Query 003835
Match_columns 792
No_of_seqs 218 out of 809
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 12:54:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003835hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167 Cullins [Cell cycle co 100.0 2E-147 5E-152 1201.9 47.5 642 147-792 2-661 (661)
2 KOG2166 Cullins [Cell cycle co 100.0 2E-128 4E-133 1123.8 64.4 679 101-790 14-725 (725)
3 COG5647 Cullin, a subunit of E 100.0 3E-127 6E-132 1066.9 60.2 684 98-792 14-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 2E-108 4E-113 858.7 48.3 651 103-792 10-728 (728)
5 PF00888 Cullin: Cullin family 100.0 1E-95 2E-100 861.5 60.3 566 108-694 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1.6E-91 3.5E-96 738.0 53.9 687 100-792 9-777 (777)
7 smart00182 CULLIN Cullin. 100.0 3.3E-37 7.2E-42 297.6 18.1 141 486-627 1-142 (142)
8 KOG2165 Anaphase-promoting com 99.8 5E-19 1.1E-23 198.7 30.4 209 482-695 444-666 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 3.4E-21 7.5E-26 161.5 4.7 66 721-786 1-68 (68)
10 KOG2167 Cullins [Cell cycle co 98.0 8.9E-05 1.9E-09 84.0 13.5 321 102-441 108-459 (661)
11 PF08539 HbrB: HbrB-like; Int 97.6 0.0011 2.3E-08 65.0 13.4 130 104-237 5-155 (158)
12 PF09012 FeoC: FeoC like trans 86.2 0.89 1.9E-05 38.1 3.7 46 732-783 4-49 (69)
13 PF09339 HTH_IclR: IclR helix- 81.7 1.6 3.4E-05 34.4 3.1 34 641-676 19-52 (52)
14 PF01726 LexA_DNA_bind: LexA D 76.0 6.3 0.00014 32.8 5.2 58 724-785 6-63 (65)
15 TIGR02698 CopY_TcrY copper tra 75.9 6.1 0.00013 37.5 5.8 60 730-792 6-65 (130)
16 PF13463 HTH_27: Winged helix 74.2 7.7 0.00017 31.7 5.4 54 730-789 5-61 (68)
17 PF08318 COG4: COG4 transport 73.3 70 0.0015 35.4 14.2 161 342-509 6-213 (331)
18 PF03965 Penicillinase_R: Peni 71.6 3.2 6.9E-05 38.4 2.7 61 729-792 4-64 (115)
19 PF02082 Rrf2: Transcriptional 69.4 8 0.00017 33.5 4.5 45 641-692 26-70 (83)
20 COG3682 Predicted transcriptio 68.1 11 0.00023 35.5 5.3 61 728-791 6-66 (123)
21 PF05732 RepL: Firmicute plasm 65.9 8.1 0.00018 38.4 4.3 52 641-701 76-127 (165)
22 PF01978 TrmB: Sugar-specific 63.2 8.8 0.00019 31.7 3.5 57 729-791 9-65 (68)
23 PF01047 MarR: MarR family; I 59.8 10 0.00022 30.2 3.1 50 730-785 5-56 (59)
24 TIGR01610 phage_O_Nterm phage 58.0 18 0.00039 32.3 4.7 46 641-694 48-93 (95)
25 smart00550 Zalpha Z-DNA-bindin 56.7 30 0.00066 28.8 5.6 54 729-788 7-62 (68)
26 smart00418 HTH_ARSR helix_turn 56.1 22 0.00049 27.9 4.7 49 733-788 2-50 (66)
27 PF12840 HTH_20: Helix-turn-he 55.4 9.5 0.00021 30.9 2.3 34 641-676 25-58 (61)
28 PF08220 HTH_DeoR: DeoR-like h 55.2 19 0.00041 28.9 4.0 47 731-783 3-49 (57)
29 smart00419 HTH_CRP helix_turn_ 54.7 27 0.00059 26.1 4.7 32 641-674 9-40 (48)
30 PF09763 Sec3_C: Exocyst compl 53.5 5.1E+02 0.011 31.8 20.3 66 361-426 629-701 (701)
31 PF04492 Phage_rep_O: Bacterio 52.3 25 0.00055 31.9 4.7 44 641-694 55-98 (100)
32 PF01022 HTH_5: Bacterial regu 48.1 20 0.00042 27.5 2.9 30 641-672 16-45 (47)
33 smart00346 HTH_ICLR helix_turn 47.9 25 0.00054 30.4 4.0 34 641-676 21-54 (91)
34 PF12108 SF3a60_bindingd: Spli 46.3 15 0.00032 25.4 1.7 14 487-500 3-16 (28)
35 PF10408 Ufd2P_core: Ubiquitin 45.0 2.8E+02 0.006 33.6 13.5 88 448-542 531-627 (629)
36 smart00344 HTH_ASNC helix_turn 44.9 35 0.00075 30.7 4.6 47 728-780 3-49 (108)
37 cd07153 Fur_like Ferric uptake 43.4 51 0.0011 30.1 5.5 51 732-783 5-56 (116)
38 PF12802 MarR_2: MarR family; 42.9 29 0.00062 27.7 3.3 48 730-783 7-56 (62)
39 PF08220 HTH_DeoR: DeoR-like h 41.6 29 0.00064 27.8 3.1 33 641-675 15-47 (57)
40 PF02186 TFIIE_beta: TFIIE bet 41.4 35 0.00077 28.4 3.6 56 729-792 6-61 (65)
41 PF04703 FaeA: FaeA-like prote 41.1 48 0.001 27.4 4.2 46 641-690 16-61 (62)
42 PF08221 HTH_9: RNA polymerase 40.2 28 0.00061 28.6 2.8 30 641-672 28-57 (62)
43 PF09756 DDRGK: DDRGK domain; 39.6 31 0.00067 35.0 3.5 58 729-792 100-157 (188)
44 PF05584 Sulfolobus_pRN: Sulfo 39.6 38 0.00082 28.8 3.5 32 641-674 19-50 (72)
45 PF13412 HTH_24: Winged helix- 39.4 52 0.0011 25.0 4.1 45 729-779 4-48 (48)
46 PF13412 HTH_24: Winged helix- 37.8 37 0.0008 25.8 3.0 25 641-665 18-42 (48)
47 smart00550 Zalpha Z-DNA-bindin 37.5 44 0.00095 27.9 3.6 33 641-675 23-55 (68)
48 smart00345 HTH_GNTR helix_turn 37.2 47 0.001 25.9 3.7 34 641-676 20-54 (60)
49 cd00092 HTH_CRP helix_turn_hel 37.2 44 0.00095 26.9 3.6 34 641-676 26-59 (67)
50 PF10771 DUF2582: Protein of u 36.6 42 0.00091 28.0 3.3 34 641-674 23-57 (65)
51 KOG3091 Nuclear pore complex, 36.5 1.4E+02 0.003 34.6 8.3 148 371-543 340-493 (508)
52 smart00420 HTH_DEOR helix_turn 35.6 66 0.0014 24.2 4.2 46 732-783 4-49 (53)
53 PF01978 TrmB: Sugar-specific 34.8 32 0.00069 28.4 2.4 32 641-674 23-54 (68)
54 TIGR03879 near_KaiC_dom probab 34.5 34 0.00073 29.3 2.4 31 641-673 33-63 (73)
55 PF13601 HTH_34: Winged helix 32.6 37 0.0008 29.4 2.5 25 641-665 15-39 (80)
56 TIGR02010 IscR iron-sulfur clu 32.3 62 0.0013 30.7 4.2 32 641-674 26-57 (135)
57 PRK10857 DNA-binding transcrip 32.2 69 0.0015 31.8 4.7 32 641-674 26-57 (164)
58 PRK10141 DNA-binding transcrip 31.9 49 0.0011 30.9 3.4 46 641-692 31-76 (117)
59 smart00762 Cog4 COG4 transport 29.2 2.7E+02 0.0059 30.7 9.2 79 342-420 6-95 (324)
60 PF01726 LexA_DNA_bind: LexA D 28.9 66 0.0014 26.7 3.3 35 641-677 26-61 (65)
61 PHA00738 putative HTH transcri 28.4 71 0.0015 29.4 3.6 47 641-693 27-73 (108)
62 PRK13713 conjugal transfer pro 28.2 1.4E+02 0.003 27.8 5.5 40 234-273 2-44 (118)
63 PF12802 MarR_2: MarR family; 28.1 53 0.0012 26.1 2.6 34 641-676 22-55 (62)
64 PRK11512 DNA-binding transcrip 28.1 1.1E+02 0.0025 29.1 5.4 41 740-786 52-94 (144)
65 PF08281 Sigma70_r4_2: Sigma-7 27.7 63 0.0014 25.1 2.9 22 641-662 27-48 (54)
66 PF10163 EnY2: Transcription f 27.2 2.4E+02 0.0051 24.7 6.7 56 104-159 28-85 (86)
67 PF12395 DUF3658: Protein of u 26.9 1.3E+02 0.0029 27.6 5.3 62 728-790 48-109 (111)
68 smart00347 HTH_MARR helix_turn 26.9 1.4E+02 0.0031 25.7 5.4 48 729-782 11-58 (101)
69 PF08784 RPA_C: Replication pr 26.9 74 0.0016 28.5 3.6 26 641-666 66-91 (102)
70 PRK03573 transcriptional regul 26.6 1.3E+02 0.0028 28.5 5.5 29 758-786 56-86 (144)
71 PF01853 MOZ_SAS: MOZ/SAS fami 26.4 56 0.0012 33.1 2.9 25 641-665 151-175 (188)
72 smart00418 HTH_ARSR helix_turn 26.1 88 0.0019 24.3 3.6 33 641-675 11-43 (66)
73 COG1414 IclR Transcriptional r 26.0 72 0.0016 33.7 3.8 35 641-677 20-54 (246)
74 PRK11920 rirA iron-responsive 26.0 1E+02 0.0022 30.1 4.6 33 641-675 25-57 (153)
75 PF08784 RPA_C: Replication pr 25.7 79 0.0017 28.3 3.5 52 726-779 45-96 (102)
76 cd07377 WHTH_GntR Winged helix 25.4 1E+02 0.0022 24.5 3.8 33 642-676 27-59 (66)
77 PF14164 YqzH: YqzH-like prote 25.2 64 0.0014 26.8 2.5 35 105-139 28-62 (64)
78 TIGR02944 suf_reg_Xantho FeS a 25.1 82 0.0018 29.5 3.7 33 641-675 26-58 (130)
79 cd00090 HTH_ARSR Arsenical Res 25.0 91 0.002 25.0 3.6 32 641-674 21-52 (78)
80 PF13730 HTH_36: Helix-turn-he 24.9 81 0.0017 24.6 3.0 24 642-665 27-50 (55)
81 PRK10163 DNA-binding transcrip 24.5 75 0.0016 34.0 3.7 35 641-677 41-75 (271)
82 COG1522 Lrp Transcriptional re 24.3 1.2E+02 0.0026 28.9 4.8 49 727-781 7-55 (154)
83 TIGR00738 rrf2_super rrf2 fami 24.2 94 0.002 29.0 3.9 32 641-674 26-57 (132)
84 PRK15090 DNA-binding transcrip 23.9 81 0.0017 33.4 3.8 35 641-677 29-63 (257)
85 PF03037 KMP11: Kinetoplastid 23.6 3.2E+02 0.0069 23.1 6.2 64 376-442 11-74 (90)
86 PRK11569 transcriptional repre 23.5 84 0.0018 33.6 3.8 35 641-677 44-78 (274)
87 PF13404 HTH_AsnC-type: AsnC-t 23.4 1.1E+02 0.0023 23.1 3.2 24 641-664 18-41 (42)
88 COG4190 Predicted transcriptio 23.2 1.4E+02 0.0031 28.5 4.6 52 641-694 79-133 (144)
89 smart00420 HTH_DEOR helix_turn 23.2 1.1E+02 0.0024 23.0 3.5 32 641-674 15-46 (53)
90 KOG2747 Histone acetyltransfer 22.7 71 0.0015 36.0 3.1 26 641-666 330-355 (396)
91 PF05261 Tra_M: TraM protein, 22.5 2E+02 0.0044 27.2 5.4 42 233-274 8-52 (127)
92 KOG2035 Replication factor C, 22.1 4.8E+02 0.01 28.5 8.8 140 317-468 176-329 (351)
93 smart00346 HTH_ICLR helix_turn 21.9 1.8E+02 0.004 24.9 5.1 45 733-783 10-55 (91)
94 PF02847 MA3: MA3 domain; Int 20.7 2.2E+02 0.0048 25.6 5.5 39 426-464 66-110 (113)
95 KOG0412 Golgi transport comple 20.5 5.5E+02 0.012 31.3 9.7 81 341-421 189-281 (773)
96 PRK11179 DNA-binding transcrip 20.3 1.7E+02 0.0037 28.3 5.0 47 728-780 9-55 (153)
97 TIGR01610 phage_O_Nterm phage 20.3 1.9E+02 0.0041 25.7 4.8 38 739-782 44-81 (95)
98 PF05186 Dpy-30: Dpy-30 motif; 20.1 1.2E+02 0.0027 22.9 3.0 30 430-459 10-39 (42)
No 1
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.3e-147 Score=1201.91 Aligned_cols=642 Identities=66% Similarity=1.012 Sum_probs=625.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc-CCCcccHHHHHHHHHHH
Q 003835 147 LYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQ-TPNVRSLWDMGLQLFRK 225 (792)
Q Consensus 147 LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~~-~~~~~sI~dlgL~lFr~ 225 (792)
||++|+..|++|+...+.++.....|.+.||..+.++|+.|+.++.+|++||.||||+|+.+ ++.++|||+||+.+||.
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 89999999999999988888777667789999999999999999999999999999999999 88899999999999999
Q ss_pred Hhcc--ccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHHhhhccHHhhHHHHHHHHHHHHHHHHHHHhhcCChhh
Q 003835 226 YLSS--YSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPD 303 (792)
Q Consensus 226 ~v~~--~~~l~~~l~~~iL~lI~~eR~g~~id~~llk~~i~ml~~L~vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~e 303 (792)
+++. .+.+..++.++++..|+++|.|+++|+.+|++++.|+.++++|.+.||+.|++.+.++|++++...+++..+++
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~e 161 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPE 161 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHH
Confidence 9998 67889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc-cchHHHHH
Q 003835 304 YLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQ 382 (792)
Q Consensus 304 YL~~ve~~l~eE~~R~~~yL~~sT~~~L~~~l~~~LI~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~-~~l~~l~~ 382 (792)
||++|+.++.+|.+|+..|+|.+|++++..+++++||..|++.|+..|+..+++.++..++.+||.|++++ ++...++.
