Query psy17466
Match_columns 226
No_of_seqs 132 out of 186
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 23:15:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17466.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17466hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0570|consensus 100.0 1.7E-64 3.7E-69 432.1 17.3 170 1-174 1-172 (223)
2 PF05983 Med7: MED7 protein; 100.0 1.8E-61 3.9E-66 405.1 12.5 156 7-166 1-162 (162)
3 KOG2391|consensus 82.1 16 0.00034 34.9 10.3 32 144-175 237-268 (365)
4 PF10018 Med4: Vitamin-D-recep 80.4 16 0.00036 31.1 9.2 61 109-169 3-63 (188)
5 PF15471 TMEM171: Transmembran 77.5 1.2 2.7E-05 41.1 1.4 21 8-28 216-236 (319)
6 PF05278 PEARLI-4: Arabidopsis 65.3 1.2E+02 0.0025 28.1 11.8 87 81-167 122-225 (269)
7 COG5178 PRP8 U5 snRNP spliceos 59.3 6.3 0.00014 43.3 2.2 23 73-96 106-128 (2365)
8 KOG3335|consensus 55.4 73 0.0016 27.8 7.7 38 130-167 101-138 (181)
9 KOG4552|consensus 53.6 1.7E+02 0.0038 26.4 12.2 38 130-167 69-106 (272)
10 KOG1924|consensus 45.5 12 0.00025 39.6 1.6 13 116-128 700-712 (1102)
11 PF06216 RTBV_P46: Rice tungro 45.2 1.3E+02 0.0029 28.0 8.1 59 110-168 53-111 (389)
12 COG1561 Uncharacterized stress 43.0 2.4E+02 0.0052 26.4 9.6 83 78-167 154-237 (290)
13 PF04340 DUF484: Protein of un 36.8 72 0.0016 27.6 5.0 31 129-160 35-65 (225)
14 PF07544 Med9: RNA polymerase 35.8 1.8E+02 0.004 21.6 7.6 54 105-158 25-82 (83)
15 smart00302 GED Dynamin GTPase 35.0 2E+02 0.0043 21.7 7.4 34 134-167 56-91 (92)
16 PF03234 CDC37_N: Cdc37 N term 33.7 2.4E+02 0.0051 24.4 7.5 24 200-223 102-125 (177)
17 KOG1924|consensus 32.2 27 0.00059 36.9 1.8 36 126-161 776-811 (1102)
18 KOG3331|consensus 30.8 2.4E+02 0.0051 25.1 7.1 83 17-126 40-129 (213)
19 cd04769 HTH_MerR2 Helix-Turn-H 30.6 2.2E+02 0.0048 22.0 6.4 29 131-159 75-103 (116)
20 cd07635 BAR_GRAF2 The Bin/Amph 30.0 2.7E+02 0.0059 24.6 7.5 58 114-171 69-129 (207)
21 cd04786 HTH_MerR-like_sg7 Heli 30.0 2.1E+02 0.0046 23.0 6.4 35 134-172 77-111 (131)
22 TIGR02116 toxin_Txe_YoeB toxin 29.9 90 0.002 22.6 3.8 30 74-103 4-36 (80)
23 cd04770 HTH_HMRTR Helix-Turn-H 29.6 1.8E+02 0.0039 22.6 5.8 34 133-166 77-110 (123)
24 PRK10227 DNA-binding transcrip 28.5 1.6E+02 0.0034 23.8 5.4 36 131-166 75-110 (135)
25 TIGR02047 CadR-PbrR Cd(II)/Pb( 28.4 1.7E+02 0.0037 23.2 5.5 52 110-167 60-111 (127)
26 PF07139 DUF1387: Protein of u 28.1 4.5E+02 0.0097 24.8 8.8 63 106-174 180-250 (302)
27 PF05659 RPW8: Arabidopsis bro 27.9 3.5E+02 0.0076 22.4 8.2 60 108-170 27-87 (147)
28 cd04783 HTH_MerR1 Helix-Turn-H 26.7 2.1E+02 0.0046 22.4 5.7 28 133-160 75-102 (126)
29 PF14649 Spatacsin_C: Spatacsi 26.3 2.9E+02 0.0063 25.7 7.3 52 83-143 105-156 (296)
30 KOG3261|consensus 26.0 45 0.00097 29.1 1.8 27 14-40 130-163 (202)
31 PF04859 DUF641: Plant protein 25.4 2E+02 0.0044 23.7 5.5 33 131-163 90-122 (131)
32 PRK09514 zntR zinc-responsive 24.5 2.7E+02 0.0058 22.5 6.1 36 130-165 76-111 (140)
33 KOG2546|consensus 23.8 59 0.0013 32.1 2.4 14 34-49 386-399 (483)
34 PF05852 DUF848: Gammaherpesvi 23.7 4.5E+02 0.0097 22.2 8.4 69 101-173 31-113 (146)
35 cd04776 HTH_GnyR Helix-Turn-He 23.4 3.7E+02 0.0079 21.1 7.7 37 133-169 78-114 (118)
36 PF10873 DUF2668: Protein of u 22.9 48 0.001 28.1 1.4 18 7-26 106-123 (155)
37 TIGR01429 AMP_deaminase AMP de 22.9 2.6E+02 0.0056 28.7 6.8 66 63-129 84-154 (611)
38 PF09457 RBD-FIP: FIP domain ; 22.1 2.4E+02 0.0052 19.4 4.5 28 133-160 2-32 (48)
39 TIGR02449 conserved hypothetic 22.1 2.8E+02 0.0062 20.2 5.1 36 139-174 25-60 (65)
40 PF05615 THOC7: Tho complex su 22.1 4.1E+02 0.0089 21.1 11.5 41 128-168 74-114 (139)
41 cd01108 HTH_CueR Helix-Turn-He 21.8 2.4E+02 0.0053 22.2 5.3 33 133-165 77-109 (127)
42 KOG0995|consensus 21.6 2.3E+02 0.0049 29.0 5.9 39 130-168 289-327 (581)
43 PF15290 Syntaphilin: Golgi-lo 21.3 1.6E+02 0.0034 27.7 4.4 110 33-168 32-143 (305)
No 1
>KOG0570|consensus
Probab=100.00 E-value=1.7e-64 Score=432.09 Aligned_cols=170 Identities=49% Similarity=0.895 Sum_probs=162.8
Q ss_pred CCCcccccCCCCCCchHhHhhcChhhhhCCCCCCCCCCccccccccCcccccCCCcCCCCcccCccccCC--CCchhHHH
