Query 008667
Match_columns 557
No_of_seqs 192 out of 969
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 15:04:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008667hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 1.8E-87 4E-92 730.8 48.5 539 1-541 51-603 (725)
2 PF00888 Cullin: Cullin family 100.0 9.4E-87 2E-91 739.5 54.9 516 2-538 32-554 (588)
3 COG5647 Cullin, a subunit of E 100.0 5.3E-83 1.2E-87 666.4 47.5 548 6-556 78-667 (773)
4 KOG2167 Cullins [Cell cycle co 100.0 9.1E-83 2E-87 650.2 39.3 519 10-538 2-532 (661)
5 KOG2284 E3 ubiquitin ligase, C 100.0 7.2E-80 1.6E-84 603.0 38.7 501 5-538 53-598 (728)
6 KOG2285 E3 ubiquitin ligase, C 100.0 8.6E-69 1.9E-73 529.8 46.7 543 6-556 55-657 (777)
7 smart00182 CULLIN Cullin. 100.0 7.5E-35 1.6E-39 262.7 16.2 139 354-492 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 7.7E-27 1.7E-31 244.0 33.3 189 348-537 442-635 (765)
9 PF08539 HbrB: HbrB-like; Int 94.8 0.26 5.6E-06 44.9 9.7 88 9-98 51-156 (158)
10 KOG2167 Cullins [Cell cycle co 91.1 0.76 1.6E-05 49.6 7.9 111 140-258 289-418 (661)
11 PF13412 HTH_24: Winged helix- 82.7 1.7 3.7E-05 30.7 3.4 36 503-538 2-37 (48)
12 PF12802 MarR_2: MarR family; 80.5 1.6 3.6E-05 32.4 2.8 37 502-538 3-41 (62)
13 PF01047 MarR: MarR family; I 72.3 2.9 6.2E-05 30.8 2.1 37 502-538 1-37 (59)
14 PF09339 HTH_IclR: IclR helix- 67.6 5.7 0.00012 28.6 2.7 33 507-539 6-39 (52)
15 PF08279 HTH_11: HTH domain; 66.7 8.7 0.00019 27.8 3.6 31 508-538 4-35 (55)
16 PF13463 HTH_27: Winged helix 66.6 8.1 0.00018 29.2 3.6 36 502-537 1-37 (68)
17 PF08220 HTH_DeoR: DeoR-like h 63.5 8.3 0.00018 28.5 3.0 32 506-537 2-33 (57)
18 TIGR02337 HpaR homoprotocatech 63.1 8.7 0.00019 32.9 3.5 50 501-550 25-77 (118)
19 PF02082 Rrf2: Transcriptional 61.6 11 0.00023 30.2 3.5 34 505-538 11-45 (83)
20 PF08318 COG4: COG4 transport 61.0 2E+02 0.0044 29.5 15.4 156 215-377 14-213 (331)
21 PF08280 HTH_Mga: M protein tr 59.9 8.4 0.00018 28.7 2.5 33 506-538 7-39 (59)
22 PF13404 HTH_AsnC-type: AsnC-t 58.3 10 0.00022 26.2 2.4 31 507-537 6-36 (42)
23 smart00347 HTH_MARR helix_turn 55.5 13 0.00029 30.1 3.3 39 499-537 5-43 (101)
24 PF01022 HTH_5: Bacterial regu 55.4 18 0.00039 25.4 3.4 36 504-540 2-37 (47)
25 PF09763 Sec3_C: Exocyst compl 54.9 3.8E+02 0.0082 30.7 20.5 138 145-295 555-701 (701)
26 PRK11512 DNA-binding transcrip 54.6 16 0.00034 32.5 3.8 52 500-551 36-90 (144)
27 PF05261 Tra_M: TraM protein, 54.3 1.5E+02 0.0032 25.8 9.3 47 93-139 8-55 (127)
28 TIGR03879 near_KaiC_dom probab 54.2 15 0.00033 28.7 3.1 30 509-538 23-52 (73)
29 PF04545 Sigma70_r4: Sigma-70, 53.9 22 0.00047 25.2 3.7 30 507-538 11-40 (50)
30 smart00550 Zalpha Z-DNA-bindin 49.6 24 0.00051 27.1 3.5 44 504-547 6-54 (68)
31 cd04764 HTH_MlrA-like_sg1 Heli 48.8 21 0.00045 27.0 3.2 38 519-556 1-38 (67)
32 smart00420 HTH_DEOR helix_turn 47.8 24 0.00052 24.7 3.2 32 507-538 3-34 (53)
33 TIGR01610 phage_O_Nterm phage 47.2 29 0.00063 28.5 4.0 40 499-538 20-67 (95)
34 PF12840 HTH_20: Helix-turn-he 47.1 22 0.00048 26.4 3.0 36 503-538 9-44 (61)
35 PF06784 UPF0240: Uncharacteri 44.6 33 0.00072 31.9 4.3 60 474-539 96-157 (179)
36 PF01978 TrmB: Sugar-specific 42.9 15 0.00034 27.9 1.6 48 502-549 6-56 (68)
37 cd01104 HTH_MlrA-CarA Helix-Tu 42.8 29 0.00063 26.1 3.2 32 519-550 1-32 (68)
38 TIGR01889 Staph_reg_Sar staphy 41.9 38 0.00083 28.5 4.0 39 500-538 21-63 (109)
39 PF02796 HTH_7: Helix-turn-hel 40.4 36 0.00079 23.6 3.0 30 508-539 13-42 (45)
40 PRK13713 conjugal transfer pro 39.8 31 0.00066 29.5 3.0 44 95-138 3-47 (118)
41 smart00421 HTH_LUXR helix_turn 39.6 41 0.0009 23.7 3.5 34 503-538 5-38 (58)
42 PF08281 Sigma70_r4_2: Sigma-7 38.6 44 0.00096 23.8 3.4 22 517-538 25-46 (54)
43 PRK13777 transcriptional regul 38.2 47 0.001 31.1 4.3 53 500-552 41-96 (185)
44 cd06170 LuxR_C_like C-terminal 37.7 46 0.001 23.5 3.5 34 503-538 2-35 (57)
45 cd04782 HTH_BltR Helix-Turn-He 36.8 41 0.00088 27.7 3.3 37 519-556 1-39 (97)
46 PF01325 Fe_dep_repress: Iron 36.8 49 0.0011 24.7 3.4 32 508-539 12-43 (60)
47 PRK03573 transcriptional regul 36.4 40 0.00086 29.8 3.4 39 500-538 27-66 (144)
48 PF09012 FeoC: FeoC like trans 36.3 26 0.00057 26.8 2.0 31 509-539 5-35 (69)
49 cd04768 HTH_BmrR-like Helix-Tu 36.2 40 0.00087 27.7 3.2 31 519-550 1-31 (96)
50 TIGR02054 MerD mercuric resist 35.5 42 0.00092 29.0 3.3 33 518-551 3-35 (120)
51 PF10408 Ufd2P_core: Ubiquitin 34.6 7.2E+02 0.016 28.1 15.7 58 73-130 322-392 (629)
52 smart00422 HTH_MERR helix_turn 34.5 49 0.0011 24.9 3.3 29 519-548 1-29 (70)
53 smart00346 HTH_ICLR helix_turn 34.2 51 0.0011 26.3 3.5 41 507-547 8-52 (91)
54 cd00090 HTH_ARSR Arsenical Res 34.2 56 0.0012 24.4 3.6 35 503-538 6-40 (78)
55 cd01282 HTH_MerR-like_sg3 Heli 34.1 46 0.001 28.3 3.3 30 519-549 1-30 (112)
56 cd04763 HTH_MlrA-like Helix-Tu 33.8 54 0.0012 24.8 3.4 31 519-549 1-31 (68)
57 cd01107 HTH_BmrR Helix-Turn-He 33.2 49 0.0011 27.9 3.3 37 519-556 1-40 (108)
58 COG4367 Uncharacterized protei 32.4 37 0.00079 27.4 2.2 25 517-541 22-46 (97)
59 PRK10857 DNA-binding transcrip 32.0 62 0.0013 29.6 4.0 32 507-538 13-45 (164)
60 PF13384 HTH_23: Homeodomain-l 31.9 41 0.00088 23.6 2.2 29 509-539 10-38 (50)
61 TIGR01884 cas_HTH CRISPR locus 31.6 55 0.0012 31.0 3.8 38 501-538 140-177 (203)
62 cd04789 HTH_Cfa Helix-Turn-Hel 31.4 54 0.0012 27.3 3.2 30 519-549 2-31 (102)
63 KOG4552 Vitamin-D-receptor int 31.2 4.6E+02 0.01 24.8 11.9 120 191-332 21-142 (272)
64 PRK15090 DNA-binding transcrip 31.0 52 0.0011 32.4 3.6 32 507-538 17-48 (257)
65 PF12324 HTH_15: Helix-turn-he 30.8 82 0.0018 24.9 3.8 37 505-541 25-61 (77)
66 cd01111 HTH_MerD Helix-Turn-He 30.3 54 0.0012 27.7 3.1 31 519-550 1-31 (107)
67 PF08784 RPA_C: Replication pr 30.1 67 0.0015 26.6 3.6 38 501-538 44-85 (102)
68 smart00344 HTH_ASNC helix_turn 29.8 64 0.0014 26.8 3.5 33 505-537 4-36 (108)
69 PF13601 HTH_34: Winged helix 29.0 36 0.00077 27.1 1.7 33 507-539 3-35 (80)
70 PF10771 DUF2582: Protein of u 29.0 53 0.0011 25.1 2.5 29 508-536 12-40 (65)
71 TIGR02844 spore_III_D sporulat 28.9 80 0.0017 25.2 3.6 34 505-539 7-40 (80)
72 cd04773 HTH_TioE_rpt2 Second H 28.8 60 0.0013 27.4 3.1 37 519-556 1-39 (108)
73 cd04766 HTH_HspR Helix-Turn-He 28.7 60 0.0013 26.3 3.0 30 519-549 2-31 (91)
74 cd04777 HTH_MerR-like_sg1 Heli 28.6 62 0.0013 27.1 3.2 37 519-556 1-37 (107)
75 TIGR02010 IscR iron-sulfur clu 28.5 80 0.0017 27.7 4.0 33 507-539 13-46 (135)
76 KOG4481 Uncharacterized conser 27.7 63 0.0014 29.5 3.1 59 474-538 95-155 (194)
77 cd04761 HTH_MerR-SF Helix-Turn 27.6 77 0.0017 21.8 3.1 27 519-545 1-27 (49)
78 cd06171 Sigma70_r4 Sigma70, re 27.3 92 0.002 21.3 3.5 36 502-538 11-46 (55)
79 cd04765 HTH_MlrA-like_sg2 Heli 27.1 70 0.0015 26.5 3.2 31 519-549 1-31 (99)
80 PF02847 MA3: MA3 domain; Int 27.1 1.3E+02 0.0028 25.1 5.0 36 297-332 68-110 (113)
81 cd04788 HTH_NolA-AlbR Helix-Tu 27.0 68 0.0015 26.4 3.1 30 519-549 1-30 (96)
82 PF00165 HTH_AraC: Bacterial r 26.6 60 0.0013 21.9 2.3 23 516-538 6-28 (42)
83 PF10078 DUF2316: Uncharacteri 26.3 59 0.0013 26.5 2.5 26 517-542 22-47 (89)
84 cd04774 HTH_YfmP Helix-Turn-He 26.2 76 0.0016 26.1 3.2 30 519-549 1-30 (96)
85 PF00376 MerR: MerR family reg 26.2 57 0.0012 21.9 2.0 26 520-546 1-26 (38)
86 PF05584 Sulfolobus_pRN: Sulfo 26.1 1E+02 0.0023 24.0 3.6 44 503-548 5-51 (72)
87 KOG2908 26S proteasome regulat 26.0 65 0.0014 33.0 3.2 38 511-548 284-327 (380)
88 cd01105 HTH_GlnR-like Helix-Tu 26.0 75 0.0016 25.6 3.1 37 519-556 2-40 (88)
89 cd04762 HTH_MerR-trunc Helix-T 25.7 83 0.0018 21.2 3.0 26 519-544 1-26 (49)
90 TIGR03209 P21_Cbot clostridium 25.5 56 0.0012 28.6 2.5 34 502-537 108-142 (142)
91 TIGR00738 rrf2_super rrf2 fami 24.9 1E+02 0.0022 26.7 4.0 33 506-538 12-45 (132)
92 cd01109 HTH_YyaN Helix-Turn-He 24.1 90 0.0019 26.4 3.4 29 519-548 1-29 (113)
93 smart00762 Cog4 COG4 transport 23.9 5.3E+02 0.012 26.4 9.6 75 215-289 14-95 (324)
94 PF04967 HTH_10: HTH DNA bindi 23.8 81 0.0018 23.0 2.5 27 512-538 17-43 (53)
95 PF11994 DUF3489: Protein of u 23.8 1.2E+02 0.0025 23.7 3.5 35 503-537 9-43 (72)
96 smart00418 HTH_ARSR helix_turn 23.7 92 0.002 22.3 3.1 23 516-538 8-30 (66)
97 cd01279 HTH_HspR-like Helix-Tu 23.3 92 0.002 25.7 3.2 30 519-549 2-31 (98)
98 PRK10870 transcriptional repre 22.8 1.1E+02 0.0025 28.1 4.1 53 500-552 51-108 (176)
99 TIGR00721 tfx DNA-binding prot 22.8 1.1E+02 0.0023 27.2 3.6 35 501-537 6-40 (137)
100 PF13413 HTH_25: Helix-turn-he 22.7 73 0.0016 23.9 2.2 23 516-538 8-30 (62)
101 PF01418 HTH_6: Helix-turn-hel 22.4 60 0.0013 25.4 1.8 36 509-544 25-60 (77)
102 PF13411 MerR_1: MerR HTH fami 22.2 80 0.0017 23.7 2.5 30 519-549 1-30 (69)
103 PRK11179 DNA-binding transcrip 21.9 1E+02 0.0022 27.7 3.5 36 501-536 6-41 (153)
104 TIGR02431 pcaR_pcaU beta-ketoa 21.9 97 0.0021 30.2 3.6 32 507-538 12-44 (248)
105 PRK11920 rirA iron-responsive 21.6 1.2E+02 0.0027 27.2 4.0 31 509-539 15-45 (153)
106 PRK13749 transcriptional regul 21.5 1.2E+02 0.0026 26.3 3.6 38 518-556 3-42 (121)
107 PF02002 TFIIE_alpha: TFIIE al 21.5 60 0.0013 27.1 1.7 33 506-538 15-47 (105)
108 PF04703 FaeA: FaeA-like prote 21.4 72 0.0016 24.1 1.9 30 509-538 5-35 (62)
109 cd01106 HTH_TipAL-Mta Helix-Tu 21.1 1E+02 0.0023 25.5 3.2 29 519-548 1-29 (103)
110 cd04775 HTH_Cfa-like Helix-Tur 21.1 1.1E+02 0.0024 25.4 3.3 28 519-547 2-29 (102)
111 PF12728 HTH_17: Helix-turn-he 20.8 90 0.002 21.9 2.4 26 519-544 2-27 (51)
112 smart00544 MA3 Domain in DAP-5 20.7 2.2E+02 0.0048 23.7 5.2 38 295-332 66-110 (113)
113 PRK11169 leucine-responsive tr 20.5 98 0.0021 28.2 3.1 35 502-536 12-46 (164)
114 COG1846 MarR Transcriptional r 20.4 1.2E+02 0.0026 25.2 3.5 50 502-551 20-72 (126)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.8e-87 Score=730.82 Aligned_cols=539 Identities=41% Similarity=0.700 Sum_probs=505.3
Q ss_pred CCCCcch----HHHHHHHHHHHHHHHHHHH-HHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCC-CCcc
Q 008667 1 MVLHKFG----EKLYSGLVSTMTLHLKEIS-KSIEAAQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPST-HKTP 74 (557)
Q Consensus 1 lc~~k~~----e~LY~~l~~~i~~~l~~i~-~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~-~~~~ 74 (557)
||++++| ++||+++++++.+|+..++ +.+.+..++.+|+.+...|.+|+.++.+++++|+||||+||+++ +..+
T Consensus 51 ~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~ 130 (725)
T KOG2166|consen 51 MCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLP 130 (725)
T ss_pred HhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 5889999 9999999999999999955 66666777899999999999999999999999999999999976 6666
Q ss_pred HHHHH-HHHHHHHhccccchHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhhC---cccchhhchhhHHHHHHHHH
Q 008667 75 VHELG-LNLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG---PSVYQEDFEKPFLEVSAEFY 150 (557)
Q Consensus 75 i~~l~-l~lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~~~~~~lk~ii~~l~~lg---~~~Y~~~FE~~~L~~t~~yY 150 (557)
+.+++ +.+|+..++.. ++.+++.++++.+|..+|.|+.+|+..|+++++++..+| ..+|...||++|++.|..||
T Consensus 131 v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y 209 (725)
T KOG2166|consen 131 TLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYY 209 (725)