T Consensus 162 Yl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~kgl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~q 241 (661)
T KOG2167|consen 162 YLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTKGLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQ 241 (661)
T ss_pred HHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhcchHHhhhhhhccchHhHHHHHHHHhcchHHHHH
Confidence 99999999999999999999999988899999999999999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHHhhcccccCchhhHHHHHHHHHHHHHHHHHHHHhcCCC--hhhhHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 003835 383 ALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKN--EAFCNTIKDAFEYLINLRQNRPAELIAKFLDEK 460 (792)
Q Consensus 383 ~~~~yI~~~G~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~--~~f~~~l~~af~~~iN~~~~~~~e~Laky~D~~ 460 (792)
.|.+|+++.|..+|.|++.++.+|++|+.||++.|-++..||-.+ +.|.+++++||+.|+|.+.++|||+||+|.|.+
T Consensus 242 q~sdylk~~G~KlV~de~kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~~rpAelIak~~dt~ 321 (661)
T KOG2167|consen 242 QWSDYLKKPGFKLVIDEEKDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRRNRPAELIAKYVDTK 321 (661)
T ss_pred HHHHHHhcccceeccCchhhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999877 999999999999999999999999999999999
Q ss_pred HhcCCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhhhhHHHHHHHHHH
Q 003835 461 LRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFK 540 (792)
Q Consensus 461 Lr~~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG~~fT~kLe~Mfk 540 (792)
||.|+|+.+|++++..+++++.|||||++|||||+||+++||||||.++|+|.|+|++|+++||.|||.+||+||||||+
T Consensus 322 Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfk 401 (661)
T KOG2167|consen 322 LRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFK 401 (661)
T ss_pred HHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCceeEEeecCcce
Q 003835 541 DIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGH 620 (792)
Q Consensus 541 Di~~S~~l~~~f~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~~~~~LP~~l~~~~~~F~~fY~~k~~gRkL~W~~~Lg~ 620 (792)
||++|++++..|+++.........++ +.|+|||.|+||+|++.++.||++|..+++.|+.||.++|+||+|.|+++||+
T Consensus 402 dme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~ 480 (661)
T KOG2167|consen 402 DMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGH 480 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcc
Confidence 99999999999999855434455566 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCCeeEEEEeecc------------ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEE
Q 003835 621 CVLKAEFPKGKKELAVSLFQ------------LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFV 688 (792)
Q Consensus 621 ~~i~~~f~~~~~el~vs~~Q------------lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~ 688 (792)
|+|+|.|+.|++||+||+|| +|++||.++|||.+.||+|+|+||+|||.|+|.++|+|+++.+||.|.
T Consensus 481 ~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~ 560 (661)
T KOG2167|consen 481 CVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFI 560 (661)
T ss_pred hhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEE
Confidence 99999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred EccCCCCCceeEEecccccccchhhhhhhhHHHHhhhhhhhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHH
Q 003835 689 FNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKR 768 (792)
Q Consensus 689 ~N~~Ft~~~~riki~~i~~ket~~e~~~t~e~v~~dR~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~ 768 (792)
||..|++|.+|||||+|++|||++|+++|.|+|.+||+++||||||||||+||+|+|+.||+|+++||+||+.| ++|+|
T Consensus 561 ~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlkfpv~~-d~kkr 639 (661)
T KOG2167|consen 561 VNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLKFPVKP-DLKKR 639 (661)
T ss_pred echhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcCCCCCh-hHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred HHHhhhhcccccCCCCCCceeecC
Q 003835 769 IESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 769 IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
||+|||||||+|| +| +.|+|||
T Consensus 640 iesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 640 IESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999999 45 8999998
No 2
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.9e-128 Score=1123.84 Aligned_cols=679 Identities=38% Similarity=0.642 Sum_probs=638.4
Q ss_pred CchHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhhccCch----hHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 003835 101 TNFEEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMG----GNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (792)
Q Consensus 101 ~~~~e~~W~~L~~AI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~----e~LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~ 176 (792)
..+.+++|.+|..|++.+..+....++|+.+|+++|++|++++| ++||+++++++.+|+.+.+.+.....++ ..+
T Consensus 14 w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~-~~~ 92 (725)
T KOG2166|consen 14 WSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHD-EYM 92 (725)
T ss_pred HHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCc-HHH
Confidence 47788999999999986665556678999999999999999999 9999999999999999999887776665 689
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCcccHHHHH-HHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcCC
Q 003835 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMG-LQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVD 255 (792)
Q Consensus 177 L~~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~~~~~~~sI~dlg-L~lFr~~v~~~~~l~~~l~~~iL~lI~~eR~g~~id 255 (792)
|..+...|.+|+.++.+++++|+||||+||.+.....++++++ +.+||..++.. ++..++++++|.+|..+|.|+.||
T Consensus 93 l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~-~~~~~~~~all~lI~~eR~ge~in 171 (725)
T KOG2166|consen 93 LRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKF-EMQSEAIDALLALIHKEREGEQID 171 (725)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHH-HHHHHHHHHHHHHHHhhccccccc
Confidence 9999999999999999999999999999999873356677666 99999998765 699999999999999999999999
Q ss_pred hHHHHHHHHHHHhhh-----ccHHhhHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHHhccccCcCcHHH
Q 003835 256 RTLLNHLLKMFTALG-----IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKP 330 (792)
Q Consensus 256 ~~llk~~i~ml~~L~-----vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~eYL~~ve~~l~eE~~R~~~yL~~sT~~~ 330 (792)
+.+|++++.|+..|| +|...||++|+++|++||..++.+|+...++++|+.+|+.++.+|.+|+..||+..+..+
T Consensus 172 ~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~ 251 (725)
T KOG2166|consen 172 RELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPK 251 (725)
T ss_pred HHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccch
Confidence 999999999999987 999999999999999999999999999889999999999999999999999999888888
Q ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHhhccCCHHHHHHHHHhhccc-cchHHHHHHHHHHHHHhhcccccCc-----hh
Q 003835 331 LIATAERQLLERHISAIL---DKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE-----EK 401 (792)
Q Consensus 331 L~~~l~~~LI~~~~~~ll---~~g~~~ll~~~~~~~L~~ly~L~~~~-~~l~~l~~~~~~yI~~~G~~iv~~~-----~~ 401 (792)
+.+.++..++..|++.++ .+||..|+.+++.++|.+||+|++|+ .|++.++..+..|++.+|..++... ..
T Consensus 252 ~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~~~~ 331 (725)
T KOG2166|consen 252 LVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETAATN 331 (725)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhcccc
Confidence 888888888888888777 58999999999999999999999999 9999999999999999998777432 45
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCCCCHHHHHhhhhchh
Q 003835 402 DKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVL 481 (792)
Q Consensus 402 ~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~~~~~~e~Laky~D~~Lr~~~k~~~~~e~e~~ld~i~ 481 (792)
++.+|+.+++++++|..++..||+++..|..+++.||+.|+|.+...++|+||+|||.+||+|.++.+|+++|..|++++
T Consensus 332 ~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~ 411 (725)
T KOG2166|consen 332 PVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVV 411 (725)
T ss_pred hHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcce
Confidence 67999999999999999999999999999999999999999998854569999999999999999999999999999999
Q ss_pred eeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhhhhHHHHHHHHHHhHHhhHHHHHHHHHHhhhccC
Q 003835 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTK 561 (792)
Q Consensus 482 ~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG~~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~ 561 (792)
.||+||++||+|+.||+++||||||+++|+|+|+|++||++||++||.+||+||++||+|+.+|++++..|+++ .+ ..
T Consensus 412 ~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~-~~-~~ 489 (725)
T KOG2166|consen 412 KLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY-AN-YS 489 (725)
T ss_pred eeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh-hc-hh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987 22 22
Q ss_pred CCCCcceEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCceeEEeecCcceEEEEEEecCCeeEEEEeecc-
Q 003835 562 LPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ- 640 (792)
Q Consensus 562 ~~~~~~f~v~VLt~~~WP~~~~~~~~LP~~l~~~~~~F~~fY~~k~~gRkL~W~~~Lg~~~i~~~f~~~~~el~vs~~Q- 640 (792)
...++||.|.|||+|+||++++.+++||++|..+.+.|..||.+||+||+|+|+|+||.|+|.++|.+++|+|+||+||
T Consensus 490 ~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm 569 (725)
T KOG2166|consen 490 ANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQM 569 (725)
T ss_pred ccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHH
Confidence 3357999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -----------ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEeccccccc
Q 003835 641 -----------LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKE 709 (792)
Q Consensus 641 -----------lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft~~~~riki~~i~~ke 709 (792)
+|++||.++|+|+.++|.+.|+||+|.|.+|+.+ |.+++ +++|.|.+|.+|+++++||+|+.+..+
T Consensus 570 ~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~- 646 (725)
T KOG2166|consen 570 AVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD- 646 (725)
T ss_pred HHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch-
Confidence 9999999999999999999999999988888888 88888 999999999999999999999987655
Q ss_pred chhhhhhhhHHHHhhhhhhhhHHHHHhhhcccccChHHHHHHHHHhc--CCCCChHHHHHHHHHhhhhcccccCCCCCCc
Q 003835 710 TVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQI 787 (792)
Q Consensus 710 t~~e~~~t~e~v~~dR~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~l--rF~~~~~~iKk~IE~LIereYl~Rd~~d~~~ 787 (792)
|.+.+.+.|++||+++||||||||||+||+|.|++|+.||++|+ ||.|+|.+||+|||.|||||||+|| +|+++
T Consensus 647 ---e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~ 722 (725)
T KOG2166|consen 647 ---ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNI 722 (725)
T ss_pred ---hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCc
Confidence 77888999999999999999999999999999999999999999 7999999999999999999999999 99999
Q ss_pred eee
Q 003835 788 YNY 790 (792)
Q Consensus 788 Y~Y 790 (792)
|+|
T Consensus 723 Y~Y 725 (725)
T KOG2166|consen 723 YRY 725 (725)
T ss_pred ccC
Confidence 998
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-127 Score=1066.90 Aligned_cols=684 Identities=36% Similarity=0.575 Sum_probs=631.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHH---hcCCCCccHHHHHHHHHhhhccC----------------chhHHHHHHHHHHHHH
Q 003835 98 TLPTNFEEDTWAKLKLAIKAIF---LKQPTSCDLEKLYQAVNDLCLHK----------------MGGNLYQRIEKECEEH 158 (792)
Q Consensus 98 ~~~~~~~e~~W~~L~~AI~~I~---~~~~~~~s~e~LY~~Vy~lC~~k----------------~~e~LY~~l~~~~~~~ 158 (792)
+++++.++.+|..++.||+.|+ ......++|+++|+.+|+.|.++ +|+.||++|....+++
T Consensus 14 ~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~ 93 (773)
T COG5647 14 TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNY 93 (773)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHH
Confidence 4567777999999999999999 44556789999999999999987 4778999999999988
Q ss_pred HHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh-----cCCCcccHHHHHHHHHHHHhccccch
Q 003835 159 ISAAIRSLVGQSPDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVK-----QTPNVRSLWDMGLQLFRKYLSSYSEV 233 (792)
Q Consensus 159 l~~~~~~l~~~~~d~~~~L~~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~-----~~~~~~sI~dlgL~lFr~~v~~~~~l 233 (792)
+...-... .....+.||..+++.|++|+.++.+++++|.||||+|++ .++ ...++++++..|+.++|. .+
T Consensus 94 i~~~~~~~--s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~-~~E~~slcl~~~~~~~f~--~i 168 (773)
T COG5647 94 IEEYNRGR--SQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTL-VFEVYSLCLVKEKIESFR--LI 168 (773)
T ss_pred HHHhcccc--cchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCcc-ceeeehhhhhHHHHHHHH--hh
Confidence 88765431 122347999999999999999999999999999999999 333 567888999999999986 89
Q ss_pred HHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHHhh-----------hccHHhhHHHHHHHHHHHHHHHHHHHhhcCChh
Q 003835 234 EHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFTAL-----------GIYSESFEKPFLECTSEFYAAEGMKYMQQSDVP 302 (792)
Q Consensus 234 ~~~l~~~iL~lI~~eR~g~~id~~llk~~i~ml~~L-----------~vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~ 302 (792)
.+.+++.+|..+++.|.|+.||+..+..++.|+..| .+|...|||.||+.|.+||..++.+.+..+++.
T Consensus 169 ~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~ 248 (773)
T COG5647 169 VDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVT 248 (773)
T ss_pred hHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHH
Confidence 999999999999999999999999999999999999 589999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHHHHHHHHHHHHHHH--HHHHHhhccCCHHHHHHHHHhhccc-cchHH
Q 003835 303 DYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILD--KGFTMLMDGHRTEDLQRMYSLFSRV-NALES 379 (792)
Q Consensus 303 eYL~~ve~~l~eE~~R~~~yL~~sT~~~L~~~l~~~LI~~~~~~ll~--~g~~~ll~~~~~~~L~~ly~L~~~~-~~l~~ 379 (792)
+||.+|+.++++|.+++..|++.+|.++|..+++++||++|.+.+.. +||..+++..+.+.|..||++++++ .++.+
T Consensus 249 eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~s~f~~~~d~~~~e~l~~lY~l~se~~~~v~p 328 (773)
T COG5647 249 EYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQP 328 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhchHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999886 4999999999999999999999999 78999
Q ss_pred HHHHHHHHHHHhh--ccccc---------------CchhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHH
Q 003835 380 LRQALAMYIRRTG--HGIVM---------------DEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLI 442 (792)
Q Consensus 380 l~~~~~~yI~~~G--~~iv~---------------~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~i 442 (792)
|++.|..||+..| ..+.. +...++.||+.++++++.+..++.++|.+|..+..++++||+.|+
T Consensus 329 l~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fi 408 (773)
T COG5647 329 LQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFI 408 (773)
T ss_pred HHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHh
Confidence 9999999999999 21111 223467999999999999999999999999999999999999999
Q ss_pred hcCC---CCchhHHHHHHHHHHhcCCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHH
Q 003835 443 NLRQ---NRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSM 519 (792)
Q Consensus 443 N~~~---~~~~e~Laky~D~~Lr~~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~m 519 (792)
|.+. ..++|+||+|+|.+||++.+......++..+..++.||||+.+||+||+||+++||||||+|+|+|.|+|++|
T Consensus 409 n~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~m 488 (773)
T COG5647 409 NGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKM 488 (773)
T ss_pred ccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHH
Confidence 9843 3689999999999999998777778899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhHHHHHHHHHHhHHhhHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCC-CCccCChHHHHHHHH
Q 003835 520 ISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDI 598 (792)
Q Consensus 520 i~kLk~ecG~~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~-~~~~LP~~l~~~~~~ 598 (792)
|++||++||.+||+|||+||+||.+|.++...|++...+ ....+||.|.|||+.+||+.|+ ..+.||++|.+.++.