Q psy17466 1 MSAPQEQVSSLPLPPVQYINNYTDELIRRGRAPKPPLPIHDSYSMFGNQFNADDTIIRPLESQGIKRLYP--QHFDRRRE 78 (226)
Q Consensus 1 M~~~~~~vss~ppPPp~y~k~ft~en~~~~~~p~PP~P~~g~y~~FG~~~~~~d~~ip~Le~~gi~qLYp--~~~D~k~E 78 (226)
|..+.+++|+|||||| |||+||++|+.++.+|+||+|+.|+|.|||+.|..+| +||||+++||+|||+ .++|+|.|
T Consensus 1 m~~~~q~~S~~PpPPp-Y~k~yt~~ni~~~sAP~pP~p~~~tY~~FG~~~~~dd-vip~Le~~Gv~qLykkd~~~d~K~E 78 (223)
T KOG0570|consen 1 MGFGPQTVSAYPPPPP-YYKLYTDENINKGSAPPPPPPILGTYKMFGEEYREDD-VIPPLEEQGVPQLYKKDNNYDYKKE 78 (223)
T ss_pred CCCCcccccCCCcCCh-HHHHhhhccccCCCCCcccCCCccchhhhccccchhc-cccChhhcChHhhCcccccccHHHH
Confidence 6677777888888876 9999999999999999999999999999999999888 899999999999999 68999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCChHHHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 79 LRKLNHSLLVNFLDLIDLLVQCPDSPRRTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHL 158 (226)
Q Consensus 79 LkkL~~SLL~nfLeLl~~L~~~P~~~~~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~ 158 (226)
|+|||+||++|||||+|+|+++|+. |++||++|++||+|||||||+|||||||||||+|||+|+++|++++++|++++
T Consensus 79 LRkLnrslllnfleL~~ILi~~P~~--~e~Kvedi~tifvnlHHLiNeyRPhQaResLi~lmE~Qi~~~~~~ve~~kk~~ 156 (223)
T KOG0570|consen 79 LRKLNRSLLLNFLELLDILIRAPDM--REEKVEDIRTIFVNLHHLINEYRPHQARESLIMLMERQIEQRSDIVEDFKKHL 156 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCchh--HHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999984 79999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCC
Q psy17466 159 DRVNQILNQAIENLPD 174 (226)
Q Consensus 159 d~~~e~L~~~l~~l~~ 174 (226)
.++.++|..++.+|..
T Consensus 157 ~~~~e~l~d~~~tL~~ 172 (223)
T KOG0570|consen 157 RQVREVLDDQFQTLRG 172 (223)
T ss_pred HHHHHHHHHHHHhhcc
Confidence 9999999999999984
No 2
>PF05983 Med7: MED7 protein; InterPro: IPR009244 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.
Probab=100.00 E-value=1.8e-61 Score=405.06 Aligned_cols=156 Identities=47% Similarity=0.801 Sum_probs=104.7
Q ss_pred ccCCCCCCchHhHhhcChhhhhCCCCCCCCCCccccccccCcccccCCCcCCCCcccCccccCCCC------chhHHHHH
Q psy17466 7 QVSSLPLPPVQYINNYTDELIRRGRAPKPPLPIHDSYSMFGNQFNADDTIIRPLESQGIKRLYPQH------FDRRRELR 80 (226)
Q Consensus 7 ~vss~ppPPp~y~k~ft~en~~~~~~p~PP~P~~g~y~~FG~~~~~~d~~ip~Le~~gi~qLYp~~------~D~k~ELk 80 (226)
||||+|||||+|||+||++|. ....+|||+|.+|+|+|||+.|++++ .+|+|+++||+||||.. .|++.||+
T Consensus 1 ~~~s~fPpPP~~yk~yt~~n~-l~~~~pPp~P~~~~y~~FG~~~~~~~-~~p~L~~~gi~qLy~~~~~~~~~~d~~~eLk 78 (162)
T PF05983_consen 1 QISSLFPPPPPFYKLYTDENE-LRFLPPPPPPIDGEYRVFGETWSTED-KLPSLESQGIRQLYPPDDDPSPSVDRKKELK 78 (162)
T ss_dssp -----S----GGGGG--HHHG-GGGGS-----SSGGGSTS-------------------------------HHHHHHHHH
T ss_pred CCCCCCCCchHHHHHcCChhh-ccCCCCcccCCCCcceeCCCEeecCC-CCCCchhccccccCCCccccCCCchHHHHHH
Confidence 466777777789999999983 33345666778999999999999999 89999999999999998 99999999
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCChHHHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 81 KLNHSLLVNFLDLIDLLVQCPDSPRRTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHLDR 160 (226)
Q Consensus 81 kL~~SLL~nfLeLl~~L~~~P~~~~~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~ 160 (226)
||++|||+|||+|+|+|+.+|+++ ++||+||++||+|||||||+||||||||||++||++|+++|++++++||++|++
T Consensus 79 kL~~sll~nfleLl~~l~~~P~~~--~~ki~~i~~L~~NmhhllNeyRPhQARetLi~~me~Ql~~kr~~i~~i~~~~~~ 156 (162)
T PF05983_consen 79 KLNKSLLLNFLELLDILSKNPSQY--ERKIEDIRLLFINMHHLLNEYRPHQARETLIMMMEEQLEEKREEIEEIRKVCEK 156 (162)
T ss_dssp HHHHHHHHHHHHHTTSS---CCCH--HHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCccH--HHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999985 579999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q psy17466 161 VNQILN 166 (226)
Q Consensus 161 ~~e~L~ 166 (226)
|+++|+
T Consensus 157 ~~~~le 162 (162)
T PF05983_consen 157 AREVLE 162 (162)
T ss_dssp HHHHH-
T ss_pred HHHHhC
Confidence 999985
No 3
>KOG2391|consensus
Probab=82.13 E-value=16 Score=34.86 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Q psy17466 144 RRQRNETSQRFHVHLDRVNQILNQAIENLPDT 175 (226)
Q Consensus 144 i~~r~e~~~~ir~~~d~~~e~L~~~l~~l~~~ 175 (226)
++++.|++....+++++.++.|++.+.+|...
