52 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=36.9
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
...||...-.++.+|-++|++.+||+..+++++|..|. ..+++.
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 34466655566789999999999999999999999999 777776
No 92
>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=44.90 E-value=36 Score=33.42 Aligned_cols=43 Identities=21% Similarity=0.285 Sum_probs=35.3
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
..|+..+-.++.+|-+||++.+||+..++++.|..|. ..+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~--e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALY--DAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCce
Confidence 3455444455689999999999999999999999999 778774
No 93
>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=44.53 E-value=30 Score=28.67 Aligned_cols=41 Identities=15% Similarity=0.303 Sum_probs=30.1
Q ss_pred HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 644 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 644 LllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
.-...+.+.+|++||+..++++++.|...|.-|+ +-+-+.+
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~--~kG~I~~ 46 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLI--RKGYIRK 46 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH--CCTSCEE
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEE
Confidence 3344566789999999999999999999999999 5444443
No 94
>PRK00215 LexA repressor; Validated
Probab=44.34 E-value=47 Score=33.76 Aligned_cols=52 Identities=21% Similarity=0.329 Sum_probs=42.2
Q ss_pred EcHHHHHHHHhhcC-----CCCCCHHHHHHHhCC-CHHHHHHHHhHhhcCCcceeeeCCC
Q 003648 636 VSLFQTVVLMLFND-----AQKLSFQDIKDATGI-EDKELRRTLQSLACGKVRVLQKLPK 689 (805)
Q Consensus 636 vs~~Qa~ILllFn~-----~~~lt~~eI~~~t~i-~~~~l~~~L~sL~~~k~~iL~k~~~ 689 (805)
++.-|..||..+.+ ....|+.||++.+|+ +...+.+.|..|. +.+++.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCC
Confidence 35568888865542 346899999999999 9999999999999 8888887654
No 95
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=44.19 E-value=28 Score=36.86 Aligned_cols=49 Identities=22% Similarity=0.478 Sum_probs=43.4
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (805)
|-.||-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.-.|
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~hGG 55 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRVHGG 55 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEEeCC
Confidence 55788888999999999999999999999999999999 88888885433
No 96
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.71 E-value=32 Score=33.02 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=41.9
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+-.-.-||-.+.++...++.+|++.+|++...+.+.+.-|. +.+|+..
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 44556788888888889999999999999999999999999 8888874
No 97
>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=42.44 E-value=24 Score=35.46 Aligned_cols=26 Identities=38% Similarity=0.617 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 652 KLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 652 ~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
.+|+++|++.|||..+++..+|+.|-
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 69999999999999999999999885
No 98
>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=41.58 E-value=42 Score=29.37 Aligned_cols=45 Identities=18% Similarity=0.370 Sum_probs=37.4
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHh-CCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
-+.||..... +...+.||.+.+ |+++..|.+.|..|. ..+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 3566766656 689999999999 999999999999999 88998764
No 99
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=39.83 E-value=40 Score=36.11 Aligned_cols=49 Identities=12% Similarity=0.179 Sum_probs=43.1
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
--|..|+-+.+..+.+++.||++.+|++...++|-|..|. ..+++.+..