T ss_pred cccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHH
Confidence 66666 99999998874 599999999999999999999999999999999999998 57999999999999999999
Q ss_pred HHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhhhhHHHhcCchhhHHhhcCCcHHHHH
Q 008667 151 KVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLG 230 (557)
Q Consensus 151 ~~~~~~~~~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~ 230 (557)
..++++|+...++.+|+.+++.++.+|..|+..|++..+.+++.+.++..++..+++.+++..++|+..|+.+++.++|.
T Consensus 210 ~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~ 289 (725)
T KOG2166|consen 210 SEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLS 289 (725)
T ss_pred HHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHH
Confidence 99999999988999999999999999999999999888888888888888888888888888899999999999999999
Q ss_pred HHHHhhccCCCChHHHHHHHHHHHHHHhhHhhcCcccC--CCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHHHH
Q 008667 231 RMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERL--KDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSSFE 308 (557)
Q Consensus 231 ~ly~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~--~~~~~~I~~ll~l~~~~~~li~~~F~~~~~f~~~i~~af~ 308 (557)
++|+|+++++.|++.+++.++.|++.+|..++...... .+|..+++.++++++++..++..||++|..|.++++.||.
T Consensus 290 ~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~ 369 (725)
T KOG2166|consen 290 RMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFE 369 (725)
T ss_pred HHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence 99999999999999999999999999998888776544 6899999999999999999999999999999999999999
Q ss_pred HhhccCCCcH-HHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHcCCCCCChHHHHHH
Q 008667 309 YFINLNPRSP-EFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSL 387 (557)
Q Consensus 309 ~~ln~~~~~~-e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~ 387 (557)
.|+|.+...+ |+||+|||.++|++.++.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|+++|+.|
T Consensus 370 ~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~m 449 (725)
T KOG2166|consen 370 EFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSL 449 (725)
T ss_pred HHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHH
Confidence 9999977666 999999999999998999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcccchhHhHHHhhhhHHhhHHHHHHHhhhcCCC-CCCcceEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHH
Q 008667 388 IVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPEL-GDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRS 466 (557)
Q Consensus 388 i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~-~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~ 466 (557)
|.+|+++||.+||+||++|++|+..|++++..|.++...+ ..+++|.|.|||.|+||.+++.++.||++|.++++.|..
T Consensus 450 Isklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~ 529 (725)
T KOG2166|consen 450 ITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYANYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKG 529 (725)
T ss_pred HHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhchhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHH
Confidence 9999999999999999999999999999999999762211 246999999999999999888889999999999999999
Q ss_pred HHhccCCCceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhhcc
Q 008667 467 YYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVPAI 541 (557)
Q Consensus 467 ~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~~~ 541 (557)
||.++|+||+|.|+|++|+|+|.++|.+ ++++++||++||+||++||+.+.+|+++|.+.|+++.+.+..++..
T Consensus 530 ~Y~~kh~gR~L~w~~~l~~~ei~~~~~~-~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~S 603 (725)
T KOG2166|consen 530 FYATKHNGRRLTWIYSLGTGEINGKFDK-KTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQS 603 (725)
T ss_pred HHhhccCCCeeeeeeccCceEEEEEecC-ceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHH
Confidence 9999999999999999999999999998 7999999999999999999999999999999999999998865443
No 2
>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=9.4e-87 Score=739.46 Aligned_cols=516 Identities=41% Similarity=0.724 Sum_probs=477.7
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCCccHHHHHHH
Q 008667 2 VLHKFGEKLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPSTHKTPVHELGLN 81 (557)
Q Consensus 2 c~~k~~e~LY~~l~~~i~~~l~~i~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~~~~i~~l~l~ 81 (557)
|.+++|++||+.+++.+.+++..+++++.+.+++++|..|..+|.+|+.++.+++++|+||||+|+.++
T Consensus 32 ~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~----------- 100 (588)
T PF00888_consen 32 CDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN----------- 100 (588)
T ss_dssp HHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT-----------
T ss_pred cCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh-----------
Confidence 567899999999999999999999999977778999999999999999999999999999999999987
Q ss_pred HHHHHhccccchHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhhC-cccchhhchhhHHHHHHHHHHHHHHHhHhc
Q 008667 82 LWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG-PSVYQEDFEKPFLEVSAEFYKVESQKFIEC 160 (557)
Q Consensus 82 lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~~~~~~lk~ii~~l~~lg-~~~Y~~~FE~~~L~~t~~yY~~~~~~~~~~ 160 (557)
+|++.|+. ++.++++++++++|.++|.|+.+++.+++++++|++++| ..+|.+.||++|+++|.+||+.++ +++
T Consensus 101 ~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~~~~~y~~~fe~~~l~~t~~yY~~~~---i~~ 175 (588)
T PF00888_consen 101 LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELGSLEVYEEEFEKPFLEETKEYYKSES---IQE 175 (588)
T ss_dssp HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTTHTHHHHHHTHHHHHHHHHHHHHHHH---HHH
T ss_pred hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccchHHhhHHHHHHHHHHHHHHHHHHHH---HHh
Confidence 99999999 799999999999999999999999999999999999997 679999999999999999999999 677
Q ss_pred CCHHHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhhhhHHHhcCchhhHHhhcCCcHHHHHHHHHhhccCC
Q 008667 161 CDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVP 240 (557)
Q Consensus 161 ~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~ 240 (557)
.++.+|+++|+.++++|.+|+..|++++|.+++.+++.++||.+|.+.| .+|+..|+++++.++|+++|+|+++++
T Consensus 176 ~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~ 251 (588)
T PF00888_consen 176 NSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVP 251 (588)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTST
T ss_pred cCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhccc
Confidence 8999999999999999999999999999999999999999999999999 479999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHHhhHhhcCcccCCCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHHHHHhhccC-CCcHH
Q 008667 241 SGLLTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSSFEYFINLN-PRSPE 319 (557)
Q Consensus 241 ~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~I~~ll~l~~~~~~li~~~F~~~~~f~~~i~~af~~~ln~~-~~~~e 319 (557)
++++.+++.|++||.+.|.++++.......+.++|+.+++++++++.++.+||++++.|.+++++||+.++|.+ .++++
T Consensus 252 ~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~e 331 (588)
T PF00888_consen 252 NGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKNNNKIPE 331 (588)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCSTSHHHH
T ss_pred CCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcCCcchHH
Confidence 99999999999999999999998765445788999999999999999999999999999999999999999987 89999
Q ss_pred HHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccch
Q 008667 320 FISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQF 399 (557)
Q Consensus 320 ~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~ 399 (557)
+||+|||.+++++.++.++++++..++.++.+|+|+++||+|+.+|+++||+|||.+++.+.+.|..++++|+.+||.++
T Consensus 332 ~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~ 411 (588)
T PF00888_consen 332 LLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSY 411 (588)
T ss_dssp HHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHH
T ss_pred HHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchh
Confidence 99999999999998778888999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHHHhhhhHHhhHHHHHHHhhhcCCCCC----CcceEEEEeccCCCCCCCCCC-CCCcHhHHHHHHHHHHHHhccCCC
Q 008667 400 TSKLEGMFTDMKTSQDTMHEFYASHPELGD----SRTLVVQVLTTGSWPTQPSVT-CNLPAEMSALCEKFRSYYLGTHTG 474 (557)
Q Consensus 400 ~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~----~~~~~~~vls~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~ 474 (557)
+++|++|++|+..|++++++|++....++. +++|+|.|||+++||..+..+ +.+|++|+++++.|++||+++|+|
T Consensus 412 ~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~ 491 (588)
T PF00888_consen 412 TSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKG 491 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTT
T ss_pred HHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCC
Confidence 999999999999999999999987664432 789999999999999887665 999999999999999999999999
Q ss_pred ceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 475 RRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 475 RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
|+|+|.|++|+|+|++++++ ++++++||++||+||++||+++++|+++|++.||++++.+...
T Consensus 492 R~L~w~~~l~~~~i~~~~~~-~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~ 554 (588)
T PF00888_consen 492 RKLTWLPSLSSVEIEFNFNN-GKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRA 554 (588)
T ss_dssp EEEEEEGGGEEEEEEEESSS-SEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHH
T ss_pred cEEEEecccCcEEEEEEecC-CceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHH
Confidence 99999999999999999998 8899999999999999999999999999999999999998864
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.3e-83 Score=666.45 Aligned_cols=548 Identities=33% Similarity=0.527 Sum_probs=492.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccc-----CCCCccHHHHHH
Q 008667 6 FGEKLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIP-----STHKTPVHELGL 80 (557)
Q Consensus 6 ~~e~LY~~l~~~i~~~l~~i~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~-----~~~~~~i~~l~l 80 (557)
.|..+|+++..+.++++..-..+......+.+|..+++.|++|..++.+++++|.||||.|++ ...+..+.++++
T Consensus 78 ~~s~li~~L~~~~k~~i~~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl 157 (773)
T COG5647 78 LGSRLIQKLVDYAKNYIEEYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCL 157 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhh
Confidence 678889999988888888754333233448999999999999999999999999999999999 234567889999
Q ss_pred HHHHHHhccccchHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhhC---------cccchhhchhhHHHHHHHHHH
Q 008667 81 NLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG---------PSVYQEDFEKPFLEVSAEFYK 151 (557)
Q Consensus 81 ~lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~~~~~~lk~ii~~l~~lg---------~~~Y~~~FE~~~L~~t~~yY~ 151 (557)
..|+..++. .+.+.+++.++..+++.|.|+.+|+..+..++.|+.++| ..+|.+.||+.||+.|..||.
