Query 007158
Match_columns 615
No_of_seqs 187 out of 1019
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 19:44:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007158.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007158hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00888 Cullin: Cullin family 100.0 2.6E-90 5.5E-95 780.6 60.2 547 29-596 1-554 (588)
2 KOG2166 Cullins [Cell cycle co 100.0 4.8E-88 1E-92 745.4 54.0 573 22-596 14-600 (725)
3 COG5647 Cullin, a subunit of E 100.0 5.5E-85 1.2E-89 689.6 54.1 598 9-611 6-664 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 7.2E-82 1.6E-86 623.7 42.2 545 17-597 6-599 (728)
5 KOG2167 Cullins [Cell cycle co 100.0 3E-80 6.5E-85 639.2 38.8 517 68-594 2-530 (661)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1.3E-71 2.8E-76 555.7 48.9 583 22-612 10-655 (777)
7 smart00182 CULLIN Cullin. 100.0 8.8E-34 1.9E-38 259.2 16.2 139 412-550 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 7.1E-25 1.5E-29 232.2 44.3 201 405-606 441-650 (765)
9 PF08539 HbrB: HbrB-like; Int 97.6 0.0017 3.6E-08 59.9 14.3 130 25-156 5-156 (158)
10 KOG2167 Cullins [Cell cycle co 95.0 0.24 5.3E-06 53.8 11.8 89 24-112 67-159 (661)
11 PF13412 HTH_24: Winged helix- 76.7 3.3 7.3E-05 29.6 3.3 36 561-596 2-37 (48)
12 PF12802 MarR_2: MarR family; 75.6 2.8 6.1E-05 31.6 2.8 38 560-597 3-42 (62)
13 PF01047 MarR: MarR family; I 64.8 5.2 0.00011 29.8 2.2 38 560-597 1-38 (59)
14 PF08220 HTH_DeoR: DeoR-like h 63.5 7.9 0.00017 29.0 2.9 31 564-594 2-32 (57)
15 PF08279 HTH_11: HTH domain; 60.5 12 0.00026 27.4 3.4 31 566-596 4-35 (55)
16 PF08318 COG4: COG4 transport 60.4 2.2E+02 0.0048 29.7 15.7 155 274-435 15-213 (331)
17 PF09339 HTH_IclR: IclR helix- 60.3 9.3 0.0002 27.9 2.7 32 565-596 6-38 (52)
18 TIGR02337 HpaR homoprotocatech 60.0 12 0.00027 32.4 4.0 50 559-608 25-77 (118)
19 PF13463 HTH_27: Winged helix 60.0 12 0.00026 28.6 3.5 37 560-596 1-38 (68)
20 PF02082 Rrf2: Transcriptional 58.7 11 0.00024 30.5 3.3 35 563-597 11-46 (83)
21 PF08280 HTH_Mga: M protein tr 57.0 9.7 0.00021 28.7 2.4 32 564-595 7-38 (59)
22 PRK11512 DNA-binding transcrip 55.6 16 0.00036 32.9 4.2 52 558-609 36-90 (144)
23 PF13404 HTH_AsnC-type: AsnC-t 55.1 11 0.00024 26.3 2.2 30 565-594 6-35 (42)
24 PF01022 HTH_5: Bacterial regu 53.9 18 0.00039 25.7 3.3 34 563-597 3-36 (47)
25 PF06784 UPF0240: Uncharacteri 50.4 23 0.00051 33.4 4.4 58 533-596 97-156 (179)
26 smart00347 HTH_MARR helix_turn 49.3 18 0.0004 29.7 3.2 41 557-597 5-45 (101)
27 TIGR03879 near_KaiC_dom probab 47.7 21 0.00046 28.3 3.0 31 567-597 23-53 (73)
28 PF04545 Sigma70_r4: Sigma-70, 47.4 29 0.00062 24.9 3.6 30 565-596 11-40 (50)
29 PF09645 F-112: F-112 protein; 46.5 10 0.00022 31.2 1.1 51 559-609 2-57 (110)
30 smart00550 Zalpha Z-DNA-bindin 44.1 31 0.00066 26.8 3.5 36 562-597 6-43 (68)
31 PF12840 HTH_20: Helix-turn-he 43.3 27 0.00059 26.3 3.0 37 561-597 9-45 (61)
32 PRK13777 transcriptional regul 42.2 35 0.00076 32.4 4.2 53 558-610 41-96 (185)
33 KOG2166 Cullins [Cell cycle co 41.1 74 0.0016 37.0 7.3 38 25-62 10-48 (725)
34 TIGR01889 Staph_reg_Sar staphy 38.7 52 0.0011 28.1 4.4 51 558-608 21-78 (109)
35 smart00420 HTH_DEOR helix_turn 38.2 39 0.00085 23.9 3.1 33 565-597 3-35 (53)
36 PF01978 TrmB: Sugar-specific 37.0 20 0.00042 27.7 1.4 47 560-606 6-55 (68)
37 smart00421 HTH_LUXR helix_turn 35.3 49 0.0011 23.7 3.3 35 560-596 4-38 (58)
38 TIGR01610 phage_O_Nterm phage 35.2 54 0.0012 27.3 3.8 40 557-596 20-67 (95)
39 PF08784 RPA_C: Replication pr 34.2 50 0.0011 27.8 3.5 39 559-597 44-86 (102)
40 PF08281 Sigma70_r4_2: Sigma-7 33.8 56 0.0012 23.6 3.4 35 561-596 12-46 (54)
41 PF05261 Tra_M: TraM protein, 33.2 62 0.0013 28.4 3.9 47 151-197 8-55 (127)
42 PF02796 HTH_7: Helix-turn-hel 33.1 48 0.001 23.3 2.7 29 566-596 13-41 (45)
43 PF05584 Sulfolobus_pRN: Sulfo 32.5 64 0.0014 25.5 3.5 39 567-606 10-51 (72)
44 cd06170 LuxR_C_like C-terminal 32.3 59 0.0013 23.3 3.3 34 561-596 2-35 (57)
45 PF09012 FeoC: FeoC like trans 32.2 34 0.00074 26.5 2.0 31 567-597 5-35 (69)
46 PRK03573 transcriptional regul 31.8 59 0.0013 29.1 3.9 50 558-607 27-80 (144)
47 PRK10857 DNA-binding transcrip 30.6 59 0.0013 30.2 3.7 34 564-597 12-46 (164)
48 PRK10870 transcriptional repre 30.3 78 0.0017 29.7 4.5 53 558-610 51-108 (176)
49 PRK13713 conjugal transfer pro 30.1 57 0.0012 28.3 3.1 42 153-194 3-45 (118)
50 PF13413 HTH_25: Helix-turn-he 29.7 44 0.00096 25.5 2.2 24 574-597 8-31 (62)
51 PF13384 HTH_23: Homeodomain-l 29.7 41 0.0009 23.9 2.0 29 567-597 10-38 (50)
52 PF09763 Sec3_C: Exocyst compl 29.6 9.5E+02 0.021 27.9 20.8 23 331-353 679-701 (701)
53 PF04967 HTH_10: HTH DNA bindi 29.4 51 0.0011 24.4 2.4 27 570-596 17-43 (53)
54 PF00165 HTH_AraC: Bacterial r 28.5 52 0.0011 22.5 2.2 23 574-596 6-28 (42)
55 PF10475 DUF2450: Protein of u 28.4 6.5E+02 0.014 25.6 26.8 70 278-347 194-282 (291)
56 TIGR02844 spore_III_D sporulat 27.9 73 0.0016 25.8 3.3 33 563-596 7-39 (80)
57 PRK15090 DNA-binding transcrip 26.9 61 0.0013 32.4 3.4 32 565-596 17-48 (257)
58 smart00346 HTH_ICLR helix_turn 26.9 74 0.0016 25.7 3.3 33 565-597 8-41 (91)
59 TIGR02010 IscR iron-sulfur clu 26.6 85 0.0018 28.0 3.9 33 565-597 13-46 (135)
60 PF13601 HTH_34: Winged helix 26.2 41 0.00089 27.1 1.6 33 565-597 3-35 (80)
61 cd00090 HTH_ARSR Arsenical Res 26.2 86 0.0019 23.7 3.5 36 561-597 6-41 (78)
62 PF10771 DUF2582: Protein of u 26.1 60 0.0013 25.1 2.4 29 566-594 12-40 (65)
63 PF10408 Ufd2P_core: Ubiquitin 25.8 1E+03 0.023 27.2 17.5 63 400-469 564-628 (629)
64 PF01325 Fe_dep_repress: Iron 25.1 94 0.002 23.5 3.3 31 567-597 13-43 (60)
65 PF10163 EnY2: Transcription f 24.9 2.9E+02 0.0063 22.5 6.4 55 26-80 29-85 (86)
66 TIGR01884 cas_HTH CRISPR locus 24.4 84 0.0018 30.2 3.7 39 559-597 140-178 (203)
67 COG4367 Uncharacterized protei 24.2 60 0.0013 26.5 2.1 26 575-600 22-47 (97)
68 KOG4481 Uncharacterized conser 24.2 80 0.0017 29.2 3.1 59 532-596 95-155 (194)
69 smart00762 Cog4 COG4 transport 24.1 8.2E+02 0.018 25.4 16.6 154 273-433 14-205 (324)
70 cd04764 HTH_MlrA-like_sg1 Heli 23.7 91 0.002 23.7 3.1 27 577-603 1-27 (67)
71 KOG4552 Vitamin-D-receptor int 23.7 6.6E+02 0.014 24.1 11.9 120 249-390 21-142 (272)
72 smart00344 HTH_ASNC helix_turn 23.6 92 0.002 26.2 3.4 34 563-596 4-37 (108)
73 PRK11920 rirA iron-responsive 23.0 94 0.002 28.5 3.5 32 566-597 14-45 (153)
74 cd06171 Sigma70_r4 Sigma70, re 22.9 1.1E+02 0.0024 21.2 3.3 36 560-596 11-46 (55)
75 PF12324 HTH_15: Helix-turn-he 22.7 1.3E+02 0.0028 24.2 3.6 35 563-597 25-59 (77)
76 TIGR00738 rrf2_super rrf2 fami 21.5 1.1E+02 0.0024 26.8 3.7 34 564-597 12-46 (132)
77 PLN02999 photosystem II oxygen 21.2 3.8E+02 0.0082 25.2 6.9 22 99-120 168-189 (190)
78 KOG1488 Translational represso 21.2 8.4E+02 0.018 27.1 10.8 50 55-108 327-377 (503)
79 PF02847 MA3: MA3 domain; Int 21.0 1.9E+02 0.0041 24.5 4.9 35 356-390 69-110 (113)
80 TIGR00721 tfx DNA-binding prot 20.6 1.2E+02 0.0025 27.4 3.5 36 559-596 6-41 (137)
81 PF01418 HTH_6: Helix-turn-hel 20.3 70 0.0015 25.4 1.8 35 567-601 25-59 (77)
82 cd00569 HTH_Hin_like Helix-tur 20.3 1.4E+02 0.003 18.4 3.2 29 564-594 11-39 (42)
No 1
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=2.6e-90 Score=780.64 Aligned_cols=547 Identities=41% Similarity=0.735 Sum_probs=506.4
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH
Q 007158 29 WKILEHAIHEIYNHNASGLSFEELYRNAYNMVLHKFGEKLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHNK 108 (615)
Q Consensus 29 W~~l~~~i~~I~~~~~~~~s~~~lY~~vy~lc~~~~~e~LY~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~~~W~~y~~ 108 (615)
|+.|++||+.|+.+..++.+||++|+.||++|.+++|++||+.+++.+.+++.++.+++.+..++++|..|...|.+|+.