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le--~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLE--KQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHH--hCCCeEEEe
Confidence 3477888899999899999999999999999999999998 777887754
No 100
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=39.29 E-value=43 Score=35.52 Aligned_cols=49 Identities=14% Similarity=0.259 Sum_probs=42.3
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCC
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 689 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~ 689 (805)
-|..|+-+.++.+.+++.||++.++++...++|-|..|. +.++|.+.-.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~~G 54 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRHHG 54 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecC
Confidence 356678778888999999999999999999999999999 7788877543
No 101
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=39.09 E-value=28 Score=35.04 Aligned_cols=46 Identities=11% Similarity=0.177 Sum_probs=40.2
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
-+..|+.+.+.++.+++.+|++.+|+++..++|=|..|. ..+++.+
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 467788889999999999999999999999999999998 6555544
No 102
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=38.39 E-value=50 Score=34.70 Aligned_cols=46 Identities=15% Similarity=0.295 Sum_probs=39.1
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
|..|+..+++++.++.+||++.+|+++..++|-|.-|. ..+.|.+.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~--~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQ--TQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 55688888888899999999999999999999999998 55556553
No 103
>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=37.41 E-value=38 Score=34.31 Aligned_cols=51 Identities=22% Similarity=0.300 Sum_probs=42.3
Q ss_pred EcHHHHHHHHhhcCC-----CCCCHHHHHHHhCCC-HHHHHHHHhHhhcCCcceeeeCC
Q 003648 636 VSLFQTVVLMLFNDA-----QKLSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 636 vs~~Qa~ILllFn~~-----~~lt~~eI~~~t~i~-~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++..|..||....+. -..|+.||++.+|++ ...+.+.|..|. +.++|.+.+
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 467788888766532 258899999999998 999999999999 889998754
No 104
>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=37.37 E-value=44 Score=23.55 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003648 653 LSFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (805)
Q Consensus 653 lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (805)
+|-+||++.+|+..+.+-|.|.-|. +.++
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~--~~gl 31 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE--RQGL 31 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH--HTTS
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH--HcCC
Confidence 6789999999999999999999887 4443
No 105
>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=36.42 E-value=74 Score=24.26 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=27.3
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
-|.-++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 4 ~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 4 REREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444444442 458999999999999998888876654
No 106
>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=35.54 E-value=81 Score=25.99 Aligned_cols=58 Identities=10% Similarity=0.094 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhcccccccC
Q 003648 735 QDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQIT 801 (805)
Q Consensus 735 ~dR~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~~ 801 (805)
.+|+..|=.+|...++..+--. =+.|+.+.+.+. ++.-+ ...|+.|.++|||.+++..
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~P---t~rEIa~~~g~~-S~~tv-----~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPP---TVREIAEALGLK-STSTV-----QRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS------HHHHHHHHTSS-SHHHH-----HHHHHHHHHTTSEEEGCCS
T ss_pred CHHHHHHHHHHHHHHHHcCCCC---CHHHHHHHhCCC-ChHHH-----HHHHHHHHHCcCccCCCCC
Confidence 3567777778888777665322 234445666665 45556 8999999999999998764
No 107
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.50 E-value=78 Score=24.02 Aligned_cols=39 Identities=23% Similarity=0.398 Sum_probs=29.0
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
+.-+.-|+.++. ..++..+|++.+|++...+.+.+..+.
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 344455555553 357999999999999999988887654
No 108
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=35.19 E-value=61 Score=34.46 Aligned_cols=42 Identities=12% Similarity=0.319 Sum_probs=35.8
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+|++.-+ ++.|++||...++++...+..+|.-|. +.+++.++
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 4554444 789999999999999999999999999 88888874
No 109
>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=34.92 E-value=99 Score=26.59 Aligned_cols=49 Identities=12% Similarity=0.361 Sum_probs=40.9
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
.++++|=+.-..+..+.-.+|++.+++++..++..+..|. ..++|.+.|
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 3556666666677899999999999999999999999999 889997544
No 110
>PRK11050 manganese transport regulator MntR; Provisional
Probab=34.28 E-value=87 Score=30.37 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=36.8
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.|+.++...+.++..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le--~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLA--RDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 455566667789999999999999999999999999 66777653
No 111
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=33.55 E-value=50 Score=37.02 Aligned_cols=67 Identities=27% Similarity=0.358 Sum_probs=42.1
Q ss_pred eeEeecCCceEEEEEEecCceE-EEE----EcHHHHHHHHhhcC-CC-CCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 611 RLMWQNSLGHCVLKAEFPKGKK-ELA----VSLFQTVVLMLFND-AQ-KLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 611 kL~W~~~lg~~~l~~~f~~~~~-~l~----vs~~Qa~ILllFn~-~~-~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
-+.+.+.||..|=++--|.+.. +|- -+-+-..||-++-+ .+ .+|+++|++.|||..+++..+|++|-
T Consensus 281 LIdFSYeLSr~E~~~GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhhcccCcCCCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 3567777887765553333211 110 02233334433333 22 39999999999999999999999986
No 112
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=32.26 E-value=87 Score=27.85 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=44.5
Q ss_pred EEEcHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 634 LAVSLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 634 l~vs~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+..+....-||..+...+.=...-|+..|+++.+++...|..|. ..++|.+..