T Consensus 158 ~~~~~~~f~--~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~ 235 (773)
T COG5647 158 VKEKIESFR--LIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYE 235 (773)
T ss_pred hHHHHHHHH--hhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHH
Confidence 999999999 999999999999999999999999999999999999995 368999999999999999999
Q ss_pred HHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhhhhHHHhcCchhhHHhhcCCcHHHHHH
Q 008667 152 VESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGR 231 (557)
Q Consensus 152 ~~~~~~~~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~ 231 (557)
.++++.+..+++.+||.+|..++++|..++..|++.++..++..+++++||..|.+.+... .+|+..+++..+.+.|..
T Consensus 236 ~ess~~i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~-~s~f~~~~d~~~~e~l~~ 314 (773)
T COG5647 236 MESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQ-GSGFREALDASNLEKLQV 314 (773)
T ss_pred HHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhc-hHHHHHHHHhhhHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999876 489999999999999999
Q ss_pred HHHhhccCCCChHHHHHHHHHHHHHHh--hHh-----hcCcc-------cCCCcHHHHHHHHHHHHHHHHHHHhhcCCCH
Q 008667 232 MYNLFRRVPSGLLTIREVMTSHLRETG--KQL-----VTDPE-------RLKDPVEFVQRLLDEKDKYDNIISSAFNNDK 297 (557)
Q Consensus 232 ly~L~~~~~~~~~~l~~~~~~~i~~~g--~~~-----~~~~~-------~~~~~~~~I~~ll~l~~~~~~li~~~F~~~~ 297 (557)
+|+++++++.++.+|++.|.+||+..| .++ +.... ....+..+++.++.+++.+..++...|.+|.
T Consensus 315 lY~l~se~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~ 394 (773)
T COG5647 315 LYRLLSETKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDG 394 (773)
T ss_pred HHHHhhhhhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcc
Confidence 999999999999999999999999999 211 11111 1126889999999999999999999999999
Q ss_pred HhHHHHHHHHHHhhcc----CCCcHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHH
Q 008667 298 TFQNALNSSFEYFINL----NPRSPEFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRL 373 (557)
Q Consensus 298 ~f~~~i~~af~~~ln~----~~~~~e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RL 373 (557)
.+.+++++||+.++|+ +..+||+||+|+|.++|++.+......++..+.+++.||+|+.+||+|+++|+++|||||
T Consensus 395 ~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRL 474 (773)
T COG5647 395 SIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRL 474 (773)
T ss_pred hHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 9999999999999997 347999999999999999876555567888999999999999999999999999999999
Q ss_pred cCCCCCChHHHHHHHHHHHHHcccchhHhHHHhhhhHHhhHHHHHHHhhhcCCCCCCcceEEEEeccCCCCCC-CCCCCC
Q 008667 374 LSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPELGDSRTLVVQVLTTGSWPTQ-PSVTCN 452 (557)
Q Consensus 374 L~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~vls~~~WP~~-~~~~~~ 452 (557)
|+++|+|.++|..||++||+.||.+||+|+++||+||..|.++...|++...+....+++.|.||+..+||.+ ++..+.
T Consensus 475 L~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~~~~Dl~v~VLt~a~WP~sp~~~~~~ 554 (773)
T COG5647 475 LNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQSYNKYLDLFVWVLTQAYWPLSPEEVSIR 554 (773)
T ss_pred hcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchhhccccchhHHHHHHhcCCCCccccccC
Confidence 9999999999999999999999999999999999999999999999987543223468999999999999954 568999
Q ss_pred CcHhHHHHHHHHHHHHhccCCCceeeeccCccceEEEEeeCCCc-EEEE-EecHHHHHHHHhhhCCCCcCHHHHHHhcCC
Q 008667 453 LPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQ-KHEL-NVSTYQMCVLMLFNNADRLSYQGNRAGNRD 530 (557)
Q Consensus 453 lP~~l~~~~~~f~~~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~-~~~l-~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~ 530 (557)
||++|.+.++.|++||.+||+||+|.|.|+||+|+|++.|+.|+ .+.+ +++++|+.|+++||+++++|+++|.+.|+|
T Consensus 555 lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l 634 (773)
T COG5647 555 LPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKL 634 (773)
T ss_pred CChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCC
Confidence 99999999999999999999999999999999999999999842 3333 488999999999999999999999999999
Q ss_pred ChHHhhhh------hccccccCC-CCCCccccc
Q 008667 531 SCFRLEKV------PAISGLCEG-EECSSERTY 556 (557)
Q Consensus 531 ~~~~l~~~------~~~~~~~~~-~~~~~~~~~ 556 (557)
+.+.+..+ +++.-+.++ +++||.-+|
T Consensus 635 ~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~f 667 (773)
T COG5647 635 STDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKF 667 (773)
T ss_pred ChhhHHHHHHHHHhhheeeeccccccCCCCceE
Confidence 99998843 566666666 788886543
No 4
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9.1e-83 Score=650.17 Aligned_cols=519 Identities=39% Similarity=0.655 Sum_probs=487.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh--hcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCC--CCccHHHHHHHHHHH
Q 008667 10 LYSGLVSTMTLHLKEISKSIEA--AQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPST--HKTPVHELGLNLWRD 85 (557)
Q Consensus 10 LY~~l~~~i~~~l~~i~~~l~~--~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~--~~~~i~~l~l~lf~~ 85 (557)
||+.+++.++++++.-...+.. .+...+|..+.++|..|...+..++++|.||||.|+... ..+++|++++.+||.
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 8999999999999964443432 123689999999999999999999999999999999983 468999999999999
Q ss_pred Hhcc--ccchHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhhCcccchhhchhhHHHHHHHHHHHHHHHhHhcCCH
Q 008667 86 NIVR--SNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLGPSVYQEDFEKPFLEVSAEFYKVESQKFIECCDC 163 (557)
Q Consensus 86 ~v~~--~~~~~~~l~~~ll~~I~~~R~g~~~~~~~lk~ii~~l~~lg~~~Y~~~FE~~~L~~t~~yY~~~~~~~~~~~~~ 163 (557)
+++. .|.+..+..++++..+++.|.|+++|+.++++++.|+.+++ +|.+.|++.|++.+.++|..+.....++..+
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~--iY~esF~~~fls~f~~lY~aE~~d~~Qel~v 159 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQ--IYKESFELTFLSLFRELYAAEGQDKRQELEV 159 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHH--hhhhhhHHHHHHHHHHHHHHHhcchhhhccc
Confidence 9999 67888999999999999999999999999999999999985 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhhhhHHHhcCchhhHHhhcCCcHHHHHHHHHhhccCCCCh
Q 008667 164 GEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGL 243 (557)
Q Consensus 164 ~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~~ 243 (557)
++||++++.++.+|..++..+++.+|...+..+++..|+..|++.|+.+ |+..+++.++..++.++|.|++++..+.
T Consensus 160 ~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~~~g~ 236 (661)
T KOG2167|consen 160 PEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRVQGGQ 236 (661)
T ss_pred HHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHHhcch
Confidence 9999999999999999999999998877799999999999999999975 8999999999999999999999999888
Q ss_pred HHHHHHHHHHHHHHhhHhhcCcccCCCcHHHHHHHHHHHHHHHHHHHhhcCCC--HHhHHHHHHHHHHhhcc-CCCcHHH
Q 008667 244 LTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKYDNIISSAFNND--KTFQNALNSSFEYFINL-NPRSPEF 320 (557)
Q Consensus 244 ~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~I~~ll~l~~~~~~li~~~F~~~--~~f~~~i~~af~~~ln~-~~~~~e~ 320 (557)
..++..|.+|+++.|..++.+.... .++|+.++.++++.+-++..||..+ ..|..++++||+.++|. .+++||+
T Consensus 237 l~l~qq~sdylk~~G~KlV~de~kD---k~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAel 313 (661)
T KOG2167|consen 237 LSLLQQWSDYLKKPGFKLVIDEEKD---KDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAEL 313 (661)
T ss_pred HHHHHHHHHHHhcccceeccCchhh---HHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHHH
Confidence 8999999999999999999876643 7999999999999999999999888 99999999999999997 5789999
Q ss_pred HHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccchh
Q 008667 321 ISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFT 400 (557)
Q Consensus 321 La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~ 400 (557)
+|+|.|..|+.|+++.++++++..++.++.||+|+..||+|+.+|++.||+|||.++|+|.|+|..|+.+||.+||..||
T Consensus 314 Iak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft 393 (661)
T KOG2167|consen 314 IAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFT 393 (661)
T ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHhhhhHHhhHHHHHHHhhhcCC-C--CCCcceEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHhccCCCcee
Q 008667 401 SKLEGMFTDMKTSQDTMHEFYASHPE-L--GDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRL 477 (557)
Q Consensus 401 ~kl~~M~~D~~~S~~l~~~f~~~~~~-~--~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL 477 (557)
+||++||+||..|++++..|+++... + +.++ +.+.|+|.++||++++.++.||++|.++++.|.+||..+|.||+|
T Consensus 394 ~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrkl 472 (661)
T KOG2167|consen 394 YKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKL 472 (661)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcce
Confidence 99999999999999999999987432 2 2234 999999999999999999999999999999999999999999999
Q ss_pred eeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 478 SWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 478 ~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.|.+++|+|.+++.|+. |++++.||++|++||++||+.+.||++||.+.|++....|...
T Consensus 473 qW~~~lg~~v~ka~f~~-gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rt 532 (661)
T KOG2167|consen 473 QWQDSLGHCVLKAEFKE-GKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRT 532 (661)
T ss_pred eeecCCcchhhhhhccC-CchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHH
Confidence 99999999999999998 6999999999999999999999999999999999988877754
No 5
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.2e-80 Score=603.01 Aligned_cols=501 Identities=26% Similarity=0.523 Sum_probs=471.7
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCC-------------
Q 008667 5 KFGEKLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPSTH------------- 71 (557)
Q Consensus 5 k~~e~LY~~l~~~i~~~l~~i~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~------------- 71 (557)
+-||.||..++.+|++|+...+..+-..+.+.+|..|++.|+.|..+..++..+|.|||+.|++++.
T Consensus 53 pl~erly~e~k~~i~~hvrq~~~~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~ 132 (728)
T KOG2284|consen 53 PLSERLYNEVKACIQEHVRQKRQDIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAF 132 (728)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcch
Confidence 4799999999999999999866665554446699999999999999999999999999999999843
Q ss_pred -----CccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhhC---------------
Q 008667 72 -----KTPVHELGLNLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVIN-RGLMRNIIKMLMDLG--------------- 130 (557)
Q Consensus 72 -----~~~i~~l~l~lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~~~-~~~lk~ii~~l~~lg--------------- 130 (557)
...|-.+|+.+||+.+.+ ++...|+..++..|.++|.|+..+ ...+.+++++|+.+.
T Consensus 133 ~~~~~~~eig~lal~~w~~~~v~--~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryk 210 (728)
T KOG2284|consen 133 LQIPDVKEIGCLALEIWKEDLVK--TILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYK 210 (728)
T ss_pred hcCCcHHHHhHHHHHHHHHHHHH--HHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchh
Confidence 234668999999999999 899999999999999999999887 678999999998773
Q ss_pred -----cccchhhchhhHHHHHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhh
Q 008667 131 -----PSVYQEDFEKPFLEVSAEFYKVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANH 205 (557)
Q Consensus 131 -----~~~Y~~~FE~~~L~~t~~yY~~~~~~~~~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~ 205 (557)
..+|++.||+|||.+|..||+++|+..+.+.++++|+.+|..++++|+.||+.||++++..+++..|++.+|.+|
T Consensus 211 a~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h 290 (728)
T KOG2284|consen 211 ARESTTAFYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAH 290 (728)
T ss_pred hccccHHHHHHHhccccccchHHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHH
Confidence 148999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHhcCchhhHHhhcCCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHhhHhhcCcccCCCcHHHHHHHHHHHHHH
Q 008667 206 MPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKY 285 (557)
Q Consensus 206 ~~~il~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~I~~ll~l~~~~ 285 (557)
.+.+ +..++.++.+.+..|++.||+|+..+..|++.+...|++||.++|.++++......-|..||+..+.+|.+|
T Consensus 291 ~~~l----ha~ch~~i~~e~~~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf 366 (728)
T KOG2284|consen 291 KDKL----HAVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKF 366 (728)
T ss_pred HHHH----HHHHHHHHhhhhhhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHH
Confidence 9999 678999999999999999999999999999999999999999999999998877778999999999999999
Q ss_pred HHHHHhhcCCCHHhHHHHHHHHHHhhcc------CCCcHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhccccchH
Q 008667 286 DNIISSAFNNDKTFQNALNSSFEYFINL------NPRSPEFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKD 359 (557)
Q Consensus 286 ~~li~~~F~~~~~f~~~i~~af~~~ln~------~~~~~e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd 359 (557)
..++...|.+|..|..+++.|+..++|. -.+.+|.||+|||.+++++.+|+++.++|.+|+..+.+|+|++|||
T Consensus 367 ~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkd 446 (728)
T KOG2284|consen 367 NDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKD 446 (728)
T ss_pred HHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHH
Confidence 9999999999999999999999999996 2589999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccchhHhHHHhhhhHHhhHHHHHHHhhhcCCCCCCcceEEEEec
Q 008667 360 VFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPELGDSRTLVVQVLT 439 (557)
Q Consensus 360 ~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~vls 439 (557)
+|.++|.++||+||+.+.|.|.|.|..||++||+.||.+||+++- +.|+..|.+++++|.+.+.