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~~~~~ 80 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWEKYKK 80 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHH
Confidence 99999999999987778899999999999999999999999999999999999999998777788999999999999999
Q ss_pred HHHHHHHHhhhhhhcccCCCCCccHhHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhhC
Q 007158 109 ALQMIRDILMYMDRTYIPSTHKTPVHELGLNLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG 188 (615)
Q Consensus 109 ~~~~l~~vf~YLdr~yv~~~~~~~i~~l~l~~f~~~v~~~~~l~~~l~~~ll~~I~~~R~g~~i~~~~lk~ii~~l~~lg 188 (615)
++.+|+++|+||||+|+.++ +|++.|+. ++.++++++++++|.++|.|+.++...++++++++.++|
T Consensus 81 ~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~ 147 (588)
T PF00888_consen 81 AIKYISDIFSYLDRNYVKRN-----------LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELG 147 (588)
T ss_dssp HHHHHHHHTHHHHHTSTTTT-----------HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhHhhhhhh-----------hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccc
Confidence 99999999999999999886 99999999 799999999999999999999999999999999999997
Q ss_pred -cccchhhchhhHHHHHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHhhhHHH
Q 007158 189 -PSVYQEDFEKPFLEVSAEFYKVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRL 267 (615)
Q Consensus 189 -~~~Y~~~FE~~~l~~t~~yY~~~s~~~i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~i 267 (615)
..+|.+.||++|++.|.+||+.++ +++.++.+|+++|+.++.+|.+|+..|++++|.+++.+++.++||.+|.+.|
T Consensus 148 ~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l 224 (588)
T PF00888_consen 148 SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL 224 (588)
T ss_dssp HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH
T ss_pred hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999 6778999999999999999999999999999999999999999999999999
Q ss_pred HhcCchhhHHhhccCcHHHHHHHHHHhccCCCChHhHHHHHHHHHHHHhhhhhcCcccCCCcHHHHHHHHHHHHHHHHHH
Q 007158 268 VHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKYDNII 347 (615)
Q Consensus 268 l~~~~~~~~~ll~~~~~~~L~~l~~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 347 (615)
.+|+..|+++++.++|+++|+|+++++++++.+++.|++||.+.|.++++.......+.++|+.++++|+++..++
T Consensus 225 ----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 225 ----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp ----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred ----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999999999999999999999876544567899999999999999999
Q ss_pred HhhcCCCHHhHHHHHHHHHHhhccC-CCcHHHHHHHHHHHhhcCCCCCChhHHHHHHHHHhhhhccccchHHHHHHHHHH
Q 007158 348 SSAFNNDKTFQNALNSSFEYFINLN-PRSPEFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQH 426 (615)
Q Consensus 348 ~~~F~~~~~f~~~i~~af~~~ln~~-~~~~e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~ 426 (615)
.++|++++.|.+++++||+.++|.. .+++++||+|||.+++++.++.+++++++.++.++.+|+|+++||+|+.+|+++
T Consensus 301 ~~~F~~~~~f~~~l~~af~~~~n~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~ 380 (588)
T PF00888_consen 301 QECFDNDSEFKKALDEAFEEFLNKNNNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKL 380 (588)
T ss_dssp HHTTTT-HHHHHHHHHHHHHHHHCSTSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHH
T ss_pred HHhccccHHHHHHHHHhHHHHHHcCCcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHH
Confidence 9999999999999999999999987 899999999999999999877888899999999999999999999999999999
Q ss_pred HHhHhcCCCCCChHHHHHHHHHHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhhcCCCCC----CccEEEEEeccCCCC
Q 007158 427 LAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPELGD----SRTLVVQVLTTGSWP 502 (615)
Q Consensus 427 L~~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~----~~~~~~~vls~~~WP 502 (615)
||+|||.+++.+.+.|..++++|+.+||.+++++|++|++|+..|+++++.|++....++. +++|+|.||++++||
T Consensus 381 L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp 460 (588)
T PF00888_consen 381 LAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWP 460 (588)
T ss_dssp HHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-
T ss_pred HHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCC
Confidence 9999999999999999999999999999999999999999999999999999987654332 789999999999999
Q ss_pred CCCCCC-CCCcHhHHHHHHHHHHHHhcCCCCcceeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCccHHH
Q 007158 503 TQPSVT-CNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQG 581 (615)
Q Consensus 503 ~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~~~~~t~~e 581 (615)
..+..+ +.+|++|+.+++.|++||+.+|+||+|+|.|++|+|+|++++++ ++++++||++||+||++||+++++|+++
T Consensus 461 ~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~-~~~~l~~s~~q~~iLl~Fn~~~~~t~~e 539 (588)
T PF00888_consen 461 KYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNN-GKYELTVSTLQAAILLLFNDNDSLTVEE 539 (588)
T ss_dssp S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSS-SEEEEEEEHHHHHHHHGGGSSSEEEHHH
T ss_pred CCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecC-CceeEEeeHHHHHHHHHHccCCCccHHH
Confidence 887655 99999999999999999999999999999999999999999998 8899999999999999999999999999
Q ss_pred HHHhcCCChhhhhhh
Q 007158 582 NRAGNRDSCFRLEKV 596 (615)
Q Consensus 582 i~~~t~~~~~~l~~~ 596 (615)
|++.||++++.+..+
T Consensus 540 i~~~~~~~~~~l~~~ 554 (588)
T PF00888_consen 540 ISEKTGISEEELKRA 554 (588)
T ss_dssp HHHHC---HHHHHHH
T ss_pred HHHHHCcCHHHHHHH
Confidence 999999999988754
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.8e-88 Score=745.41 Aligned_cols=573 Identities=40% Similarity=0.680 Sum_probs=526.2
Q ss_pred hhhHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhhcCCch----HHHHHHHHHHHHHHHHHHH-HHHHhccchHHH
Q 007158 22 PKYAEKTWKILEHAIHEIYNHNASGLSFEELYRNAYNMVLHKFG----EKLYSGLVSTMTLHLKEIS-KSIEAAQGGSFL 96 (615)
Q Consensus 22 ~~~f~~~W~~l~~~i~~I~~~~~~~~s~~~lY~~vy~lc~~~~~----e~LY~~l~~~i~~~~~~i~-~~l~~~~~~~~L 96 (615)
..+++++|..|..+++.+.+.--++.+++.+|+++|++|+++.| ++||.++++++.+|+.+++ +.+....++.+|
T Consensus 14 w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~~~~l 93 (725)
T KOG2166|consen 14 WSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHDEYML 93 (725)
T ss_pred HHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHH
Confidence 35566667777666664432223567899999999999999988 9999999999999999955 555666778999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhcccCCC-CCccHhHHH-HHHHHHHHhcchhhHHHHHHHHHHHHHHHhcCCCCCh
Q 007158 97 EELNRKWNDHNKALQMIRDILMYMDRTYIPST-HKTPVHELG-LNLWRDNIVRSNKIQTRLLNTLLELVHRERTGEVINR 174 (615)
Q Consensus 97 ~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~-~~~~i~~l~-l~~f~~~v~~~~~l~~~l~~~ll~~I~~~R~g~~i~~ 174 (615)
+.+.+.|.+|+.++.+++++|.||||+||.+. +..++.+++ +.+|+..++.. ++.++++++++.+|..+|.|+.+|+
T Consensus 94 ~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~in~ 172 (725)
T KOG2166|consen 94 RELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQIDR 172 (725)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhcccccccH
Confidence 99999999999999999999999999999965 555666665 99999998874 5999999999999999999999999
Q ss_pred HHHHHHHHHHHhhC---cccchhhchhhHHHHHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhcCChhhHHHH
Q 007158 175 GLMRNIIKMLMDLG---PSVYQEDFEKPFLEVSAEFYKVESQKFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKI 251 (615)
Q Consensus 175 ~~lk~ii~~l~~lg---~~~Y~~~FE~~~l~~t~~yY~~~s~~~i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~~l 251 (615)
..|+++++++..+| .++|...||++|++.|..||..+++.|+...++.+|+.+++.++.+|..|+..|++..+.+++
T Consensus 173 ~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~ 252 (725)
T KOG2166|consen 173 ELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPKL 252 (725)
T ss_pred HHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccchh
Confidence 99999999999998 569999999999999999999999999998899999999999999999999998888777888
Q ss_pred HHHHHHHHHHhhhHHHHhcCchhhHHhhccCcHHHHHHHHHHhccCCCChHhHHHHHHHHHHHHhhhhhcCcccC--CCc
Q 007158 252 TNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERL--KDP 329 (615)
Q Consensus 252 ~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~l~~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~--~~~ 329 (615)
.+.+...++..+++.+++...+||..++.+++.++|.+||+|+++++.|++.+++.++.|++.+|..++...... .+|
T Consensus 253 ~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~~ 332 (725)
T KOG2166|consen 253 VEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATNP 332 (725)
T ss_pred hHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccch
Confidence 888888888888888887778999999999999999999999999999999999999999999998888766544 689
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHHHHHhhccCCCcH-HHHHHHHHHHhhcCCCCCChhHHHHHHHHHhh
Q 007158 330 VEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSSFEYFINLNPRSP-EFISLFVDDKLRKGLKGVSEEDVETILDKVMM 408 (615)
Q Consensus 330 ~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~i~~af~~~ln~~~~~~-e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~ 408 (615)
.++++.++++++++..++..||++|..|.++++.||..|+|.+...+ |+||+|||..+|++.++.++++++..+++++.
T Consensus 333 ~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~ 412 (725)
T KOG2166|consen 333 VEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVVK 412 (725)
T ss_pred HHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhccee
Confidence 99999999999999999999999999999999999999999977666 99999999999999899999999999999999
Q ss_pred hhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhhcCCC-CC
Q 007158 409 LFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPEL-GD 487 (615)
Q Consensus 409 lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~-~~ 487 (615)
+|+|+++||+|+.+|++.||||||+++|.|++.|+.||.+|+++||.+||.||++|++|+..|++++..|.++...+ ..
T Consensus 413 l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~~~~~~ 492 (725)
T KOG2166|consen 413 LLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYANYSANL 492 (725)
T ss_pred eeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhchhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999762111 23
Q ss_pred CccEEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHhcCCCCcceeeccCccceEEEEeeCCCcEEEEEecHHHHHH
Q 007158 488 SRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCV 567 (615)
Q Consensus 488 ~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~i 567 (615)
+++|.|.|||.|+||.+++.++.||++|.++++.|..||..+|+||+|.|+|++|+|+|.++|.+ ++++|+||++||+|
T Consensus 493 ~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~-~~~~l~vst~Qm~V 571 (725)
T KOG2166|consen 493 GIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDK-KTVELQVSTYQMAV 571 (725)
T ss_pred CCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecC-ceEEEEEEhHHHHH
Confidence 69999999999999998888899999999999999999999999999999999999999999998 79999999999999
Q ss_pred HHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 568 LMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 568 Ll~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
|++||+.+.+|+++|.++|+++.+.+..+
T Consensus 572 LlLFN~~d~lt~~eI~~~t~i~~~~l~~~ 600 (725)
T KOG2166|consen 572 LLLFNNTEKLTYEEILEQTNLGHEDLARL 600 (725)
T ss_pred HHHccchhhccHHHHHHHhCCCHHHHHHH
Confidence 99999999999999999999999998744
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.5e-85 Score=689.61 Aligned_cols=598 Identities=33% Similarity=0.517 Sum_probs=524.3
Q ss_pred cccccCCCCCCCChhhHHHHHHHHHHHHHHHHhhC---CCCCCHHHHHHHHHHhhcCC----------------chHHHH
Q 007158 9 FQIEAFKHRVVVDPKYAEKTWKILEHAIHEIYNHN---ASGLSFEELYRNAYNMVLHK----------------FGEKLY 69 (615)
Q Consensus 9 ~~i~~~~~~~~~~~~~f~~~W~~l~~~i~~I~~~~---~~~~s~~~lY~~vy~lc~~~----------------~~e~LY 69 (615)
++|..|+. +.++++|+..|+.++.||++|+... ...++|+++|+.+|+.|.+. .++.+|
T Consensus 6 ~ki~vp~~--~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li 83 (773)
T COG5647 6 IKIDVPRK--TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLI 83 (773)
T ss_pred cccccCcc--CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHH
Confidence 44444444 5677889999999999999999543 34678999999999999986 456677
Q ss_pred HHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccC-----CCCCccHhHHHHHHHHHH
Q 007158 70 SGLVSTMTLHLKEISKSIEAAQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIP-----STHKTPVHELGLNLWRDN 144 (615)
Q Consensus 70 ~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~-----~~~~~~i~~l~l~~f~~~ 144 (615)
+++.....+++............+.+|..+++.|.++..+..+++.+|.||||.|++ ......+.++++..|+..