T Consensus 489 is~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~ 565 (773)
T COG5647 489 ISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEG 565 (773)
T ss_pred HHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHH
Confidence 999999999999999999999999999999999986533 2246899999999999997665 679999999999999
Q ss_pred HHHHHHhcCCceeEEeecCcceEEEEEEecCCeeEEEEeecc---------------ccHHHHHHHhCCCHHHHHHHHHH
Q 003835 599 FKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ---------------LSFQDIKDATGIEDKELRRTLQS 663 (792)
Q Consensus 599 F~~fY~~k~~gRkL~W~~~Lg~~~i~~~f~~~~~el~vs~~Q---------------lt~~eI~~~T~i~~~eL~r~L~s 663 (792)
|++||.+||+||+|.|.++||+|+|+++|+.+++.+.+|+++ +||+||.+.|+|+.++|+++|+|
T Consensus 566 f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~s 645 (773)
T COG5647 566 FKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQS 645 (773)
T ss_pred HHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHH
Confidence 999999999999999999999999999999999888887655 99999999999999999999999
Q ss_pred hhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEEecccccccchhhhhhhhHHHHhhhhhhhhHHHHHhhhccccc
Q 003835 664 LACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVL 743 (792)
Q Consensus 664 L~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft~~~~riki~~i~~ket~~e~~~t~e~v~~dR~~~i~AaIVRIMK~rK~l 743 (792)
|+|.|..+|.+. ++.++|++.|.+|.+|++++.|||||.+..++..+++..|+++|++||+++.|||||||||+||+|
T Consensus 646 l~~ak~~~l~~~--~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l 723 (773)
T COG5647 646 LSCAKLVVLLKD--DKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKL 723 (773)
T ss_pred HHhhheeeeccc--cccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 998887777665 889999999999999999999999999888777778889999999999999999999999999999
Q ss_pred ChHHHHHHHHHhc--CCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 744 SHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 744 ~h~~Li~ev~~~l--rF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
.|++|+.||+.|+ ||.|+|+|||++||.|||||||+|.++| .+|+|+|
T Consensus 724 ~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 724 KHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 9999999999999 8999999999999999999999999988 8999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-108 Score=858.71 Aligned_cols=651 Identities=27% Similarity=0.494 Sum_probs=603.6
Q ss_pred hHHHHHHHHHHHHHHHHhcCCC-CccHHHHHHHHHhhhccC---chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHH
Q 003835 103 FEEDTWAKLKLAIKAIFLKQPT-SCDLEKLYQAVNDLCLHK---MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLS 178 (792)
Q Consensus 103 ~~e~~W~~L~~AI~~I~~~~~~-~~s~e~LY~~Vy~lC~~k---~~e~LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~L~ 178 (792)
.++++|.+|...|.+|..-++. ...|..-|..||.+|..- .||.||...+.++++|++..+...... +++.+|.
T Consensus 10 ~fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~~~v~~--~p~~~l~ 87 (728)
T KOG2284|consen 10 EFDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQDIVDV--DPDLLLQ 87 (728)
T ss_pred eHHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhhhhhcC--CHHHHHH
Confidence 3589999999999999887775 468999999999999874 699999999999999999877766543 3357999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCC-----------------CcccHHHHHHHHHHHHhccccchHHHHHHHH
Q 003835 179 LVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-----------------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGL 241 (792)
Q Consensus 179 ~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~~~~-----------------~~~sI~dlgL~lFr~~v~~~~~l~~~l~~~i 241 (792)
.|.+.|+.|..+..++..+|.|||..|+++++ .+..|..++|++||+.++. ++...++..+
T Consensus 88 ~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~--~i~~~lv~~l 165 (728)
T KOG2284|consen 88 EYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVK--TILPQLVKLL 165 (728)
T ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHH--HHHHHHHHHH
Confidence 99999999999999999999999999999864 3457888999999999976 8999999999
Q ss_pred HHHHHHHhcCCcCC-hHHHHHHHHHHHhhh----------------------ccHHhhHHHHHHHHHHHHHHHHHHHhhc
Q 003835 242 LRMIERERLGEAVD-RTLLNHLLKMFTALG----------------------IYSESFEKPFLECTSEFYAAEGMKYMQQ 298 (792)
Q Consensus 242 L~lI~~eR~g~~id-~~llk~~i~ml~~L~----------------------vY~~~FE~~fL~~T~~yY~~es~~~l~~ 298 (792)
|..|.++|.|+..+ ...+..+|..|+.+. +|++.||.|||.+|.+||+.+++.++++
T Consensus 166 l~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~ 245 (728)
T KOG2284|consen 166 LIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQKMLTD 245 (728)
T ss_pred HHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHHHHhh
Confidence 99999999999766 467788888887652 8999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc-cch
Q 003835 299 SDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NAL 377 (792)
Q Consensus 299 ~s~~eYL~~ve~~l~eE~~R~~~yL~~sT~~~L~~~l~~~LI~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~-~~l 377 (792)
.+|++|+.+|..+|++|+-||..||++++..+++..|++.+|..|.+.| +-.+.++|.+++..||+.||.|+..+ -|+
T Consensus 246 ~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l-ha~ch~~i~~e~~~d~~nmy~ll~~i~~gl 324 (728)
T KOG2284|consen 246 LSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL-HAVCHDLITNEENKDLRNMYRLLKPIQAGL 324 (728)
T ss_pred ccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhhhhhhHHHHHHHHHHHhcCc
Confidence 9999999999999999999999999999999999999999999999874 66799999999999999999999999 999
Q ss_pred HHHHHHHHHHHHHhhcccccCchh---hHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHhcCC-----CCc
Q 003835 378 ESLRQALAMYIRRTGHGIVMDEEK---DKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQ-----NRP 449 (792)
Q Consensus 378 ~~l~~~~~~yI~~~G~~iv~~~~~---~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~~-----~~~ 449 (792)
..+...|.+||.+.|...+++.+. +..||+.+|++|.+|..++...|.+|..|..+++.|...++|.+. .+.
T Consensus 325 ~~mv~e~~~~v~~~gl~a~s~lt~en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka 404 (728)
T KOG2284|consen 325 SVMVKEFEEYVKKKGLEAVSRLTGENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKA 404 (728)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccch
Confidence 999999999999999998876433 679999999999999999999999999999999999999999754 367
Q ss_pred hhHHHHHHHHHHhcCCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhhh
Q 003835 450 AELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGS 529 (792)
Q Consensus 450 ~e~Laky~D~~Lr~~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG~ 529 (792)
+|.||+|||.+||++.|++++.++|..|+..+.+||||.|||+|.+||.++||+||+.+.|.|.|+|..||.|||+.||.
T Consensus 405 ~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacgy 484 (728)
T KOG2284|consen 405 SERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGY 484 (728)
T ss_pred HHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhHHhhHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCc
Q 003835 530 QFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSG 609 (792)
Q Consensus 530 ~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~~~~~LP~~l~~~~~~F~~fY~~k~~g 609 (792)
+||+++. +.|+++|.+++++|.+.+.+ +.||.+|+..++.||.||..+|+|
T Consensus 485 efts~~~--~td~~~s~~lnn~f~~~i~n---------------------------f~~pq~l~~~iq~fe~fyt~~~~g 535 (728)
T KOG2284|consen 485 EFTSSWP--LTDPQLSTNLNNQFAQDIAN---------------------------FHLPQILQPVIQEFEKFYTGKHNG 535 (728)
T ss_pred eecccCC--CCChhhccccchhHHHHHHh---------------------------ccchHHHHHHHHHHHHHhccccCC
Confidence 9999999 99999999999999875442 679999999999999999999999
Q ss_pred eeEEeecCcceEEEEEEecCCeeEEEEeecc------------ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCC
Q 003835 610 RRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ------------LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 610 RkL~W~~~Lg~~~i~~~f~~~~~el~vs~~Q------------lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
|||+|.|.|++++|+.+|-++.|.-.|.+|| +++.||.+.||+++++|.+++.+|. .+++|+-..
T Consensus 536 rkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~til--dv~~~~~d~- 612 (728)
T KOG2284|consen 536 RKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCDD- 612 (728)
T ss_pred ceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHH--hceeecccc-
Confidence 9999999999999999999999999999999 8999999999999999999999998 788887644
Q ss_pred CCCCCCCCeEEEccCCCCCceeEEeccccc-ccchhhhhhhhHHHHhhhhhhhhHHHHHhhhcccccChHHHHHHHHHhc
Q 003835 678 GRDVEDDDSFVFNEGFTAPLYRIKVNAIQM-KETVEENTSTTERVFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL 756 (792)
Q Consensus 678 ~~~i~~~d~f~~N~~Ft~~~~riki~~i~~-ket~~e~~~t~e~v~~dR~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~l 756 (792)
.++..+..|++|.+|++++.|.||...++ |.+++|.+.+...|.+||++..+||||||||+||.+.|+-|++||+.|.
T Consensus 613 -~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt 691 (728)
T KOG2284|consen 613 -QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQT 691 (728)
T ss_pred -cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhh
Confidence 47778889999999999999999976544 5677888999999999999999999999999999999999999999999
Q ss_pred --CCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 757 --KFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 757 --rF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
||.|++++|||+||.||||.||+|.+.+ +.|.|+|
T Consensus 692 ~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 692 KGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred cccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 7999999999999999999999997766 7899998
No 5
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=1e-95 Score=861.50 Aligned_cols=566 Identities=42% Similarity=0.708 Sum_probs=516.1
Q ss_pred HHHHHHHHHHHHhcCCCCccHHHHHHHHHhhhccCchhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHH
Q 003835 108 WAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSLVERCWQDL 187 (792)
Q Consensus 108 W~~L~~AI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~L~~~~~~W~~~ 187 (792)
|..|++||+.|+.+.....+|+++|++||++|..++|++||+++++.+..|+..++..+....+ ..+|..+..+|.+|
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~--~~~l~~~~~~w~~~ 78 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSD--EDLLEEYVQEWEKY 78 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTT--CHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcCh--hHHHHHHHHHHHHH
Confidence 9999999999999899999999999999999999999999999999999999998888776533 58999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhhhcCCCcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhcCCcCChHHHHHHHHHHH
Q 003835 188 CDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERLGEAVDRTLLNHLLKMFT 267 (792)
Q Consensus 188 ~~~l~~i~~iF~YLDR~Yv~~~~~~~sI~dlgL~lFr~~v~~~~~l~~~l~~~iL~lI~~eR~g~~id~~llk~~i~ml~ 267 (792)
+.++.+|+++|+||||+|+.++ +|++.|+. ++.++++.+++.+|.++|.|+.+|+.+++.+++|+.
T Consensus 79 ~~~~~~i~~if~yLdr~yv~~~------------~f~~~v~~--~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~ 144 (588)
T PF00888_consen 79 KKAIKYISDIFSYLDRNYVKRN------------LFREQVFK--PLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFV 144 (588)
T ss_dssp HHHHHHHHHHTHHHHHTSTTTT------------HHHHHTTT--SHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHhhhhhh------------hHHHHHHH--HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence 9999999999999999999885 99999987 599999999999999999999999999999999999
Q ss_pred hhh---ccHHhhHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHHHHHHHHHH
Q 003835 268 ALG---IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLLYLDVSTRKPLIATAERQLLERHI 344 (792)
Q Consensus 268 ~L~---vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~eYL~~ve~~l~eE~~R~~~yL~~sT~~~L~~~l~~~LI~~~~ 344 (792)
+|| +|.+.||++||++|.+||+.++ +++.++.+||.+|+.++.+|.+||..||+++|..++.++++++||..|.