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 44566777888888887766677899999999999999999999 899998754
No 113
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=31.79 E-value=73 Score=23.95 Aligned_cols=30 Identities=20% Similarity=0.427 Sum_probs=21.2
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999988774
No 114
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=31.42 E-value=72 Score=34.27 Aligned_cols=39 Identities=33% Similarity=0.472 Sum_probs=30.7
Q ss_pred HHHHHHHhh-cCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 639 FQTVVLMLF-NDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 639 ~Qa~ILllF-n~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
+...|+-.+ +....+|+++|++.|||..+++..+|++|-
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 444555443 335689999999999999999999999875
No 115
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=30.89 E-value=1.3e+02 Score=24.93 Aligned_cols=55 Identities=11% Similarity=0.146 Sum_probs=41.3
Q ss_pred HHHHHHHHhhccCCC--CChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhcccccccCCCCC
Q 003648 740 QVDAAIVRIMKTRKV--LSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQITNITW 805 (805)
Q Consensus 740 ~I~AaIVRIMK~rK~--l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~~~~~~ 805 (805)
..+..|...||.+.. ++-.+|-.++ -.+...+ .+.+..|.+.+||.++....=.|
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~l------gl~~~~v-----~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNL------GLPKKEV-----NRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHH------CCCHHHH-----HHHHHHHHHCCCEEecCCCCCce
Confidence 355678889999877 9988777554 3345566 89999999999999977543445
No 116
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.35 E-value=92 Score=29.64 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=36.0
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
.|..+.+..+..++.+|++.++++...+.+.|..|. +.+++.+
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~--~~Gli~~ 54 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD--KDEYLIY 54 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH--HCCCEEE
Confidence 344455667788999999999999999999999999 7787764
No 117
>PHA02943 hypothetical protein; Provisional
Probab=30.26 E-value=84 Score=30.51 Aligned_cols=43 Identities=23% Similarity=0.261 Sum_probs=34.6
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
||-.+ ..+..|..||++.+|++-.+++-.|.-|. +-+.+.+..
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~ 58 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVE 58 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEe
Confidence 44444 66678899999999999999999999998 777666543
No 118
>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=30.07 E-value=84 Score=27.17 Aligned_cols=34 Identities=6% Similarity=0.133 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHH
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTL 673 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L 673 (805)
=|+.|+-...+ +.+|+.+|++..|++...+.+.|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 36678877888 89999999999999999988866
No 119
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=29.85 E-value=1.2e+02 Score=23.13 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=26.0
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhH
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQS 675 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~s 675 (805)
+.+.|+.+.-+. .|+.+|+..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344455444332 69999999999999999998765
No 120
>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=29.78 E-value=1.2e+02 Score=22.74 Aligned_cols=45 Identities=7% Similarity=0.201 Sum_probs=34.8
Q ss_pred HHHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhccc
Q 003648 741 VDAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWT 796 (805)
Q Consensus 741 I~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~ 796 (805)
.+-.|+..+.....++..+|-..+ ..+..-+ .+.|..|.+.|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv-----~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL------GISRSTV-----NRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHH-----HHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHH-----HHHHHHHHHCcCcC
Confidence 456788888889999999988766 3456666 89999999999985
No 121
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=29.52 E-value=83 Score=26.58 Aligned_cols=49 Identities=18% Similarity=0.249 Sum_probs=40.8
Q ss_pred HHHHHHHHhhcCC--CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 638 LFQTVVLMLFNDA--QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 638 ~~Qa~ILllFn~~--~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
..|.++|...-.. .+++-.+|...+|++...+-..++.|. +.+++.+.+
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 4577788777653 578899999999999999999999999 888888754
No 122
>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=29.31 E-value=2.1e+02 Score=24.92 Aligned_cols=55 Identities=9% Similarity=0.200 Sum_probs=40.3
Q ss_pred HHHH-HHHHHHHHHHHhc-CCCCCcHHHHHHHHHhhhccCchhHHHHHHHHHHHHHH
Q 003648 105 EDTW-AKLKLAIKAIFLK-QPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHI 159 (805)
Q Consensus 105 e~~W-~~L~~aI~~I~~~-~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~L~~~i~~~l 159 (805)
+.+| ..++..+..+... ...+++|++|+..|.-.++....+.+...+-..|.+++
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 5678 4777777777765 45678999999999999998877777666666666554
No 123
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=28.89 E-value=1.1e+02 Score=25.98 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=38.7
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcce
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRV 683 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~i 683 (805)