T Consensus 84 ~~L~~~~k~~i~~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~ 163 (773)
T COG5647 84 QKLVDYAKNYIEEYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIE 163 (773)
T ss_pred HHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHH
Confidence 777777777776644332222347899999999999999999999999999999999 234556778999999999
Q ss_pred HhcchhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhhC---------cccchhhchhhHHHHHHHHHHHHHHHh
Q 007158 145 IVRSNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLG---------PSVYQEDFEKPFLEVSAEFYKVESQKF 215 (615)
Q Consensus 145 v~~~~~l~~~l~~~ll~~I~~~R~g~~i~~~~lk~ii~~l~~lg---------~~~Y~~~FE~~~l~~t~~yY~~~s~~~ 215 (615)
++. .+.+.+++.++..+.+.|.|+++|+..+..++.|+.+++ ..+|.+.||+.||+.|.+||..++++.
T Consensus 164 ~f~--~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~ 241 (773)
T COG5647 164 SFR--LIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEV 241 (773)
T ss_pred HHH--hhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHH
Confidence 999 999999999999999999999999999999999999995 268999999999999999999999999
Q ss_pred HhcCCHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHhhhHHHHhcCchhhHHhhccCcHHHHHHHHHHhc
Q 007158 216 IECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFR 295 (615)
Q Consensus 216 i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~l~~L~~ 295 (615)
+..+++.+||.+|..++++|..++..|++.++..++..+++++||..|.+.+.+. .+|+..+++..+.+.|..+|++++
T Consensus 242 i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~-~s~f~~~~d~~~~e~l~~lY~l~s 320 (773)
T COG5647 242 IELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQ-GSGFREALDASNLEKLQVLYRLLS 320 (773)
T ss_pred HHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhc-hHHHHHHHHhhhHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999876 379999999999999999999999
Q ss_pred cCCCChHhHHHHHHHHHHHHh--hh-hhc----Ccc-------cCCCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHH
Q 007158 296 RVPSGLLTIREVMTSHLRETG--KQ-LVT----DPE-------RLKDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNAL 361 (615)
Q Consensus 296 ~~~~~~~~l~~~~~~~i~~~g--~~-~~~----~~~-------~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~i 361 (615)
+++.++.+|++.|.+||+..| .. ... ... ..-.+..+++.++.+++.+..++..+|.+|..+.+++
T Consensus 321 e~~~~v~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l 400 (773)
T COG5647 321 ETKYGVQPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKAL 400 (773)
T ss_pred hhhhhhhhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHH
Confidence 999999999999999999999 11 111 111 1125789999999999999999999999999999999
Q ss_pred HHHHHHhhcc----CCCcHHHHHHHHHHHhhcCCCCCChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCCCC
Q 007158 362 NSSFEYFINL----NPRSPEFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTV 437 (615)
Q Consensus 362 ~~af~~~ln~----~~~~~e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~ 437 (615)
++||+.|+|+ +..++|+||+|+|.++|++.+......++..+.+++.||+|+.+||+|+++|+++||||||+++|.
T Consensus 401 ~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~ 480 (773)
T COG5647 401 GNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSA 480 (773)
T ss_pred HHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCc
Confidence 9999999997 247999999999999999876655567888999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhhcCCCCCCccEEEEEeccCCCCCC-CCCCCCCcHhHH
Q 007158 438 SDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPELGDSRTLVVQVLTTGSWPTQ-PSVTCNLPAEMS 516 (615)
Q Consensus 438 ~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~vls~~~WP~~-~~~~~~lP~~l~ 516 (615)
+.+.|..||++||+.||.+||+|+++||+||..|.++...|++...+....+++.|.||+..+||.+ ++..+.||++|.
T Consensus 481 s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~ 560 (773)
T COG5647 481 SAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQSYNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELV 560 (773)
T ss_pred chHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchhhccccchhHHHHHHhcCCCCccccccCCChHHH
Confidence 9999999999999999999999999999999999999999987542222368999999999999954 568999999999
Q ss_pred HHHHHHHHHHhcCCCCcceeeccCccceEEEEeeCCCc-E-EEEEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 517 ALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQ-K-HELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 517 ~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~g~-~-~~l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
+.++.|++||.+||+||+|.|.|+||+|+|++.|+.|+ . ...+++.+|+.|+++||+++++|+++|.+.|+|+.+.+.
T Consensus 561 p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~ 640 (773)
T COG5647 561 PILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLK 640 (773)
T ss_pred HHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHH
Confidence 99999999999999999999999999999999999842 2 233478999999999999999999999999999999998
Q ss_pred hh------hccccccCC-CCCCcc
Q 007158 595 KV------PAISGLCEG-EECSSE 611 (615)
Q Consensus 595 ~~------~~~~~l~~~-~~~~~~ 611 (615)
.+ +++..+..+ ..-||.
T Consensus 641 ~~L~sl~~ak~~~l~~~~~~~~p~ 664 (773)
T COG5647 641 RVLQSLSCAKLVVLLKDDKLVSPN 664 (773)
T ss_pred HHHHHHHhhheeeeccccccCCCC
Confidence 43 355555554 224443
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.2e-82 Score=623.72 Aligned_cols=545 Identities=26% Similarity=0.518 Sum_probs=507.1
Q ss_pred CCCCChhhHHHHHHHHHHHHHHHHhhCC-CCCCHHHHHHHHHHhhcC---CchHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 007158 17 RVVVDPKYAEKTWKILEHAIHEIYNHNA-SGLSFEELYRNAYNMVLH---KFGEKLYSGLVSTMTLHLKEISKSIEAAQG 92 (615)
Q Consensus 17 ~~~~~~~~f~~~W~~l~~~i~~I~~~~~-~~~s~~~lY~~vy~lc~~---~~~e~LY~~l~~~i~~~~~~i~~~l~~~~~ 92 (615)
|+.++ |++.|..|.+.|..|..-++ ...+|..-|+.||.+|.. +-||.||...+..|++|+..-+..+-..+.
T Consensus 6 p~vv~---fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~~p 82 (728)
T KOG2284|consen 6 PKVVE---FDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDVDP 82 (728)
T ss_pred ceeee---HHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcCCH
Confidence 56778 99999999999999998776 467899999999999986 478999999999999999864444433344
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCCC------------------CccHhHHHHHHHHHHHhcchhhHHH
Q 007158 93 GSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPSTH------------------KTPVHELGLNLWRDNIVRSNKIQTR 154 (615)
Q Consensus 93 ~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~------------------~~~i~~l~l~~f~~~v~~~~~l~~~ 154 (615)
+.+|..|++.|+.|..+..++..+|.|||..|++.+. ...|-.+|+.+|++.+.+ ++...
T Consensus 83 ~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~--~i~~~ 160 (728)
T KOG2284|consen 83 DLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVK--TILPQ 160 (728)
T ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHH--HHHHH
Confidence 6699999999999999999999999999999999742 234667889999999999 99999
Q ss_pred HHHHHHHHHHHHhcCCCCC-hHHHHHHHHHHHhhC--------------------cccchhhchhhHHHHHHHHHHHHHH
Q 007158 155 LLNTLLELVHRERTGEVIN-RGLMRNIIKMLMDLG--------------------PSVYQEDFEKPFLEVSAEFYKVESQ 213 (615)
Q Consensus 155 l~~~ll~~I~~~R~g~~i~-~~~lk~ii~~l~~lg--------------------~~~Y~~~FE~~~l~~t~~yY~~~s~ 213 (615)
|+..++..|.++|.|+..+ ...+.+++++|+.+. ..+|++.||+|||.+|.+||+++++
T Consensus 161 lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~ 240 (728)
T KOG2284|consen 161 LVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQ 240 (728)
T ss_pred HHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHH
Confidence 9999999999999999877 678899999998762 1479999999999999999999999
Q ss_pred HhHhcCCHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHhhhHHHHhcCchhhHHhhccCcHHHHHHHHHH
Q 007158 214 KFIECCDCGEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNL 293 (615)
Q Consensus 214 ~~i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~l~~L 293 (615)
..+.+.++++||.+|.-++++|+-||.+||++++..+++..|++.+|.+|.+.+ ...+..++.+.+..|++.||.|
T Consensus 241 ~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~~nmy~l 316 (728)
T KOG2284|consen 241 KMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDLRNMYRL 316 (728)
T ss_pred HHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999 5689999999999999999999
Q ss_pred hccCCCChHhHHHHHHHHHHHHhhhhhcCcccCCCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHHHHHhhcc--
Q 007158 294 FRRVPSGLLTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSSFEYFINL-- 371 (615)
Q Consensus 294 ~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~i~~af~~~ln~-- 371 (615)
+..+..|+..+...|.+||.++|.++++......-|..||+..+.+|.+|..++...|++|..|..++++|+..++|.
T Consensus 317 l~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~e 396 (728)
T KOG2284|consen 317 LKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKE 396 (728)
T ss_pred HHHHhcCchHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCC
Confidence 999999999999999999999999999877666678999999999999999999999999999999999999999995
Q ss_pred ----CCCcHHHHHHHHHHHhhcCCCCCChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHH
Q 007158 372 ----NPRSPEFISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIV 447 (615)
Q Consensus 372 ----~~~~~e~La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~ 447 (615)
-++.||.||+|||.+++++.||+++.++|.+++..+.+|+|++|||+|.++|.++||+||+.+.|.|.|.|..||+
T Consensus 397 pg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~min 476 (728)
T KOG2284|consen 397 PGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMIN 476 (728)
T ss_pred CCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHH
Confidence 2589999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhhcCCCCCCccEEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHh
Q 007158 448 KLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPELGDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYL 527 (615)
Q Consensus 448 ~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~ 527 (615)
+||+.||.+||+++. +.|+..|.+++++|.+.+. ++.+|.+|+...+.|+.||.
T Consensus 477 klkqacgyefts~~~--~td~~~s~~lnn~f~~~i~------------------------nf~~pq~l~~~iq~fe~fyt 530 (728)
T KOG2284|consen 477 KLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA------------------------NFHLPQILQPVIQEFEKFYT 530 (728)
T ss_pred HHHHHhCceecccCC--CCChhhccccchhHHHHHH------------------------hccchHHHHHHHHHHHHHhc
Confidence 999999999999998 9999999999999987653 28999999999999999999
Q ss_pred cCCCCcceeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 528 GTHTGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 528 ~~~~~R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
.+|+||||+|++.++++++++++-+ +.|.-.++++||++|++||..+.+++.||.+.+|++.+.|-+.+
T Consensus 531 ~~~~grkltwl~~~~~g~v~~~yl~-k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti 599 (728)
T KOG2284|consen 531 GKHNGRKLTWLFNMSQGDVRLTYLD-KQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTI 599 (728)
T ss_pred cccCCceehhhhhhcccceeeeecC-chHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHH
Confidence 9999999999999999999999997 89999999999999999999999999999999999999998664
No 5
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3e-80 Score=639.19 Aligned_cols=517 Identities=39% Similarity=0.655 Sum_probs=485.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh--ccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCC-C-CCccHhHHHHHHHHH
Q 007158 68 LYSGLVSTMTLHLKEISKSIEA--AQGGSFLEELNRKWNDHNKALQMIRDILMYMDRTYIPS-T-HKTPVHELGLNLWRD 143 (615)
Q Consensus 68 LY~~l~~~i~~~~~~i~~~l~~--~~~~~~L~~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~-~-~~~~i~~l~l~~f~~ 143 (615)
||+.|++.++.+++.-...+.. .....+|+.+.++|..|+..+..++++|.|+||.|+.. + ..+|+|++++.+|+.