T Consensus 237 lkRt~EeL~~G~~kL~~~~etLEqq~~~L~~n 268 (365)
T KOG2391|consen 237 LKRTEEELNIGKQKLVAMKETLEQQLQSLQKN 268 (365)
T ss_pred HHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 66677777777777777777777777666553
No 4
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=80.36 E-value=16 Score=31.09 Aligned_cols=61 Identities=15% Similarity=0.122 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 109 KVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQAI 169 (226)
Q Consensus 109 ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l 169 (226)
.+++|...=..+..+|.+++-||.+..-|.-|+.++..+-+.+..+.+.+..++..|...+
T Consensus 3 ~~~~L~~~d~~L~~~L~~l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 3 LAEDLIEADDELSSALEELQEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666677888999999999999999999999999999999999999999999999876
No 5
>PF15471 TMEM171: Transmembrane protein family 171
Probab=77.53 E-value=1.2 Score=41.11 Aligned_cols=21 Identities=24% Similarity=0.482 Sum_probs=14.6
Q ss_pred cCCCCCCchHhHhhcChhhhh
Q psy17466 8 VSSLPLPPVQYINNYTDELIR 28 (226)
Q Consensus 8 vss~ppPPp~y~k~ft~en~~ 28 (226)
|=-||||||+||.......+.
T Consensus 216 ViiFPPPPPPYF~ess~~a~t 236 (319)
T PF15471_consen 216 VIIFPPPPPPYFPESSASAVT 236 (319)
T ss_pred EEEcCCccCCCCCCCCccccc
Confidence 346999999998766544443
No 6
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=65.30 E-value=1.2e+02 Score=28.12 Aligned_cols=87 Identities=15% Similarity=0.177 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCh-------H----------HHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHH
Q psy17466 81 KLNHSLLVNFLDLIDLLVQCPDSP-------R----------RTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQ 143 (226)
Q Consensus 81 kL~~SLL~nfLeLl~~L~~~P~~~-------~----------~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Q 143 (226)
++=..+|...+.++..|...|... . ..=+|.||+..+.-+--....|.-|++|+.-+..+++.
T Consensus 122 ~~RS~yLe~Lc~IIqeLq~t~~~~LS~~dl~e~~~~l~DLesa~vkV~WLR~~L~Ei~Ea~e~~~~~~~~e~eke~~~r~ 201 (269)
T PF05278_consen 122 QFRSYYLECLCDIIQELQSTPLKELSESDLKEMIATLKDLESAKVKVDWLRSKLEEILEAKEIYDQHETREEEKEEKDRK 201 (269)
T ss_pred HHHHHHHHHHHHHHHHHhcCcHhhhhHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333445555667777777777321 0 11235566655544333333344467777777767777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 144 RRQRNETSQRFHVHLDRVNQILNQ 167 (226)
Q Consensus 144 i~~r~e~~~~ir~~~d~~~e~L~~ 167 (226)
++..+.+.+.....++++...+.+
T Consensus 202 l~~~~~ELe~~~EeL~~~Eke~~e 225 (269)
T PF05278_consen 202 LELKKEELEELEEELKQKEKEVKE 225 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666665555555555444444
No 7
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=59.34 E-value=6.3 Score=43.25 Aligned_cols=23 Identities=30% Similarity=0.365 Sum_probs=11.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHH
Q psy17466 73 FDRRRELRKLNHSLLVNFLDLIDL 96 (226)
Q Consensus 73 ~D~k~ELkkL~~SLL~nfLeLl~~ 96 (226)
.|+|..|-.| +-|-.+.++|+..
T Consensus 106 ~Dkrs~lgal-kylPhavlkLLeN 128 (2365)
T COG5178 106 VDKRSYLGAL-KYLPHAVLKLLEN 128 (2365)
T ss_pred hhhHhhhhhh-hhchHHHHHHHhc
Confidence 4555544433 3344455555554
No 8
>KOG3335|consensus
Probab=55.43 E-value=73 Score=27.79 Aligned_cols=38 Identities=11% Similarity=0.208 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 130 HQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQ 167 (226)
Q Consensus 130 hQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~ 167 (226)
++.|..=++-++.+++....+++++++.++...+.+.+
T Consensus 101 ee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~~~l~~ 138 (181)
T KOG3335|consen 101 EEKRKQEIMELRLKVEKLENAIAELTKFFSQLHSKLNK 138 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 88888888888888888888888888888876644444
No 9
>KOG4552|consensus
Probab=53.58 E-value=1.7e+02 Score=26.45 Aligned_cols=38 Identities=29% Similarity=0.402 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 130 HQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQ 167 (226)
Q Consensus 130 hQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~ 167 (226)
.|-||.++..||..++.|-+.|+++++.+..|.-+|..
T Consensus 69 q~k~e~~m~~Lea~VEkrD~~IQqLqk~LK~aE~iLtt 106 (272)
T KOG4552|consen 69 QQKREQLMRTLEAHVEKRDEVIQQLQKNLKSAEVILTT 106 (272)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999999888877765
No 10
>KOG1924|consensus
Probab=45.50 E-value=12 Score=39.57 Aligned_cols=13 Identities=23% Similarity=0.370 Sum_probs=6.7
Q ss_pred HHHHHHHHHhhcC
Q psy17466 116 LFIHIHHLLNEFR 128 (226)
Q Consensus 116 L~iNmHHLLNeyR 128 (226)
+.-|+--++-+||
T Consensus 700 taQnLsIflgS~r 712 (1102)
T KOG1924|consen 700 TAQNLSIFLGSFR 712 (1102)
T ss_pred HHHHHHHHHhhcc
Confidence 3455555555555
No 11
>PF06216 RTBV_P46: Rice tungro bacilliform virus P46 protein; InterPro: IPR009347 This family consists of several Rice tungro bacilliform virus P46 proteins. The function of this family is unknown.