T Consensus 145 ~l~~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~ 221 (588)
T PF00888_consen 145 ELGSLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHL 221 (588)
T ss_dssp HTTHTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGH
T ss_pred ccchHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHH
Confidence 775 8999999999999999999999 6777999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHHHhhccc-cchHHHHHHHHHHHHHhhcccccCc---hhhHHHHHHHHHHHHHHHHHH
Q 003835 345 SAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMDE---EKDKDMVSSLLEFKASLDTIW 420 (792)
Q Consensus 345 ~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~-~~l~~l~~~~~~yI~~~G~~iv~~~---~~~~~~V~~Ll~l~~~~~~ii 420 (792)
+.| .+|+..|+++++.++|++||+|++++ ++++.++..|++||.+.|..++.+. ..++.||+.|++++++++.++
T Consensus 222 ~~l-~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~ 300 (588)
T PF00888_consen 222 DEL-SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEKSSDPKEFIEDLLELYDKYEKLI 300 (588)
T ss_dssp HHH-HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCCGGGCHHHHHHHHHHHHHHHHHH
T ss_pred HHH-HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhcccccchHHHHHHHHHHHHHHHHHH
Confidence 987 88999999999999999999999998 9999999999999999999998753 567899999999999999999
Q ss_pred HHhcCCChhhhHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHH
Q 003835 421 EQSFSKNEAFCNTIKDAFEYLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKD 500 (792)
Q Consensus 421 ~~~F~~~~~f~~~l~~af~~~iN~~~~~~~e~Laky~D~~Lr~~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~ 500 (792)
.+||++++.|..++++||+.|+|....+++|+||+|||.+||++.++.++++++..++.++.||+|+++||+|+.+|+++
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 99999999999999999999999996689999999999999999888889999999999999999999999999999999
Q ss_pred HHHHhcCCCCCChHHHHHHHHHHHHhhhhhHHHHHHHHHHhHHhhHHHHHHHHHHhhhccCCCC--CcceEEEEeecCCC
Q 003835 501 LAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPS--GIEMSVHVLTTGYW 578 (792)
Q Consensus 501 LakRLL~~~s~s~d~E~~mi~kLk~ecG~~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~~~~--~~~f~v~VLt~~~W 578 (792)
||+|||.+++.+.|.|+.||.+||.+||.+||+||++||+|++.|++++++|++.... .+... +++|+|.|||+|+|
T Consensus 381 L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~-~~~~~~~~~~~~~~vls~~~W 459 (588)
T PF00888_consen 381 LAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQ-NNIQLIPPFDFNVKVLSKGYW 459 (588)
T ss_dssp HHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TT-SS--CCEEEEEEEETTTS
T ss_pred HHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhh-ccccccCCCceEEEEecCCCC
Confidence 9999999999999999999999999999999999999999999999999999998665 22222 79999999999999
Q ss_pred CCCCCCC-ccCChHHHHHHHHHHHHHHhcCCceeEEeecCcceEEEEEEecCCeeEEEEeecc------------ccHHH
Q 003835 579 PTYPPMD-VRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ------------LSFQD 645 (792)
Q Consensus 579 P~~~~~~-~~LP~~l~~~~~~F~~fY~~k~~gRkL~W~~~Lg~~~i~~~f~~~~~el~vs~~Q------------lt~~e 645 (792)
|.++..+ +.||++|+.+++.|++||..+|+||+|+|.|+||+|+|+++|++++|+|.||++| +|++|
T Consensus 460 p~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~e 539 (588)
T PF00888_consen 460 PKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEE 539 (588)
T ss_dssp -S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHH
T ss_pred CCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHH
Confidence 9999877 9999999999999999999999999999999999999999999999999999999 89999
Q ss_pred HHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 003835 646 IKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 694 (792)
Q Consensus 646 I~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft 694 (792)
|++.|||++++|+++|.+|...+..++.+.|++++++++|.|+||.+||
T Consensus 540 i~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 540 ISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999999966655555889999999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-91 Score=737.99 Aligned_cols=687 Identities=27% Similarity=0.453 Sum_probs=615.1
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCCC-CccHHHHHHHHHhhhccC--chhHHHHHHHHHHHHHHHHHHHhhhcCCCcHHHH
Q 003835 100 PTNFEEDTWAKLKLAIKAIFLKQPT-SCDLEKLYQAVNDLCLHK--MGGNLYQRIEKECEEHISAAIRSLVGQSPDLVVF 176 (792)
Q Consensus 100 ~~~~~e~~W~~L~~AI~~I~~~~~~-~~s~e~LY~~Vy~lC~~k--~~e~LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~ 176 (792)
+.+-+|+.|...++.+-+++..... ..-|+.||.+||.+|.+. ....+|+.|+..+.+++.+.........+| ..+
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d-~aL 87 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSLQTD-GAL 87 (777)
T ss_pred chhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhhccc-cHH
Confidence 3455689999999999988876554 568999999999999986 567899999999999999877777665555 689
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCC-------CcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHh
Q 003835 177 LSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTP-------NVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERER 249 (792)
Q Consensus 177 L~~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~~~~-------~~~sI~dlgL~lFr~~v~~~~~l~~~l~~~iL~lI~~eR 249 (792)
|..|..+|.+|..+..++.--|.-||.+-....+ .-.+|..+-|.-|.+++|. .+++++....+.+++.||
T Consensus 88 L~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~--nIk~rLq~sAmklVhaER 165 (777)
T KOG2285|consen 88 LIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFM--NIKERLQVSAMKLVHAER 165 (777)
T ss_pred HHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999998654432 2357999999999999997 799999999999999999
Q ss_pred cCCcCChHHHHHHHHHHHhhh--------ccHHhhHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHHHHHhcc
Q 003835 250 LGEAVDRTLLNHLLKMFTALG--------IYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEEHERCLL 321 (792)
Q Consensus 250 ~g~~id~~llk~~i~ml~~L~--------vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~eYL~~ve~~l~eE~~R~~~ 321 (792)
+|+.+|.+++-++-..++.|. +|.+.||..||++|.+||+..+..++++.++-+|+++|...++||+.|..+
T Consensus 166 ~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkR 245 (777)
T KOG2285|consen 166 DGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKR 245 (777)
T ss_pred ccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHH
Confidence 999999999999999999885 999999999999999999999999999999999999999999999999999
Q ss_pred ccCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc-cchHHHHHHHHHHHHHhhcccccC
Q 003835 322 YLDV--STRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV-NALESLRQALAMYIRRTGHGIVMD 398 (792)
Q Consensus 322 yL~~--sT~~~L~~~l~~~LI~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~-~~l~~l~~~~~~yI~~~G~~iv~~ 398 (792)
||.. .|..+++..+.+.||..|.+.|+. .+..||...+++-|.+||+|+.|+ .|++++...+..||.+.|.+-+..
T Consensus 246 YLE~~~~s~~~lme~~VnaLv~sf~~tIlA-EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~ 324 (777)
T KOG2285|consen 246 YLEMNSPSSGKLMEKAVNALVESFEDTILA-ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRN 324 (777)
T ss_pred hhccCCCcHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHh
Confidence 9864 889999999999999999999996 489999999999999999999999 999999999999999999764422
Q ss_pred -----chhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHhcC--------------------CCCchhHH
Q 003835 399 -----EEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLR--------------------QNRPAELI 453 (792)
Q Consensus 399 -----~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~--------------------~~~~~e~L 453 (792)
.++...||+.||.++++|..++.++|..|+.|..+-+.||..++|.. .+++||+|
T Consensus 325 aaE~ittDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELL 404 (777)
T KOG2285|consen 325 AAENITTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELL 404 (777)
T ss_pred hhhhccCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHH
Confidence 12345899999999999999999999999999999999999999973 15789999
Q ss_pred HHHHHHHHhcCC--CCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhh--h
Q 003835 454 AKFLDEKLRAGN--KGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECG--S 529 (792)
Q Consensus 454 aky~D~~Lr~~~--k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG--~ 529 (792)
|.|||.+||+.. |..+.+|+|..|.+++-+++|+++||||..|.+-||+|||+.+.|+..+.|..|+..|+ ||| .
T Consensus 405 ANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPa 483 (777)
T KOG2285|consen 405 ANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPA 483 (777)
T ss_pred HHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcH
Confidence 999999999864 67889999999999999999999999999999999999999999999999999999999 788 6
Q ss_pred hHHHHHHHHHHhHHhhHHHHHHHHHHhhhccCCCCCcceEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHhcCC
Q 003835 530 QFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYS 608 (792)
Q Consensus 530 ~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~-~~~~LP~~l~~~~~~F~~fY~~k~~ 608 (792)
.|.+||-.||+||++|+|++.+|+......+.....-..++.||..|+|-.... ..+.||.+|+..+-.-++||.++|+
T Consensus 484 DyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hs 563 (777)
T KOG2285|consen 484 DYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHS 563 (777)
T ss_pred HHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccC
Confidence 799999999999999999999999976652222223458999999999998754 5699999999999999999999999
Q ss_pred ceeEEeecCcceEEEEEEecCCeeEEEEeecc--------------ccHHHHHHHhCCCHHHHHHHHHHhhc-CC--cee
Q 003835 609 GRRLMWQNSLGHCVLKAEFPKGKKELAVSLFQ--------------LSFQDIKDATGIEDKELRRTLQSLAC-GK--VRV 671 (792)
Q Consensus 609 gRkL~W~~~Lg~~~i~~~f~~~~~el~vs~~Q--------------lt~~eI~~~T~i~~~eL~r~L~sL~~-~k--~ki 671 (792)
||+|.|.|+++.++|++.-+-|.|+|.|++|| +|++.+.-+|.+|+.||+|+|.||+. || ..|
T Consensus 564 grkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~Qi 643 (777)
T KOG2285|consen 564 GRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQI 643 (777)
T ss_pred ccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhhe
Confidence 99999999999999988766699999999999 99999999999999999999999988 76 678
Q ss_pred eecCCCC----CCCCCCCeEEEccCCCC-----CceeEEeccc---ccccchhhhhhhhHHHHhhhhhhhhHHHHHhhhc
Q 003835 672 LQKLPKG----RDVEDDDSFVFNEGFTA-----PLYRIKVNAI---QMKETVEENTSTTERVFQDRQYQVDAAIVRIMKT 739 (792)
Q Consensus 672 L~k~p~~----~~i~~~d~f~~N~~Ft~-----~~~riki~~i---~~ket~~e~~~t~e~v~~dR~~~i~AaIVRIMK~ 739 (792)
|..+|+. +++.++..|.+|..|.- ...|-|||-| |+. +....++.++.|.+-|-..+|-|||+|||.
T Consensus 644 LL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLs-tEr~~eeenesIVqLRiLRtQEaIikImK~ 722 (777)
T KOG2285|consen 644 LLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLS-TERNAEEENESIVQLRILRTQEAIIKIMKT 722 (777)
T ss_pred eeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeeh-hhhhhhhhcchhHHHHHHHHHHHHHHHHHH
Confidence 8888853 67888999999999952 2356777765 222 222234456778999999999999999999
Q ss_pred ccccChHHHHHHHHHhcC--CCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 740 RKVLSHTLLITELFQQLK--FPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 740 rK~l~h~~Li~ev~~~lr--F~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
||+++..+|..|+++.|+ |-|...+||..||.|||.-|++||++|-++|+|+|
T Consensus 723 RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 723 RKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999999994 99999999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=3.3e-37 Score=297.56 Aligned_cols=141 Identities=55% Similarity=0.904 Sum_probs=133.6
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhhhhHHHHHHHHHHhHHhhHHHHHHHHHHhhhccCCCCC
Q 003835 486 FIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSG 565 (792)
Q Consensus 486 ~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG~~fT~kLe~MfkDi~~S~~l~~~f~~~~~~~~~~~~~ 565 (792)
||++||+|+.+|+++||+|||.+++++.|.|+.||++||.+||.+||+|||+||+||+.|++++++|++.... .....+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~-~~~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLEN-NSNKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999987665 223356
Q ss_pred cceEEEEeecCCCCCCCC-CCccCChHHHHHHHHHHHHHHhcCCceeEEeecCcceEEEEEEe
Q 003835 566 IEMSVHVLTTGYWPTYPP-MDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEF 627 (792)
Q Consensus 566 ~~f~v~VLt~~~WP~~~~-~~~~LP~~l~~~~~~F~~fY~~k~~gRkL~W~~~Lg~~~i~~~f 627 (792)
++|+|.|||.|+||.++. .++.||++|+.+++.|++||..+|+||+|+|.|+||+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999988 88999999999999999999999999999999999999999986
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=5e-19 Score=198.75 Aligned_cols=209 Identities=26% Similarity=0.367 Sum_probs=187.8
Q ss_pred eeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhhhhHHHHHHHHHHhHHhhHHHHHHHHHHhh-hc-
Q 003835 482 VLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQ-AR- 559 (792)
Q Consensus 482 ~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~ecG~~fT~kLe~MfkDi~~S~~l~~~f~~~~~-~~- 559 (792)
.|...+.+|+.|.+-|+..||-|||.....+.|-|..-+.-||-.+|..--+.+|+|++|+.-|+++++++++... .+
T Consensus 444 mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~ 523 (765)
T KOG2165|consen 444 MLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRG 523 (765)
T ss_pred HHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhcc
Confidence 4556778999999999999999999999999999999999999999999999999999999999999999987421 10
Q ss_pred cCCCCCcceEEEEeecCCCCCCCCCCccCChHHHHHHHHHHHHHHhcCCceeEEeecCcceEEEEEEecCCeeEEEEeec
Q 003835 560 TKLPSGIEMSVHVLTTGYWPTYPPMDVRLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKAEFPKGKKELAVSLF 639 (792)
Q Consensus 560 ~~~~~~~~f~v~VLt~~~WP~~~~~~~~LP~~l~~~~~~F~~fY~~k~~gRkL~W~~~Lg~~~i~~~f~~~~~el~vs~~ 639 (792)
....+.+.+.+.||++-+||......+.||..++..++.|.+-|..-..+|+|.|.+++|.++|..+|.+.+-+++||.-
T Consensus 524 ~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~ 603 (765)
T KOG2165|consen 524 AEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPE 603 (765)
T ss_pred cccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHH
Confidence 11223578899999999999998889999999999999999999999999999999999999999999999999999987
Q ss_pred c------------ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCCC
Q 003835 640 Q------------LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTA 695 (792)
Q Consensus 640 Q------------lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft~ 695 (792)
| +|++|+++.+|||..-|+|.|.=+. +.++|..+|.. +++.+|+++++=.+
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~~---s~tgt~T~iEse~d 666 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPII---SDTGTLTVIESEMD 666 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCCC---CCCceeeecccccc
Confidence 6 9999999999999999999999998 88999988753 77789999995443
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.83 E-value=3.4e-21 Score=161.52 Aligned_cols=66 Identities=59% Similarity=0.959 Sum_probs=60.7
Q ss_pred HHhhhhhhhhHHHHHhhhcccccChHHHHHHHHHhc--CCCCChHHHHHHHHHhhhhcccccCCCCCC
Q 003835 721 VFQDRQYQVDAAIVRIMKTRKVLSHTLLITELFQQL--KFPIKPADLKKRIESLIDREYLERDKNNPQ 786 (792)
Q Consensus 721 v~~dR~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~l--rF~~~~~~iKk~IE~LIereYl~Rd~~d~~ 786 (792)
|++||.+.|+||||||||++|+|+|++|+.+|++++ +|+|+..+||++||+||+||||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 578999999999999999999999999999999999 699999999999999999999999999875
No 10
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.95 E-value=8.9e-05 Score=83.95 Aligned_cols=321 Identities=11% Similarity=0.038 Sum_probs=206.7
Q ss_pred chHHHHHHHHHHHHHHHHhcCCC----CccHHHHHHHHHhhhccCc--hhHHHHHHHHHHHHHHHHHHHhhh---cCC--
Q 003835 102 NFEEDTWAKLKLAIKAIFLKQPT----SCDLEKLYQAVNDLCLHKM--GGNLYQRIEKECEEHISAAIRSLV---GQS-- 170 (792)
Q Consensus 102 ~~~e~~W~~L~~AI~~I~~~~~~----~~s~e~LY~~Vy~lC~~k~--~e~LY~~l~~~~~~~l~~~~~~l~---~~~-- 170 (792)
.++...|..|++++..|...... ...|-.+++.+|+-|..+. ..++.+-++..+..+..+...-+. ..+
T Consensus 108 sgeAvdrslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k 187 (661)
T KOG2167|consen 108 SGEAVDRSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKK 187 (661)
T ss_pred hcchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhccccccc
Confidence 34466788999999888765433 3456678999999998873 445666666666666665322222 111
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCcccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHhc
Q 003835 171 PDLVVFLSLVERCWQDLCDQMLMIRGIALYLDRTYVKQTPNVRSLWDMGLQLFRKYLSSYSEVEHKTVTGLLRMIERERL 250 (792)
Q Consensus 171 ~d~~~~L~~~~~~W~~~~~~l~~i~~iF~YLDR~Yv~~~~~~~sI~dlgL~lFr~~v~~~~~l~~~l~~~iL~lI~~eR~ 250 (792)
.....+.+.+...|-+....... +.-+|-+ +.++...+|+++-..+....-.-+...+-+.+....+|..++.