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 7999999999999864444432 12367999999999999999999999999999999998 3 368999999999999
Q ss_pred HHhc--chhhHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhhCcccchhhchhhHHHHHHHHHHHHHHHhHhcCCH
Q 007158 144 NIVR--SNKIQTRLLNTLLELVHRERTGEVINRGLMRNIIKMLMDLGPSVYQEDFEKPFLEVSAEFYKVESQKFIECCDC 221 (615)
Q Consensus 144 ~v~~--~~~l~~~l~~~ll~~I~~~R~g~~i~~~~lk~ii~~l~~lg~~~Y~~~FE~~~l~~t~~yY~~~s~~~i~~~~~ 221 (615)
+++. .|.+..+..++++..++++|.|+++|+++|+.++.|+.+++ +|.+.|+..|++.+.++|.++..+..++..+
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 9998 67889999999999999999999999999999999999986 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHhhhHHHHhcCchhhHHhhccCcHHHHHHHHHHhccCCCCh
Q 007158 222 GEYLKKAERRLNEEMERVTHYLDAKSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGL 301 (615)
Q Consensus 222 ~~Yl~~v~~~l~~E~~r~~~~l~~~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~l~~L~~~~~~~~ 301 (615)
.+||++++.++.+|.+++..+++.+|..++..+++.+|+..|++.|+.+ |+..+++..+..++.+||.|++++.++.
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 9999999999999999999999988877799999999999999999965 8999999999999999999999998888
Q ss_pred HhHHHHHHHHHHHHhhhhhcCcccCCCcHHHHHHHHHHHHHHHHHHHhhcCCC--HHhHHHHHHHHHHhhcc-CCCcHHH
Q 007158 302 LTIREVMTSHLRETGKQLVTDPERLKDPVEFVQRLLDEKDKYDNIISSAFNND--KTFQNALNSSFEYFINL-NPRSPEF 378 (615)
Q Consensus 302 ~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~--~~f~~~i~~af~~~ln~-~~~~~e~ 378 (615)
..++..|.+|+++.|..++.+.... .++|+.++.++++.+-++..+|..+ ..|..++++||+.|+|. .+++||+
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 8999999999999999999876543 7999999999999999999999888 99999999999999997 5689999
Q ss_pred HHHHHHHHhhcCCCCCChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhccchhh
Q 007158 379 ISLFVDDKLRKGLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFT 458 (615)
Q Consensus 379 La~y~D~~lk~~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~ 458 (615)
+|+|.|..|+.|+++.++++++..++.++.+|+|+.+||+|+.+|++.||+|||.++|+|.|+|.+|+.+||.+||..||
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 HhHHHhhhhHHhhHHHHHHHhhhcCCC---CCCccEEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHhcCCCCcce
Q 007158 459 SKLEGMFTDMKTSQDTMHEFYASHPEL---GDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRL 535 (615)
Q Consensus 459 ~kl~~M~~D~~~S~~l~~~f~~~~~~~---~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L 535 (615)
+||++|++|+..|++++..|+++...+ +.++ +.+.|+|.++||++++.++.||++|.++++.|..||-.+|.||+|
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 999999999999999999999984322 2234 999999999999999999999999999999999999999999999
Q ss_pred eeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 536 SWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 536 ~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
+|.+++|+|.+++.|+. |++++.||++|++||++||++++||++||.+.|++....|.
T Consensus 473 qW~~~lg~~v~ka~f~~-gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~ 530 (661)
T KOG2167|consen 473 QWQDSLGHCVLKAEFKE-GKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELR 530 (661)
T ss_pred eeecCCcchhhhhhccC-CchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHH
Confidence 99999999999999998 69999999999999999999999999999999999766665
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-71 Score=555.71 Aligned_cols=583 Identities=24% Similarity=0.450 Sum_probs=519.9
Q ss_pred hhhHHHHHHHHHHHHHHHHhhCC-CCCCHHHHHHHHHHhhcCC--chHHHHHHHHHHHHHHHHHHHHHHHhcc-chHHHH
Q 007158 22 PKYAEKTWKILEHAIHEIYNHNA-SGLSFEELYRNAYNMVLHK--FGEKLYSGLVSTMTLHLKEISKSIEAAQ-GGSFLE 97 (615)
Q Consensus 22 ~~~f~~~W~~l~~~i~~I~~~~~-~~~s~~~lY~~vy~lc~~~--~~e~LY~~l~~~i~~~~~~i~~~l~~~~-~~~~L~ 97 (615)
.+-|++.|+...+.+-+++...+ +...|+.+|..||..|.+. ...++|+.+...|.+++.....++...+ +..+|.
T Consensus 10 r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL~ 89 (777)
T KOG2285|consen 10 RDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTDGALLI 89 (777)
T ss_pred hhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence 34599999999999999999875 3456999999999999985 6678999999999999998777776544 468999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhcccCCCC--------CccHhHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHhcC
Q 007158 98 ELNRKWNDHNKALQMIRDILMYMDRTYIPSTH--------KTPVHELGLNLWRDNIVRSNKIQTRLLNTLLELVHRERTG 169 (615)
Q Consensus 98 ~~~~~W~~y~~~~~~l~~vf~YLdr~yv~~~~--------~~~i~~l~l~~f~~~v~~~~~l~~~l~~~ll~~I~~~R~g 169 (615)
.|..+|.+|....+++...|.-|+.+-....+ -.+++.+.+..|.+.+|. .++.++..+.+.++..+|+|
T Consensus 90 ~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER~G 167 (777)
T KOG2285|consen 90 GYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAERDG 167 (777)
T ss_pred HHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999987544321 247999999999999999 99999999999999999999
Q ss_pred CCCChHHHHHHHHHHHhhC------cccchhhchhhHHHHHHHHHHHHHHHhHhcCCHHHHHHHHHHHHHHHHHHHhhcC
Q 007158 170 EVINRGLMRNIIKMLMDLG------PSVYQEDFEKPFLEVSAEFYKVESQKFIECCDCGEYLKKAERRLNEEMERVTHYL 243 (615)
Q Consensus 170 ~~i~~~~lk~ii~~l~~lg------~~~Y~~~FE~~~l~~t~~yY~~~s~~~i~~~~~~~Yl~~v~~~l~~E~~r~~~~l 243 (615)
+.+|.+++-++-++++.+. ..+|+++||..|+++|.+||+..+..++++.++.+||++++..+++|+.|+.+||
T Consensus 168 ~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYL 247 (777)
T KOG2285|consen 168 NAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYL 247 (777)
T ss_pred chhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhh
Confidence 9999999999999999986 3589999999999999999999999999999999999999999999999999999
Q ss_pred Ch--hhHHHHHHHHHHHHHHhhhHHHHhcCchhhHHhhccCcHHHHHHHHHHhccCCCChHhHHHHHHHHHHHHhhhhhc
Q 007158 244 DA--KSEAKITNVVEKEMIANHMPRLVHMDNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVT 321 (615)
Q Consensus 244 ~~--~t~~~l~~~~~~~Li~~~~~~il~~~~~~~~~ll~~~~~~~L~~l~~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~ 321 (615)
.+ .|..+++..+..+||.++.+.|+. .+..|+...+++.|++||+|+.++..|++++...+..||+..|..-+-
T Consensus 248 E~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~ 323 (777)
T KOG2285|consen 248 EMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMR 323 (777)
T ss_pred ccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHH
Confidence 87 578999999999999999999984 688999999999999999999999999999999999999999986542
Q ss_pred C-cc-cCCCcHHHHHHHHHHHHHHHHHHHhhcCCCHHhHHHHHHHHHHhhcc---------------------CCCcHHH
Q 007158 322 D-PE-RLKDPVEFVQRLLDEKDKYDNIISSAFNNDKTFQNALNSSFEYFINL---------------------NPRSPEF 378 (615)
Q Consensus 322 ~-~~-~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~i~~af~~~ln~---------------------~~~~~e~ 378 (615)
. .. -+.++..||+.|+.++++|..++.++|.+||.|..|-+.||+.++|. ..+.||+
T Consensus 324 ~aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpEL 403 (777)
T KOG2285|consen 324 NAAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPEL 403 (777)
T ss_pred hhhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHH
Confidence 2 22 22478999999999999999999999999999999999999999994 1378999
Q ss_pred HHHHHHHHhhcCC--CCCChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhcc--
Q 007158 379 ISLFVDDKLRKGL--KGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECG-- 454 (615)
Q Consensus 379 La~y~D~~lk~~~--~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~G-- 454 (615)
||.|||.++|+.. |.++.++++.++++++.+++|..+||+|..+++.+|++||+...|++.+.|..|+..|+ +||
T Consensus 404 LANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMP 482 (777)
T KOG2285|consen 404 LANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMP 482 (777)
T ss_pred HHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCc
Confidence 9999999999975 67888999999999999999999999999999999999999999999999999999999 677
Q ss_pred chhhHhHHHhhhhHHhhHHHHHHHhhhcCCCC---CCccEEEEEeccCCCCCC-CCCCCCCcHhHHHHHHHHHHHHhcCC
Q 007158 455 YQFTSKLEGMFTDMKTSQDTMHEFYASHPELG---DSRTLVVQVLTTGSWPTQ-PSVTCNLPAEMSALCEKFRSYYLGTH 530 (615)
Q Consensus 455 ~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~---~~~~~~~~vls~~~WP~~-~~~~~~lP~~l~~~~~~f~~~Y~~~~ 530 (615)
.+|++|+..||+|++.|+++++.|+.....+. ..-.++++||+.|.|... ....+.||.+|++.+-..++||+.+|
T Consensus 483 aDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~h 562 (777)
T KOG2285|consen 483 ADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKH 562 (777)
T ss_pred HHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhccc
Confidence 49999999999999999999999999876331 234689999999999954 45788999999999999999999999
Q ss_pred CCcceeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--CCCccHHHHHHhcCCChhhhhh-------hhcccc
Q 007158 531 TGRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEK-------VPAISG 601 (615)
Q Consensus 531 ~~R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~--~~~~t~~ei~~~t~~~~~~l~~-------~~~~~~ 601 (615)
+||+|+|.|+++.++++..-.- |.|.+.|+++||+||.+||+ ++.+|++.+.-+|.++-..|.. .++++.
T Consensus 563 sgrkl~w~h~msNG~itf~n~~-GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~ 641 (777)
T KOG2285|consen 563 SGRKLQWYHHMSNGTITFVNNF-GRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKY 641 (777)
T ss_pred CccchhhhhhccCCeeEeeccc-ccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhh
Confidence 9999999999999998543333 78999999999999999998 6789999999999999887772 234433
Q ss_pred ---ccCCCCCCccc
Q 007158 602 ---LCEGEECSSER 612 (615)
Q Consensus 602 ---l~~~~~~~~~~ 612 (615)
||.+---++.|
T Consensus 642 QiLL~ep~~~~spk 655 (777)
T KOG2285|consen 642 QILLCEPPTTVSPK 655 (777)
T ss_pred heeeecCcccCCcc
Confidence 77775544443
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=8.8e-34 Score=259.25 Aligned_cols=139 Identities=50% Similarity=0.875 Sum_probs=131.3
Q ss_pred cccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhhcCC--CCCCc
Q 007158 412 YLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYASHPE--LGDSR 489 (615)
Q Consensus 412 ~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~--~~~~~ 489 (615)
|+++||+|+.+|+++||+|||..++++.+.|..||++|+.+||.+++++|++|++|++.|++++++|++.... ...++
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-CCCCCcHhHHHHHHHHHHHHhcCCCCcceeeccCccceEEEEee
Q 007158 490 TLVVQVLTTGSWPTQPS-VTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATF 550 (615)
Q Consensus 490 ~~~~~vls~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~l~~~~ 550 (615)
+|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|.|++|+|+|+++|
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 99999999999998776 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=7.1e-25 Score=232.16 Aligned_cols=201 Identities=22% Similarity=0.273 Sum_probs=183.7
Q ss_pred HHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhccchhhHhHHHhhhhHHhhHHHHHHHhhh--c
Q 007158 405 KVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTECGYQFTSKLEGMFTDMKTSQDTMHEFYAS--H 482 (615)
Q Consensus 405 ~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~--~ 482 (615)
-+-.+...+.+|+.|++.||.+||.||++...++.+.|..-++.||-++|....+.|++|++|+..|+++++.++.. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 35567777889999999999999999999999999999999999999999999999999999999999999999984 1
Q ss_pred C---CCCCCccEEEEEeccCCCCCCCCCCCCCcHhHHHHHHHHHHHHhcCCCCcceeeccCccceEEEEeeCCCcEEEEE
Q 007158 483 P---ELGDSRTLVVQVLTTGSWPTQPSVTCNLPAEMSALCEKFRSYYLGTHTGRRLSWQTNMGSADIKATFGKGQKHELN 559 (615)
Q Consensus 483 ~---~~~~~~~~~~~vls~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~g~~~~l~ 559 (615)
. .+...+.+++.+||+.+||......+.+|.+++..++.|.+.|.+.+++|+|.|.+++|+|+++++|.+ ++..++
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~D-Rtl~~t 599 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFED-RTLVLT 599 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcC-eEEEEe
Confidence 1 122357899999999999998888999999999999999999999999999999999999999999999 999999
Q ss_pred ecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh----hccccccCCC
Q 007158 560 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV----PAISGLCEGE 606 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~----~~~~~l~~~~ 606 (615)
||+.||+|+++|.+.++||++|+++.+||+++.++.. ....+||.-.