T Consensus 447 ifqkfys~mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~-------------- 510 (728)
T KOG2284|consen 447 IFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA-------------- 510 (728)
T ss_pred HHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH--------------
Confidence 999999999999999999999999999999999999999999998 9999999999999987653
Q ss_pred cCCCCCCCCCCCCCcHhHHHHHHHHHHHHhccCCCceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCc
Q 008667 440 TGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRL 519 (557)
Q Consensus 440 ~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~~~~l 519 (557)
++.+|.+|+...+.|+.||..+|+||||+|.+.++++++++++-+ +.|.-.|++|||++|++||..+.+
T Consensus 511 ----------nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~-k~yva~~~~yqma~ll~f~~~~~i 579 (728)
T KOG2284|consen 511 ----------NFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLD-KQYVAQMYVYQMAALLCFERRDAI 579 (728)
T ss_pred ----------hccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecC-chHHHHHHHHHHHHHHHhcccccc
Confidence 378999999999999999999999999999999999999999997 999999999999999999999999
Q ss_pred CHHHHHHhcCCChHHhhhh
Q 008667 520 SYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 520 t~~ei~~~t~~~~~~l~~~ 538 (557)
++.+|.+.+|++.+-|.+.
T Consensus 580 ~~k~i~~~~~~~~~~l~kt 598 (728)
T KOG2284|consen 580 LVKDIGEEIGVSGDYLLKT 598 (728)
T ss_pred hHHhhhhhhCccHHHHHHH
Confidence 9999999999999998875
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.6e-69 Score=529.76 Aligned_cols=543 Identities=24% Similarity=0.456 Sum_probs=487.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhh-cchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCCC--------CccHH
Q 008667 6 FGEKLYSGLVSTMTLHLKEISKSIEAA-QGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPSTH--------KTPVH 76 (557)
Q Consensus 6 ~~e~LY~~l~~~i~~~l~~i~~~l~~~-~~~~~L~~~~~~W~~~~~~~~~l~~if~YLdr~yv~~~~--------~~~i~ 76 (557)
-...+|+-++..|.+|+......+... .+..+|..|...|.+|.....++.-.|.-|+..-...++ -.++.
T Consensus 55 GpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vR 134 (777)
T KOG2285|consen 55 GPAKIRDILTRDINEFIHQAQKRVRSLQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVR 134 (777)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHH
Confidence 445699999999999999877777654 446899999999999999999999999999987554421 24799
Q ss_pred HHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhhC------cccchhhchhhHHHHHHHHH
Q 008667 77 ELGLNLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG------PSVYQEDFEKPFLEVSAEFY 150 (557)
Q Consensus 77 ~l~l~lf~~~v~~~~~~~~~l~~~ll~~I~~~R~g~~~~~~~lk~ii~~l~~lg------~~~Y~~~FE~~~L~~t~~yY 150 (557)
.+.+..|-+++|. .++.++..+.+.++..+|.|+.+|.+++-++-++|+.+. ..+|.+.||..||++|.+||
T Consensus 135 klMLd~WNe~IF~--nIk~rLq~sAmklVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efY 212 (777)
T KOG2285|consen 135 KLMLDKWNEIIFM--NIKERLQVSAMKLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFY 212 (777)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 999999999999999999999999999999999999996 36999999999999999999
Q ss_pred HHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhhcCc--chHHHHHHHHHHHHHhhhhhHHHhcCchhhHHhhcCCcHHH
Q 008667 151 KVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDA--KSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYED 228 (557)
Q Consensus 151 ~~~~~~~~~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~--~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~ 228 (557)
+..+.+++++.++.+|+++++..+++|+.|+.+||.+ .|..+++..+..+||.++.+.|+. ++..|+...+++.
T Consensus 213 r~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etEr 288 (777)
T KOG2285|consen 213 RKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETER 288 (777)
T ss_pred HHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHH
Confidence 9999999999999999999999999999999999976 578999999999999999999985 6889999999999
Q ss_pred HHHHHHhhccCCCChHHHHHHHHHHHHHHhhHhhcCc-cc-CCCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHH
Q 008667 229 LGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDP-ER-LKDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSS 306 (557)
Q Consensus 229 L~~ly~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~-~~-~~~~~~~I~~ll~l~~~~~~li~~~F~~~~~f~~~i~~a 306 (557)
|.+||+|+.++..|++++.+-+..||...|.+-+-.. +. +.++..||+.|+.++++|..++.++|.+|+.|..|.+.|
T Consensus 289 L~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkA 368 (777)
T KOG2285|consen 289 LQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKA 368 (777)
T ss_pred HHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHH
Confidence 9999999999999999999999999999998655322 22 237899999999999999999999999999999999999
Q ss_pred HHHhhcc---------------------CCCcHHHHHHHHHHHhhcCC--CCCChHHHHHHHHHHhhhhccccchHHHHH
Q 008667 307 FEYFINL---------------------NPRSPEFISLFVDDKLRKGL--KGVSEEDVETILDKVMMLFRYLQEKDVFEK 363 (557)
Q Consensus 307 f~~~ln~---------------------~~~~~e~La~y~D~~lk~~~--~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~ 363 (557)
|+.++|. ..++||+||.|||.++|+.. +.++.++++.++++++-+++|+.+||+|+.
T Consensus 369 fkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMR 448 (777)
T KOG2285|consen 369 FKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMR 448 (777)
T ss_pred HHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHH
Confidence 9999994 14789999999999999976 678889999999999999999999999999
Q ss_pred HHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcc--cchhHhHHHhhhhHHhhHHHHHHHhhhcCCC---CCCcceEEEEe
Q 008667 364 YYKQHLAKRLLSGKTVSDDAERSLIVKLKTECG--YQFTSKLEGMFTDMKTSQDTMHEFYASHPEL---GDSRTLVVQVL 438 (557)
Q Consensus 364 ~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G--~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~---~~~~~~~~~vl 438 (557)
+++.+|++||+...|++.+.|..|+..|+ +|| .+|.+|+..||+|++.|+++++.|+..++.+ ...-.++++||
T Consensus 449 yHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiL 527 (777)
T KOG2285|consen 449 YHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKIL 527 (777)
T ss_pred HHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeee
Confidence 99999999999999999999999999999 688 4999999999999999999999999887643 12346889999
Q ss_pred ccCCCCCC-CCCCCCCcHhHHHHHHHHHHHHhccCCCceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--
Q 008667 439 TTGSWPTQ-PSVTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN-- 515 (557)
Q Consensus 439 s~~~WP~~-~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~-- 515 (557)
..|.|... ....+.||.+|++.+..-+.||+.+|+||||+|.|+++.++++..-.- |.|++.|+++||+||.+||+
T Consensus 528 NaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~-GryDLevTTFQmAVLFawNqR~ 606 (777)
T KOG2285|consen 528 NAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNF-GRYDLEVTTFQMAVLFAWNQRA 606 (777)
T ss_pred cccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeeccc-ccceeeeehhhHHHHHHhcccc
Confidence 99999964 457889999999999999999999999999999999999999543333 78999999999999999998
Q ss_pred CCCcCHHHHHHhcCCChHHhh-------hhhc---cccccCCCCCCccccc
Q 008667 516 ADRLSYQGNRAGNRDSCFRLE-------KVPA---ISGLCEGEECSSERTY 556 (557)
Q Consensus 516 ~~~lt~~ei~~~t~~~~~~l~-------~~~~---~~~~~~~~~~~~~~~~ 556 (557)
++.+|++.+.-+|.+|...|. +.|+ =+-||+|...++.|.+
T Consensus 607 hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDF 657 (777)
T KOG2285|consen 607 HDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDF 657 (777)
T ss_pred ccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccc
Confidence 689999999999999988766 2344 3668998776666543
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=7.5e-35 Score=262.66 Aligned_cols=139 Identities=50% Similarity=0.875 Sum_probs=131.5
Q ss_pred cccchHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccchhHhHHHhhhhHHhhHHHHHHHhhhcCC--CCCCc
Q 008667 354 YLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPE--LGDSR 431 (557)
Q Consensus 354 ~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~--~~~~~ 431 (557)
|+++||+|+.+|+++||+|||..++++.+.|..||++||.+||.+++++|++|++|++.|++++++|++...+ ...++
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~~~~~~ 80 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNSNKPII 80 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999987654 23468
Q ss_pred ceEEEEeccCCCCCCCC-CCCCCcHhHHHHHHHHHHHHhccCCCceeeeccCccceEEEEee
Q 008667 432 TLVVQVLTTGSWPTQPS-VTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATF 492 (557)
Q Consensus 432 ~~~~~vls~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~w~~~lg~~~l~~~~ 492 (557)
+|+|.|||+++||..+. .++.+|++|+.+++.|++||..+|+||+|+|.|++|+|+|+++|
T Consensus 81 ~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 81 DLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred ceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 99999999999998876 89999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=7.7e-27 Score=244.02 Aligned_cols=189 Identities=23% Similarity=0.304 Sum_probs=176.6
Q ss_pred HhhhhccccchHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccchhHhHHHhhhhHHhhHHHHHHHhhh--cC
Q 008667 348 VMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYAS--HP 425 (557)
Q Consensus 348 i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~--~~ 425 (557)
+-.+...+.+|+.|.+.||.+||.||+....++.+.|..-++.||-+||....+.|++|++|+..|+++++.++.. ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 4456677789999999999999999999999999999999999999999999999999999999999999999974 22
Q ss_pred ---CCCCCcceEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHhccCCCceeeeccCccceEEEEeeCCCcEEEEEe
Q 008667 426 ---ELGDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNV 502 (557)
Q Consensus 426 ---~~~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~~l~v 502 (557)
.+...+.+++.+||+.+||......+.+|.+++..++.|.+-|.+.+++|+|.|.+++|.|+++++|.+ ++.+++|
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~D-Rtl~~tV 600 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFED-RTLVLTV 600 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcC-eEEEEee
Confidence 112357899999999999998889999999999999999999999999999999999999999999998 9999999
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
|+.||+|+.+|.+.++||++++++.+|||++.++.
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrr 635 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRR 635 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999884
No 9
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=94.76 E-value=0.26 Score=44.88 Aligned_cols=88 Identities=17% Similarity=0.256 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHH-HHHHHHHHHhhhhhhccccC-----------------C
Q 008667 9 KLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHN-KALQMIRDILMYMDRTYIPS-----------------T 70 (557)
Q Consensus 9 ~LY~~l~~~i~~~l~~i~~~l~~~~~~~~L~~~~~~W~~~~-~~~~~l~~if~YLdr~yv~~-----------------~ 70 (557)
.+-+.+++.+..-+..+.+.+...+++.+|..++..|.-|. .-+-++..+|..|++.+-.. .
T Consensus 51 ~~~~dl~elL~tg~~~L~~~l~~~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~ 130 (158)
T PF08539_consen 51 YFLEDLEELLTTGMYILENQLNEVPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAG 130 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCC
Confidence 34456666666666667777877788999999999999955 55678999999999654332 2
Q ss_pred CCccHHHHHHHHHHHHhccccchHHHHH
Q 008667 71 HKTPVHELGLNLWRDNIVRSNKIQTRLL 98 (557)
Q Consensus 71 ~~~~i~~l~l~lf~~~v~~~~~~~~~l~ 98 (557)
+..+|+.+++..||+.|+- +..+++.
T Consensus 131 ~~l~Vr~l~L~~FRD~IvL--P~y~~l~ 156 (158)
T PF08539_consen 131 SELDVRRLLLIAFRDSIVL--PYYQRLK 156 (158)
T ss_pred CCCcHHHHHHHHHHHHhhh--cchHhhh
Confidence 3469999999999999987 6666553
No 10
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=91.10 E-value=0.76 Score=49.56 Aligned_cols=111 Identities=13% Similarity=0.051 Sum_probs=60.1
Q ss_pred hhHHHHHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHH--HHHHhhhcCcchHHHH-----------------HHHHHHH
Q 008667 140 KPFLEVSAEFYKVESQKFIECCDCGEYLKKAERRLNEE--MERVTHYLDAKSEAKI-----------------TNVVEKE 200 (557)
Q Consensus 140 ~~~L~~t~~yY~~~~~~~~~~~~~~~Yl~~~~~~l~~E--~~r~~~~l~~~t~~~l-----------------~~~~~~~ 200 (557)
.+|+..+..+|...++. +...+.+|+.+.....-.+ ++-++.-| ..+..++ .+.+-+-
T Consensus 289 e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~gnk~~~d~~l-~~~~d~i~~lfr~i~gkdvfeA~ykkdLakr 365 (661)
T KOG2167|consen 289 EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRAGNKETSDEEL-EFVLDKILVLFRFIHGKDVFEAFYKKDLAKR 365 (661)
T ss_pred HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHhccccccchhH-HHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 78999999999999993 5566889998887776555 22222111 0111122 2222223
Q ss_pred HHhhhhhHHHhcCchhhHHhhcCCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHh
Q 008667 201 MIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETG 258 (557)
Q Consensus 201 Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~~~~l~~~~~~~i~~~g 258 (557)
|+..|...+ ..|+.-+-.-+.....+..|+|...+++ .+...+..+.|....|
T Consensus 366 LLl~kSAsv----dae~~ml~~lk~ecgs~ft~kLegMfkd-me~sk~i~~~f~~~~~ 418 (661)
T KOG2167|consen 366 LLLGKSASV----DAEKSMLSKLKLECGSAFTYKLEGMFKD-MELSKEINRAFKQSKG 418 (661)
T ss_pred HHhccchhh----cchhHHHHHhhhhcchHHHHHHHHhhhh-HHHHHHHHHHHHHHHH
Confidence 333332222 1122222233445678889998887754 3445555555544434
No 11
>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=82.73 E-value=1.7 Score=30.69 Aligned_cols=36 Identities=11% Similarity=0.008 Sum_probs=28.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+..+..||....+++.+|..||++.+|+|...+...