Probab=45.21 E-value=1.3e+02 Score=27.98 Aligned_cols=59 Identities=12% Similarity=0.107 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 110 VEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQA 168 (226)
Q Consensus 110 i~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~ 168 (226)
.+.+|.|.+=.-||-|.=--.|+...=..-|.+|+...+.+.+..|+++...+++|+|.
T Consensus 53 tervrklh~~~~~~y~~e~e~~sy~~e~~~l~~qvs~l~~~~~~~r~~~~~~~~~~egl 111 (389)
T PF06216_consen 53 TERVRKLHIISDYIYNKEFERQSYSNEWISLNDQVSHLQHQNSEQRQQIREMREIIEGL 111 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34445555566777776667788888888899999999999999999999999999993
No 12
>COG1561 Uncharacterized stress-induced protein [Function unknown]
Probab=43.04 E-value=2.4e+02 Score=26.35 Aligned_cols=83 Identities=17% Similarity=0.195 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh-CCCChHHHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 78 ELRKLNHSLLVNFLDLIDLLVQ-CPDSPRRTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHV 156 (226)
Q Consensus 78 ELkkL~~SLL~nfLeLl~~L~~-~P~~~~~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~ 156 (226)
.|+.+...-|...-.+++.+.. .|.- .....+ .+.-++.++...+.|- |=.-...+-.|.-.-.|++.+++.
T Consensus 154 ~L~~~l~~~L~~ie~~v~~v~~~~P~~--~~~~~~---~l~~ri~~~~~~~d~~--rl~qE~al~a~K~DI~EEldRL~s 226 (290)
T COG1561 154 ALKADLLQRLDAIEELVEKVESLMPEI--LEWYRE---RLVARLNEAQDQLDED--RLEQEVALLAQKADIAEELDRLKS 226 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhChHH--HHHHHH---HHHHHHHHHhcccChH--HHHHHHHHHHHHhhHHHHHHHHHH
Confidence 3444555555555555555432 2321 122233 3334444444444432 111134444566677899999999
Q ss_pred HHHHHHHHHHH
Q psy17466 157 HLDRVNQILNQ 167 (226)
Q Consensus 157 ~~d~~~e~L~~ 167 (226)
|+.+++.+|++
T Consensus 227 Hv~~~~~iL~~ 237 (290)
T COG1561 227 HVKEFRNILEK 237 (290)
T ss_pred HHHHHHHHHhc
Confidence 99999999965
No 13
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=36.80 E-value=72 Score=27.61 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 129 PHQARETLRVMMELQRRQRNETSQRFHVHLDR 160 (226)
Q Consensus 129 PhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~ 160 (226)
||+.+ ..+.+.|+|++.-|+.+++++.+++.
T Consensus 35 ph~~~-~avSL~erQ~~~LR~~~~~L~~~l~~ 65 (225)
T PF04340_consen 35 PHPSG-GAVSLVERQLERLRERNRQLEEQLEE 65 (225)
T ss_dssp -------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCC-CcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 57765 58899999998888888888877765
No 14
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=35.82 E-value=1.8e+02 Score=21.60 Aligned_cols=54 Identities=17% Similarity=0.197 Sum_probs=42.0
Q ss_pred HHHhHHHHHHHHHHHHHHHHhhc----ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 105 RRTEKVEDISLLFIHIHHLLNEF----RPHQARETLRVMMELQRRQRNETSQRFHVHL 158 (226)
Q Consensus 105 ~~~~ki~di~~L~iNmHHLLNey----RPhQAREtLi~mme~Qi~~r~e~~~~ir~~~ 158 (226)
.+...+..|+.=+-|+--++.++ |...-.+.-+..+++|++.+++.+.+++..|
T Consensus 25 d~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 25 DLDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888888888888888764 7777788888888888888888887777665
No 15
>smart00302 GED Dynamin GTPase effector domain.
Probab=34.98 E-value=2e+02 Score=21.67 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=20.9
Q ss_pred HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 134 ETLRVMMELQ--RRQRNETSQRFHVHLDRVNQILNQ 167 (226)
Q Consensus 134 EtLi~mme~Q--i~~r~e~~~~ir~~~d~~~e~L~~ 167 (226)
+.+-.+|++. +.+||+...+.-+.+.+|..+|..