T Consensus 188 ~l~atV~~~LL~~hL~~IL~kgl----~~lvDm~---q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~k 260 (661)
T KOG2167|consen 188 PLIATVERCLLSRHLDLILTKGL----DSLVDMR---QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEK 260 (661)
T ss_pred chHHHHHHHHHHHHHHHHHhcch----HHhhhhh---hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchh
Confidence 23467888888888877555444 4444443 2234677888888887444333346778888888888888888
Q ss_pred CCcCCh--HHHHHHHHHHHhhhccHHhhHHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHHH--HHHhcc-----
Q 003835 251 GEAVDR--TLLNHLLKMFTALGIYSESFEKPFLECTSEFYAAEGMKYMQQSDVPDYLKHVEIRLHEE--HERCLL----- 321 (792)
Q Consensus 251 g~~id~--~llk~~i~ml~~L~vY~~~FE~~fL~~T~~yY~~es~~~l~~~s~~eYL~~ve~~l~eE--~~R~~~----- 321 (792)
++.... -..|+.++|......++..- .+|+..++++|..+++. +...+.+|+++....+-.+ .+-|..
T Consensus 261 Dk~mVqELL~FK~k~Dii~~~sF~~~v~-e~f~~~~~~afe~fink--~~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~ 337 (661)
T KOG2167|consen 261 DKDMVQELLDFKKKVDIIVDESFLKYVA-EKFLNSMSKAFETFINK--RRNRPAELIAKYVDTKLRAGNKETSDEELEFV 337 (661)
T ss_pred hHHHHHHHHHHHHHhhHHHHHHHHHhhH-HHHHHHHHHHHHHHHhc--ccCCHHHHHHHHHHHHHHhccccccchhHHHH
Confidence 776333 45688899988887766555 89999999999999994 6667899999887766555 111111
Q ss_pred ---------ccCcC--cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccccchHHHHHHHHHHHHH
Q 003835 322 ---------YLDVS--TRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRVNALESLRQALAMYIRR 390 (792)
Q Consensus 322 ---------yL~~s--T~~~L~~~l~~~LI~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~~~l~~l~~~~~~yI~~ 390 (792)
|++.. ...-....+.+.|+..|... ++.|+.-|.+-....+.+.+|+|.+..+..+...+..+.|+..
T Consensus 338 ~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs-vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~ 416 (661)
T KOG2167|consen 338 LDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS-VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQS 416 (661)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh-hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 11100 01112233444444444432 3566655666677889999999999887777777777777666
Q ss_pred hhcccccCchhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHH
Q 003835 391 TGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYL 441 (792)
Q Consensus 391 ~G~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~ 441 (792)
.|..--. ...|+.++--.+.+|-.||..+..+-..+++.|+-|
T Consensus 417 ~~~~~~~--------~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F 459 (661)
T KOG2167|consen 417 KGANNRL--------EGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIF 459 (661)
T ss_pred HHhhccC--------cCCceEEEeecccccCCCCchhccCCHHHHHHHHHH
Confidence 5433111 112233334456788888888877777777666655
No 11
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.62 E-value=0.0011 Score=65.03 Aligned_cols=130 Identities=13% Similarity=0.131 Sum_probs=93.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhhccCchh----HHHHHHHHHHHHHHHHHHHhhhcCCCcHHHHHHH
Q 003835 104 EEDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLCLHKMGG----NLYQRIEKECEEHISAAIRSLVGQSPDLVVFLSL 179 (792)
Q Consensus 104 ~e~~W~~L~~AI~~I~~~~~~~~s~e~LY~~Vy~lC~~k~~e----~LY~~l~~~~~~~l~~~~~~l~~~~~d~~~~L~~ 179 (792)
.++.|..+..++-.+|+++....+.|+|-+.|.-.+....+. .+-+.+++.+..-+......+... ++..+|..
T Consensus 5 ~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~--~~~~~l~r 82 (158)
T PF08539_consen 5 SDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEV--PDNRLLKR 82 (158)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhc--chhHHHHH
Confidence 478999999999999999999899999998887654443332 344455555555444444444332 23689999
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHhhhhhhhcC----------------CCcccHHHHHHHHHHHHhccccchHHHH
Q 003835 180 VERCWQDLC-DQMLMIRGIALYLDRTYVKQT----------------PNVRSLWDMGLQLFRKYLSSYSEVEHKT 237 (792)
Q Consensus 180 ~~~~W~~~~-~~l~~i~~iF~YLDR~Yv~~~----------------~~~~sI~dlgL~lFr~~v~~~~~l~~~l 237 (792)
+...|.-+. .-+-++..||+.|++.+-... ....+|..++|..||++|+. +..+++
T Consensus 83 L~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvL--P~y~~l 155 (158)
T PF08539_consen 83 LVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVL--PYYQRL 155 (158)
T ss_pred HHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhh--cchHhh
Confidence 999999954 556689999999996543221 23589999999999999986 444444
No 12
>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=86.24 E-value=0.89 Score=38.09 Aligned_cols=46 Identities=26% Similarity=0.418 Sum_probs=37.6
Q ss_pred HHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 732 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 732 aIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
.|-.+|+.++.++..+|-.+ |..+++.+...+|.||.++||++.+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~------~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELARE------FGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHH------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 35678999999999988775 99999999999999999999999643
No 13
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=81.72 E-value=1.6 Score=34.38 Aligned_cols=34 Identities=26% Similarity=0.484 Sum_probs=29.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+|+.||++.+|+|...+.|.|.+|. ..+.+.++|
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~dp 52 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTLV--EEGYVERDP 52 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEECS
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecCc
Confidence 7899999999999999999999998 666776654
No 14
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=75.96 E-value=6.3 Score=32.76 Aligned_cols=58 Identities=17% Similarity=0.329 Sum_probs=42.3
Q ss_pred hhhhhhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCC
Q 003835 724 DRQYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNP 785 (792)
Q Consensus 724 dR~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~ 785 (792)
+|+..|=.+|...++...--- =+.|+.+.+.+. ++..+...++.|.+++||+|+++-+
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~P---t~rEIa~~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPP---TVREIAEALGLK-STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS------HHHHHHHHTSS-SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred HHHHHHHHHHHHHHHHcCCCC---CHHHHHHHhCCC-ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 466667777777777655443 255666666666 7888999999999999999998643
No 15
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=75.88 E-value=6.1 Score=37.54 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=43.8
Q ss_pred hHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 730 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 730 ~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
+..|.+++-....++-.+++..+-+ +..+....|...|..|.+||||+|..+.+ .|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~--~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAE--KKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhh--ccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEe
Confidence 4567777766777776665544322 35678889999999999999999986554 577754
No 16
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=74.24 E-value=7.7 Score=31.74 Aligned_cols=54 Identities=13% Similarity=0.276 Sum_probs=36.6
Q ss_pred hHHHHHhhh-cccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhccccc--CCCCCCcee
Q 003835 730 DAAIVRIMK-TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER--DKNNPQIYN 789 (792)
Q Consensus 730 ~AaIVRIMK-~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~R--d~~d~~~Y~ 789 (792)
|..|.+.+. ....++-.+|... +..+.+.+-+.|..|++++||+| |+.|...+.
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~ 61 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER------LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKR 61 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH------TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEE
T ss_pred HHHHHHHHHccCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeE
Confidence 566777777 7777777665554 66777888899999999999977 555555433
No 17
>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=73.30 E-value=70 Score=35.41 Aligned_cols=161 Identities=14% Similarity=0.220 Sum_probs=96.9
Q ss_pred HHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc----cchHHHHHHHHHHHHHhhcccccCc-------hhhHHHHHHHH
Q 003835 342 RHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLL 410 (792)
Q Consensus 342 ~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~----~~l~~l~~~~~~yI~~~G~~iv~~~-------~~~~~~V~~Ll 410 (792)
+++..++.+.|..-...++.+.+.|.+.||-.+ .|++....-+...|.......+... ..+.-|+..|.
T Consensus 6 ~~L~~~f~~~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~~~~~~~~~~~lt 85 (331)
T PF08318_consen 6 ESLCEIFLKKFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSDSRSPVFYADALT 85 (331)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccHHHHHH
Confidence 344556667799999999999999999999887 4666666666666655555444322 22335667777
Q ss_pred HHHHHHHHH-------HHHhcCCChh------hhHHHHH----HHHHHHhcCC-CCchhHHHHHHHHHHhc---------
Q 003835 411 EFKASLDTI-------WEQSFSKNEA------FCNTIKD----AFEYLINLRQ-NRPAELIAKFLDEKLRA--------- 463 (792)
Q Consensus 411 ~l~~~~~~i-------i~~~F~~~~~------f~~~l~~----af~~~iN~~~-~~~~e~Laky~D~~Lr~--------- 463 (792)
.|++.+-.+ |..+|+..-. ++...+. -+..|...+. .+...-+..|-...+.+
T Consensus 86 ~LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 165 (331)
T PF08318_consen 86 KLFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSS 165 (331)
T ss_pred HHHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhccccccccccc
Confidence 777666554 5667764331 1111121 2333444332 11223344554444433
Q ss_pred ---------CCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCC
Q 003835 464 ---------GNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGK 509 (792)
Q Consensus 464 ---------~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~ 509 (792)
+....+--+++..|+++..+...- ..|.+++++|.....
T Consensus 166 ~~~~~~~~~~~~~~d~reld~lL~Eis~i~~~w-------~lY~rFi~~k~~~~~ 213 (331)
T PF08318_consen 166 SRAASSSQSEDEGIDPRELDALLNEISLILQRW-------SLYCRFISRKWNEFS 213 (331)
T ss_pred cccccccccccCCCCHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhccc
Confidence 011234477888888888777654 489999999988743
No 18
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=71.64 E-value=3.2 Score=38.43 Aligned_cols=61 Identities=15% Similarity=0.249 Sum_probs=44.0
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
.+..|.+|+=....++-.+++..+-+. ..+....|+.-+..|.+|+||+|...++ .|.|-|
T Consensus 4 ~E~~IM~~lW~~~~~t~~eI~~~l~~~--~~~~~sTv~t~L~rL~~Kg~l~~~~~gr-~~~Y~p 64 (115)
T PF03965_consen 4 LELEIMEILWESGEATVREIHEALPEE--RSWAYSTVQTLLNRLVEKGFLTREKIGR-AYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHCTT--SS--HHHHHHHHHHHHHTTSEEEEEETT-CEEEEE
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhc--cccchhHHHHHHHHHHhCCceeEeecCC-ceEEEe
Confidence 356677777777777776655554333 6778999999999999999999986543 677753
No 19
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=69.38 E-value=8 Score=33.51 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=34.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 692 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~ 692 (792)
+|.+||++.+++|...+.+.|+.|. +..++...+ .++.-|.++.+
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~ 70 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARP 70 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCC
Confidence 7899999999999999999999999 777776543 23456777664
No 20
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=68.14 E-value=11 Score=35.52 Aligned_cols=61 Identities=18% Similarity=0.275 Sum_probs=52.1
Q ss_pred hhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeec
Q 003835 728 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 791 (792)
Q Consensus 728 ~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~Yl 791 (792)
..++.|.+||=.++..+-.|++.++-+. +.+....||--|..|..||.|.|..+++ .|.|=
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~--~ews~sTV~TLl~RL~KKg~l~~~kdgr-~~~y~ 66 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD--REWSYSTVKTLLNRLVKKGLLTRKKDGR-AFRYS 66 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc--ccccHHHHHHHHHHHHhccchhhhhcCC-eeeee
Confidence 3578899999999999999988887666 8889999999999999999999987654 46663
No 21
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=65.88 E-value=8.1 Score=38.35 Aligned_cols=52 Identities=19% Similarity=0.367 Sum_probs=42.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCCCCceeEE
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFTAPLYRIK 701 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft~~~~rik 701 (792)
.|..+|++.+|++...+.|++..|. +.+||.+... ..|.+|++|--+-.+.+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~~-------G~Y~iNP~~~~kG~~~~ 127 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIRN-------GAYMINPNFFFKGDRDK 127 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEccC-------CeEEECcHHheeCcHHH
Confidence 5789999999999999999999998 7888887532 37999999865544444
No 22
>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=63.21 E-value=8.8 Score=31.74 Aligned_cols=57 Identities=18% Similarity=0.335 Sum_probs=43.0
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeec
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYL 791 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~Yl 791 (792)
.++.|-+.+-.+..++-.+|..++ ..+...+-+.++.|.++|+++|.++++..|..+
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~l------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEEL------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHHH------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 455555555577778877766553 567788999999999999999998877666654
No 23
>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=59.80 E-value=10 Score=30.20 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=36.0
Q ss_pred hHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhccccc--CCCCC
Q 003835 730 DAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER--DKNNP 785 (792)
Q Consensus 730 ~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~R--d~~d~ 785 (792)
|..|..+.-....++..+|-.. +..+.+.+-+.|..|.++|||+| +++|+
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~------~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEK------LGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHHHHHHcCCCCHHHHHHH------HCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 4455566666666777665543 56788999999999999999999 45554
No 24
>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=58.05 E-value=18 Score=32.31 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=37.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 694 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft 694 (792)
+|-.||++.+|++..-+.|.|..|. +-+++.+.. ....|.+|.+.+
T Consensus 48 is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~~ 93 (95)
T TIGR01610 48 VTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPLS 93 (95)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCcc
Confidence 7889999999999999999999998 777776532 135799998764
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=56.70 E-value=30 Score=28.81 Aligned_cols=54 Identities=9% Similarity=0.246 Sum_probs=41.8
Q ss_pred hhHHHHHhhhcccc--cChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCce
Q 003835 729 VDAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 788 (792)
Q Consensus 729 i~AaIVRIMK~rK~--l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y 788 (792)
++..|...||.+.. ++-.+|-.+ .-.+...+.+.+..|.+++|++++++.+..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKN------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 45678889999877 886665554 3556668999999999999999988765554
No 26
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=56.13 E-value=22 Score=27.87 Aligned_cols=49 Identities=12% Similarity=0.310 Sum_probs=34.6
Q ss_pred HHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCce
Q 003835 733 IVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIY 788 (792)
Q Consensus 733 IVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y 788 (792)
|++.+. +..++-.++..+ +..+.+.+.+.|+.|.+++++.+..+.+..|
T Consensus 2 il~~l~-~~~~~~~~i~~~------l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~ 50 (66)
T smart00418 2 ILKLLA-EGELCVCELAEI------LGLSQSTVSHHLKKLREAGLVESRREGKRVY 50 (66)
T ss_pred HHHHhh-cCCccHHHHHHH------HCCCHHHHHHHHHHHHHCCCeeeeecCCEEE
Confidence 445555 666676664443 3467788999999999999999876544433
No 27
>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=55.35 E-value=9.5 Score=30.90 Aligned_cols=34 Identities=12% Similarity=0.326 Sum_probs=28.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+|+.||++.+|++...+.++|..|. +..++....