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~ 37 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRY 37 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHH
Confidence 456778898899899999999999999999988754
No 12
>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=80.46 E-value=1.6 Score=32.44 Aligned_cols=37 Identities=16% Similarity=0.080 Sum_probs=31.4
Q ss_pred ecHHHHHHHHhhhCCCC--cCHHHHHHhcCCChHHhhhh
Q 008667 502 VSTYQMCVLMLFNNADR--LSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~--lt~~ei~~~t~~~~~~l~~~ 538 (557)
+|+.|+.||......+. +|..+|++.+++++..+..+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~ 41 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRI 41 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence 57889999988887776 99999999999999988754
No 13
>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=72.26 E-value=2.9 Score=30.83 Aligned_cols=37 Identities=8% Similarity=0.057 Sum_probs=32.0
Q ss_pred ecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 502 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+|+.|+.+|....+.+.+|..+|++.++++...+..+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~ 37 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRI 37 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHH
Confidence 3788999999999888999999999999999988754
No 14
>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=67.60 E-value=5.7 Score=28.61 Aligned_cols=33 Identities=6% Similarity=0.001 Sum_probs=26.3
Q ss_pred HHHHHhhhCCC-CcCHHHHHHhcCCChHHhhhhh
Q 008667 507 MCVLMLFNNAD-RLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 507 a~iLl~Fn~~~-~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
+.||..|.+.. .+|+.||++.+|++...+-.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L 39 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLL 39 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 45888998865 4899999999999998877543
No 15
>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=66.74 E-value=8.7 Score=27.80 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=23.5
Q ss_pred HHHHhh-hCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 508 CVLMLF-NNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 508 ~iLl~F-n~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.||..+ +..+.+|.++|++.+|+|..++...
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~ 35 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRD 35 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHH
Confidence 345444 6666699999999999999998864
No 16
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=66.60 E-value=8.1 Score=29.16 Aligned_cols=36 Identities=11% Similarity=-0.026 Sum_probs=26.8
Q ss_pred ecHHHHHHHHhhh-CCCCcCHHHHHHhcCCChHHhhh
Q 008667 502 VSTYQMCVLMLFN-NADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 502 vs~~Qa~iLl~Fn-~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
+|..|..||.... .....|..+|++.++++...+-.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~ 37 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSR 37 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHH
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHH
Confidence 4678999999998 78899999999999999887664
No 17
>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=63.46 E-value=8.3 Score=28.47 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=28.1
Q ss_pred HHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 506 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 506 Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
|..|+...+++..+|+++|++.+|+|+.++..
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRR 33 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHH
Confidence 45678888999999999999999999998774
No 18
>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=63.11 E-value=8.7 Score=32.86 Aligned_cols=50 Identities=10% Similarity=0.066 Sum_probs=39.0
Q ss_pred EecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh---hccccccCCCCC
Q 008667 501 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV---PAISGLCEGEEC 550 (557)
Q Consensus 501 ~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~---~~~~~~~~~~~~ 550 (557)
.+++.|+.||.....++.+|..+|++.++++...+-.+ +.=-|++.++.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~ 77 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKA 77 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccC
Confidence 56899999999998888999999999999999887643 222366655433
No 19
>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=61.63 E-value=11 Score=30.21 Aligned_cols=34 Identities=12% Similarity=-0.020 Sum_probs=24.2
Q ss_pred HHHHHHHhhhCCC-CcCHHHHHHhcCCChHHhhhh
Q 008667 505 YQMCVLMLFNNAD-RLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 505 ~Qa~iLl~Fn~~~-~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+++.+.+..+..+ .+|.++|++.+++|+..+.++
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~ki 45 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKI 45 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 3444455444444 499999999999999999976
No 20
>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=60.97 E-value=2e+02 Score=29.52 Aligned_cols=156 Identities=13% Similarity=0.232 Sum_probs=88.9
Q ss_pred hhhHHhhcCCcHHHHHHHHHhhccCC---CChHHHHHHHHHHHHHHhhHhhcCccc----CCCcHHHHHHHHHHHHHHHH
Q 008667 215 SGLVNMLLDDKYEDLGRMYNLFRRVP---SGLLTIREVMTSHLRETGKQLVTDPER----LKDPVEFVQRLLDEKDKYDN 287 (557)
Q Consensus 215 ~~~~~ll~~~~~~~L~~ly~L~~~~~---~~~~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~I~~ll~l~~~~~~ 287 (557)
..|..-.+.+|.+.+.++++||.-+. .|++...+-+.+.|.....+.++.... ...+.-|+..|..+++..-.
T Consensus 14 ~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~ia~ 93 (331)
T PF08318_consen 14 KKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEHIAT 93 (331)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHHHHH
Confidence 35777788899999999999998664 356666666666666666666654422 23456677777777777666
Q ss_pred HH-------HhhcCCCHH------hHHHHHHHHHHhhcc---CC---CcHHHHHHHHHHHhhc-----------------
Q 008667 288 II-------SSAFNNDKT------FQNALNSSFEYFINL---NP---RSPEFISLFVDDKLRK----------------- 331 (557)
Q Consensus 288 li-------~~~F~~~~~------f~~~i~~af~~~ln~---~~---~~~e~La~y~D~~lk~----------------- 331 (557)
++ ..+|+.... +.+..+.-...++.. .. +....+-.|-...+.+
T Consensus 94 ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (331)
T PF08318_consen 94 IIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSRAASSSQ 173 (331)
T ss_pred HHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhccccccccccccccccccc
Confidence 55 458876531 111111111112221 11 1222233333333322
Q ss_pred -CCCCCChHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHcCCC
Q 008667 332 -GLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGK 377 (557)
Q Consensus 332 -~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~ 377 (557)
+..+.+-.+++..|+.+..+++. -..|.++++.|.-...
T Consensus 174 ~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 174 SEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFS 213 (331)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhccc
Confidence 00112334677778877777643 3589999999987743
No 21
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=59.90 E-value=8.4 Score=28.66 Aligned_cols=33 Identities=12% Similarity=0.003 Sum_probs=25.7
Q ss_pred HHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 506 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 506 Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
|.-+|.++-+.+.+|+++|++.+|+|...+..-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHH
Confidence 555665555588999999999999999998864
No 22
>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=58.30 E-value=10 Score=26.17 Aligned_cols=31 Identities=19% Similarity=0.094 Sum_probs=23.1
Q ss_pred HHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 507 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 507 a~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
-.||.....+...|+.+|++.+|+|+..+..
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHH
Confidence 3577777777899999999999999988753
No 23
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=55.50 E-value=13 Score=30.08 Aligned_cols=39 Identities=18% Similarity=0.092 Sum_probs=34.1
Q ss_pred EEEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 499 ELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 499 ~l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
++.++..+..||........+|..+|++.++++...+..
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~ 43 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTR 43 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHH
Confidence 456788999999999888889999999999999888774
No 24
>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=55.39 E-value=18 Score=25.37 Aligned_cols=36 Identities=11% Similarity=-0.006 Sum_probs=27.4
Q ss_pred HHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhhc
Q 008667 504 TYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVPA 540 (557)
Q Consensus 504 ~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~~ 540 (557)
+...-|+.+.-+ .+.++.||++.+|++...+-..++
T Consensus 2 ~~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 2 PTRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHH
Confidence 345567777777 679999999999999999876544
No 25
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=54.90 E-value=3.8e+02 Score=30.74 Aligned_cols=138 Identities=14% Similarity=0.228 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhhcCcchHHHHHHHHHHHHHhhhhhHHHhc-CchhhHHhhcC
Q 008667 145 VSAEFYKVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHM-DNSGLVNMLLD 223 (557)
Q Consensus 145 ~t~~yY~~~~~~~~~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~-~~~~~~~ll~~ 223 (557)
-..-||...+..-+ ...+.++.+.+...++++.+..-..+-.....+|.+-++.+ +.++.. .++++.....
T Consensus 555 N~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~gv------e~l~~~~~~~ei~~~~~- 626 (701)
T PF09763_consen 555 NYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFEGV------EALLQTVSPEEISYQAA- 626 (701)
T ss_pred HHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHH------HHHHhccCchhcccchh-
Confidence 33344444444322 24456677777777776666543332222234444433321 111110 0111111111
Q ss_pred CcHHHHHHHHHhhc--cCCCChHHHHHHHHHHHHHHhh------HhhcCcccCCCcHHHHHHHHHHHHHHHHHHHhhcCC
Q 008667 224 DKYEDLGRMYNLFR--RVPSGLLTIREVMTSHLRETGK------QLVTDPERLKDPVEFVQRLLDEKDKYDNIISSAFNN 295 (557)
Q Consensus 224 ~~~~~L~~ly~L~~--~~~~~~~~l~~~~~~~i~~~g~------~~~~~~~~~~~~~~~I~~ll~l~~~~~~li~~~F~~ 295 (557)
-....|+.+..-+. .+..+++.+.+.+.+|+...+. .++.. -=..+-+..+..|.++..++..|+.|
T Consensus 627 ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~-----vW~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 627 YSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQV-----VWSAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred ccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHH-----HHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 12345555555432 3334556666666666511111 11110 01234567888899999999999865
No 26
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=54.60 E-value=16 Score=32.53 Aligned_cols=52 Identities=15% Similarity=0.034 Sum_probs=40.2
Q ss_pred EEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhhc---cccccCCCCCC
Q 008667 500 LNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVPA---ISGLCEGEECS 551 (557)
Q Consensus 500 l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~~---~~~~~~~~~~~ 551 (557)
..+|+.|+.||......+.+|..+|++.+++++..+-.+++ =-|++.++.+.
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~ 90 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP 90 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence 35788999999887777889999999999999999875422 24677665543
No 27
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=54.32 E-value=1.5e+02 Score=25.79 Aligned_cols=47 Identities=21% Similarity=0.486 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHhcCCCCCH-HHHHHHHHHHHhhCcccchhhch
Q 008667 93 IQTRLLNTLLELVHRERTGEVINR-GLMRNIIKMLMDLGPSVYQEDFE 139 (557)
Q Consensus 93 ~~~~l~~~ll~~I~~~R~g~~~~~-~~lk~ii~~l~~lg~~~Y~~~FE 139 (557)
+++++.+.|-.++...|...+.+. --+.++..||..||+-+|...-|
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~Q~E 55 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEAQME 55 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHHCCH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHHHHh
Confidence 456677788888888886554332 23789999999999767765444
No 28
>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=54.22 E-value=15 Score=28.73 Aligned_cols=30 Identities=3% Similarity=-0.168 Sum_probs=23.3
Q ss_pred HHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 509 VLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 509 iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+..++...+.+|+.||++.+|+|+..+...
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 333334456789999999999999998864
No 29
>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=53.86 E-value=22 Score=25.18 Aligned_cols=30 Identities=7% Similarity=0.038 Sum_probs=22.8
Q ss_pred HHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 507 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 507 a~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
..|-+.| ...+|++||++.+|+|...+...
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHH
Confidence 3444666 56789999999999999988753
No 30
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=49.60 E-value=24 Score=27.09 Aligned_cols=44 Identities=9% Similarity=-0.030 Sum_probs=32.8
Q ss_pred HHHHHHHHhhhCCCC--cCHHHHHHhcCCChHHhhhhh---ccccccCC
Q 008667 504 TYQMCVLMLFNNADR--LSYQGNRAGNRDSCFRLEKVP---AISGLCEG 547 (557)
Q Consensus 504 ~~Qa~iLl~Fn~~~~--lt~~ei~~~t~~~~~~l~~~~---~~~~~~~~ 547 (557)
...-.||..+.+... +|..||++.+|++...+..++ .=.|++..
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 445568888888765 999999999999999888652 33455543
No 31
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=48.84 E-value=21 Score=27.00 Aligned_cols=38 Identities=11% Similarity=-0.097 Sum_probs=27.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCCCccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEECSSERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 556 (557)
+|+.|+++.+|+++..+.....-.++..|...+--|.|
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~~~~g~R~y 38 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYY 38 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCCCCCceee
Confidence 47899999999999999987665556545444444444
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=47.77 E-value=24 Score=24.65 Aligned_cols=32 Identities=13% Similarity=0.036 Sum_probs=25.9
Q ss_pred HHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 507 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 507 a~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
-.|+..+.+...+|..+|++.++++...+...
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~ 34 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRD 34 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHH
Confidence 34666666667899999999999999998754
No 33
>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=47.16 E-value=29 Score=28.55 Aligned_cols=40 Identities=15% Similarity=0.053 Sum_probs=33.4
Q ss_pred EEEecHHHHHHHHhhh--------CCCCcCHHHHHHhcCCChHHhhhh
Q 008667 499 ELNVSTYQMCVLMLFN--------NADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 499 ~l~vs~~Qa~iLl~Fn--------~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
...+++-|+.+|+..- ....+|-.||++.+|++...+..+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~ 67 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDA 67 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHH
Confidence 3567889999888665 477899999999999999988764
No 34
>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=47.07 E-value=22 Score=26.36 Aligned_cols=36 Identities=8% Similarity=-0.027 Sum_probs=29.7
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
++.-..||..+...++.|+.+|++.+|++...+-..