T Consensus 56 ~~~~~LL~E~~~i~~kR~~~~~~l~~L~~A~~~l~~ 91 (92)
T smart00302 56 ELLDELLEEDPEIASKRKELKKRLELLKKARQIIAA 91 (92)
T ss_pred ccHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4455566554 566666666666677777766643
No 16
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=33.65 E-value=2.4e+02 Score=24.37 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=17.1
Q ss_pred ccCCCCchhhHHHhhhhcCCCCCC
Q psy17466 200 SVDGVNPYDRLMCELVDNMPLTND 223 (226)
Q Consensus 200 ~~~~~~~~~~~~~~~~d~~~~~~~ 223 (226)
.....-..+..|-+|+|.+....+
T Consensus 102 ~~~~~p~y~~Mi~~L~~qvk~~~d 125 (177)
T PF03234_consen 102 KDPEQPTYDEMIEDLLDQVKKEPD 125 (177)
T ss_pred CCCCCCCHHHHHHHHHHHHhcccC
Confidence 344456788999999999865443
No 17
>KOG1924|consensus
Probab=32.21 E-value=27 Score=36.94 Aligned_cols=36 Identities=8% Similarity=0.125 Sum_probs=18.2
Q ss_pred hcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 126 EFRPHQARETLRVMMELQRRQRNETSQRFHVHLDRV 161 (226)
Q Consensus 126 eyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~ 161 (226)
.+||.=.-=...+..++|++.-+=.|-.+-.+|+++
T Consensus 776 rL~pRL~~ilFKl~fse~vnniKP~i~avt~ACEE~ 811 (1102)
T KOG1924|consen 776 RLRPRLSAILFKLTFSEQVNNIKPDIVAVTAACEEL 811 (1102)
T ss_pred ccChhHHHHHHHhhHHHHHhhcChHHHHHHHHHHHH
Confidence 344443333444555666666665555444444443
No 18
>KOG3331|consensus
Probab=30.75 E-value=2.4e+02 Score=25.14 Aligned_cols=83 Identities=24% Similarity=0.462 Sum_probs=47.9
Q ss_pred HhHhhcChhhhhCCCCCCCCCCccccccccCcccccCCCcCCCCcccCccccCCCCchhHHHHHHHH------HHHHHHH
Q psy17466 17 QYINNYTDELIRRGRAPKPPLPIHDSYSMFGNQFNADDTIIRPLESQGIKRLYPQHFDRRRELRKLN------HSLLVNF 90 (226)
Q Consensus 17 ~y~k~ft~en~~~~~~p~PP~P~~g~y~~FG~~~~~~d~~ip~Le~~gi~qLYp~~~D~k~ELkkL~------~SLL~nf 90 (226)
+.|.+|.++...+...-.| =..||..|+.++ ++ |+|- .+|++|- +-+|++-
T Consensus 40 pL~qFFddk~~~~~~~~~p-------~~k~GR~W~aeE--LR-~KS~-------------nDLH~LWYvcLkErNmL~T~ 96 (213)
T KOG3331|consen 40 PLWQFFDDKKFDRSADEEP-------PVKHGRAWSAEE--LR-LKSF-------------NDLHKLWYVCLKERNMLATM 96 (213)
T ss_pred cHHHHhhhhhccCChhhcC-------CcccCCccchHH--Hh-cchh-------------hHHHHHHHHHHHHHHHHHHH
Confidence 3678887665322111112 145899998877 22 2221 2455551 2233333
Q ss_pred HH-HHHHHhhCCCChHHHhHHHHHHHHHHHHHHHHhh
Q psy17466 91 LD-LIDLLVQCPDSPRRTEKVEDISLLFIHIHHLLNE 126 (226)
Q Consensus 91 Le-Ll~~L~~~P~~~~~~~ki~di~~L~iNmHHLLNe 126 (226)
-. +-++...-|. .+.|..++.-.-++-|.|||
T Consensus 97 ~~~~k~~~~~~Pn----pERi~kV~~TM~~I~~Vl~E 129 (213)
T KOG3331|consen 97 RHELKNIVGSFPN----PERIDKVRTTMWRIEHVLNE 129 (213)
T ss_pred HHHHHHHHhcCCC----HHHHHHHHHHHHHHHHHHHH
Confidence 33 4444444565 26799999999999999997
No 19
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.60 E-value=2.2e+02 Score=22.02 Aligned_cols=29 Identities=10% Similarity=0.110 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 131 QARETLRVMMELQRRQRNETSQRFHVHLD 159 (226)
Q Consensus 131 QAREtLi~mme~Qi~~r~e~~~~ir~~~d 159 (226)
++...+..++++|.+.-.+.++++++...
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~l~~~~~ 103 (116)
T cd04769 75 LPWPHLQQALEDKKQEIRAQITELQQLLA 103 (116)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566777888876666666654444443
No 20
>cd07635 BAR_GRAF2 The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase 2 (GRAF2), also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA which regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death. It is highly expressed in skeletal muscle and also interacts with PKNbeta, which is a target of Rho. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related prote
Probab=30.02 E-value=2.7e+02 Score=24.60 Aligned_cols=58 Identities=19% Similarity=0.139 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhhcCh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy17466 114 SLLFIHIHHLLNEFRP---HQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQAIEN 171 (226)
Q Consensus 114 ~~L~iNmHHLLNeyRP---hQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l~~ 171 (226)
-.=|+|+|--|+.+|- .||-.+|+.-|+.=+++-...+.+.++..|++.+-...++..
T Consensus 69 l~ef~~~~~el~d~r~~L~~~~~~~l~~pL~~F~kedl~~~Ke~KK~FdK~se~~~~Al~K 129 (207)
T cd07635 69 LQEFSNFLKNLEEQREIMALNVTETLIKPLERFRKEQLGAVKEEKKKFDKETEKNYSLLEK 129 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 3347899999999995 566666666665544444445556677788777777776554
No 21
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=29.96 E-value=2.1e+02 Score=22.95 Aligned_cols=35 Identities=14% Similarity=0.117 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy17466 134 ETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQAIENL 172 (226)
Q Consensus 134 EtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l~~l 172 (226)
+.+..+++.++++-.+.++ .+.+.++.|...+..+
T Consensus 77 ~~~~~~l~~k~~~i~~~i~----~L~~~~~~L~~~i~~~ 111 (131)
T cd04786 77 DELLAALERKVADIEALEA----RLAQNKAQLLVLIDLI 111 (131)
T ss_pred HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 4455666666555555554 3333444455544444
No 22
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=29.88 E-value=90 Score=22.59 Aligned_cols=30 Identities=17% Similarity=0.207 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHH---HHHHHHHHHHHHhhCCCC
Q psy17466 74 DRRRELRKLNHS---LLVNFLDLIDLLVQCPDS 103 (226)
Q Consensus 74 D~k~ELkkL~~S---LL~nfLeLl~~L~~~P~~ 103 (226)
+...+|++|-++ +...|.+.+..|..+|-.