T Consensus 600 Vsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~ 650 (765)
T KOG2165|consen 600 VSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEP 650 (765)
T ss_pred eCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCC
Confidence 9999999999999999999999999999999999854 3566677544
No 9
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.65 E-value=0.0017 Score=59.85 Aligned_cols=130 Identities=16% Similarity=0.292 Sum_probs=101.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHH---HhhcCCch-HHHHHHHHHHHHHHHHHHHHHHHhccchHHHHHHH
Q 007158 25 AEKTWKILEHAIHEIYNHNASGLSFEELYRNAY---NMVLHKFG-EKLYSGLVSTMTLHLKEISKSIEAAQGGSFLEELN 100 (615)
Q Consensus 25 f~~~W~~l~~~i~~I~~~~~~~~s~~~lY~~vy---~lc~~~~~-e~LY~~l~~~i~~~~~~i~~~l~~~~~~~~L~~~~ 100 (615)
.++.|+.+..++-.+++++....+-+++-..|- +.|.++.. ..+-+.+.+.+..-...+...+....++.+|..++
T Consensus 5 ~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~~~~~~l~rL~ 84 (158)
T PF08539_consen 5 SDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEVPDNRLLKRLV 84 (158)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHH
Confidence 689999999999999999887777777777664 56766643 44556677777777767777787778889999999
Q ss_pred HHHHHHH-HHHHHHHHHhhhhhhcccCC-----------------CCCccHhHHHHHHHHHHHhcchhhHHHHH
Q 007158 101 RKWNDHN-KALQMIRDILMYMDRTYIPS-----------------THKTPVHELGLNLWRDNIVRSNKIQTRLL 156 (615)
Q Consensus 101 ~~W~~y~-~~~~~l~~vf~YLdr~yv~~-----------------~~~~~i~~l~l~~f~~~v~~~~~l~~~l~ 156 (615)
..|.-|. .-+-++..+|.+|++.+-.. .+..+|+.+++..||+.|+- +..+++.
T Consensus 85 eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL--P~y~~l~ 156 (158)
T PF08539_consen 85 EIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL--PYYQRLK 156 (158)
T ss_pred HHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh--cchHhhh
Confidence 9999955 55689999999999654322 23478999999999999987 6666553
No 10
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=95.04 E-value=0.24 Score=53.84 Aligned_cols=89 Identities=13% Similarity=0.227 Sum_probs=57.0
Q ss_pred hHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHh-hcCCchHHHHHHHHHHHHHHHHHHH---HHHHhccchHHHHHH
Q 007158 24 YAEKTWKILEHAIHEIYNHNASGLSFEELYRNAYNM-VLHKFGEKLYSGLVSTMTLHLKEIS---KSIEAAQGGSFLEEL 99 (615)
Q Consensus 24 ~f~~~W~~l~~~i~~I~~~~~~~~s~~~lY~~vy~l-c~~~~~e~LY~~l~~~i~~~~~~i~---~~l~~~~~~~~L~~~ 99 (615)
+..+.|.-..+.+.+.+..++...-.....+.++.. |....|+.+++.+-..+...+.... ++.....-+.+...|
T Consensus 67 ~v~siWem~l~LFR~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY 146 (661)
T KOG2167|consen 67 YVLSIWEMGLQLFRAHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELY 146 (661)
T ss_pred CcCCHHHhhHHHHHHHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence 477899999999999988855333344445555533 5566788888555555554444321 222222235678889
Q ss_pred HHHHHHHHHHHHH
Q 007158 100 NRKWNDHNKALQM 112 (615)
Q Consensus 100 ~~~W~~y~~~~~~ 112 (615)
..+|.++...+.+
T Consensus 147 ~aE~~d~~Qel~v 159 (661)
T KOG2167|consen 147 AAEGQDKRQELEV 159 (661)
T ss_pred HHHhcchhhhccc
Confidence 9999999887754
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=76.71 E-value=3.3 Score=29.57 Aligned_cols=36 Identities=11% Similarity=0.008 Sum_probs=28.6
Q ss_pred cHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 561 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 561 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
+..+..||....+++.+|..||++.+|+|...+...
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 456778888888888999999999999999888754
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=75.65 E-value=2.8 Score=31.60 Aligned_cols=38 Identities=16% Similarity=0.062 Sum_probs=31.9
Q ss_pred ecHHHHHHHHhhhCCCC--ccHHHHHHhcCCChhhhhhhh
Q 007158 560 VSTYQMCVLMLFNNADR--LSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~--~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+|+.|+.||......+. +|..||++.+++++..+-.+.
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 57889999988887766 999999999999999988554
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=64.81 E-value=5.2 Score=29.83 Aligned_cols=38 Identities=8% Similarity=0.033 Sum_probs=32.4
Q ss_pred ecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 560 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+|..|+.+|....+.+++|..+|++.++++...+-.++
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence 47789999999988888999999999999998887554
No 14
>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=7.9 Score=28.98 Aligned_cols=31 Identities=16% Similarity=0.115 Sum_probs=27.7
Q ss_pred HHHHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 564 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 564 Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
|..|+...++.+.+|++||++.+|+|+..+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiR 32 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIR 32 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHH
Confidence 4568888899999999999999999999887
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=60.51 E-value=12 Score=27.44 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=23.1
Q ss_pred HHHHhh-hCCCCccHHHHHHhcCCChhhhhhh
Q 007158 566 CVLMLF-NNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 566 ~iLl~F-n~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
.||..+ +..+.+|.++|++.+|+|...+..-
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 445444 6666699999999999999888743
No 16
>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=60.38 E-value=2.2e+02 Score=29.72 Aligned_cols=155 Identities=13% Similarity=0.231 Sum_probs=88.5
Q ss_pred hhHHhhccCcHHHHHHHHHHhccC---CCChHhHHHHHHHHHHHHhhhhhcCccc----CCCcHHHHHHHHHHHHHHHHH
Q 007158 274 GLVNMLLDDKYEDLGRMYNLFRRV---PSGLLTIREVMTSHLRETGKQLVTDPER----LKDPVEFVQRLLDEKDKYDNI 346 (615)
Q Consensus 274 ~~~~ll~~~~~~~L~~l~~L~~~~---~~~~~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~i~~ll~l~~~~~~l 346 (615)
.|..-.+.+|.+.+.+.++||--+ +.|++....-+.+.|.....+.+..... ...+.-|...|..+++.+-.+
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt~LFe~ia~i 94 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALTKLFEHIATI 94 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHHHHHHHHHHH
Confidence 566777888999999999999765 3466666666666666666666554322 235567788888888877776
Q ss_pred HHh-------hcCCCHH------hHHHHHHHHHHhhcc---CCCc---HHHHHHHHHHHhhc------------------
Q 007158 347 ISS-------AFNNDKT------FQNALNSSFEYFINL---NPRS---PEFISLFVDDKLRK------------------ 389 (615)
Q Consensus 347 ~~~-------~F~~~~~------f~~~i~~af~~~ln~---~~~~---~e~La~y~D~~lk~------------------ 389 (615)
+++ +|+.... +.+..+.-...++.. ..++ ...+-.|-...+.+
T Consensus 95 i~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 174 (331)
T PF08318_consen 95 IEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSRAASSSQS 174 (331)
T ss_pred HHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccccccccccc
Confidence 544 7775531 112222212222221 1112 22233333333322
Q ss_pred CCCCCChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCC
Q 007158 390 GLKGVSEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGK 435 (615)
Q Consensus 390 ~~~~~~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~ 435 (615)
...+.+-.+++..|+.+..+++- -..|.+++++|.-...
T Consensus 175 ~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 175 EDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFS 213 (331)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhccc
Confidence 00112234567777777766542 5689999999987643
No 17
>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=60.28 E-value=9.3 Score=27.86 Aligned_cols=32 Identities=6% Similarity=0.024 Sum_probs=25.7
Q ss_pred HHHHHhhhCCC-CccHHHHHHhcCCChhhhhhh
Q 007158 565 MCVLMLFNNAD-RLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 565 a~iLl~Fn~~~-~~t~~ei~~~t~~~~~~l~~~ 596 (615)
+.||..|.+.+ .+|+.||++.+|++...+-.+
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~ 38 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRL 38 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 46888898855 489999999999999888654
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=60.04 E-value=12 Score=32.37 Aligned_cols=50 Identities=10% Similarity=0.066 Sum_probs=39.7
Q ss_pred EecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh---ccccccCCCCC
Q 007158 559 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEEC 608 (615)
Q Consensus 559 ~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~~ 608 (615)
.++..|..||.....++.+|..+|++.+|++...+-.+. --.|++.+..+
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 468899999999988889999999999999998876443 34466655443
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=59.99 E-value=12 Score=28.65 Aligned_cols=37 Identities=11% Similarity=0.003 Sum_probs=27.3
Q ss_pred ecHHHHHHHHhhh-CCCCccHHHHHHhcCCChhhhhhh
Q 007158 560 VSTYQMCVLMLFN-NADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 560 vs~~Qa~iLl~Fn-~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
+|..|..||.... .....|..+|++.++++...+-..
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~ 38 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRI 38 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHH
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHH
Confidence 4678999999888 788999999999999998887644
No 20
>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=58.74 E-value=11 Score=30.48 Aligned_cols=35 Identities=11% Similarity=-0.041 Sum_probs=25.2
Q ss_pred HHHHHHHhhhCCC-CccHHHHHHhcCCChhhhhhhh
Q 007158 563 YQMCVLMLFNNAD-RLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 563 ~Qa~iLl~Fn~~~-~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+++.+.+..+..+ .+|.++|++.+++++..+.++.
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil 46 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKIL 46 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445555545544 3999999999999999999775
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=57.00 E-value=9.7 Score=28.72 Aligned_cols=32 Identities=13% Similarity=0.033 Sum_probs=25.2
Q ss_pred HHHHHHhhhCCCCccHHHHHHhcCCChhhhhh
Q 007158 564 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLEK 595 (615)
Q Consensus 564 Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~ 595 (615)
|.-+|.++-+.+.+|+++|++.+|+|...+..
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHH
Confidence 56667555558899999999999999998873
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=55.61 E-value=16 Score=32.92 Aligned_cols=52 Identities=15% Similarity=0.036 Sum_probs=41.0
Q ss_pred EEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh---ccccccCCCCCC
Q 007158 558 LNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEECS 609 (615)
Q Consensus 558 l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~~~ 609 (615)
..+|+.|+.||......+++|..+|++.+++++..+-.++ --.|++.+..|.