.+=|+.++-++...+.-|+++|++.||-..-.++-+|..+.-.|.++
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 34589999888888899999999999999999999998886224444
No 124
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=28.85 E-value=70 Score=25.86 Aligned_cols=37 Identities=19% Similarity=0.458 Sum_probs=31.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 650 AQKL-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 650 ~~~l-t~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
++.+ |..+|++..|++-..++++|.-|. ..+++...|
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~--~~g~i~~~~ 58 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLE--AEGLIERRP 58 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHH--HCCcEEEEC
Confidence 4678 999999999999999999999999 888887755
No 125
>PRK06474 hypothetical protein; Provisional
Probab=28.63 E-value=1.5e+02 Score=29.59 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=40.7
Q ss_pred EEcHHHHHHHHhhcCCC-CCCHHHHHHHh-CCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 635 AVSLFQTVVLMLFNDAQ-KLSFQDIKDAT-GIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 635 ~vs~~Qa~ILllFn~~~-~lt~~eI~~~t-~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
-.++.-..||-.+-..+ .+|..+|.+.+ +++...+-++|..|. +.+++...+
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 34555666775554444 49999999999 799999999999999 889988643
No 126
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=28.48 E-value=75 Score=33.86 Aligned_cols=51 Identities=18% Similarity=0.337 Sum_probs=43.4
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003648 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKG 690 (805)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (805)
.-|.++-++-+.++.++-+||..++|+|...+-|.|..|. |.+++.+...|
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~K~G 246 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKEKKG 246 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEEEeC
Confidence 3466666777777889999999999999999999999999 99998876554
No 127
>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=28.11 E-value=85 Score=27.48 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=31.7
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
...++.-++....++++++|++.++++.+++...+..++
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 344444555677899999999999999999999999998
No 128
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.47 E-value=1.4e+02 Score=22.04 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=27.6
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHh
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSL 676 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL 676 (805)
+..+..++.++- .+.++..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444444432 245899999999999999988877654
No 129
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.39 E-value=1.2e+02 Score=29.66 Aligned_cols=45 Identities=13% Similarity=0.270 Sum_probs=38.1
Q ss_pred HHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 642 VVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 642 ~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+|..++.+.+.....+|++.+++++..+...++-|. +.+++...|
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 344555567789999999999999999999999999 888888755
No 130
>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=26.27 E-value=1.5e+02 Score=26.92 Aligned_cols=57 Identities=18% Similarity=0.325 Sum_probs=41.1
Q ss_pred HHHHhhcC-CCCCCHHHHHHHh-----CCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEec
Q 003648 642 VVLMLFND-AQKLSFQDIKDAT-----GIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNE 703 (805)
Q Consensus 642 ~ILllFn~-~~~lt~~eI~~~t-----~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~ 703 (805)
.||-.+.+ ...+|.+||.+.+ +++...+-|+|..|. ..+++.+...+. ....|.++.
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 45544444 4579999999988 689999999999999 888888743211 124566664
No 131
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=26.23 E-value=1.9e+02 Score=24.90 Aligned_cols=34 Identities=21% Similarity=0.343 Sum_probs=29.6
Q ss_pred HHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 644 LMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 644 LllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
++..++.+.+|-++|++.+|++...+-++++.|-
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHH
Confidence 3445566789999999999999999999999998
No 132
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=25.90 E-value=94 Score=32.87 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=36.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 639 FQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 639 ~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
=|..|+-+.+.++.+++.+|++.+|+++..++|=|..|.
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 477899999999999999999999999999999999987
No 133
>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=25.86 E-value=1.6e+02 Score=25.26 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=27.8
Q ss_pred HHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 640 QTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 640 Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
.-.+|-+.-+...+|..+|+..+|.+.+++...|..+.
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 34466677788899999999999999999999998875
No 134
>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=25.61 E-value=75 Score=24.94 Aligned_cols=49 Identities=12% Similarity=0.166 Sum_probs=34.8
Q ss_pred HHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhcccccccC
Q 003648 742 DAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQIT 801 (805)
Q Consensus 742 ~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~~ 801 (805)
+..|..+.-....++..+|-..+ ..++.-+ -+.|+.|+++|||++.+..