T Consensus 4 ~a~kdlkkl~k~~~~~~~~i~~~i~~l~~~P~~ 36 (80)
T TIGR02116 4 EAWEDYKKWQEADKKLKKKINELIKDVRRDPFK 36 (80)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHHHHHcCCCC
Confidence 456799999766 989999999888888863
No 23
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.61 E-value=1.8e+02 Score=22.55 Aligned_cols=34 Identities=9% Similarity=0.159 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 133 RETLRVMMELQRRQRNETSQRFHVHLDRVNQILN 166 (226)
Q Consensus 133 REtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~ 166 (226)
.+.+..+|+.|+++-.+.++++++........+.
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~ 110 (123)
T cd04770 77 CAEVRALLEEKLAEVEAKIAELQALRAELAGLLS 110 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777887776666666555444444333333
No 24
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=28.52 E-value=1.6e+02 Score=23.84 Aligned_cols=36 Identities=6% Similarity=0.035 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 131 QARETLRVMMELQRRQRNETSQRFHVHLDRVNQILN 166 (226)
Q Consensus 131 QAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~ 166 (226)
+....+..+++.|+.+-.+.++++++..+.....+.
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 110 (135)
T PRK10227 75 RHSADVKRRTLEKVAEIERHIEELQSMRDQLLALAN 110 (135)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445566666655555555544444444333333
No 25
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=28.36 E-value=1.7e+02 Score=23.22 Aligned_cols=52 Identities=6% Similarity=0.211 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 110 VEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQ 167 (226)
Q Consensus 110 i~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~ 167 (226)
+++|+.++-. ...++++.+.+..+++.|+++-.+.++++++..+.....+..
T Consensus 60 L~eI~~~l~~------~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 111 (127)
T TIGR02047 60 LAEIRQLLRY------QDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDLRGR 111 (127)
T ss_pred HHHHHHHHHh------hhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5566655421 123455556667777777766666665555554444444433
No 26
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=28.15 E-value=4.5e+02 Score=24.75 Aligned_cols=63 Identities=17% Similarity=0.273 Sum_probs=45.3
Q ss_pred HHhHHHHHHHHHHHHH--------HHHhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy17466 106 RTEKVEDISLLFIHIH--------HLLNEFRPHQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQAIENLPD 174 (226)
Q Consensus 106 ~~~ki~di~~L~iNmH--------HLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l~~l~~ 174 (226)
...-|..|+.-|--+| +|+.|+.-++|....|.+ .|+..++.+++..|.|-.+=+.+|..|..
T Consensus 180 ~d~S~k~ik~~F~~l~~cL~dREvaLl~EmdkVK~EAmeiL~------aRqkkAeeLkrltd~A~~MsE~Ql~ELRa 250 (302)
T PF07139_consen 180 MDSSIKKIKQTFAELQSCLMDREVALLAEMDKVKAEAMEILD------ARQKKAEELKRLTDRASQMSEEQLAELRA 250 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHhhcCHHHHHHHHH
Confidence 3456777777777776 456677777776655533 36677778888888888888888888765
No 27
>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].
Probab=27.86 E-value=3.5e+02 Score=22.36 Aligned_cols=60 Identities=12% Similarity=0.212 Sum_probs=40.4
Q ss_pred hHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy17466 108 EKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRR-QRNETSQRFHVHLDRVNQILNQAIE 170 (226)
Q Consensus 108 ~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~-~r~e~~~~ir~~~d~~~e~L~~~l~ 170 (226)
.|.-..+.++-++--.||..-|.=.. |.-+...+. .|+++++++.+.+++++++++.|..
T Consensus 27 ~k~~~fk~~l~~L~sTl~~i~P~i~e---I~~~~~eld~~~~ee~e~L~~~L~~g~~LV~k~sk 87 (147)
T PF05659_consen 27 KKSLSFKSILKRLESTLESIIPIIKE---IDKLNVELDRPRQEEIERLKELLEKGKELVEKCSK 87 (147)
T ss_pred HHHHhhhhHHHHHHHHHHHhhhHHHH---HHHHhhhcCCchhHHHHHHHHHHHHHHHHHHHhcc
Confidence 45556666667777777777774222 223333344 3488999999999999999988654
No 28
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.73 E-value=2.1e+02 Score=22.43 Aligned_cols=28 Identities=11% Similarity=0.036 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 133 RETLRVMMELQRRQRNETSQRFHVHLDR 160 (226)
Q Consensus 133 REtLi~mme~Qi~~r~e~~~~ir~~~d~ 160 (226)
...+..+++.|++.-.+.++++++..+.
T Consensus 75 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 102 (126)
T cd04783 75 CSEARELAEQKLAEVDEKIADLQRMRAS 102 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456777777766666666544444443
No 29
>PF14649 Spatacsin_C: Spatacsin C-terminus
Probab=26.30 E-value=2.9e+02 Score=25.65 Aligned_cols=52 Identities=21% Similarity=0.397 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCChHHHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHH
Q psy17466 83 NHSLLVNFLDLIDLLVQCPDSPRRTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQ 143 (226)
Q Consensus 83 ~~SLL~nfLeLl~~L~~~P~~~~~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Q 143 (226)
+|..|++|+.= .+|.+. ++ -.+-.+.+||+|=+-++.-.+|+..+..+...+
T Consensus 105 lk~all~ylk~-----~~P~d~---e~-~~mv~l~F~m~~Eia~~~e~~A~~~l~~l~~~~ 156 (296)
T PF14649_consen 105 LKMALLDYLKR-----CCPEDK---EK-FSMVALHFNMYREIAELWEKRARQILKKLVSQP 156 (296)
T ss_pred HHHHHHHHHHh-----cCCCCH---HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 44445555442 367763 33 345678899999999999999999998887754
No 30
>KOG3261|consensus
Probab=26.00 E-value=45 Score=29.11 Aligned_cols=27 Identities=30% Similarity=0.602 Sum_probs=16.0
Q ss_pred CchHhHhhcChhhhhC----C--CCCCCC-CCcc
Q psy17466 14 PPVQYINNYTDELIRR----G--RAPKPP-LPIH 40 (226)
Q Consensus 14 PPp~y~k~ft~en~~~----~--~~p~PP-~P~~ 40 (226)
+-|.|+|+|.++.--- + ++|||| ||+.