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 3578899999988777788999999999999999987554 345677666553
No 23
>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=55.10 E-value=11 Score=26.33 Aligned_cols=30 Identities=20% Similarity=0.067 Sum_probs=22.4
Q ss_pred HHHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 565 MCVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 565 a~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
-.||..+..+...|+.+|++.+|+|+..+.
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHH
Confidence 356777777788999999999999988774
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=53.87 E-value=18 Score=25.70 Aligned_cols=34 Identities=12% Similarity=-0.003 Sum_probs=26.4
Q ss_pred HHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 563 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 563 ~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
...-|+.+.-+ ++.++.||++.+|++...+-.+.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHH
Confidence 44567766766 67999999999999999887654
No 25
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=50.41 E-value=23 Score=33.40 Aligned_cols=58 Identities=10% Similarity=0.041 Sum_probs=46.1
Q ss_pred cceeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--CCCccHHHHHHhcCCChhhhhhh
Q 007158 533 RRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 533 R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~--~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
|.-.|.+.+|..+++ +.+.| .||+.||.-|+.-.. ...||.+.||+..+|..+.++-+
T Consensus 97 r~~~~~~~fg~~ep~-~vPkG-----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~i 156 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPE-KVPKG-----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNI 156 (179)
T ss_pred CCCcccccccccCcc-cCCCC-----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHH
Confidence 444588899998886 45554 689999998887655 45799999999999999888755
No 26
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=49.30 E-value=18 Score=29.71 Aligned_cols=41 Identities=20% Similarity=0.096 Sum_probs=35.3
Q ss_pred EEEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 557 ELNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 557 ~l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
++.++..+..||........+|..+|++.++++...+....
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l 45 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence 45678899999999988888999999999999998887553
No 27
>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=47.69 E-value=21 Score=28.30 Aligned_cols=31 Identities=3% Similarity=-0.187 Sum_probs=23.6
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+..++.....+|+.||++.+|+|+..+....
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l 53 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHL 53 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3333344467899999999999999998653
No 28
>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=47.44 E-value=29 Score=24.88 Aligned_cols=30 Identities=7% Similarity=0.038 Sum_probs=22.7
Q ss_pred HHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 565 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 565 a~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
..|-+.| ..++|++||++.+|+|...+..+
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 56789999999999999988754
No 29
>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.
Probab=46.50 E-value=10 Score=31.22 Aligned_cols=51 Identities=18% Similarity=0.410 Sum_probs=32.3
Q ss_pred EecHHHHHHHH--hhhCCCCccHHHHHHhcCCChhhhhhh-hcccccc--CCCCCC
Q 007158 559 NVSTYQMCVLM--LFNNADRLSYQGNRAGNRDSCFRLEKV-PAISGLC--EGEECS 609 (615)
Q Consensus 559 ~vs~~Qa~iLl--~Fn~~~~~t~~ei~~~t~~~~~~l~~~-~~~~~l~--~~~~~~ 609 (615)
+++-+|++-+| -.....++|+.||.....+|+..--.+ ..+..+| |+++|-
T Consensus 2 tlN~~q~A~~l~kiLq~K~Eit~eDIlaqfeIS~s~Ay~I~~~lr~iCe~hq~eC~ 57 (110)
T PF09645_consen 2 TLNSYQMAEILYKILQEKKEITLEDILAQFEISYSRAYNIQRVLRKICEQHQDECE 57 (110)
T ss_dssp ---HHHHHHHHHHHHHHHSEE-HHHHHHHH---HHHHHHHHHHHHHHHHH-TTTEE
T ss_pred cccHHHHHHHHHHHHHHcCcCcHHHHHHHhccchhhhhHHHHHHHHHHHhCcchhh
Confidence 35667776553 345678999999999999998876544 5778899 678774
No 30
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=44.13 E-value=31 Score=26.83 Aligned_cols=36 Identities=8% Similarity=-0.022 Sum_probs=29.4
Q ss_pred HHHHHHHHhhhCCCC--ccHHHHHHhcCCChhhhhhhh
Q 007158 562 TYQMCVLMLFNNADR--LSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 562 ~~Qa~iLl~Fn~~~~--~t~~ei~~~t~~~~~~l~~~~ 597 (615)
...-.||..+.+... +|..||++.+|++...+..+.
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L 43 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVL 43 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 345567888887655 999999999999999988664
No 31
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=43.32 E-value=27 Score=26.27 Aligned_cols=37 Identities=8% Similarity=-0.047 Sum_probs=30.0
Q ss_pred cHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 561 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 561 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
++.-..||..+...++.|+.+|++.+|++...+-.+.
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 4566778888877889999999999999999887554
No 32
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=42.17 E-value=35 Score=32.44 Aligned_cols=53 Identities=6% Similarity=-0.110 Sum_probs=41.3
Q ss_pred EEecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh---ccccccCCCCCCc
Q 007158 558 LNVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEECSS 610 (615)
Q Consensus 558 l~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~~~~ 610 (615)
+.+|..|..||.....++++|..+|++.++++...+-.+. --.|++.+..|..
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 4578899999999999899999999999999877765432 3457777665543
No 33
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=41.07 E-value=74 Score=36.96 Aligned_cols=38 Identities=18% Similarity=0.169 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHhhCC-CCCCHHHHHHHHHHhhcC
Q 007158 25 AEKTWKILEHAIHEIYNHNA-SGLSFEELYRNAYNMVLH 62 (615)
Q Consensus 25 f~~~W~~l~~~i~~I~~~~~-~~~s~~~lY~~vy~lc~~ 62 (615)
++..|+.++++++++.+... ....+|++|+.+|..|+.
T Consensus 10 ~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~ 48 (725)
T KOG2166|consen 10 LEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTI 48 (725)
T ss_pred hhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHH
Confidence 89999999999999998874 223389999999998885
No 34
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=38.68 E-value=52 Score=28.11 Aligned_cols=51 Identities=18% Similarity=0.154 Sum_probs=38.0
Q ss_pred EEecHHHHHHHHhhh----CCCCccHHHHHHhcCCChhhhhhhh---ccccccCCCCC
Q 007158 558 LNVSTYQMCVLMLFN----NADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEEC 608 (615)
Q Consensus 558 l~vs~~Qa~iLl~Fn----~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~~ 608 (615)
+.+|+.|..||.... +.+++|..+|++.++++...+-.++ --.|+..+..|
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~ 78 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERS 78 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCC
Confidence 356888998887666 5578999999999999999887654 33455554443
No 35
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=38.19 E-value=39 Score=23.88 Aligned_cols=33 Identities=12% Similarity=0.012 Sum_probs=26.3
Q ss_pred HHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 565 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 565 a~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
-.|+..+.+...+|+.+|++.++++...+....
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 346666666678999999999999999887553
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=37.04 E-value=20 Score=27.69 Aligned_cols=47 Identities=15% Similarity=0.018 Sum_probs=34.2
Q ss_pred ecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh---ccccccCCC
Q 007158 560 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGE 606 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~ 606 (615)
.|-.++-|+...-..+..|..||++.+|++...+..+. .-.||+.+.
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 35566667766657788999999999999999988554 334555443
No 37
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.26 E-value=49 Score=23.65 Aligned_cols=35 Identities=14% Similarity=0.013 Sum_probs=26.6
Q ss_pred ecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 560 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
+|.-+..++.++. .++|..+|++.+|+|...+...
T Consensus 4 l~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 4 LTPREREVLRLLA--EGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHH
Confidence 3555666666664 4579999999999999998855
No 38
>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=35.20 E-value=54 Score=27.33 Aligned_cols=40 Identities=15% Similarity=0.053 Sum_probs=33.4
Q ss_pred EEEecHHHHHHHHhhh--------CCCCccHHHHHHhcCCChhhhhhh
Q 007158 557 ELNVSTYQMCVLMLFN--------NADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 557 ~l~vs~~Qa~iLl~Fn--------~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
...+++-|+.+|+..- ....+|-.||++.+|++...+...
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 4567889999888665 467899999999999999988754
No 39
>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=34.21 E-value=50 Score=27.79 Aligned_cols=39 Identities=15% Similarity=0.015 Sum_probs=31.8
Q ss_pred EecHHHHHHHHhhhC----CCCccHHHHHHhcCCChhhhhhhh
Q 007158 559 NVSTYQMCVLMLFNN----ADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 559 ~vs~~Qa~iLl~Fn~----~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
.++..|-.||..+.+ .+.+++++|++.++++...++...
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al 86 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKAL 86 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHH
Confidence 688999999999987 568999999999999999988553
No 40
>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=33.82 E-value=56 Score=23.63 Aligned_cols=35 Identities=14% Similarity=-0.022 Sum_probs=20.2
Q ss_pred cHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 561 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 561 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
++-|-.++.+.- -.++|++||++.+|+|+..+...
T Consensus 12 ~~~~r~i~~l~~-~~g~s~~eIa~~l~~s~~~v~~~ 46 (54)
T PF08281_consen 12 PERQREIFLLRY-FQGMSYAEIAEILGISESTVKRR 46 (54)
T ss_dssp -HHHHHHHHHHH-TS---HHHHHHHCTS-HHHHHHH
T ss_pred CHHHHHHHHHHH-HHCcCHHHHHHHHCcCHHHHHHH
Confidence 334444443322 24689999999999999988754
No 41
>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=33.22 E-value=62 Score=28.36 Aligned_cols=47 Identities=21% Similarity=0.486 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHHhcCCCCCh-HHHHHHHHHHHhhCcccchhhch
Q 007158 151 IQTRLLNTLLELVHRERTGEVINR-GLMRNIIKMLMDLGPSVYQEDFE 197 (615)
Q Consensus 151 l~~~l~~~ll~~I~~~R~g~~i~~-~~lk~ii~~l~~lg~~~Y~~~FE 197 (615)
+++++.+.|-+++...|...+-+. --..++..||.+||+.+|+..-|
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 345566677777888887554332 23678999999999888875443
No 42
>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=33.09 E-value=48 Score=23.33 Aligned_cols=29 Identities=10% Similarity=-0.050 Sum_probs=19.2
Q ss_pred HHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 566 CVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 566 ~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
-|+-++.++ .|+.+|++.+|+|...+-.+
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHH
Confidence 344555554 89999999999998877544
No 43
>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=32.48 E-value=64 Score=25.49 Aligned_cols=39 Identities=15% Similarity=0.093 Sum_probs=29.1
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhh---ccccccCCC
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGE 606 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~ 606 (615)
||+..... ..|.++|.+.||++...|-+.. +-.|++.++
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 44444444 8999999999999999987663 556676554
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=32.26 E-value=59 Score=23.29 Aligned_cols=34 Identities=12% Similarity=-0.101 Sum_probs=25.0
Q ss_pred cHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 561 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 561 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
+..|..++.++- +.+|..+|++.+|++...+...
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 4689999999999999988854
No 45
>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=32.22 E-value=34 Score=26.54 Aligned_cols=31 Identities=13% Similarity=-0.059 Sum_probs=22.6
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
|.....++..+|++||+..++++++.++.+.
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 3344556788999999999999999999664
No 46
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=31.76 E-value=59 Score=29.13 Aligned_cols=50 Identities=12% Similarity=-0.011 Sum_probs=37.8
Q ss_pred EEecHHHHHHHHhhhC-CCCccHHHHHHhcCCChhhhhhhh---ccccccCCCC
Q 007158 558 LNVSTYQMCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEE 607 (615)
Q Consensus 558 l~vs~~Qa~iLl~Fn~-~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~ 607 (615)
+.+|..|..+|..... .+..|..||++.+++++..+-.++ --.|+..+..
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 4578889999988775 457899999999999999988654 3345554443
No 47
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=30.64 E-value=59 Score=30.23 Aligned_cols=34 Identities=15% Similarity=0.023 Sum_probs=27.0
Q ss_pred HHHHHHhhhC-CCCccHHHHHHhcCCChhhhhhhh
Q 007158 564 QMCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 564 Qa~iLl~Fn~-~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
.+.+.+.|+. ...+|.++|++.+++|...++++.