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~h 44 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYH 44 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHH
Confidence 566678888887788999999999999999987754
No 35
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=44.63 E-value=33 Score=31.94 Aligned_cols=60 Identities=10% Similarity=0.018 Sum_probs=46.4
Q ss_pred CceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--CCCcCHHHHHHhcCCChHHhhhhh
Q 008667 474 GRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 474 ~RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~--~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
.|.-.|.+.+|..+.+ ..+.| .||+.||.-|+.-+. -..||.+-||+..++..+.++.++
T Consensus 96 ~r~~~~~~~fg~~ep~-~vPkG-----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL 157 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPE-KVPKG-----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNIL 157 (179)
T ss_pred CCCCcccccccccCcc-cCCCC-----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHH
Confidence 3445688999998886 34544 679999998877665 357999999999999988887553
No 36
>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=42.89 E-value=15 Score=27.86 Aligned_cols=48 Identities=17% Similarity=0.043 Sum_probs=34.8
Q ss_pred ecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh---hccccccCCCC
Q 008667 502 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV---PAISGLCEGEE 549 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~---~~~~~~~~~~~ 549 (557)
.|-.++-|+...-.....|..||++.+|++...+..+ +.=-|++....
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3556677776665777899999999999999998764 23346665544
No 37
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=42.83 E-value=29 Score=26.11 Aligned_cols=32 Identities=13% Similarity=-0.133 Sum_probs=26.4
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEEC 550 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~ 550 (557)
+|+.|+++.+|++...|....+-.|+..|...
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~~~~~r~ 32 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRT 32 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCCCCCCcC
Confidence 47899999999999999987666678776543
No 38
>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=41.93 E-value=38 Score=28.49 Aligned_cols=39 Identities=18% Similarity=0.159 Sum_probs=32.3
Q ss_pred EEecHHHHHHHHhhh----CCCCcCHHHHHHhcCCChHHhhhh
Q 008667 500 LNVSTYQMCVLMLFN----NADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 500 l~vs~~Qa~iLl~Fn----~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+.+|+.|..||.... ..+.+|..+|++.++++...+-.+
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~ 63 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKI 63 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHH
Confidence 356888999987766 557899999999999999988764
No 39
>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=40.42 E-value=36 Score=23.60 Aligned_cols=30 Identities=10% Similarity=-0.074 Sum_probs=20.4
Q ss_pred HHHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 508 CVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 508 ~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
-|+-++.++ .|+.+|++.+|+|..++-.++
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHH
Confidence 345566665 899999999999998876553
No 40
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=39.84 E-value=31 Score=29.48 Aligned_cols=44 Identities=18% Similarity=0.420 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhhCcccchhhc
Q 008667 95 TRLLNTLLELVHRERTGEVINRG-LMRNIIKMLMDLGPSVYQEDF 138 (557)
Q Consensus 95 ~~l~~~ll~~I~~~R~g~~~~~~-~lk~ii~~l~~lg~~~Y~~~F 138 (557)
+++.+.|-+++...|.....+.+ -+.++..||..||+-+|.-..
T Consensus 3 ~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGLRVYeaQ~ 47 (118)
T PRK13713 3 NEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYEAQM 47 (118)
T ss_pred hHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhHHHHHHHH
Confidence 45667777888888865442222 378999999999977775433
No 41
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.55 E-value=41 Score=23.68 Aligned_cols=34 Identities=15% Similarity=-0.004 Sum_probs=26.0
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
|.-|..++.++. ...|..+|++.+|+|...+...
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHH
Confidence 555566666654 3579999999999999998854
No 42
>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=38.61 E-value=44 Score=23.84 Aligned_cols=22 Identities=14% Similarity=-0.059 Sum_probs=15.7
Q ss_pred CCcCHHHHHHhcCCChHHhhhh
Q 008667 517 DRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 517 ~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
..+|+.||++.+|+|+..+...
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~ 46 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRR 46 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHH
Confidence 3689999999999999988753
No 43
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=38.20 E-value=47 Score=31.15 Aligned_cols=53 Identities=6% Similarity=-0.127 Sum_probs=41.3
Q ss_pred EEecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh---hccccccCCCCCCc
Q 008667 500 LNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV---PAISGLCEGEECSS 552 (557)
Q Consensus 500 l~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~---~~~~~~~~~~~~~~ 552 (557)
+.+|+.|..||.....++.+|..+|++.++++..++..+ +-=-|++.++.+..
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~ 96 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKED 96 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence 467899999999999999999999999999997776543 22247777665544
No 44
>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=37.69 E-value=46 Score=23.50 Aligned_cols=34 Identities=12% Similarity=-0.101 Sum_probs=24.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+.-|..++.++- +.+|..+|++.+|+|...+...
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHH
Confidence 344555554443 4689999999999999998853
No 45
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.84 E-value=41 Score=27.75 Aligned_cols=37 Identities=19% Similarity=-0.027 Sum_probs=28.4
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCCC--ccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEECS--SERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~--~~~~~ 556 (557)
+|+.|+++.+|+|+..+.-.-+ .||+.|...+ --|.|
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~~~~~gyR~Y 39 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGLFKPEIVKENGYRYY 39 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccC
Confidence 5789999999999999998766 4888776433 33554
No 46
>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=36.80 E-value=49 Score=24.68 Aligned_cols=32 Identities=6% Similarity=-0.085 Sum_probs=25.0
Q ss_pred HHHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 508 CVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 508 ~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
+|..+-.+...++..+|++.+|++++++..++
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 34445557889999999999999999988653
No 47
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=36.37 E-value=40 Score=29.83 Aligned_cols=39 Identities=10% Similarity=-0.073 Sum_probs=32.7
Q ss_pred EEecHHHHHHHHhhhCC-CCcCHHHHHHhcCCChHHhhhh
Q 008667 500 LNVSTYQMCVLMLFNNA-DRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 500 l~vs~~Qa~iLl~Fn~~-~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+.+|+.|..||...... +..|..+|++.+++++..+..+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~ 66 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHH
Confidence 45788999999888754 5689999999999999988764
No 48
>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=36.34 E-value=26 Score=26.81 Aligned_cols=31 Identities=13% Similarity=-0.059 Sum_probs=22.3
Q ss_pred HHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 509 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 509 iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
|.....++...|++||+..++++++.++.++
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3444556788999999999999999998653
No 49
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.18 E-value=40 Score=27.72 Aligned_cols=31 Identities=19% Similarity=0.050 Sum_probs=26.1
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEEC 550 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~ 550 (557)
+|++|+++.+|+++..|.-.-+. ||+.|...
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~ 31 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKI 31 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcc
Confidence 48899999999999999987666 88877643
No 50
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=35.54 E-value=42 Score=29.03 Aligned_cols=33 Identities=9% Similarity=-0.066 Sum_probs=28.0
Q ss_pred CcCHHHHHHhcCCChHHhhhhhccccccCCCCCC
Q 008667 518 RLSYQGNRAGNRDSCFRLEKVPAISGLCEGEECS 551 (557)
Q Consensus 518 ~lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~ 551 (557)
.+|++|+++.+|+|...+.-.-++ ||+.|...+
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r~ 35 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLR-GLLHPVRRT 35 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCccC
Confidence 589999999999999999988666 888876543
No 51
>PF10408 Ufd2P_core: Ubiquitin elongating factor core; InterPro: IPR019474 This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (IPR003613 from INTERPRO), which has ligase activity. Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.; GO: 0034450 ubiquitin-ubiquitin ligase activity, 0006511 ubiquitin-dependent protein catabolic process, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 2KRE_A 3M63_A 2QIZ_A 2QJ0_A 3M62_A.
Probab=34.59 E-value=7.2e+02 Score=28.07 Aligned_cols=58 Identities=14% Similarity=0.388 Sum_probs=34.3
Q ss_pred ccHHHHHHHHHHHH-hccccchHHHHHHHHHHHHHHHhcCCC------------CCHHHHHHHHHHHHhhC
Q 008667 73 TPVHELGLNLWRDN-IVRSNKIQTRLLNTLLELVHRERTGEV------------INRGLMRNIIKMLMDLG 130 (557)
Q Consensus 73 ~~i~~l~l~lf~~~-v~~~~~~~~~l~~~ll~~I~~~R~g~~------------~~~~~lk~ii~~l~~lg 130 (557)
.++-.+++...... .+.||.++.++...+...+...+.+.. ....++.++++.|++++
T Consensus 322 ~~l~~f~i~fm~s~~~ikNP~LraklvevL~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~sLm~~yidvE 392 (629)
T PF10408_consen 322 DELVTFCITFMGSPEYIKNPHLRAKLVEVLFSLLPPDRDGRRGVLGSLFESHPLAQEHLVPSLMKFYIDVE 392 (629)
T ss_dssp HHHHHHHHHHHH-TTS---HHHHHHHHHHHHHCCS--TTS---TTHHHHHH-HHHHCCHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHhCChhhcCCHHHHHHHHHHHHHhcCcccccccccHHHHHHcCHHHHHHHHHHHHHHHHHHH
Confidence 35556666666555 677888999998888877766662211 11236788888888885
No 52
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=34.48 E-value=49 Score=24.91 Aligned_cols=29 Identities=14% Similarity=-0.103 Sum_probs=24.1
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGE 548 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~ 548 (557)
+|+.|+++.+|+++..+....+ -|++.|.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-~gli~~~ 29 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-IGLLPPP 29 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCC
Confidence 4789999999999999998755 6777664
No 53
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=34.23 E-value=51 Score=26.31 Aligned_cols=41 Identities=15% Similarity=0.029 Sum_probs=30.3
Q ss_pred HHHHHhhhCC-CCcCHHHHHHhcCCChHHhhhhhc---cccccCC
Q 008667 507 MCVLMLFNNA-DRLSYQGNRAGNRDSCFRLEKVPA---ISGLCEG 547 (557)
Q Consensus 507 a~iLl~Fn~~-~~lt~~ei~~~t~~~~~~l~~~~~---~~~~~~~ 547 (557)
..||..+... ..+|+.||++.+|++...+...++ =.|++..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 3477777776 689999999999999999875422 2455543
No 54
>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=34.22 E-value=56 Score=24.38 Aligned_cols=35 Identities=11% Similarity=0.008 Sum_probs=28.8
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+..+..|+..+.+.. ++..||++.+|++...+...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~ 40 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHH
Confidence 456777888777766 99999999999999987754
No 55
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.14 E-value=46 Score=28.26 Aligned_cols=30 Identities=20% Similarity=0.021 Sum_probs=25.5
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
++++|+++.+|+|+..+.-.-+. ||+.|.-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~p~r 30 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLLVPER 30 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCCCCCc
Confidence 47899999999999999987675 8887744
No 56
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=33.82 E-value=54 Score=24.81 Aligned_cols=31 Identities=10% Similarity=-0.139 Sum_probs=25.6
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
+|+.|+++.+|+++..+...-.-.|+..|..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~~~~r 31 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQR 31 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCc
Confidence 4789999999999999998766667876644
No 57
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=33.23 E-value=49 Score=27.86 Aligned_cols=37 Identities=19% Similarity=0.055 Sum_probs=29.1
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCCC---ccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEECS---SERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~---~~~~~ 556 (557)
+|++|+++.+|+|+..+.-.-.. ||+.|...+ .-|.|
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~ngyR~Y 40 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDTGYRYY 40 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCCCcccc
Confidence 47899999999999999987665 888886543 34555
No 58
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.44 E-value=37 Score=27.37 Aligned_cols=25 Identities=20% Similarity=0.080 Sum_probs=22.4
Q ss_pred CCcCHHHHHHhcCCChHHhhhhhcc
Q 008667 517 DRLSYQGNRAGNRDSCFRLEKVPAI 541 (557)
Q Consensus 517 ~~lt~~ei~~~t~~~~~~l~~~~~~ 541 (557)
..+|.++|+.++|.++..+++++++
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~~ 46 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQV 46 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHHH
Confidence 4799999999999999999998755
No 59
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=32.04 E-value=62 Score=29.65 Aligned_cols=32 Identities=16% Similarity=0.064 Sum_probs=25.9
Q ss_pred HHHHHhhhC-CCCcCHHHHHHhcCCChHHhhhh
Q 008667 507 MCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 507 a~iLl~Fn~-~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+.+.+.|+. ...+|.++|++.+++|..-++++
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kI 45 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQL 45 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHH
Confidence 444555765 45799999999999999999986
No 60
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.89 E-value=41 Score=23.59 Aligned_cols=29 Identities=10% Similarity=-0.068 Sum_probs=20.2
Q ss_pred HHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 509 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 509 iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
++.++.+ .+|..+|++.+|+|..++....
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHH
Confidence 4555554 7899999999999999987653
No 61
>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=31.62 E-value=55 Score=30.97 Aligned_cols=38 Identities=13% Similarity=0.066 Sum_probs=33.7
Q ss_pred EecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 501 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 501 ~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.++.-|..||..+.++...|..+|++.+|++...+...
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~ 177 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRH 177 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 56888999999999888899999999999999988753
No 62
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.36 E-value=54 Score=27.32 Aligned_cols=30 Identities=17% Similarity=0.042 Sum_probs=25.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
+|++|+++.+|+|+..+.-.-+. ||+.|..