T Consensus 130 ~a~~y~k~faSDRsHMk~~~G~w~~pPPpyp~I~ 163 (202)
T KOG3261|consen 130 HAPLYFKHFASDRSHMKEPDGSWTAPPPPYPPIV 163 (202)
T ss_pred ccHHHHHHhhcchhhhcCCCCCccCCCCCCCccc
Confidence 4457999998764311 2 346666 5553
No 31
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=25.41 E-value=2e+02 Score=23.69 Aligned_cols=33 Identities=21% Similarity=0.360 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 131 QARETLRVMMELQRRQRNETSQRFHVHLDRVNQ 163 (226)
Q Consensus 131 QAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e 163 (226)
..+|.+..-|+.|++.|-.+|..+|..++.+..
T Consensus 90 ~~yE~~~~kLe~e~~~Kdsei~~Lr~~L~~~~~ 122 (131)
T PF04859_consen 90 KTYEIVVKKLEAELRAKDSEIDRLREKLDELNR 122 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888999999999999999999887543
No 32
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.52 E-value=2.7e+02 Score=22.53 Aligned_cols=36 Identities=3% Similarity=0.106 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 130 HQARETLRVMMELQRRQRNETSQRFHVHLDRVNQIL 165 (226)
Q Consensus 130 hQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L 165 (226)
.++.+.+..+++.|++.-.+.++++++........+
T Consensus 76 ~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 111 (140)
T PRK09514 76 HHTCQEVKGIVDEKLAEVEAKIAELQHMRRSLQRLN 111 (140)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566777888877666666655444443333333
No 33
>KOG2546|consensus
Probab=23.80 E-value=59 Score=32.08 Aligned_cols=14 Identities=36% Similarity=0.562 Sum_probs=7.6
Q ss_pred CCCCCccccccccCcc
Q psy17466 34 KPPLPIHDSYSMFGNQ 49 (226)
Q Consensus 34 ~PP~P~~g~y~~FG~~ 49 (226)
+||||..+.| ||..
T Consensus 386 ppPp~~~~~~--~g~e 399 (483)
T KOG2546|consen 386 PPPPPKSLSD--LGRE 399 (483)
T ss_pred CCCCCCcccc--cccc
Confidence 4444444556 8853
No 34
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=23.67 E-value=4.5e+02 Score=22.16 Aligned_cols=69 Identities=10% Similarity=0.085 Sum_probs=38.6
Q ss_pred CCChHHHhHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHH
Q psy17466 101 PDSPRRTEKVEDISLLFIHIHHLLNEFRPHQARETLRVMMELQRRQRNETSQR--------------FHVHLDRVNQILN 166 (226)
Q Consensus 101 P~~~~~~~ki~di~~L~iNmHHLLNeyRPhQAREtLi~mme~Qi~~r~e~~~~--------------ir~~~d~~~e~L~ 166 (226)
++++-+....+.-+...... |..|-+....+++.-++..|++++.++.. +...+++.++.|+
T Consensus 31 ~~~~LF~~Qf~~t~~~~r~~----~~~r~~~~~~~~v~~~~~~i~~k~~El~~L~~~d~~kv~~~E~L~d~v~eLkeel~ 106 (146)
T PF05852_consen 31 KSSSLFRAQFQFTKKSLRSH----NSLREECEIKNKVSSLETEISEKKKELSHLKKFDRKKVEDLEKLTDRVEELKEELE 106 (146)
T ss_pred CCcHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445555555444443 44566777777777777776666655544 4444555555555
Q ss_pred HHHhcCC
Q psy17466 167 QAIENLP 173 (226)
Q Consensus 167 ~~l~~l~ 173 (226)
..+..+.
T Consensus 107 ~el~~l~ 113 (146)
T PF05852_consen 107 FELERLQ 113 (146)
T ss_pred HHHHHHh
Confidence 5554443
No 35
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.44 E-value=3.7e+02 Score=21.06 Aligned_cols=37 Identities=11% Similarity=0.155 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 133 RETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQAI 169 (226)
Q Consensus 133 REtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l 169 (226)
.+....+++.|+..-.+.++++++.++.....+..+-
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~~ 114 (118)
T cd04776 78 LEKMLEKIEKRRAELEQQRRDIDAALAELDAAEERCR 114 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566777766666666666666665555555543
No 36
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=22.94 E-value=48 Score=28.10 Aligned_cols=18 Identities=44% Similarity=0.800 Sum_probs=13.1
Q ss_pred ccCCCCCCchHhHhhcChhh
Q psy17466 7 QVSSLPLPPVQYINNYTDEL 26 (226)
Q Consensus 7 ~vss~ppPPp~y~k~ft~en 26 (226)
.|+|+|-+||+| -|+.|-
T Consensus 106 ~v~SyP~apPpy--sy~~e~ 123 (155)
T PF10873_consen 106 AVSSYPAAPPPY--SYDHEM 123 (155)
T ss_pred cccccCCCCCCc--cccccc
Confidence 578899777778 666554
No 37
>TIGR01429 AMP_deaminase AMP deaminase. This model describes AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the region included in the model.
Probab=22.91 E-value=2.6e+02 Score=28.74 Aligned_cols=66 Identities=18% Similarity=0.256 Sum_probs=35.6
Q ss_pred cCccccCCCCchhHHHHH--H---HHHHHHHHHHHHHHHHhhCCCChHHHhHHHHHHHHHHHHHHHHhhcCh
Q psy17466 63 QGIKRLYPQHFDRRRELR--K---LNHSLLVNFLDLIDLLVQCPDSPRRTEKVEDISLLFIHIHHLLNEFRP 129 (226)
Q Consensus 63 ~gi~qLYp~~~D~k~ELk--k---L~~SLL~nfLeLl~~L~~~P~~~~~~~ki~di~~L~iNmHHLLNeyRP 129 (226)
.|+.++|....+....-. . =.+....-|-.|+.+++..|.-.--..+++=|.- =.|||.+||+.+-
T Consensus 84 ~gv~~v~~~~~~~~~~~~~~~~~~~~~~f~~D~~~l~~~~~~g~~~s~~~~RL~~Le~-kf~L~~llN~~~E 154 (611)
T TIGR01429 84 GGVLFVYDNDTMLERQEPHFLVPPTLKTYYVDMEHLLALISDGPTKSFCFRRLQYLES-KFNLHELLNEMSE 154 (611)
T ss_pred CCEEEEEcCcchhhcCCccccCCCCHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHH-HHHHHHHhhhhhh
Confidence 477777765433211000 0 1344555566677777777753212233333332 2699999998854
No 38
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=22.12 E-value=2.4e+02 Score=19.36 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=19.4
Q ss_pred HHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Q psy17466 133 RETLRVMMELQ---RRQRNETSQRFHVHLDR 160 (226)
Q Consensus 133 REtLi~mme~Q---i~~r~e~~~~ir~~~d~ 160 (226)
|+.|+.++..| ..++...+.+++..+|.