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~------~~~~~~~-----t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKL------GISRSTV-----TRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHH------TS-HHHH-----HHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH------CCChhHH-----HHHHHHHHHCCCEEeccCC
Confidence 44556666667777777666443 4456666 8999999999999987653
No 135
>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=25.60 E-value=98 Score=24.60 Aligned_cols=44 Identities=16% Similarity=0.246 Sum_probs=37.6
Q ss_pred HHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhcccc
Q 003648 743 AAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTM 797 (805)
Q Consensus 743 AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~ 797 (805)
..|+..++.++.++..+|.+. |.+++.-| ++-+..|.++++|.+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~------~~VS~~Ti-----RRDl~~L~~~g~i~r 46 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE------FGVSEMTI-----RRDLNKLEKQGLIKR 46 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH------HCcCHHHH-----HHHHHHHHHCCCEEE
Confidence 468888999999999999854 57788888 999999999998875
No 136
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=25.31 E-value=98 Score=35.50 Aligned_cols=38 Identities=32% Similarity=0.465 Sum_probs=29.9
Q ss_pred HHHHHH-hhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 640 QTVVLM-LFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 640 Qa~ILl-lFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
-..||- +.+..+.+|+++|++.|||..+++..+|++|-
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~ 399 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLN 399 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 334442 33444689999999999999999999999885
No 137
>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=25.26 E-value=81 Score=29.53 Aligned_cols=50 Identities=12% Similarity=0.151 Sum_probs=40.0
Q ss_pred EcHHHHHHHHh--hcC--------CCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 636 VSLFQTVVLML--FND--------AQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 636 vs~~Qa~ILll--Fn~--------~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+-.+.-..++. .|. .-+.|.++|+..++-+.+.++.+|..|. +.+++...
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34556666666 444 3479999999999999999999999999 99998753
No 138
>smart00753 PAM PCI/PINT associated module.
Probab=24.61 E-value=1.3e+02 Score=25.74 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003648 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (805)
Q Consensus 649 ~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (805)
....+++++|++.++++.+++...+..++ ..+.|
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 139
>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=24.61 E-value=1.3e+02 Score=25.74 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCccee
Q 003648 649 DAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVL 684 (805)
Q Consensus 649 ~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL 684 (805)
....+++++|++.++++.+++...+..++ ..+.|
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 140
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.57 E-value=87 Score=23.70 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=21.5
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
|+.++.+ .+|..+|++.+|++...+.+-+.-+.
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 4444444 78999999999999999888776654
No 141
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=24.56 E-value=1.9e+02 Score=27.30 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=39.4
Q ss_pred EcHHHHHHHHhhcCCCCCCHHHHHHHh----CCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 636 VSLFQTVVLMLFNDAQKLSFQDIKDAT----GIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 636 vs~~Qa~ILllFn~~~~lt~~eI~~~t----~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+|..+..|+..+=+.+..|..||.+.+ ++....+...|.-|. +-+++.+.
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~--~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLV--DKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHH--HCCceeee
Confidence 456678888776667789999977665 788899999999999 77887653
No 142
>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=24.50 E-value=4.2e+02 Score=29.14 Aligned_cols=53 Identities=15% Similarity=0.378 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHhccc----chhHHHHHHHHHHHHHhhhhh
Q 003648 343 HISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGI 395 (805)
Q Consensus 343 ~~~~ll~~gl~~ll~~~~~~~L~~ly~Ll~~~----~~l~~l~~~~~~yI~~~g~~i 395 (805)
.+..++.+.|..-+++++...+.+.++||-.+ .|++....-+.+.|......+
T Consensus 7 ~L~~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~ 63 (324)
T smart00762 7 TLTELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSL 63 (324)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHH
Confidence 44455667788889999999999999999877 456666655555555544433
No 143
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.47 E-value=1.2e+02 Score=31.34 Aligned_cols=37 Identities=19% Similarity=0.268 Sum_probs=32.7
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 648 NDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 648 n~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+....+|.++|++.+++++..++.++..|+ .++++..
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~--~~~~~~~ 210 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLV--NCHILFT 210 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHH--hCCEEEE
Confidence 335689999999999999999999999999 8888854
No 144
>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=24.23 E-value=1.7e+02 Score=25.84 Aligned_cols=40 Identities=15% Similarity=0.414 Sum_probs=26.4
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceee
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 685 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~ 685 (805)
+..+..+... ++..|.+.||||.-.++.+|.+|. ..+|-+
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 3344555555 999999999999999999999998 655543
No 145
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=24.05 E-value=1.1e+02 Score=26.91 Aligned_cols=46 Identities=11% Similarity=0.247 Sum_probs=35.6
Q ss_pred HHHHHhhcCCCCCCHHHHHHHh--CCCHHHHHHHHhHhhcCCcceeeeCC
Q 003648 641 TVVLMLFNDAQKLSFQDIKDAT--GIEDKELRRTLQSLACGKVRVLQKLP 688 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t--~i~~~~l~~~L~sL~~~k~~iL~k~~ 688 (805)
+.||...-+++-+|..++.+.+ .+....+.+++.-|+ |.+++.+++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSG 66 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSG 66 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccC
Confidence 4456666677788999999976 788999999999999 999998864
No 146
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=23.76 E-value=1.4e+02 Score=30.99 Aligned_cols=43 Identities=23% Similarity=0.324 Sum_probs=36.0
Q ss_pred HHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 643 VLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 643 ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.+-..++...+|..+|++.++++...+.+.|..|. +.+++.+.