T Consensus 25 ~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~~ 58 (61)
T PF12840_consen 25 MTVSELAEELGISQSTVSYHLKKLE--EAGLIEVER 58 (61)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 7899999999999999999999998 667766543
No 28
>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=55.16 E-value=19 Score=28.89 Aligned_cols=47 Identities=17% Similarity=0.368 Sum_probs=41.7
Q ss_pred HHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 731 AAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 731 AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
..|+..++.+..++-.+|..+ |.+++..|.+-+..|-+.+.|.|--+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~------~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE------FGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 468889999999999988875 89999999999999999999999643
No 29
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=54.69 E-value=27 Score=26.10 Aligned_cols=32 Identities=28% Similarity=0.496 Sum_probs=28.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
+|..||++.+|++...+.+.|..|. +.+++.+
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 6889999999999999999999998 7777765
No 30
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=53.46 E-value=5.1e+02 Score=31.80 Aligned_cols=66 Identities=14% Similarity=0.331 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhc--cc-cchHHHHHHHHHHHHHhhcccccCch-hh---HHHHHHHHHHHHHHHHHHHHhcCC
Q 003835 361 TEDLQRMYSLFS--RV-NALESLRQALAMYIRRTGHGIVMDEE-KD---KDMVSSLLEFKASLDTIWEQSFSK 426 (792)
Q Consensus 361 ~~~L~~ly~L~~--~~-~~l~~l~~~~~~yI~~~G~~iv~~~~-~~---~~~V~~Ll~l~~~~~~ii~~~F~~ 426 (792)
...|+.+-.-+. .+ .+++.|.+.+.+|+...+..-..+.. -+ ..+-...++.|.++..|+..|+.|
T Consensus 629 k~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 629 KQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVVWSAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 455555555532 23 67777777777777332211000000 01 256777999999999999999864
No 31
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=52.26 E-value=25 Score=31.86 Aligned_cols=44 Identities=18% Similarity=0.328 Sum_probs=36.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGFT 694 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~Ft 694 (792)
+|..+|++.||++.+.+.+.|..|. +-+||... |-.+-+|.+.+
T Consensus 55 Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 55 ISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred eeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 7889999999999999999999999 88898653 45666666543
No 32
>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=48.09 E-value=20 Score=27.47 Aligned_cols=30 Identities=13% Similarity=0.419 Sum_probs=25.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceee
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVL 672 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL 672 (792)
+++.||++.+|++...+.++|..|. +.+++
T Consensus 16 ~~~~el~~~l~~s~~~vs~hL~~L~--~~glV 45 (47)
T PF01022_consen 16 LTVSELAEELGLSQSTVSHHLKKLR--EAGLV 45 (47)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred CchhhHHHhccccchHHHHHHHHHH--HCcCe
Confidence 6889999999999999999999997 44444
No 33
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=47.85 E-value=25 Score=30.45 Aligned_cols=34 Identities=15% Similarity=0.358 Sum_probs=30.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+|..||++.+|++...+.|.|..|. ..+++.+.+
T Consensus 21 ~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~ 54 (91)
T smart00346 21 LTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDG 54 (91)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 7899999999999999999999998 677777654
No 34
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=46.26 E-value=15 Score=25.35 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=9.0
Q ss_pred ccChhHHHHHHHHH
Q 003835 487 IQGKDVFEAFYKKD 500 (792)
Q Consensus 487 i~~KD~Fe~~Yk~~ 500 (792)
|++.|.|++||++.
T Consensus 3 is~~d~f~eFY~rl 16 (28)
T PF12108_consen 3 ISGGDPFSEFYERL 16 (28)
T ss_dssp --S--HHHHHHHHH
T ss_pred CCCCChHHHHHHHH
Confidence 56889999999875
No 35
>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=45.04 E-value=2.8e+02 Score=33.62 Aligned_cols=88 Identities=19% Similarity=0.234 Sum_probs=44.8
Q ss_pred CchhHHHHHHHHHHhcCC---CCCCHH----HHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHH
Q 003835 448 RPAELIAKFLDEKLRAGN---KGTSEE----ELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMI 520 (792)
Q Consensus 448 ~~~e~Laky~D~~Lr~~~---k~~~~~----e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi 520 (792)
+.|.+|.-+++.+.-... |-.+-+ +-...|.+++.++-.|.+.|.|...=-++ ++|.+.+.=..-+
T Consensus 531 RlA~MLn~~L~~L~Gpk~~~LkVk~~~~y~F~P~~ll~~i~~iy~~l~~~~~F~~ava~D-------~Rsy~~~lf~~a~ 603 (629)
T PF10408_consen 531 RLAAMLNYNLDQLVGPKCSELKVKNPEKYGFDPKELLSQIVDIYLNLSDSDKFVQAVAND-------GRSYSPELFEKAV 603 (629)
T ss_dssp HHHHHHHHHHHHHHSHHHHT---SSGGGGT--HHHHHHHHHHHHHHCTT-HHHHHHHHH--------TTT--HHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCchhcccCCChhhcCCcHHHHHHHHHHHHhhcCCchHHHHHHHhC-------CCCCCHHHHHHHH
Confidence 456666667766653211 111111 23467888889999998888776543332 5666665544445
Q ss_pred HHHHHhh--hhhHHHHHHHHHHhH
Q 003835 521 SKLKTEC--GSQFTNKLEGMFKDI 542 (792)
Q Consensus 521 ~kLk~ec--G~~fT~kLe~MfkDi 542 (792)
..|+..- +.....+++.+.+.+
T Consensus 604 ~~l~~~~l~~~~~i~~f~~l~~~v 627 (629)
T PF10408_consen 604 RILRRIGLKSEDEIEKFEELAKKV 627 (629)
T ss_dssp HHHTTSTSSTHHHHHHHHHHCCHH
T ss_pred HHHHHhCCCCHHHHHHHHHHHHHH
Confidence 5554432 344444554444433
No 36
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.94 E-value=35 Score=30.74 Aligned_cols=47 Identities=15% Similarity=0.333 Sum_probs=41.1
Q ss_pred hhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhccccc
Q 003835 728 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 780 (792)
Q Consensus 728 ~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~R 780 (792)
.+|-.|++.+.....++..+|-.+ +-.+++.+.++|..|.++++|+|
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~------l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKK------VGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHH------HCcCHHHHHHHHHHHHHCCCeec
Confidence 367789999999999998887765 47889999999999999999996
No 37
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=43.39 E-value=51 Score=30.06 Aligned_cols=51 Identities=16% Similarity=0.129 Sum_probs=41.0
Q ss_pred HHHHhhhc-ccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 732 AIVRIMKT-RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 732 aIVRIMK~-rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
+|..+|.. .+-++..+|..++.++. ..++.+.|=+.++.|.+.+.|.|-..
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 46666665 56799999988886653 46899999999999999999999543
No 38
>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=42.94 E-value=29 Score=27.70 Aligned_cols=48 Identities=13% Similarity=0.286 Sum_probs=33.2
Q ss_pred hHHHHHhhhcccc--cChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 730 DAAIVRIMKTRKV--LSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 730 ~AaIVRIMK~rK~--l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
+..|..+...+.. ++-.+|... +-.+++.+-+.|..|++++||+|..+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAER------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4455555555555 666555544 46677889999999999999999643
No 39
>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=41.62 E-value=29 Score=27.80 Aligned_cols=33 Identities=21% Similarity=0.521 Sum_probs=28.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 675 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~ 675 (792)
+|++||++.+|++...++|-|..|. +..++.+.
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~ 47 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRT 47 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 7899999999999999999999998 55555553
No 40
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=41.42 E-value=35 Score=28.39 Aligned_cols=56 Identities=25% Similarity=0.348 Sum_probs=34.9
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
.=|.||..||+| .|---+.|+.+.+.+.++. +.++.|-+.+=|+-|+++ +.|.|.+
T Consensus 6 ql~~~VeymK~r---~~Plt~~eI~d~l~~d~~~----~~~~~Lk~npKI~~d~~~-~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKR---DHPLTLEEILDYLSLDIGK----KLKQWLKNNPKIEYDPDG-NTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH----S-B-HHHHHHHHTSSS-H----HHHHHHHH-TTEEEE-TT--CEEE--
T ss_pred HHHHHHHHHHhc---CCCcCHHHHHHHHcCCCCH----HHHHHHHcCCCEEEecCC-CEEEecc
Confidence 347899999998 6666777777777765553 355777788888888743 6788864
No 41
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.12 E-value=48 Score=27.37 Aligned_cols=46 Identities=26% Similarity=0.341 Sum_probs=32.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEc
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFN 690 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N 690 (792)
++..||++++||+.-..++.|..|. +.+.+.+.|.++... ..+.+|
T Consensus 16 ~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~~--~~W~l~ 61 (62)
T PF04703_consen 16 LKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGKS--TYWRLN 61 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSSS---EEEES
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCcc--eeeeec
Confidence 6789999999999999999999999 555556655543332 245555
No 42
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=40.15 E-value=28 Score=28.57 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=24.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceee
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVL 672 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL 672 (792)
+|+.+|.+.|++|.+.++..|..|. +.+++
T Consensus 28 ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v 57 (62)
T PF08221_consen 28 LTLREIVRRTGLSPKQVKKALVVLI--QHNLV 57 (62)
T ss_dssp EEHHHHHHHHT--HHHHHHHHHHHH--HTTSE
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHH--HcCCe
Confidence 7899999999999999999999998 55554
No 43
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=39.59 E-value=31 Score=35.03 Aligned_cols=58 Identities=21% Similarity=0.323 Sum_probs=42.7
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceeecC
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNYLA 792 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~YlA 792 (792)
+=...|-..|.+|.+...+|-.+ |...++++-.+|..|...|=|.=--+|+.-|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~------f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAE------FGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHH------H-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHH------cCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 55677889999999999888775 89999999999999999999998778889999984
No 44
>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=39.58 E-value=38 Score=28.81 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=27.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
.|++||.+.||++..+|...|.-|+ +-.|+.+
T Consensus 19 ~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 19 CTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 7999999999999999999999998 6555543
No 45
>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=39.44 E-value=52 Score=24.97 Aligned_cols=45 Identities=13% Similarity=0.313 Sum_probs=36.1
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccc
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 779 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~ 779 (792)
.+-.|+..+.....++..+|-..+ -.+.+.+.+.|..|.++|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHHHHHCcCcC
Confidence 456788888889999988877653 578889999999999999985
No 46
>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=37.81 E-value=37 Score=25.84 Aligned_cols=25 Identities=20% Similarity=0.458 Sum_probs=22.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhh
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLA 665 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~ 665 (792)
+|..||++.+|++...+.+.|..|.
T Consensus 18 ~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 18 ITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 7899999999999999999999997
No 47
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=37.53 E-value=44 Score=27.86 Aligned_cols=33 Identities=27% Similarity=0.295 Sum_probs=28.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 675 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~ 675 (792)
+|..||++.+|++...+.|+|..|. +...+.+.
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~ 55 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQ 55 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 6889999999999999999999998 55555543
No 48
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.25 E-value=47 Score=25.89 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=29.5
Q ss_pred c-cHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 L-SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 l-t~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+ |..||++..|++...+.+.|..|. +.+++...+
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 5 899999999999999999999998 666776544
No 49
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=37.24 E-value=44 Score=26.93 Aligned_cols=34 Identities=26% Similarity=0.424 Sum_probs=30.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+|..||++.+|++...+.+.|..|. +.+++.+.+
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~~ 59 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELE--EEGLISRRG 59 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 7999999999999999999999998 667776644
No 50
>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=36.58 E-value=42 Score=28.00 Aligned_cols=34 Identities=35% Similarity=0.466 Sum_probs=29.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhc-CCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLAC-GKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~-~k~kiL~k 674 (792)
+|+.||+..||+++.++-..|-=|+. +|+.+-.+
T Consensus 23 ~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~ 57 (65)
T PF10771_consen 23 WSVSELKKATGLSDKEVYLAIGWLARENKIEFEEK 57 (65)
T ss_dssp EEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEE
T ss_pred cCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEee
Confidence 79999999999999999999999997 66766654
No 51
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=36.55 E-value=1.4e+02 Score=34.62 Aligned_cols=148 Identities=19% Similarity=0.197 Sum_probs=87.9
Q ss_pred hccccchHHHHHHHHHHHHHhhcccccCchhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHH-HHhcCC--C
Q 003835 371 FSRVNALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEY-LINLRQ--N 447 (792)
Q Consensus 371 ~~~~~~l~~l~~~~~~yI~~~G~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~-~iN~~~--~ 447 (792)
..|++..+...+..+.+|+..+..+-.=....-+.+.+|++.++|...|-... |+-.-.- .+.... -
T Consensus 340 ~~R~K~Q~q~~~~~r~ri~~i~e~v~eLqk~~ad~~~KI~~~k~r~~~Ls~Ri----------LRv~ikqeilr~~G~~L 409 (508)
T KOG3091|consen 340 RQRLKVQDQEVKQHRIRINAIGERVTELQKHHADAVAKIEEAKNRHVELSHRI----------LRVMIKQEILRKRGYAL 409 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHhccCCcC
Confidence 34445555666777778877776654333344578888999888876653321 1111111 112111 1
Q ss_pred Cch-hHHHHHHHHHHhcCCCCCCHHHHHhhhhchheeeecccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHh
Q 003835 448 RPA-ELIAKFLDEKLRAGNKGTSEEELEGTLDKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTE 526 (792)
Q Consensus 448 ~~~-e~Laky~D~~Lr~~~k~~~~~e~e~~ld~i~~lF~~i~~KD~Fe~~Yk~~LakRLL~~~s~s~d~E~~mi~kLk~e 526 (792)
.+. |-|..=+|.+++.-+.. .|+...|+.++.+.|-.. -+.++...--...|.+..|.+.|+.+
T Consensus 410 ~~~EE~Lr~Kldtll~~ln~P---nq~k~Rl~~L~e~~r~q~------------~~~~~~~~~~iD~~~~~e~~e~lt~~ 474 (508)
T KOG3091|consen 410 TPDEEELRAKLDTLLAQLNAP---NQLKARLDELYEILRMQN------------SQLKLQESYWIDFDKLIEMKEHLTQE 474 (508)
T ss_pred CccHHHHHHHHHHHHHHhcCh---HHHHHHHHHHHHHHHhhc------------chhccccceeechhhhHHHHHHHHHH
Confidence 122 56888889998864333 788888887777776665 23344433344567777888888876
Q ss_pred h--hhhHHHHHHHHHHhHH
Q 003835 527 C--GSQFTNKLEGMFKDIE 543 (792)
Q Consensus 527 c--G~~fT~kLe~MfkDi~ 543 (792)
- =.-+.+=|.+|.+||+
T Consensus 475 ~e~l~~Lv~Ilk~d~edi~ 493 (508)
T KOG3091|consen 475 QEALTKLVNILKGDQEDIK 493 (508)
T ss_pred HHHHHHHHHHHHhHHHHHH
Confidence 3 2234555667777774
No 52
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=35.64 E-value=66 Score=24.23 Aligned_cols=46 Identities=13% Similarity=0.254 Sum_probs=34.8
Q ss_pred HHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 732 AIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 732 aIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
.|.+.+..+..++-.+|... |..++..+.+.|..|.++++|.+..+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQGKVSVEELAEL------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 35566666666666665554 57789999999999999999998653
No 53
>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=34.75 E-value=32 Score=28.37 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=27.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
.|..||++.+|++...+.+.|..|. +-.+..+
T Consensus 23 ~t~~eIa~~l~i~~~~v~~~L~~L~--~~GlV~~ 54 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYRALKSLE--EKGLVER 54 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHHHHHHHH--HTTSEEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEE
Confidence 7899999999999999999999998 4444444
No 54
>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=34.45 E-value=34 Score=29.25 Aligned_cols=31 Identities=19% Similarity=0.269 Sum_probs=25.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeee
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQ 673 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~ 673 (792)
+|+.||++.+|++...++..+..+. +..+|.