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~~r 31 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLITGTR 31 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCc
Confidence 68999999999999999988776 8887643
No 63
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=31.23 E-value=4.6e+02 Score=24.85 Aligned_cols=120 Identities=11% Similarity=0.264 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHhhhhhHHHhc-CchhhHHhhcCCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHhhHhhcCcccCC
Q 008667 191 AKITNVVEKEMIANHMPRLVHM-DNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERLK 269 (557)
Q Consensus 191 ~~l~~~~~~~Li~~~~~~il~~-~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~ 269 (557)
+.|.+.+.+.||...-+.++.. +...+..++..+ .++++.|..|--.. ...+.+-..++.+|.+.-
T Consensus 21 E~i~kelie~l~~~~~qk~l~~gE~v~il~Ll~~k-d~ef~~llkla~eq-~k~e~~m~~Lea~VEkrD----------- 87 (272)
T KOG4552|consen 21 EHIVKELIETLINRDKQKMLKNGETVNILKLLDSK-DDEFKTLLKLAPEQ-QKREQLMRTLEAHVEKRD----------- 87 (272)
T ss_pred HHHHHHHHHHHHhhhHHHHHhcchHHHHHHHHHhc-cHHHHHHHHHhHhH-HHHHHHHHHHHHHHHHhH-----------
Confidence 4444555555555445555543 112233344433 24455554433222 123344444555444433
Q ss_pred CcHHHHHHHHHHHHHHHHHHH-hhcCCCHHhHHHHHHHHHHhhccCCCcHHHHHHHHHHHhhcC
Q 008667 270 DPVEFVQRLLDEKDKYDNIIS-SAFNNDKTFQNALNSSFEYFINLNPRSPEFISLFVDDKLRKG 332 (557)
Q Consensus 270 ~~~~~I~~ll~l~~~~~~li~-~~F~~~~~f~~~i~~af~~~ln~~~~~~e~La~y~D~~lk~~ 332 (557)
..|+.|-.-.+..+.++. .||.-+..+ +.|++| ++.+-.+|.|-+|.|.+-+.+
T Consensus 88 ---~~IQqLqk~LK~aE~iLtta~fqA~qKL-ksi~~A-----~krpvsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 88 ---EVIQQLQKNLKSAEVILTTACFQANQKL-KSIKEA-----EKRPVSSEELIKYAHRISKHN 142 (272)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-----hcCCCCHHHHHHHHHHhhhcc
Confidence 334554444444444443 377655442 334433 335667899999999987654
No 64
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=31.04 E-value=52 Score=32.40 Aligned_cols=32 Identities=6% Similarity=-0.033 Sum_probs=27.9
Q ss_pred HHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 507 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 507 a~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
..||.+|.....+|+.||++.+|++..++--+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rl 48 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRF 48 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHH
Confidence 45889998888899999999999999998754
No 65
>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=30.80 E-value=82 Score=24.93 Aligned_cols=37 Identities=11% Similarity=-0.035 Sum_probs=26.8
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhhcc
Q 008667 505 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVPAI 541 (557)
Q Consensus 505 ~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~~~ 541 (557)
+.-.+|-+.-+...+|+.+|+..+|.+.+.+..+++-
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 3445777788899999999999999999999887543
No 66
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=30.32 E-value=54 Score=27.66 Aligned_cols=31 Identities=13% Similarity=-0.094 Sum_probs=25.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEEC 550 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~ 550 (557)
+|++|+++.+|+|+..+.-.-+. ||+.|..-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~~r 31 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLHPVAR 31 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCc
Confidence 47899999999999999987666 88877533
No 67
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=30.05 E-value=67 Score=26.58 Aligned_cols=38 Identities=16% Similarity=0.036 Sum_probs=31.3
Q ss_pred EecHHHHHHHHhhhC----CCCcCHHHHHHhcCCChHHhhhh
Q 008667 501 NVSTYQMCVLMLFNN----ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 501 ~vs~~Qa~iLl~Fn~----~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.+++.|-.||..+.. .+.+++++|++.++++...+++.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~a 85 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKA 85 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHH
Confidence 588999999999988 56799999999999999998864
No 68
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=29.84 E-value=64 Score=26.78 Aligned_cols=33 Identities=12% Similarity=-0.034 Sum_probs=28.1
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 505 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 505 ~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
..-.||..+..+...|+.+|++.+|+|+..+..
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~ 36 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHN 36 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHH
Confidence 345688888888899999999999999999864
No 69
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=29.03 E-value=36 Score=27.07 Aligned_cols=33 Identities=12% Similarity=0.093 Sum_probs=25.3
Q ss_pred HHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 507 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 507 a~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
..|+...+..+++++.+|.+.+|++...+-+.+
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL 35 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHL 35 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHH
Confidence 456666666788999999999999999988653
No 70
>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=28.96 E-value=53 Score=25.11 Aligned_cols=29 Identities=17% Similarity=0.004 Sum_probs=23.3
Q ss_pred HHHHhhhCCCCcCHHHHHHhcCCChHHhh
Q 008667 508 CVLMLFNNADRLSYQGNRAGNRDSCFRLE 536 (557)
Q Consensus 508 ~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~ 536 (557)
.|-.+.++...+|+.+|++.||++...+.
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~ 40 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVY 40 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHH
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHH
Confidence 46678888899999999999999766554
No 71
>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=28.90 E-value=80 Score=25.21 Aligned_cols=34 Identities=6% Similarity=-0.169 Sum_probs=29.4
Q ss_pred HHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 505 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 505 ~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
=|+.|+-...+ ...|+.+|++..|+|..++-..+
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 36778888888 89999999999999999988754
No 72
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=28.79 E-value=60 Score=27.37 Aligned_cols=37 Identities=14% Similarity=-0.009 Sum_probs=28.5
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCC--Cccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEEC--SSERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~--~~~~~~ 556 (557)
+|+.|+++.+|+|+..+...-.. |++.|... +.-|.|
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gll~p~~~~~~g~R~Y 39 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GLLSPDREPETGYRVY 39 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCceee
Confidence 58899999999999999988675 78877543 234544
No 73
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.67 E-value=60 Score=26.31 Aligned_cols=30 Identities=10% Similarity=-0.141 Sum_probs=25.9
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
+|++++++.+|+++..+.-.-. .|++.|..
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~p~r 31 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLLSPSR 31 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCcCCCc
Confidence 5899999999999999998877 58888754
No 74
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.59 E-value=62 Score=27.13 Aligned_cols=37 Identities=11% Similarity=-0.015 Sum_probs=26.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCCCccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEECSSERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 556 (557)
++++|+++.+|+|...+.=.=+ .||+.|...+.-|.|
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~-~GLl~p~~~~g~r~Y 37 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYID-LGLLIPEKKGGQYFF 37 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCcCCccCCCcccc
Confidence 5789999999999999986533 366667554444554
No 75
>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=28.51 E-value=80 Score=27.72 Aligned_cols=33 Identities=12% Similarity=0.011 Sum_probs=25.4
Q ss_pred HHHHHhhhCC-CCcCHHHHHHhcCCChHHhhhhh
Q 008667 507 MCVLMLFNNA-DRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 507 a~iLl~Fn~~-~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
+.+.+.++.. ..+|.++|++.+++|+.-+++++
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil 46 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLF 46 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3344555543 47999999999999999999863
No 76
>KOG4481 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.66 E-value=63 Score=29.51 Aligned_cols=59 Identities=10% Similarity=0.103 Sum_probs=49.0
Q ss_pred CceeeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--CCCcCHHHHHHhcCCChHHhhhh
Q 008667 474 GRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 474 ~RkL~w~~~lg~~~l~~~~~~~~~~~l~vs~~Qa~iLl~Fn~--~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.+++-|-++.+...++ ..+.| .++..||.-++.|++ .++||.+-|++...++.++++-+
T Consensus 95 e~r~p~~~~f~~~~i~-rIpkg-----kit~~eAL~~ln~hkL~petw~AekIA~ey~l~~~~v~~i 155 (194)
T KOG4481|consen 95 EFRLPKDYHFDEINIK-RIPKG-----KITIVEALTFLNNHKLLPETWTAEKIAQEYHLEQEDVNDI 155 (194)
T ss_pred hcCCcccccCCCcCcc-cCCCC-----ceeHHHHHHHHhhhhcChhhhHHHHHHHHHhhchhhHHHH
Confidence 5678999999998887 46664 578999999998876 67899999999999998887744
No 77
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.61 E-value=77 Score=21.81 Aligned_cols=27 Identities=15% Similarity=-0.151 Sum_probs=22.3
Q ss_pred cCHHHHHHhcCCChHHhhhhhcccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLC 545 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~ 545 (557)
+|..|+++.+|+++..+....+-.-+.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 478999999999999999876655554
No 78
>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=27.33 E-value=92 Score=21.26 Aligned_cols=36 Identities=17% Similarity=0.040 Sum_probs=25.8
Q ss_pred ecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 502 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
+++.+..++.++- ...+|..+|++.+|++...+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHH
Confidence 3555555554443 24689999999999999988753
No 79
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.13 E-value=70 Score=26.54 Aligned_cols=31 Identities=6% Similarity=-0.318 Sum_probs=25.9
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
+|+.|+++.+|+|+..+...-...|+..|..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli~p~r 31 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVK 31 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCCCCcC
Confidence 4789999999999999998877777776643
No 80
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=27.08 E-value=1.3e+02 Score=25.10 Aligned_cols=36 Identities=19% Similarity=0.496 Sum_probs=27.6
Q ss_pred HHhHHHHHHHHHHhhcc-------CCCcHHHHHHHHHHHhhcC
Q 008667 297 KTFQNALNSSFEYFINL-------NPRSPEFISLFVDDKLRKG 332 (557)
Q Consensus 297 ~~f~~~i~~af~~~ln~-------~~~~~e~La~y~D~~lk~~ 332 (557)
......+..||+.+++. .++.++++|+++..++..+
T Consensus 68 ~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~ 110 (113)
T PF02847_consen 68 LISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADG 110 (113)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcC
Confidence 33456677788888774 4789999999999998865
No 81
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.95 E-value=68 Score=26.36 Aligned_cols=30 Identities=13% Similarity=-0.040 Sum_probs=24.9
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
++++|+++.+|+|+..+.-.-+ .||+.|..
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~-~Gll~p~~ 30 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH-IGLLSPSQ 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCc
Confidence 5789999999999999998766 56777643
No 82
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.64 E-value=60 Score=21.88 Aligned_cols=23 Identities=9% Similarity=0.027 Sum_probs=16.3
Q ss_pred CCCcCHHHHHHhcCCChHHhhhh
Q 008667 516 ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 516 ~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
...||+++||+..|+|+.-+...
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~ 28 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRL 28 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHH
Confidence 56799999999999998887753
No 83
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.33 E-value=59 Score=26.51 Aligned_cols=26 Identities=27% Similarity=0.132 Sum_probs=23.8
Q ss_pred CCcCHHHHHHhcCCChHHhhhhhccc
Q 008667 517 DRLSYQGNRAGNRDSCFRLEKVPAIS 542 (557)
Q Consensus 517 ~~lt~~ei~~~t~~~~~~l~~~~~~~ 542 (557)
..+|.++|++.+|+|+..|+.|+++-
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 47999999999999999999998875
No 84
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.24 E-value=76 Score=26.13 Aligned_cols=30 Identities=17% Similarity=0.013 Sum_probs=25.3
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
++++|+++.+|+++..+...-.. ||+.|..
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~p~r 30 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVSPER 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCc
Confidence 47899999999999999988775 8887644
No 85
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=26.24 E-value=57 Score=21.87 Aligned_cols=26 Identities=15% Similarity=-0.174 Sum_probs=20.0
Q ss_pred CHHHHHHhcCCChHHhhhhhccccccC
Q 008667 520 SYQGNRAGNRDSCFRLEKVPAISGLCE 546 (557)
Q Consensus 520 t~~ei~~~t~~~~~~l~~~~~~~~~~~ 546 (557)
|+.|+++.+|++...|.-.-.. ||+.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~-Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE-GLLP 26 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT-TSS-
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-CCCC
Confidence 5789999999999999977555 5663
No 86
>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=26.09 E-value=1e+02 Score=24.01 Aligned_cols=44 Identities=16% Similarity=0.089 Sum_probs=30.5
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh---hccccccCCC
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV---PAISGLCEGE 548 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~---~~~~~~~~~~ 548 (557)
+..|. ||...... ..|++||.+.||++...|-+. ++=.|+|+++
T Consensus 5 t~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 5 TVTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred hHHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 34444 44444444 899999999999999988764 3445777655
No 87
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=25.98 E-value=65 Score=33.02 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=28.2
Q ss_pred HhhhC---CCCcCHHHHHHhcCCChHHhhh--hhccc-cccCCC
Q 008667 511 MLFNN---ADRLSYQGNRAGNRDSCFRLEK--VPAIS-GLCEGE 548 (557)
Q Consensus 511 l~Fn~---~~~lt~~ei~~~t~~~~~~l~~--~~~~~-~~~~~~ 548 (557)
+.|.. ...+|+++|+++|++|.+.++- +-+++ ||++++
T Consensus 284 i~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~ 327 (380)
T KOG2908|consen 284 ITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGS 327 (380)
T ss_pred HHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeee
Confidence 56665 4579999999999999999994 34443 556554
No 88
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.97 E-value=75 Score=25.64 Aligned_cols=37 Identities=16% Similarity=0.081 Sum_probs=28.4
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCCCC--ccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEECS--SERTY 556 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~~--~~~~~ 556 (557)
+|+.|+++.+|+++..|...-+. |++.|...+ .-|.|
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~p~r~~~~g~R~Y 40 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDGGGQRKY 40 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCceec
Confidence 68999999999999999987665 677676554 34544
No 89
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.72 E-value=83 Score=21.25 Aligned_cols=26 Identities=15% Similarity=-0.111 Sum_probs=21.0
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGL 544 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~ 544 (557)
+|..|+++.+|++...+....+-..+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999986554433
No 90
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=25.50 E-value=56 Score=28.61 Aligned_cols=34 Identities=15% Similarity=-0.022 Sum_probs=23.3
Q ss_pred ecHHHHH-HHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 502 VSTYQMC-VLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 502 vs~~Qa~-iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
+++-|-. +.|.+- +.+|++|||+.+|+|+..+.+
T Consensus 108 Lp~~~r~v~~l~~~--~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 108 LPNKQKKIIYMKFF--EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHhhcC
Confidence 3444444 444333 358999999999999988754
No 91
>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=24.93 E-value=1e+02 Score=26.66 Aligned_cols=33 Identities=18% Similarity=0.075 Sum_probs=24.3
Q ss_pred HHHHHHhhhC-CCCcCHHHHHHhcCCChHHhhhh
Q 008667 506 QMCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 506 Qa~iLl~Fn~-~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
++.+.+.-++ ...+|.++|++.+++|+..+.++
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~i 45 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKI 45 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHH
Confidence 3334444343 34899999999999999999875
No 92
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.08 E-value=90 Score=26.41 Aligned_cols=29 Identities=14% Similarity=-0.069 Sum_probs=23.6
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGE 548 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~ 548 (557)
+|++|+++.+|+|+..|.-.-+. ||+.|.