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 33344455679999999999999999999999999 88888774
No 147
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=23.62 E-value=1.9e+02 Score=32.92 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=35.1
Q ss_pred hcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 647 FNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 647 Fn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
+.....+|.++|++.++++...+.+.|..|. +.+++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEec
Confidence 5666789999999999999999999999999 99999863
No 148
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=23.41 E-value=1.9e+02 Score=31.14 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=31.8
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHHhHhhcCCcceeeeCCCC
Q 003648 652 KLSFQDIKDATG--IEDKELRRTLQSLACGKVRVLQKLPKG 690 (805)
Q Consensus 652 ~lt~~eI~~~t~--i~~~~l~~~L~sL~~~k~~iL~k~~~~ 690 (805)
..+.++|++.++ |+.++++.+|.-|. +.++|.++.+|
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~--~~glikk~~~g 175 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLE--RLGLIKKNEDG 175 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHH--HCCCeeECCCC
Confidence 346889999999 89999999999999 99999986433
No 149
>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=23.27 E-value=1.1e+02 Score=28.53 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=39.2
Q ss_pred cHHHHHHHHhhcCC--------CCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 637 SLFQTVVLMLFNDA--------QKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 637 s~~Qa~ILllFn~~--------~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
-.+.-..|+..|.. -+.+.++|+..++-+.+.++.+|..|. +.+++..
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 34555566666654 378999999999999999999999999 9998875
No 150
>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=23.17 E-value=1.3e+02 Score=28.66 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=27.7
Q ss_pred EcHHHHHHHHh-hcCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 636 VSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 636 vs~~Qa~ILll-Fn~~~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
+|.-|..|+.+ |- ++++++||++.+|++...++..+.
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45556666655 43 468999999999999988887654
No 151
>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=23.13 E-value=1.1e+02 Score=25.32 Aligned_cols=33 Identities=21% Similarity=0.423 Sum_probs=30.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 652 KLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 652 ~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
.+|-++|++.+|++...+.+.|.-|. +.+++..
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 7788865
No 152
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=22.80 E-value=1.4e+02 Score=28.03 Aligned_cols=53 Identities=11% Similarity=0.102 Sum_probs=45.7
Q ss_pred HHHHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhcccccc
Q 003648 740 QVDAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQ 799 (805)
Q Consensus 740 ~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~ 799 (805)
..++.|++||=+++..+.+|++.++.+. +.....-+ +--|..|+.+|.|.+.-
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~--~ews~sTV-----~TLl~RL~KKg~l~~~k 58 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD--REWSYSTV-----KTLLNRLVKKGLLTRKK 58 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc--ccccHHHH-----HHHHHHHHhccchhhhh
Confidence 3678899999999999999999988776 66777777 89999999999997653
No 153
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=22.77 E-value=1.5e+02 Score=25.12 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=31.4
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeee
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 686 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k 686 (805)
+-||.... .+..+..+|+..+|++...+.+.|..|. +.+++..
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 34566665 5678899999999999999999999999 7777743
No 154
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=22.72 E-value=8.4e+02 Score=28.66 Aligned_cols=30 Identities=23% Similarity=0.288 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHhhhccCcCcHHHHHHHHHH
Q 003648 305 LKHVEIRLHEEHERCLLYLDVSTRKPLIATAER 337 (805)
Q Consensus 305 l~~v~~~l~eE~~r~~~yl~~~t~~~l~~~l~~ 337 (805)
++.+..++.....+.++| +..++++..|++
T Consensus 468 ~~~i~~rI~~h~~~Lrk~---syGKhIia~lek 497 (503)
T KOG1488|consen 468 RELIKSRVKPHASRLRKF---SYGKHIIAKLEK 497 (503)
T ss_pred HHHHHHHHHHHHHHHccC---ccHHHHHHHHHH
Confidence 666777777777777765 445666666554
No 155
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=22.45 E-value=1.5e+02 Score=23.30 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=30.7
Q ss_pred cHHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 637 SLFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 637 s~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
|.-+.-||.++..+ .+..+|++..|+++..+...+..+.