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 8999999999999999999888765 444443
No 55
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=32.63 E-value=37 Score=29.35 Aligned_cols=25 Identities=28% Similarity=0.630 Sum_probs=22.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhh
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLA 665 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~ 665 (792)
++|.+|++.+|+++..|-++|..|.
T Consensus 15 ~~f~~L~~~l~lt~g~Ls~hL~~Le 39 (80)
T PF13601_consen 15 ATFSELKEELGLTDGNLSKHLKKLE 39 (80)
T ss_dssp EEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 7899999999999999999999998
No 56
>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=32.30 E-value=62 Score=30.75 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=29.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
+|.+||++.+++|...|.+.|+.|. +..++..
T Consensus 26 ~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 26 VTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 7899999999999999999999998 7777754
No 57
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=32.24 E-value=69 Score=31.75 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=29.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
+|.++|++.+|+|...|.+.|+.|. +.+++..
T Consensus 26 vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 26 VPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 7999999999999999999999999 7888764
No 58
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=31.85 E-value=49 Score=30.89 Aligned_cols=46 Identities=20% Similarity=0.245 Sum_probs=37.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEG 692 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~ 692 (792)
.++.||++.+|++...+-++|.-|. ..+++.....|+.+ .|++|.+
T Consensus 31 ~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr~~----~Y~l~~~ 76 (117)
T PRK10141 31 LCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGKWV----HYRLSPH 76 (117)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcCEE----EEEECch
Confidence 6889999999999999999999998 78888877665433 5777653
No 59
>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=29.20 E-value=2.7e+02 Score=30.74 Aligned_cols=79 Identities=14% Similarity=0.270 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHhhccCCHHHHHHHHHhhcccc----chHHHHHHHHHHHHHhhcccccCc-------hhhHHHHHHHH
Q 003835 342 RHISAILDKGFTMLMDGHRTEDLQRMYSLFSRVN----ALESLRQALAMYIRRTGHGIVMDE-------EKDKDMVSSLL 410 (792)
Q Consensus 342 ~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~~----~l~~l~~~~~~yI~~~G~~iv~~~-------~~~~~~V~~Ll 410 (792)
+.+..++.+.|..-+++++.+.+.+.+.||-.+| |++....-+.+.|......+.... ...-.|+..|.
T Consensus 6 ~~L~~~~~~~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~~~~~~~~~a~~lt 85 (324)
T smart00762 6 ETLTELFKERFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASDDTRAAVFYADTLT 85 (324)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccccccccchHHHHHH
Confidence 3445566677999999999999999999998873 565555555555544433333211 11224666565
Q ss_pred HHHHHHHHHH
Q 003835 411 EFKASLDTIW 420 (792)
Q Consensus 411 ~l~~~~~~ii 420 (792)
.+++.+-.+|
T Consensus 86 ~Lfe~ia~ii 95 (324)
T smart00762 86 HLFENVATII 95 (324)
T ss_pred HHHHHHHHHH
Confidence 6655554443
No 60
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=28.94 E-value=66 Score=26.71 Aligned_cols=35 Identities=20% Similarity=0.460 Sum_probs=28.0
Q ss_pred ccHHHHHHHhCCC-HHHHHHHHHHhhcCCceeeecCCC
Q 003835 641 LSFQDIKDATGIE-DKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 641 lt~~eI~~~T~i~-~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
-|+.||++.+|+. ..-+.++|..|. +-..|.+.|.
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~~ 61 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDPG 61 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGCC
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCCC
Confidence 5899999999996 999999999998 6666666553
No 61
>PHA00738 putative HTH transcription regulator
Probab=28.43 E-value=71 Score=29.38 Aligned_cols=47 Identities=19% Similarity=0.154 Sum_probs=39.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCCCeEEEccCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDDDSFVFNEGF 693 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~d~f~~N~~F 693 (792)
+++.||++.++|+..-+-++|.-|- ..+++.....|+.+ .|++|.+-
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~v----yY~Ln~~~ 73 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRTL----YAKIRENS 73 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCEE----EEEECCCc
Confidence 6788999999999999999999997 78888877766544 57777764
No 62
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=28.23 E-value=1.4e+02 Score=27.83 Aligned_cols=40 Identities=18% Similarity=0.375 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHhcCCcCChH-HHHHHHHHHHhhh--ccH
Q 003835 234 EHKTVTGLLRMIERERLGEAVDRT-LLNHLLKMFTALG--IYS 273 (792)
Q Consensus 234 ~~~l~~~iL~lI~~eR~g~~id~~-llk~~i~ml~~L~--vY~ 273 (792)
.+++.+.|-++++..|...+-+.+ -+.++..||.+|| ||+
T Consensus 2 s~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGLRVYe 44 (118)
T PRK13713 2 SNEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYE 44 (118)
T ss_pred chHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhHHHHH
Confidence 356677788888888876553332 3678999999998 554
No 63
>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=28.10 E-value=53 Score=26.10 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=28.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
+|..||++.++++..-+.+.+..|. +-.++.+.+
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 6899999999999999999999998 666666544
No 64
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=28.10 E-value=1.1e+02 Score=29.07 Aligned_cols=41 Identities=15% Similarity=0.295 Sum_probs=30.1
Q ss_pred ccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccC--CCCCC
Q 003835 740 RKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD--KNNPQ 786 (792)
Q Consensus 740 rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd--~~d~~ 786 (792)
...++-.+|-.. +-.+++.+=+.|+.|.++|||+|. ++|+.
T Consensus 52 ~~~~t~~eLa~~------l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 52 AACITPVELKKV------LSVDLGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred cCCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 445555554443 577888899999999999999994 45554
No 65
>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=27.73 E-value=63 Score=25.11 Aligned_cols=22 Identities=27% Similarity=0.679 Sum_probs=17.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHH
Q 003835 641 LSFQDIKDATGIEDKELRRTLQ 662 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~ 662 (792)
+|++||++.+|++...++..|.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 8999999999999999887764
No 66
>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=27.20 E-value=2.4e+02 Score=24.74 Aligned_cols=56 Identities=9% Similarity=0.179 Sum_probs=39.8
Q ss_pred HHHHHH-HHHHHHHHHHhc-CCCCccHHHHHHHHHhhhccCchhHHHHHHHHHHHHHH
Q 003835 104 EEDTWA-KLKLAIKAIFLK-QPTSCDLEKLYQAVNDLCLHKMGGNLYQRIEKECEEHI 159 (792)
Q Consensus 104 ~e~~W~-~L~~AI~~I~~~-~~~~~s~e~LY~~Vy~lC~~k~~e~LY~~l~~~~~~~l 159 (792)
.+.+|. .++..+..+... ....++|++|+..|.-.++..-.+.+...+...+..++
T Consensus 28 ~e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 28 IECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HHTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HHCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 366884 777777777765 45678999999999999988777766666665555544
No 67
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=26.95 E-value=1.3e+02 Score=27.58 Aligned_cols=62 Identities=21% Similarity=0.201 Sum_probs=44.3
Q ss_pred hhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCCCCCceee
Q 003835 728 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKNNPQIYNY 790 (792)
Q Consensus 728 ~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~d~~~Y~Y 790 (792)
.+|+.|++-- ...=..-..+|.+|+.+....+...-+--||+.||+.|-|+=..+-..+.+|
T Consensus 48 ~yD~~Il~~~-~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQA-PDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhcC-CccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 4677777721 1222334578899999986568888999999999999999987655554444
No 68
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=26.93 E-value=1.4e+02 Score=25.69 Aligned_cols=48 Identities=17% Similarity=0.299 Sum_probs=36.9
Q ss_pred hhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCC
Q 003835 729 VDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 782 (792)
Q Consensus 729 i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~ 782 (792)
.+..|..++.....++-.+|..+ +.++.+.|-+.|..|.+++||++..
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKR------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 45667777777777777766544 4567788999999999999998753
No 69
>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=26.88 E-value=74 Score=28.53 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=23.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhc
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLAC 666 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~ 666 (792)
+++++|++.+++++.+++..|.-|+.
T Consensus 66 v~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 66 VHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp EEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 68999999999999999999999984
No 70
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.63 E-value=1.3e+02 Score=28.55 Aligned_cols=29 Identities=14% Similarity=0.386 Sum_probs=23.4
Q ss_pred CCCChHHHHHHHHHhhhhcccccC--CCCCC
Q 003835 758 FPIKPADLKKRIESLIDREYLERD--KNNPQ 786 (792)
Q Consensus 758 F~~~~~~iKk~IE~LIereYl~Rd--~~d~~ 786 (792)
+-.+++.+-+.|+.|.++|||+|. ++|+.
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR 86 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQTCASDRR 86 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeecCCCCcC
Confidence 566677888999999999999995 44554
No 71
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=26.45 E-value=56 Score=33.13 Aligned_cols=25 Identities=40% Similarity=0.640 Sum_probs=22.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhh
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLA 665 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~ 665 (792)
+|+++|++.|||..+++..+|+.|-
T Consensus 151 isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 151 ISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred EEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 7999999999999999999999986
No 72
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=26.11 E-value=88 Score=24.30 Aligned_cols=33 Identities=12% Similarity=0.329 Sum_probs=28.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 675 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~ 675 (792)
.|+.+|++.+|++...+.+.|..|. +.+++...
T Consensus 11 ~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~~ 43 (66)
T smart00418 11 LCVCELAEILGLSQSTVSHHLKKLR--EAGLVESR 43 (66)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 6889999999999999999999998 55666543
No 73
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=26.02 E-value=72 Score=33.70 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=31.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
+++.||++.+|+|...+.|.|.+|. ..+.+.+.+.
T Consensus 20 l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~~ 54 (246)
T COG1414 20 LSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDPE 54 (246)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcCC
Confidence 5799999999999999999999999 8888888664
No 74
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=25.95 E-value=1e+02 Score=30.07 Aligned_cols=33 Identities=21% Similarity=0.337 Sum_probs=29.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 675 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~ 675 (792)
+|..+|++..|+|..-|.+.|+.|. +..++...
T Consensus 25 ~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~ 57 (153)
T PRK11920 25 SRIPEIARAYGVSELFLFKILQPLV--EAGLVETV 57 (153)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEee
Confidence 5889999999999999999999998 88877654
No 75
>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=25.73 E-value=79 Score=28.34 Aligned_cols=52 Identities=13% Similarity=0.241 Sum_probs=34.3
Q ss_pred hhhhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccc
Q 003835 726 QYQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLE 779 (792)
Q Consensus 726 ~~~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~ 779 (792)
...++..|..++|......+--=+.++.++| -.+..+|+++|+.|++.++|=
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEe
Confidence 3456677788888844444433456666776 557889999999999999773
No 76
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.43 E-value=1e+02 Score=24.48 Aligned_cols=33 Identities=18% Similarity=0.437 Sum_probs=28.1
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCC
Q 003835 642 SFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLP 676 (792)
Q Consensus 642 t~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p 676 (792)
|..+|++.+|++...+.+.|..|. +.+++...+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~~ 59 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE--AEGLVERRP 59 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 589999999999999999999998 666666543
No 77
>PF14164 YqzH: YqzH-like protein
Probab=25.17 E-value=64 Score=26.78 Aligned_cols=35 Identities=20% Similarity=0.236 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhhh
Q 003835 105 EDTWAKLKLAIKAIFLKQPTSCDLEKLYQAVNDLC 139 (792)
Q Consensus 105 e~~W~~L~~AI~~I~~~~~~~~s~e~LY~~Vy~lC 139 (792)
+..|+.|..+|......++..-=||-.+..||..+
T Consensus 28 ~~E~~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~yi 62 (64)
T PF14164_consen 28 DEEWEELCKHIQERKNEEPDEDLHEIVEDVVYDYI 62 (64)
T ss_pred HHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHh
Confidence 57899999999999888765434444444444443
No 78
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=25.14 E-value=82 Score=29.51 Aligned_cols=33 Identities=18% Similarity=0.352 Sum_probs=29.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKL 675 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~ 675 (792)
+|..||++.+|+|...+.+.|..|. +.+++...