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl 46 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLF 46 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3444556765 457999999999999999999875
No 48
>PRK10870 transcriptional repressor MprA; Provisional
Probab=30.33 E-value=78 Score=29.72 Aligned_cols=53 Identities=9% Similarity=0.103 Sum_probs=39.5
Q ss_pred EEecHHHHHHHHhhhC--CCCccHHHHHHhcCCChhhhhhhh---ccccccCCCCCCc
Q 007158 558 LNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKVP---AISGLCEGEECSS 610 (615)
Q Consensus 558 l~vs~~Qa~iLl~Fn~--~~~~t~~ei~~~t~~~~~~l~~~~---~~~~l~~~~~~~~ 610 (615)
..+|..|..||..... ..++|..||++.++++...+-.++ --.||+.+..+..
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 3466788888877764 467999999999999999986443 4566777666543
No 49
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=30.06 E-value=57 Score=28.27 Aligned_cols=42 Identities=19% Similarity=0.420 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHhcCCCCChH-HHHHHHHHHHhhCcccchh
Q 007158 153 TRLLNTLLELVHRERTGEVINRG-LMRNIIKMLMDLGPSVYQE 194 (615)
Q Consensus 153 ~~l~~~ll~~I~~~R~g~~i~~~-~lk~ii~~l~~lg~~~Y~~ 194 (615)
+++.+.|-+++.+.|...+-+.+ -+.++..||.+||+.+|+-
T Consensus 3 ~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGLRVYea 45 (118)
T PRK13713 3 NEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYEA 45 (118)
T ss_pred hHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhHHHHHH
Confidence 44556666777777765542221 2678899999999777753
No 50
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=29.69 E-value=44 Score=25.49 Aligned_cols=24 Identities=25% Similarity=0.184 Sum_probs=17.5
Q ss_pred CCCccHHHHHHhcCCChhhhhhhh
Q 007158 574 ADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 574 ~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
...+|++|+++.|+++...++++.
T Consensus 8 ~~glsl~~va~~t~I~~~~l~aiE 31 (62)
T PF13413_consen 8 AKGLSLEDVAEETKISVSYLEAIE 31 (62)
T ss_dssp CTT--HHHHHHHCS--HHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 568999999999999999998773
No 51
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.68 E-value=41 Score=23.89 Aligned_cols=29 Identities=10% Similarity=-0.068 Sum_probs=20.1
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
++.++.+ .+|..+|++.+|+|...+....
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 4555555 7999999999999999887553
No 52
>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=29.59 E-value=9.5e+02 Score=27.94 Aligned_cols=23 Identities=4% Similarity=0.394 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC
Q 007158 331 EFVQRLLDEKDKYDNIISSAFNN 353 (615)
Q Consensus 331 ~~i~~ll~l~~~~~~l~~~~F~~ 353 (615)
.+-+..+..|.++..++..|+.|
T Consensus 679 ~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 679 AMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Confidence 44566888899999999999865
No 53
>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=29.43 E-value=51 Score=24.38 Aligned_cols=27 Identities=11% Similarity=0.031 Sum_probs=22.8
Q ss_pred hhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 570 LFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 570 ~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
.|+.....|.+||++.+|+|+..+..+
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 456677899999999999999988754
No 54
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=28.46 E-value=52 Score=22.55 Aligned_cols=23 Identities=9% Similarity=0.027 Sum_probs=16.2
Q ss_pred CCCccHHHHHHhcCCChhhhhhh
Q 007158 574 ADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 574 ~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
...||+++||+..|+|+..+...
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 56799999999999998887644
No 55
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=28.36 E-value=6.5e+02 Score=25.62 Aligned_cols=70 Identities=20% Similarity=0.243 Sum_probs=43.5
Q ss_pred hhccCcHHHHHHHHHHhccCCCChHhHHHHHHHHHHHHhhhhhcCcccC-------------------CCcHHHHHHHHH
Q 007158 278 MLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERL-------------------KDPVEFVQRLLD 338 (615)
Q Consensus 278 ll~~~~~~~L~~l~~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~-------------------~~~~~~i~~ll~ 338 (615)
-++.+.+..+..-|.++.++....+.+...|.+.|.....+++...... -++..|++.|+.
T Consensus 194 ~Fd~~~Y~~v~~AY~lLgk~~~~~dkl~~~f~~~i~~~~~~vv~~~~~~~~~~~~~~~~~~y~~lC~~v~~~~~~~cl~~ 273 (291)
T PF10475_consen 194 DFDPDKYSKVQEAYQLLGKTQSAMDKLQMHFTSAIHSTTFSVVRSYVEQSESSEERSSKMSYKDLCKQVPSDQFIPCLLE 273 (291)
T ss_pred hCCHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccCCHHHHHhhCCHHHHHHHHHH
Confidence 3456667888888888887755556666666666666665554322110 145667777777
Q ss_pred HHHHHHHHH
Q 007158 339 EKDKYDNII 347 (615)
Q Consensus 339 l~~~~~~l~ 347 (615)
+...+..++
T Consensus 274 l~~~l~~im 282 (291)
T PF10475_consen 274 LLEVLWDIM 282 (291)
T ss_pred HHHHHHHHH
Confidence 776665554
No 56
>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=27.90 E-value=73 Score=25.77 Aligned_cols=33 Identities=6% Similarity=-0.157 Sum_probs=28.9
Q ss_pred HHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 563 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 563 ~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
-++.|+....+ ..+|+.+|++.+|+|...+-..
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~ 39 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKD 39 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHH
Confidence 46788888888 9999999999999999988754
No 57
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=26.92 E-value=61 Score=32.40 Aligned_cols=32 Identities=6% Similarity=-0.033 Sum_probs=27.9
Q ss_pred HHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 565 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 565 a~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
..||.+|.....+|+.||++.+|+++..+--+
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 46888998877899999999999999988654
No 58
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=26.92 E-value=74 Score=25.71 Aligned_cols=33 Identities=12% Similarity=-0.006 Sum_probs=26.9
Q ss_pred HHHHHhhhCC-CCccHHHHHHhcCCChhhhhhhh
Q 007158 565 MCVLMLFNNA-DRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 565 a~iLl~Fn~~-~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
..||..+.+. +.+|+.||++.+|++...+....
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l 41 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 4567777766 68999999999999999987553
No 59
>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=26.60 E-value=85 Score=27.96 Aligned_cols=33 Identities=12% Similarity=0.011 Sum_probs=25.9
Q ss_pred HHHHHhhhCC-CCccHHHHHHhcCCChhhhhhhh
Q 007158 565 MCVLMLFNNA-DRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 565 a~iLl~Fn~~-~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+.+.+.++.. ..+|.++|++.+++|+..++++.
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil 46 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLF 46 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3444555543 47999999999999999999875
No 60
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.24 E-value=41 Score=27.11 Aligned_cols=33 Identities=12% Similarity=0.093 Sum_probs=25.7
Q ss_pred HHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 565 MCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 565 a~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
..||...+..+++++.+|.+.+|++...+-.+.
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 456666677788999999999999999998664
No 61
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=26.20 E-value=86 Score=23.66 Aligned_cols=36 Identities=11% Similarity=-0.013 Sum_probs=29.2
Q ss_pred cHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 561 STYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 561 s~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+..+..|+..+.+.+ ++..||++.+|++...+....
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l 41 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHL 41 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHH
Confidence 456778888777766 999999999999998887543
No 62
>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=26.09 E-value=60 Score=25.13 Aligned_cols=29 Identities=17% Similarity=0.004 Sum_probs=23.6
Q ss_pred HHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 566 CVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 566 ~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
.|-.+.++...+|+.+|++.||++...+.
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 46677888899999999999999877763
No 63
>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=25.80 E-value=1e+03 Score=27.18 Aligned_cols=63 Identities=14% Similarity=0.240 Sum_probs=36.9
Q ss_pred HHHHHHHhhhhccccchHHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhc--cchhhHhHHHhhhhHH
Q 007158 400 ETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLSGKTVSDDAERSLIVKLKTEC--GYQFTSKLEGMFTDMK 469 (615)
Q Consensus 400 e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~s~~~~~E~~~i~~Lk~~~--G~~~~~kl~~M~~D~~ 469 (615)
.+.+.+++.++-.|.+.|.|...-.+ .++|++.+.=...++.|+..- +.+...+++.+.+.++
T Consensus 564 ~~ll~~i~~iy~~l~~~~~F~~ava~-------D~Rsy~~~lf~~a~~~l~~~~l~~~~~i~~f~~l~~~ve 628 (629)
T PF10408_consen 564 KELLSQIVDIYLNLSDSDKFVQAVAN-------DGRSYSPELFEKAVRILRRIGLKSEDEIEKFEELAKKVE 628 (629)
T ss_dssp HHHHHHHHHHHHHCTT-HHHHHHHHH--------TTT--HHHHHHHHHHHTTSTSSTHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHhhcCCchHHHHHHHh-------CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHh
Confidence 46788999999999888887765332 245666555445555555432 3455566666555543
No 64
>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=25.08 E-value=94 Score=23.48 Aligned_cols=31 Identities=6% Similarity=-0.093 Sum_probs=24.6
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
|..+-.+...++..+|++.+|+++..+-.+.
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 4444457889999999999999999998664
No 65
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=24.87 E-value=2.9e+02 Score=22.50 Aligned_cols=55 Identities=18% Similarity=0.309 Sum_probs=36.3
Q ss_pred HHHHH-HHHHHHHHHHhh-CCCCCCHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHH
Q 007158 26 EKTWK-ILEHAIHEIYNH-NASGLSFEELYRNAYNMVLHKFGEKLYSGLVSTMTLHL 80 (615)
Q Consensus 26 ~~~W~-~l~~~i~~I~~~-~~~~~s~~~lY~~vy~lc~~~~~e~LY~~l~~~i~~~~ 80 (615)
+.+|. .++..+..+... ...+.++.+++..|--.+.....+.+...+-..|..++
T Consensus 29 e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 29 ECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 45774 677777777766 33567888888888877777666666555555555544
No 66
>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=24.40 E-value=84 Score=30.19 Aligned_cols=39 Identities=13% Similarity=0.045 Sum_probs=34.2
Q ss_pred EecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 559 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 559 ~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
.++..|..||..+.+++..|..+|++.+|+++..+..+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L 178 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHL 178 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 568889999999988788999999999999999887553
No 67
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.19 E-value=60 Score=26.51 Aligned_cols=26 Identities=19% Similarity=0.096 Sum_probs=22.6
Q ss_pred CCccHHHHHHhcCCChhhhhhhhccc
Q 007158 575 DRLSYQGNRAGNRDSCFRLEKVPAIS 600 (615)
Q Consensus 575 ~~~t~~ei~~~t~~~~~~l~~~~~~~ 600 (615)
..+|.++|+..+|.++..++++.++.
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~~t 47 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQVT 47 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 46999999999999999999887543
No 68
>KOG4481 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.17 E-value=80 Score=29.24 Aligned_cols=59 Identities=10% Similarity=0.103 Sum_probs=48.7
Q ss_pred CcceeeccCccceEEEEeeCCCcEEEEEecHHHHHHHHhhhC--CCCccHHHHHHhcCCChhhhhhh
Q 007158 532 GRRLSWQTNMGSADIKATFGKGQKHELNVSTYQMCVLMLFNN--ADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 532 ~R~L~w~~~lg~~~l~~~~~~g~~~~l~vs~~Qa~iLl~Fn~--~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
.+++-|-++.+...++ ..++| .++..||.-++.|.+ .++|+.+-|++...++.+.++-+
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 4578899999988886 45654 578899999999876 67999999999999998888744
No 69
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=24.06 E-value=8.2e+02 Score=25.37 Aligned_cols=154 Identities=14% Similarity=0.272 Sum_probs=83.9
Q ss_pred hhhHHhhccCcHHHHHHHHHHhccC---CCChHhHHHHHHHHHHHHhhhhhcCccc----CCCcHHHHHHHHHHHHHHHH
Q 007158 273 SGLVNMLLDDKYEDLGRMYNLFRRV---PSGLLTIREVMTSHLRETGKQLVTDPER----LKDPVEFVQRLLDEKDKYDN 345 (615)
Q Consensus 273 ~~~~~ll~~~~~~~L~~l~~L~~~~---~~~~~~l~~~~~~~i~~~g~~~~~~~~~----~~~~~~~i~~ll~l~~~~~~ 345 (615)
..|..-+++++...+.++++||.-+ +.|++....-+.+.|....+...+.... ...+..|...+..+++.+-.