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 44566777777664 7899999999999999999988876
No 156
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.95 E-value=1.1e+02 Score=29.64 Aligned_cols=30 Identities=27% Similarity=0.348 Sum_probs=27.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHhHhhc
Q 003648 649 DAQKLSFQDIKDATGIEDKELRRTLQSLAC 678 (805)
Q Consensus 649 ~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~ 678 (805)
..+.+|-++|++.+||+..+|++.|..|..
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 157
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.93 E-value=2.1e+02 Score=26.90 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=40.1
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeC
Q 003648 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 687 (805)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~ 687 (805)
.+.+-|+-+--+++.+|+.++...||++-..+++.+.-|+ -.+-|...
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 3566788888888999999999999999999999999999 55555543
No 158
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=21.33 E-value=4.7e+02 Score=26.47 Aligned_cols=111 Identities=16% Similarity=0.161 Sum_probs=61.2
Q ss_pred ChHHHHHHHHHHHHHHccCCCceeEeecCCceEEEEEE--ec-------CceEEEEEcHHHHHHHHhhcCCCCCCHHHHH
Q 003648 589 PHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAE--FP-------KGKKELAVSLFQTVVLMLFNDAQKLSFQDIK 659 (805)
Q Consensus 589 P~~l~~~~~~F~~fY~~k~~~RkL~W~~~lg~~~l~~~--f~-------~~~~~l~vs~~Qa~ILllFn~~~~lt~~eI~ 659 (805)
|.++..+++....-|.....| +.-...=|...+..+ +. .....-..|...+-+|-..--+..+|-.+|+
T Consensus 34 ~~~v~~~l~~L~~~y~~~~~g--i~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDDRG--LKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCCCC--EEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 357899999999999865333 333222222222221 00 0111123344444445444444689999999
Q ss_pred HHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCCC
Q 003648 660 DATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 706 (805)
Q Consensus 660 ~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F~ 706 (805)
+.+|++. ...+..|. ..+++...+..........|.++..|-
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 45566776 566766432221122344566777763
No 159
>PLN03239 histone acetyltransferase; Provisional
Probab=21.21 E-value=1.3e+02 Score=33.30 Aligned_cols=40 Identities=23% Similarity=0.387 Sum_probs=30.0
Q ss_pred HHHHHHHHhh-cCC---CCCCHHHHHHHhCCCHHHHHHHHhHhh
Q 003648 638 LFQTVVLMLF-NDA---QKLSFQDIKDATGIEDKELRRTLQSLA 677 (805)
Q Consensus 638 ~~Qa~ILllF-n~~---~~lt~~eI~~~t~i~~~~l~~~L~sL~ 677 (805)
-....|+-.+ +.. ..+|+++|++.|||..+++..+|+.|-
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 469999999999999999999998874
No 160
>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=20.95 E-value=73 Score=21.82 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=8.6
Q ss_pred ecchHHHHHHHHHH
Q 003648 487 IQGKDVFEAFYKKD 500 (805)
Q Consensus 487 l~~KD~Fe~~Y~k~ 500 (805)
+++.|.|.+||.++
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 45789999999875
No 161
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.84 E-value=1.1e+02 Score=24.79 Aligned_cols=36 Identities=8% Similarity=-0.015 Sum_probs=27.3
Q ss_pred CCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhccc
Q 003648 753 KVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWT 796 (805)
Q Consensus 753 K~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~ 796 (805)
++++++||++ +.|++..+. ++|+++=+.||++||=-
T Consensus 2 ~tv~k~dLi~-----lGf~~~tA~---~IIrqAK~~lV~~G~~~ 37 (59)
T PF11372_consen 2 KTVTKKDLIE-----LGFSESTAR---DIIRQAKALLVQKGFSF 37 (59)
T ss_pred CccCHHHHHH-----cCCCHHHHH---HHHHHHHHHHHHcCCCc
Confidence 5788999984 368876442 35899999999999843
No 162
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.80 E-value=1.4e+02 Score=29.35 Aligned_cols=37 Identities=11% Similarity=0.149 Sum_probs=26.6
Q ss_pred EcHHHHHHHHh-hcCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 636 VSLFQTVVLML-FNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 636 vs~~Qa~ILll-Fn~~~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
++.-|-.|+.+ +- +++|++||++.+|++...++..|.