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~ 58 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSK 58 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEec
Confidence 7999999999999999999999998 77787653
No 79
>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=25.00 E-value=91 Score=25.02 Aligned_cols=32 Identities=16% Similarity=0.454 Sum_probs=27.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
++..||++.+|++...+.+.|..|. ...++..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~ 52 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLE--EAGLVES 52 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEE
Confidence 6889999999999999999999997 4455544
No 80
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.86 E-value=81 Score=24.58 Aligned_cols=24 Identities=17% Similarity=0.444 Sum_probs=22.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhh
Q 003835 642 SFQDIKDATGIEDKELRRTLQSLA 665 (792)
Q Consensus 642 t~~eI~~~T~i~~~eL~r~L~sL~ 665 (792)
|.+.|++.+|+....+.+.|..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 789999999999999999999997
No 81
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=24.54 E-value=75 Score=34.01 Aligned_cols=35 Identities=17% Similarity=0.080 Sum_probs=30.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
+|+.||++.+|||...+.|.|.+|. ..+.|.+.+.
T Consensus 41 ~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~~ 75 (271)
T PRK10163 41 SSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDSQ 75 (271)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC
Confidence 6889999999999999999999999 7778877543
No 82
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.31 E-value=1.2e+02 Score=28.94 Aligned_cols=49 Identities=18% Similarity=0.366 Sum_probs=42.6
Q ss_pred hhhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccC
Q 003835 727 YQVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERD 781 (792)
Q Consensus 727 ~~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd 781 (792)
-.+|..|++++...-+++..+|-.++ -.+++.+.+||+.|.++|.|+|-
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l------glS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV------GLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH------CCCHHHHHHHHHHHHHCCceeeE
Confidence 35888999999999999998877665 37888999999999999999984
No 83
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=24.21 E-value=94 Score=29.02 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=28.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
+|.++|++.+|+|...+.+.|..|. +.+++..
T Consensus 26 ~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 26 VSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 7899999999999999999999998 6777754
No 84
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.88 E-value=81 Score=33.37 Aligned_cols=35 Identities=9% Similarity=0.217 Sum_probs=31.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
+|+.||++.+|||...+.|.|.+|. ..+.|.+.+.
T Consensus 29 l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~~ 63 (257)
T PRK15090 29 IGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEGE 63 (257)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC
Confidence 7899999999999999999999999 7778877553
No 85
>PF03037 KMP11: Kinetoplastid membrane protein 11; InterPro: IPR004132 Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. It stimulates T-cell proliferation and may play a role in the immunlogy of the dieases Leishmaniasis.; GO: 0006952 defense response, 0008284 positive regulation of cell proliferation
Probab=23.59 E-value=3.2e+02 Score=23.10 Aligned_cols=64 Identities=9% Similarity=0.244 Sum_probs=47.3
Q ss_pred chHHHHHHHHHHHHHhhcccccCchhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHH
Q 003835 376 ALESLRQALAMYIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLI 442 (792)
Q Consensus 376 ~l~~l~~~~~~yI~~~G~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~i 442 (792)
.++.|-..|..-+..+......|..++.+.-..+-+-|+++..+|++- .+.|.+.+++--+.|-
T Consensus 11 kldrld~ef~kkm~eqn~kffadkpdestlspemkehyekfe~miqeh---tdkfnkkm~ehsehfk 74 (90)
T PF03037_consen 11 KLDRLDAEFNKKMQEQNKKFFADKPDESTLSPEMKEHYEKFERMIQEH---TDKFNKKMHEHSEHFK 74 (90)
T ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCcccccCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 456667777777777777777776666778888888999999999874 5567777777666663
No 86
>PRK11569 transcriptional repressor IclR; Provisional
Probab=23.49 E-value=84 Score=33.64 Aligned_cols=35 Identities=9% Similarity=0.368 Sum_probs=31.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPK 677 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~ 677 (792)
+|+.||++.+|+|...+.|.|.+|. ..+.|.+.+.
T Consensus 44 ~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~~ 78 (274)
T PRK11569 44 VALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVGE 78 (274)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcCC
Confidence 6899999999999999999999999 7788877543
No 87
>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=23.44 E-value=1.1e+02 Score=23.11 Aligned_cols=24 Identities=21% Similarity=0.595 Sum_probs=19.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHh
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSL 664 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL 664 (792)
.|+.+|++.+|++...+.+-+.-|
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHh
Confidence 799999999999999998877654
No 88
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=23.16 E-value=1.4e+02 Score=28.48 Aligned_cols=52 Identities=23% Similarity=0.364 Sum_probs=41.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeecCCCCCCCCCC---CeEEEccCCC
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQKLPKGRDVEDD---DSFVFNEGFT 694 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k~p~~~~i~~~---d~f~~N~~Ft 694 (792)
.|+.|+++.+|=+.+.+.|+|..|+ .+.|+..+.+|+...|. |.|.+|-.|.
T Consensus 79 ~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 79 ASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred ccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 7899999999999999999999999 88888776666655443 4556666664
No 89
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=23.16 E-value=1.1e+02 Score=23.00 Aligned_cols=32 Identities=22% Similarity=0.526 Sum_probs=27.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhcCCceeeec
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLACGKVRVLQK 674 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~~k~kiL~k 674 (792)
+|..+|++.+|++...+.+.|..|. +.+++.+
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~L~--~~g~i~~ 46 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNKLE--EQGLLTR 46 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 6889999999999999999999997 4455544
No 90
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=22.72 E-value=71 Score=36.01 Aligned_cols=26 Identities=38% Similarity=0.580 Sum_probs=24.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhhc
Q 003835 641 LSFQDIKDATGIEDKELRRTLQSLAC 666 (792)
Q Consensus 641 lt~~eI~~~T~i~~~eL~r~L~sL~~ 666 (792)
+|+++|++.|||..+|+.-+|++|-.
T Consensus 330 isI~~iS~~Tgi~~~DIisTL~~L~m 355 (396)
T KOG2747|consen 330 ISIKEISKETGIRPDDIISTLQSLNM 355 (396)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHhhCC
Confidence 89999999999999999999999964
No 91
>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=22.54 E-value=2e+02 Score=27.15 Aligned_cols=42 Identities=21% Similarity=0.436 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHHHHHHhcCCcCCh-HHHHHHHHHHHhhh--ccHH
Q 003835 233 VEHKTVTGLLRMIERERLGEAVDR-TLLNHLLKMFTALG--IYSE 274 (792)
Q Consensus 233 l~~~l~~~iL~lI~~eR~g~~id~-~llk~~i~ml~~L~--vY~~ 274 (792)
+++++.+.|-++++..|...+-+. --+.++..||.+|| ||+-
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~ 52 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEA 52 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHH
Confidence 567788888899999998655433 34789999999998 5653
No 92
>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=22.09 E-value=4.8e+02 Score=28.51 Aligned_cols=140 Identities=19% Similarity=0.317 Sum_probs=87.1
Q ss_pred HHhccc-cCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc---------cchHHHHHHHHH
Q 003835 317 ERCLLY-LDVSTRKPLIATAERQLLERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV---------NALESLRQALAM 386 (792)
Q Consensus 317 ~R~~~y-L~~sT~~~L~~~l~~~LI~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~---------~~l~~l~~~~~~ 386 (792)
.||-.- ...-+...+..++.+++=.+.+. ++.++-.-+.+.-.-+|++--=++..+ ++.....--|.-
T Consensus 176 SRCl~iRvpaps~eeI~~vl~~v~~kE~l~--lp~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~ 253 (351)
T KOG2035|consen 176 SRCLFIRVPAPSDEEITSVLSKVLKKEGLQ--LPKELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEI 253 (351)
T ss_pred hheeEEeCCCCCHHHHHHHHHHHHHHhccc--CcHHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHH
Confidence 455432 34556777888887777666543 234444434333333555533333211 233445567999
Q ss_pred HHHHhhcccccCchhhHHHHHHHHHHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHhcCCCCc----hhHHHHHHHHHHh
Q 003835 387 YIRRTGHGIVMDEEKDKDMVSSLLEFKASLDTIWEQSFSKNEAFCNTIKDAFEYLINLRQNRP----AELIAKFLDEKLR 462 (792)
Q Consensus 387 yI~~~G~~iv~~~~~~~~~V~~Ll~l~~~~~~ii~~~F~~~~~f~~~l~~af~~~iN~~~~~~----~e~Laky~D~~Lr 462 (792)
||.+.+..|+++.. ...|++++.++-.++..|-.-+. .+++-.+.++++.+... .++ |.|.+.-++
T Consensus 254 ~i~e~a~~i~~eQs-----~~~L~~vR~~LYeLL~~CIPP~~----Ilk~Ll~~Ll~~~d~~~k~~~~~~-Aa~yEhRl~ 323 (351)
T KOG2035|consen 254 YIQEIARVILKEQS-----PAKLLEVRGRLYELLSHCIPPNT----ILKELLEELLLKCDTQLKLEVIQH-AAKYEHRLR 323 (351)
T ss_pred HHHHHHHHHHhccC-----HHHHHHHHHHHHHHHhccCChHH----HHHHHHHHHHhcCCchhHHHHHHH-HHHHHHHHh
Confidence 99999999886543 57899999999999998865433 45666777888655322 333 444588899
Q ss_pred cCCCCC
Q 003835 463 AGNKGT 468 (792)
Q Consensus 463 ~~~k~~ 468 (792)
-|+|..
T Consensus 324 lG~KaI 329 (351)
T KOG2035|consen 324 LGQKAI 329 (351)
T ss_pred hcchhh
Confidence 888763
No 93
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.91 E-value=1.8e+02 Score=24.87 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=34.6
Q ss_pred HHHhhhcc-cccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCCC
Q 003835 733 IVRIMKTR-KVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDKN 783 (792)
Q Consensus 733 IVRIMK~r-K~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~~ 783 (792)
|...+..+ ..++-.+|..++ ..+.+.+-+.+..|.+.+||+|+++
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 44555544 578877776664 5678889999999999999999864
No 94
>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=20.66 E-value=2.2e+02 Score=25.60 Aligned_cols=39 Identities=23% Similarity=0.361 Sum_probs=27.8
Q ss_pred CChhhhHHHHHHHHHHHhcC------CCCchhHHHHHHHHHHhcC
Q 003835 426 KNEAFCNTIKDAFEYLINLR------QNRPAELIAKFLDEKLRAG 464 (792)
Q Consensus 426 ~~~~f~~~l~~af~~~iN~~------~~~~~e~Laky~D~~Lr~~ 464 (792)
.+......+..||+.+++.- ..+..+++|+++..++..|
T Consensus 66 ~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~ 110 (113)
T PF02847_consen 66 RKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADG 110 (113)
T ss_dssp TTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred cCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcC
Confidence 44555667777888888752 2357899999999998764
No 95
>KOG0412 consensus Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.52 E-value=5.5e+02 Score=31.29 Aligned_cols=81 Identities=14% Similarity=0.268 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHHhhccCCHHHHHHHHHhhccc----cchHHHHHHHHHHHHHhhcccccC--------chhhHHHHHH
Q 003835 341 ERHISAILDKGFTMLMDGHRTEDLQRMYSLFSRV----NALESLRQALAMYIRRTGHGIVMD--------EEKDKDMVSS 408 (792)
Q Consensus 341 ~~~~~~ll~~g~~~ll~~~~~~~L~~ly~L~~~~----~~l~~l~~~~~~yI~~~G~~iv~~--------~~~~~~~V~~ 408 (792)
.+.+..|+.+-|..-.++++..++.|+|.+|..+ .|++....-+.+-|...+.....+ .....-|.+.
T Consensus 189 ~e~L~~l~~~~f~eA~r~~D~~ei~RffKmFPliG~~~eGL~~ys~ylc~iIA~kar~~l~n~~~~~~~~~r~qv~fad~ 268 (773)
T KOG0412|consen 189 KERLSKLFKERFTEAVRKQDLKEITRFFKMFPLIGEEDEGLQLYSVYLCQIIASKARKNLANVKAGMEDDNRRQVFFADT 268 (773)
T ss_pred HHHHHHHHHHHHHHHHhcccHHHHHHHHHHccccCCchhhHHHHHHHHHHHHHHHHHHHHHHHHhccccCchhHhHHHHH
Confidence 3445667777788889999999999999999877 588877777777777777665532 1223478888
Q ss_pred HHHHHHHHHHHHH
Q 003835 409 LLEFKASLDTIWE 421 (792)
Q Consensus 409 Ll~l~~~~~~ii~ 421 (792)
|..|++-+-.||+
T Consensus 269 Lt~lfe~va~IIe 281 (773)
T KOG0412|consen 269 LTMLFEGVARIIE 281 (773)
T ss_pred HHHHHHHHHHHHH
Confidence 8888877766653
No 96
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=20.34 E-value=1.7e+02 Score=28.31 Aligned_cols=47 Identities=13% Similarity=0.268 Sum_probs=41.5
Q ss_pred hhhHHHHHhhhcccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhccccc
Q 003835 728 QVDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLER 780 (792)
Q Consensus 728 ~i~AaIVRIMK~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~R 780 (792)
.+|-.|.+.+...-++++.+|-.++ -.+++.+.+||+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeee
Confidence 4788899999999999999877765 6788999999999999999985
No 97
>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=20.30 E-value=1.9e+02 Score=25.69 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=30.6
Q ss_pred cccccChHHHHHHHHHhcCCCCChHHHHHHHHHhhhhcccccCC
Q 003835 739 TRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLERDK 782 (792)
Q Consensus 739 ~rK~l~h~~Li~ev~~~lrF~~~~~~iKk~IE~LIereYl~Rd~ 782 (792)
....++|++|... .-.+.+.+-+.|..|.+++||+|..
T Consensus 44 ~~~~is~~eLa~~------~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAEL------TGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHH------HCcCHHHHHHHHHHHHHCCCeeeec
Confidence 5677888776654 3557778999999999999999876
No 98
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=20.12 E-value=1.2e+02 Score=22.89 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=23.2
Q ss_pred hhHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 003835 430 FCNTIKDAFEYLINLRQNRPAELIAKFLDE 459 (792)
Q Consensus 430 f~~~l~~af~~~iN~~~~~~~e~Laky~D~ 459 (792)
+...+-+|.......++..|.++||.|+-.
T Consensus 10 v~p~L~~gL~~l~~~rP~DPi~~La~~Ll~ 39 (42)
T PF05186_consen 10 VGPVLTEGLAELAKERPEDPIEFLAEYLLK 39 (42)
T ss_dssp THHHHHHHHHHHHHH--SSHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCChHHHHHHHHHH
Confidence 456788888889998988899999999753
Done!