T Consensus 2 ~eeL~~~l~~~e~~~~~k~~~v~eLe~YiD~ 32 (48)
T PF09457_consen 2 REELISLLKKQEEENARKDSRVRELEDYIDN 32 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67788887776 45556666667777775
No 39
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=22.06 E-value=2.8e+02 Score=20.20 Aligned_cols=36 Identities=14% Similarity=0.224 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy17466 139 MMELQRRQRNETSQRFHVHLDRVNQILNQAIENLPD 174 (226)
Q Consensus 139 mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~l~~l~~ 174 (226)
.|..|+..-..+-..+....+.|+..|+..+..|+.
T Consensus 25 ~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI~RLk~ 60 (65)
T TIGR02449 25 LLRAQEKTWREERAQLLEKNEQARQKVEAMITRLKA 60 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 344454444444455667788888888888777775
No 40
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=22.05 E-value=4.1e+02 Score=21.14 Aligned_cols=41 Identities=15% Similarity=0.241 Sum_probs=29.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 128 RPHQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQA 168 (226)
Q Consensus 128 RPhQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~ 168 (226)
|-.+..+.+..-++..++.-++.++.++..+..|+.+....
T Consensus 74 ~e~e~Y~~~~~~i~~~i~~~k~~ie~lk~~L~~ak~~r~~k 114 (139)
T PF05615_consen 74 RERENYEQLNEEIEQEIEQAKKEIEELKEELEEAKRVRQNK 114 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666777777777778888888888887777663
No 41
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.83 E-value=2.4e+02 Score=22.19 Aligned_cols=33 Identities=3% Similarity=0.048 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 133 RETLRVMMELQRRQRNETSQRFHVHLDRVNQIL 165 (226)
Q Consensus 133 REtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L 165 (226)
.+.+..+++.|++.-.+.++++++........+
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~ 109 (127)
T cd01108 77 SADVKALALEHIAELERKIAELQAMRRTLQQLA 109 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566777776666666655444444333333
No 42
>KOG0995|consensus
Probab=21.59 E-value=2.3e+02 Score=28.99 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 130 HQARETLRVMMELQRRQRNETSQRFHVHLDRVNQILNQA 168 (226)
Q Consensus 130 hQAREtLi~mme~Qi~~r~e~~~~ir~~~d~~~e~L~~~ 168 (226)
-|+++..+.+|...++.+.++++.+++..+..+..|+.+
T Consensus 289 ~~~~~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie~Q 327 (581)
T KOG0995|consen 289 KQHMEKKLEMLKSEIEEKEEEIEKLQKENDELKKQIELQ 327 (581)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 488999999999999999999999999999888877764
No 43
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=21.28 E-value=1.6e+02 Score=27.67 Aligned_cols=110 Identities=14% Similarity=0.147 Sum_probs=59.0
Q ss_pred CCCCCCccccccccCcccccCCCcCCCCcccCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHhhCCCChHHHhHHHH
Q psy17466 33 PKPPLPIHDSYSMFGNQFNADDTIIRPLESQGIKRLYPQHFDRRRELRKLNHSLLVNFLDLIDLLVQCPDSPRRTEKVED 112 (226)
Q Consensus 33 p~PP~P~~g~y~~FG~~~~~~d~~ip~Le~~gi~qLYp~~~D~k~ELkkL~~SLL~nfLeLl~~L~~~P~~~~~~~ki~d 112 (226)
-.|..-..|.|+.-|+++-.+. |=-+|=++.|- +..=-...||.-++.- .+.|- +|+.-|++
T Consensus 32 ~Sp~~rr~~rY~~C~dNHGikP----P~PEQYLTPLQ-QKEV~iRHLkakLkes-------~~~l~------dRetEI~e 93 (305)
T PF15290_consen 32 SSPTMRRSGRYMSCGDNHGIKP----PNPEQYLTPLQ-QKEVCIRHLKAKLKES-------ENRLH------DRETEIDE 93 (305)
T ss_pred CCCCCCCCCceeecccCCCCCC----CCHHHhcChHH-HHHHHHHHHHHHHHHH-------HHHHH------hhHHHHHH
Confidence 3444556789999999886654 11122221110 0111223344333321 22221 24566777
Q ss_pred HHHHHHHHHHHHhhcChHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17466 113 ISLLFIHIHHLLNEFRPHQARETLRVMMELQ--RRQRNETSQRFHVHLDRVNQILNQA 168 (226)
Q Consensus 113 i~~L~iNmHHLLNeyRPhQAREtLi~mme~Q--i~~r~e~~~~ir~~~d~~~e~L~~~ 168 (226)
|+.-+--|.-= =.|-=++..|.| +++.|.+|.++++.++-++..|...
T Consensus 94 LksQL~RMrED--------WIEEECHRVEAQLALKEARkEIkQLkQvieTmrssL~ek 143 (305)
T PF15290_consen 94 LKSQLARMRED--------WIEEECHRVEAQLALKEARKEIKQLKQVIETMRSSLAEK 143 (305)
T ss_pred HHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchh
Confidence 77766555210 012335677777 5777888888888888888776554
Done!