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 3567777889999999999999765 3466656556666665555544433211 12356677777777777666
Q ss_pred HH-------HhhcCCCHH------hHHHHHHHHHHhhcc---CCCc---HHHHHHHHHHHhhcC------------CCCC
Q 007158 346 II-------SSAFNNDKT------FQNALNSSFEYFINL---NPRS---PEFISLFVDDKLRKG------------LKGV 394 (615)
Q Consensus 346 l~-------~~~F~~~~~------f~~~i~~af~~~ln~---~~~~---~e~La~y~D~~lk~~------------~~~~ 394 (615)
++ ..+|+.+.. +....+.-...++.. ..++ ...+..|.-..+..+ ..+.
T Consensus 94 ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (324)
T smart00762 94 IIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERRIDRLISDINSYNHAQLHAGASNDARASSNGEDEGL 173 (324)
T ss_pred HHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhccccccccccccccccccccCCC
Confidence 54 446664321 112222222222221 1111 111223322211110 0123
Q ss_pred ChhHHHHHHHHHhhhhccccchHHHHHHHHHHHHhHhcC
Q 007158 395 SEEDVETILDKVMMLFRYLQEKDVFEKYYKQHLAKRLLS 433 (615)
Q Consensus 395 ~~~~~e~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~ 433 (615)
+-.+++..|+.+..+.+- -..|.+++++|.-.
T Consensus 174 d~revd~lL~Eis~i~~~-------~~lY~rFi~~k~~~ 205 (324)
T smart00762 174 DPRELDAILEEISQILSR-------WELYCRFISRKINE 205 (324)
T ss_pred CHHHHHHHHHHHHHHHHh-------HHHHHHHHHHHHhh
Confidence 445677777777777642 46788999888764
No 70
>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=23.72 E-value=91 Score=23.73 Aligned_cols=27 Identities=7% Similarity=-0.203 Sum_probs=21.4
Q ss_pred ccHHHHHHhcCCChhhhhhhhcccccc
Q 007158 577 LSYQGNRAGNRDSCFRLEKVPAISGLC 603 (615)
Q Consensus 577 ~t~~ei~~~t~~~~~~l~~~~~~~~l~ 603 (615)
+|+.|+++.+|+++..|..-..-.++.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~ 27 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLY 27 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999665444444
No 71
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=23.66 E-value=6.6e+02 Score=24.14 Aligned_cols=120 Identities=10% Similarity=0.257 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHhhhHHHHhc-CchhhHHhhccCcHHHHHHHHHHhccCCCChHhHHHHHHHHHHHHhhhhhcCcccCC
Q 007158 249 AKITNVVEKEMIANHMPRLVHM-DNSGLVNMLLDDKYEDLGRMYNLFRRVPSGLLTIREVMTSHLRETGKQLVTDPERLK 327 (615)
Q Consensus 249 ~~l~~~~~~~Li~~~~~~il~~-~~~~~~~ll~~~~~~~L~~l~~L~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~ 327 (615)
+.|.+.+.+.|+...-+.++.. +...+-.++..+ .++++.|..|--.- ...+.+-..++.++...-.
T Consensus 21 E~i~kelie~l~~~~~qk~l~~gE~v~il~Ll~~k-d~ef~~llkla~eq-~k~e~~m~~Lea~VEkrD~---------- 88 (272)
T KOG4552|consen 21 EHIVKELIETLINRDKQKMLKNGETVNILKLLDSK-DDEFKTLLKLAPEQ-QKREQLMRTLEAHVEKRDE---------- 88 (272)
T ss_pred HHHHHHHHHHHHhhhHHHHHhcchHHHHHHHHHhc-cHHHHHHHHHhHhH-HHHHHHHHHHHHHHHHhHH----------
Confidence 4444555555555445555533 111233334333 24455544433221 1223444444544444332
Q ss_pred CcHHHHHHHHHHHHHHHHHH-HhhcCCCHHhHHHHHHHHHHhhccCCCcHHHHHHHHHHHhhcC
Q 007158 328 DPVEFVQRLLDEKDKYDNII-SSAFNNDKTFQNALNSSFEYFINLNPRSPEFISLFVDDKLRKG 390 (615)
Q Consensus 328 ~~~~~i~~ll~l~~~~~~l~-~~~F~~~~~f~~~i~~af~~~ln~~~~~~e~La~y~D~~lk~~ 390 (615)
.|+.|-.--+..+.++ ..||.-+..+ +.|++| ++.+-.+|.|-+|.|++-+.+
T Consensus 89 ----~IQqLqk~LK~aE~iLtta~fqA~qKL-ksi~~A-----~krpvsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 89 ----VIQQLQKNLKSAEVILTTACFQANQKL-KSIKEA-----EKRPVSSEELIKYAHRISKHN 142 (272)
T ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-----hcCCCCHHHHHHHHHHhhhcc
Confidence 3444433333333333 3366544432 223333 335667899999999986653
No 72
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=23.60 E-value=92 Score=26.21 Aligned_cols=34 Identities=12% Similarity=-0.052 Sum_probs=28.5
Q ss_pred HHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 563 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 563 ~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
..-.||..+..+...|+.+|++.+|+++..+...
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~ 37 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNR 37 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 3456788888888899999999999999998743
No 73
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=22.99 E-value=94 Score=28.48 Aligned_cols=32 Identities=13% Similarity=-0.103 Sum_probs=25.8
Q ss_pred HHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 566 CVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 566 ~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
.+.+..+..+.+|..+|++..++|+..|+++.
T Consensus 14 L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl 45 (153)
T PRK11920 14 LMYCAANDGKLSRIPEIARAYGVSELFLFKIL 45 (153)
T ss_pred HHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 34455556667899999999999999999875
No 74
>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=22.94 E-value=1.1e+02 Score=21.16 Aligned_cols=36 Identities=17% Similarity=0.040 Sum_probs=25.7
Q ss_pred ecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 560 VSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 560 vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
++..+..++.++- ..++|..+|++.+|++...+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHH
Confidence 3555555554443 25689999999999999888644
No 75
>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=22.68 E-value=1.3e+02 Score=24.17 Aligned_cols=35 Identities=9% Similarity=-0.052 Sum_probs=25.3
Q ss_pred HHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhhh
Q 007158 563 YQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 563 ~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
+.-.+|-+.-++..+|+.+|+..+|.+.+.+..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L 59 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAAL 59 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 34457777788999999999999999999988664
No 76
>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=21.49 E-value=1.1e+02 Score=26.77 Aligned_cols=34 Identities=18% Similarity=0.050 Sum_probs=25.2
Q ss_pred HHHHHHhhhC-CCCccHHHHHHhcCCChhhhhhhh
Q 007158 564 QMCVLMLFNN-ADRLSYQGNRAGNRDSCFRLEKVP 597 (615)
Q Consensus 564 Qa~iLl~Fn~-~~~~t~~ei~~~t~~~~~~l~~~~ 597 (615)
++.+.+.-++ ...+|.++|++.+++++..+..+.
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il 46 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKIL 46 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHH
Confidence 3344444343 348999999999999999999764
No 77
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=21.24 E-value=3.8e+02 Score=25.25 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhh
Q 007158 99 LNRKWNDHNKALQMIRDILMYM 120 (615)
Q Consensus 99 ~~~~W~~y~~~~~~l~~vf~YL 120 (615)
..+.|.-|..-+.-|.+|+.+|
T Consensus 168 ~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 168 VYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred hHHHHHHHHHHHHHHHHHHHHh
Confidence 5578999999999999999887
No 78
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=21.24 E-value=8.4e+02 Score=27.09 Aligned_cols=50 Identities=12% Similarity=0.204 Sum_probs=29.6
Q ss_pred HHHHhhcCCchHHHHHHHHHHHHHHHHH-HHHHHHhccchHHHHHHHHHHHHHHH
Q 007158 55 NAYNMVLHKFGEKLYSGLVSTMTLHLKE-ISKSIEAAQGGSFLEELNRKWNDHNK 108 (615)
Q Consensus 55 ~vy~lc~~~~~e~LY~~l~~~i~~~~~~-i~~~l~~~~~~~~L~~~~~~W~~y~~ 108 (615)
.++.+|+.++|-++-.++-+.+.+.=.. +.++|.. .+-.....+|.+|-+
T Consensus 327 ~~~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~----~~~~L~~dQygNYVI 377 (503)
T KOG1488|consen 327 NLLELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIR----NCDQLAQDQYGNYVI 377 (503)
T ss_pred ceeEeeccCcccHHHHHHhhcCChHhhhHHHHHHHH----HHHHHHhhhhhhHHH
Confidence 5677899999988777777766654333 4444422 222333455666543
No 79
>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=21.00 E-value=1.9e+02 Score=24.46 Aligned_cols=35 Identities=20% Similarity=0.530 Sum_probs=26.8
Q ss_pred HhHHHHHHHHHHhhcc-------CCCcHHHHHHHHHHHhhcC
Q 007158 356 TFQNALNSSFEYFINL-------NPRSPEFISLFVDDKLRKG 390 (615)
Q Consensus 356 ~f~~~i~~af~~~ln~-------~~~~~e~La~y~D~~lk~~ 390 (615)
.....+..||+.++.. .++.++.+|+++...+..+
T Consensus 69 ~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~ 110 (113)
T PF02847_consen 69 ISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADG 110 (113)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcC
Confidence 3456677778877774 4789999999999998764
No 80
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=20.60 E-value=1.2e+02 Score=27.37 Aligned_cols=36 Identities=17% Similarity=0.083 Sum_probs=30.0
Q ss_pred EecHHHHHHHHhhhCCCCccHHHHHHhcCCChhhhhhh
Q 007158 559 NVSTYQMCVLMLFNNADRLSYQGNRAGNRDSCFRLEKV 596 (615)
Q Consensus 559 ~vs~~Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~ 596 (615)
..|.-|..|+.++ ..++|.+||++.+|+|...+..+
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~ 41 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAI 41 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHH
Confidence 3577888888886 46799999999999999988744
No 81
>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=20.31 E-value=70 Score=25.42 Aligned_cols=35 Identities=11% Similarity=-0.087 Sum_probs=23.5
Q ss_pred HHHhhhCCCCccHHHHHHhcCCChhhhhhhhcccc
Q 007158 567 VLMLFNNADRLSYQGNRAGNRDSCFRLEKVPAISG 601 (615)
Q Consensus 567 iLl~Fn~~~~~t~~ei~~~t~~~~~~l~~~~~~~~ 601 (615)
|+....+-..+|+.||++.+|+|+..+-.....+|
T Consensus 25 il~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 25 ILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp HHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 34444455689999999999999999887665555
No 82
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=20.29 E-value=1.4e+02 Score=18.36 Aligned_cols=29 Identities=14% Similarity=-0.256 Sum_probs=20.9
Q ss_pred HHHHHHhhhCCCCccHHHHHHhcCCChhhhh
Q 007158 564 QMCVLMLFNNADRLSYQGNRAGNRDSCFRLE 594 (615)
Q Consensus 564 Qa~iLl~Fn~~~~~t~~ei~~~t~~~~~~l~ 594 (615)
...|+..+.+ ..|+.++++.+|++...+-
T Consensus 11 ~~~i~~~~~~--~~s~~~ia~~~~is~~tv~ 39 (42)
T cd00569 11 IEEARRLLAA--GESVAEIARRLGVSRSTLY 39 (42)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHCCCHHHHH
Confidence 3445555653 4599999999999887664
Done!