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~-gll~~~ 29 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKE-GLLPPV 29 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCC
Confidence 47899999999999999977664 666543
No 93
>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=23.89 E-value=5.3e+02 Score=26.39 Aligned_cols=75 Identities=15% Similarity=0.267 Sum_probs=48.6
Q ss_pred hhhHHhhcCCcHHHHHHHHHhhccCC---CChHHHHHHHHHHHHHHhhHhhcCccc----CCCcHHHHHHHHHHHHHHHH
Q 008667 215 SGLVNMLLDDKYEDLGRMYNLFRRVP---SGLLTIREVMTSHLRETGKQLVTDPER----LKDPVEFVQRLLDEKDKYDN 287 (557)
Q Consensus 215 ~~~~~ll~~~~~~~L~~ly~L~~~~~---~~~~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~I~~ll~l~~~~~~ 287 (557)
..|..-.+++|...+.++++||..+. .|++....-+.+.|........+.... ...+.-|+..|..+++..-.
T Consensus 14 ~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~~~~~~~~~a~~lt~Lfe~ia~ 93 (324)
T smart00762 14 ERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASDDTRAAVFYADTLTHLFENVAT 93 (324)
T ss_pred HHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccccccccchHHHHHHHHHHHHHH
Confidence 35777888999999999999998664 356555556666666666555433211 12345677777777766555
Q ss_pred HH
Q 008667 288 II 289 (557)
Q Consensus 288 li 289 (557)
++
T Consensus 94 ii 95 (324)
T smart00762 94 II 95 (324)
T ss_pred HH
Confidence 44
No 94
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=23.78 E-value=81 Score=23.00 Aligned_cols=27 Identities=11% Similarity=0.031 Sum_probs=22.1
Q ss_pred hhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 512 LFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 512 ~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.|+.-...|.+||++.+|+|+..+...
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 455556899999999999999987643
No 95
>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=23.76 E-value=1.2e+02 Score=23.75 Aligned_cols=35 Identities=6% Similarity=-0.016 Sum_probs=30.6
Q ss_pred cHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 503 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 503 s~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
.+=|+.++-++..-+.-|+++|++.||..+-++..
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRg 43 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRG 43 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHH
Confidence 56689999999998899999999999998877753
No 96
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=23.71 E-value=92 Score=22.31 Aligned_cols=23 Identities=9% Similarity=-0.263 Sum_probs=19.8
Q ss_pred CCCcCHHHHHHhcCCChHHhhhh
Q 008667 516 ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 516 ~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.+..|..+|++.+|++...+...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~ 30 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHH 30 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHH
Confidence 56789999999999999887753
No 97
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.33 E-value=92 Score=25.71 Aligned_cols=30 Identities=10% Similarity=-0.161 Sum_probs=25.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
+|+.++++.+|+|...|..... .|++.|..
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gli~p~r 31 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGLVSPAR 31 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCCCCCc
Confidence 5899999999999999999877 67887743
No 98
>PRK10870 transcriptional repressor MprA; Provisional
Probab=22.79 E-value=1.1e+02 Score=28.15 Aligned_cols=53 Identities=9% Similarity=0.086 Sum_probs=38.4
Q ss_pred EEecHHHHHHHHhhhC--CCCcCHHHHHHhcCCChHHhhhh---hccccccCCCCCCc
Q 008667 500 LNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKV---PAISGLCEGEECSS 552 (557)
Q Consensus 500 l~vs~~Qa~iLl~Fn~--~~~lt~~ei~~~t~~~~~~l~~~---~~~~~~~~~~~~~~ 552 (557)
..+|..|..||..... ..++|..+|++.++++...+..+ +-=-|++.+..+..
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~ 108 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN 108 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 3467789888877764 46799999999999999998643 22247776655543
No 99
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.76 E-value=1.1e+02 Score=27.23 Aligned_cols=35 Identities=17% Similarity=0.056 Sum_probs=29.3
Q ss_pred EecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhh
Q 008667 501 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 537 (557)
Q Consensus 501 ~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~ 537 (557)
..|.-|..|+.++ ...+|.+||++.+|+|...+..
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~ 40 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSA 40 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHH
Confidence 3577888888886 4679999999999999998773
No 100
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=22.68 E-value=73 Score=23.94 Aligned_cols=23 Identities=26% Similarity=0.199 Sum_probs=16.3
Q ss_pred CCCcCHHHHHHhcCCChHHhhhh
Q 008667 516 ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 516 ~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
...+|++++++.|+++...++.+
T Consensus 8 ~~glsl~~va~~t~I~~~~l~ai 30 (62)
T PF13413_consen 8 AKGLSLEDVAEETKISVSYLEAI 30 (62)
T ss_dssp CTT--HHHHHHHCS--HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 45799999999999999998864
No 101
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=22.43 E-value=60 Score=25.43 Aligned_cols=36 Identities=11% Similarity=-0.066 Sum_probs=24.4
Q ss_pred HHHhhhCCCCcCHHHHHHhcCCChHHhhhhhccccc
Q 008667 509 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVPAISGL 544 (557)
Q Consensus 509 iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~~~~~~ 544 (557)
|+....+-..+|+.||++.+|+|+..+-...+=+|.
T Consensus 25 il~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~ 60 (77)
T PF01418_consen 25 ILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGF 60 (77)
T ss_dssp HHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTT
T ss_pred HHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCC
Confidence 444445566899999999999999998877665554
No 102
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.24 E-value=80 Score=23.70 Aligned_cols=30 Identities=10% Similarity=-0.206 Sum_probs=23.2
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGEE 549 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~ 549 (557)
.|+.|+++.+|+|+..|....+.. ++.|..
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~g-ll~~~~ 30 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREG-LLPPPR 30 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTT-SSTTBE
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhc-Cccccc
Confidence 378999999999999999875543 355544
No 103
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.94 E-value=1e+02 Score=27.71 Aligned_cols=36 Identities=11% Similarity=0.016 Sum_probs=31.0
Q ss_pred EecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhh
Q 008667 501 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 536 (557)
Q Consensus 501 ~vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~ 536 (557)
.++..--.||..+..+...|+.+|++.+|+|+..+.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~ 41 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIH 41 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHH
Confidence 345666778999998899999999999999999876
No 104
>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=21.85 E-value=97 Score=30.23 Aligned_cols=32 Identities=13% Similarity=0.148 Sum_probs=27.0
Q ss_pred HHHHHhhhC-CCCcCHHHHHHhcCCChHHhhhh
Q 008667 507 MCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 507 a~iLl~Fn~-~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
..||.+|.. ...+|+.||++.+|++..++--+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~Rl 44 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRF 44 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 458889986 56799999999999999987754
No 105
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=21.62 E-value=1.2e+02 Score=27.24 Aligned_cols=31 Identities=13% Similarity=-0.091 Sum_probs=24.8
Q ss_pred HHHhhhCCCCcCHHHHHHhcCCChHHhhhhh
Q 008667 509 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 539 (557)
Q Consensus 509 iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~ 539 (557)
+.+..+..+.+|..+|++..++|+.-|+++.
T Consensus 15 ~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl 45 (153)
T PRK11920 15 MYCAANDGKLSRIPEIARAYGVSELFLFKIL 45 (153)
T ss_pred HHHHhCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3444555667899999999999999999863
No 106
>PRK13749 transcriptional regulator MerD; Provisional
Probab=21.54 E-value=1.2e+02 Score=26.32 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=28.7
Q ss_pred CcCHHHHHHhcCCChHHhhhhhccccccCCCCC--Cccccc
Q 008667 518 RLSYQGNRAGNRDSCFRLEKVPAISGLCEGEEC--SSERTY 556 (557)
Q Consensus 518 ~lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~~~--~~~~~~ 556 (557)
.+|++|+++.+|+|...+.-.=++ ||+.|... +.-|.|
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r~~~gyR~Y 42 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLR-GLLRPVACTTGGYGLF 42 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCcCCCCCccC
Confidence 479999999999999999977554 77766544 344544
No 107
>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=21.48 E-value=60 Score=27.09 Aligned_cols=33 Identities=9% Similarity=-0.043 Sum_probs=22.7
Q ss_pred HHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhh
Q 008667 506 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 506 Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
.+.|+..+..+..++-++|++.+|++...+.++
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRki 47 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKI 47 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHH
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHH
Confidence 345666666667899999999999999999875
No 108
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=21.39 E-value=72 Score=24.11 Aligned_cols=30 Identities=10% Similarity=0.026 Sum_probs=22.9
Q ss_pred HHHhhhC-CCCcCHHHHHHhcCCChHHhhhh
Q 008667 509 VLMLFNN-ADRLSYQGNRAGNRDSCFRLEKV 538 (557)
Q Consensus 509 iLl~Fn~-~~~lt~~ei~~~t~~~~~~l~~~ 538 (557)
||..++. +.++|..||++.+|+|.......
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~y 35 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYY 35 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Confidence 5556666 78899999999999998887754
No 109
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=21.14 E-value=1e+02 Score=25.50 Aligned_cols=29 Identities=14% Similarity=-0.066 Sum_probs=23.6
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEGE 548 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~~ 548 (557)
+|+.|+++.+|+++..+.-.-+ -|++.|.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~-~Gll~~~ 29 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE-IGLLKPS 29 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCC
Confidence 4789999999999999998755 4666554
No 110
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=21.05 E-value=1.1e+02 Score=25.39 Aligned_cols=28 Identities=18% Similarity=-0.037 Sum_probs=23.8
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccccCC
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGLCEG 547 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~~~~ 547 (557)
+|+.|+++.+|+|+..|.-.-+. ||+.|
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~~ 29 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLIPS 29 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCC
Confidence 68999999999999999987776 77733
No 111
>PF12728 HTH_17: Helix-turn-helix domain
Probab=20.82 E-value=90 Score=21.92 Aligned_cols=26 Identities=8% Similarity=-0.187 Sum_probs=21.0
Q ss_pred cCHHHHHHhcCCChHHhhhhhccccc
Q 008667 519 LSYQGNRAGNRDSCFRLEKVPAISGL 544 (557)
Q Consensus 519 lt~~ei~~~t~~~~~~l~~~~~~~~~ 544 (557)
+|++|+++.+|+|...+....+-.++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 68999999999999999876544433
No 112
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=20.66 E-value=2.2e+02 Score=23.72 Aligned_cols=38 Identities=13% Similarity=0.181 Sum_probs=29.2
Q ss_pred CCHHhHHHHHHHHHHhhcc-------CCCcHHHHHHHHHHHhhcC
Q 008667 295 NDKTFQNALNSSFEYFINL-------NPRSPEFISLFVDDKLRKG 332 (557)
Q Consensus 295 ~~~~f~~~i~~af~~~ln~-------~~~~~e~La~y~D~~lk~~ 332 (557)
.+......+..||..+++. .++.++.+|+++..++..|
T Consensus 66 ~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~ 110 (113)
T smart00544 66 ANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDG 110 (113)
T ss_pred cCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcC
Confidence 3444567788888888885 3588999999999988764
No 113
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=20.48 E-value=98 Score=28.19 Aligned_cols=35 Identities=11% Similarity=-0.091 Sum_probs=30.5
Q ss_pred ecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhh
Q 008667 502 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 536 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~ 536 (557)
+.-.-..||....++...|+.+|++.+|+|...+.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~ 46 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCL 46 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHH
Confidence 45566778999999999999999999999998866
No 114
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.41 E-value=1.2e+02 Score=25.23 Aligned_cols=50 Identities=14% Similarity=0.043 Sum_probs=38.3
Q ss_pred ecHHHHHHHHhhhCCCCcCHHHHHHhcCCChHHhhhhh---ccccccCCCCCC
Q 008667 502 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEECS 551 (557)
Q Consensus 502 vs~~Qa~iLl~Fn~~~~lt~~ei~~~t~~~~~~l~~~~---~~~~~~~~~~~~ 551 (557)
+++.|..+|......+..+..+|++.+++++..+..++ -=-|++.++...
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 78999999988888777776999999999999887542 224666555443
Done!