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 44445555544 33 469999999999999988877653
No 163
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.50 E-value=1.4e+02 Score=29.09 Aligned_cols=32 Identities=16% Similarity=0.428 Sum_probs=23.6
Q ss_pred HHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 641 TVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 641 a~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
.+++|.+-+ +++++||++.+|++...++..|.
T Consensus 126 ~i~~l~~~~--~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 126 TVLVLYYYE--QYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHH
Confidence 344444433 48999999999999988877654
No 164
>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=20.49 E-value=1.4e+02 Score=32.07 Aligned_cols=58 Identities=21% Similarity=0.362 Sum_probs=32.4
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhCCCHHHHHHHHhHhhcCCcceeeeCCCCCCCCCCCeEEEecCC
Q 003648 638 LFQTVVLMLFNDAQKLSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 705 (805)
Q Consensus 638 ~~Qa~ILllFn~~~~lt~~eI~~~t~i~~~~l~~~L~sL~~~k~~iL~k~~~~~~i~~~d~f~~N~~F 705 (805)
-+--.|.-+|..+..|++.+|.+.|+-|+..|+.+|..++ ++.+.+. -...|.+=.+|
T Consensus 216 eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 216 ELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 3445567799999999999999999999999999999987 5655421 12456555544
No 165
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.46 E-value=1.4e+02 Score=28.49 Aligned_cols=24 Identities=29% Similarity=0.313 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHh
Q 003648 651 QKLSFQDIKDATGIEDKELRRTLQ 674 (805)
Q Consensus 651 ~~lt~~eI~~~t~i~~~~l~~~L~ 674 (805)
+++|++||++.+|++...++..|.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 358999999999999998876653
No 166
>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=20.29 E-value=1.4e+02 Score=23.54 Aligned_cols=48 Identities=6% Similarity=0.093 Sum_probs=32.9
Q ss_pred HHHHHHhhccCCC--CChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhhhccccccc
Q 003648 742 DAAIVRIMKTRKV--LSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQSYWTMPQI 800 (805)
Q Consensus 742 ~AaIVRIMK~rK~--l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~eyl~~~~~ 800 (805)
+..|..++..+.. ++..+|...+ ..+++-+ .+.|..|+++|||++.+.
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l------~~~~~~v-----s~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERL------GISKSTV-----SRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHH------TS-HHHH-----HHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH------CcCHHHH-----HHHHHHHHHCCCEEEeCC
Confidence 4555666666665 7777766544 3345666 889999999999998754
No 167
>PF10798 YmgB: Biofilm development protein YmgB/AriR; InterPro: IPR024753 YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid, which indicates that YmgB has an important function in acid-resistance []. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole) [].; GO: 0042710 biofilm formation, 0071229 cellular response to acid; PDB: 2OXL_B.
Probab=20.04 E-value=2.5e+02 Score=22.95 Aligned_cols=53 Identities=11% Similarity=0.162 Sum_probs=36.4
Q ss_pred HHHHHHHHHHhhccCCCCChHHHHHHHHHhcCCCCChhhHHHhhhhhHHHHHHhh
Q 003648 738 QYQVDAAIVRIMKTRKVLSHTLLITELFQQVLPPVLQFELFIYLKHNKISHIQSQ 792 (805)
Q Consensus 738 ~~~I~AaIVRIMK~rK~l~h~~Li~ev~~~l~F~~~~~~i~~~~~k~~ie~Li~~ 792 (805)
+..+.+++.-+|.+.+.++..+++..++..|....+.... +..++.+|..+.+
T Consensus 4 ~~vL~~iv~ell~~g~~vsnKaII~~LI~~LE~e~Dv~~~--dvyR~~LEiVv~~ 56 (61)
T PF10798_consen 4 SEVLGAIVRELLASGGHVSNKAIILKLIHRLESESDVVQL--DVYRNALEIVVGR 56 (61)
T ss_dssp HHHHHHHHHHHHHTT---SHHHHHHHHHHHHHT---HHHH--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccccHHHH--HHHHHHHHHHHcc
Confidence 3467888888999999999999999999999755444333 3458888887653
Done!