Query psy14608
Match_columns 199
No_of_seqs 163 out of 689
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 16:04:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0810|consensus 100.0 2.4E-28 5.1E-33 211.6 16.2 186 11-199 64-269 (297)
2 KOG0811|consensus 99.8 7.8E-18 1.7E-22 144.0 15.2 139 60-199 87-243 (269)
3 KOG0809|consensus 99.7 9.2E-16 2E-20 131.1 11.6 141 58-199 130-281 (305)
4 cd00179 SynN Syntaxin N-termin 99.6 1.6E-14 3.4E-19 113.2 13.8 117 12-161 31-149 (151)
5 COG5074 t-SNARE complex subuni 99.5 8.9E-13 1.9E-17 109.7 13.6 134 65-199 97-248 (280)
6 COG5325 t-SNARE complex subuni 99.4 4.7E-12 1E-16 107.7 11.8 68 131-199 191-258 (283)
7 KOG0810|consensus 99.0 5.7E-08 1.2E-12 84.7 18.6 95 104-198 127-261 (297)
8 PF05739 SNARE: SNARE domain; 98.9 1.4E-09 3.1E-14 73.2 3.7 60 135-195 4-63 (63)
9 cd00193 t_SNARE Soluble NSF (N 98.5 5.8E-08 1.2E-12 64.0 2.7 56 134-190 5-60 (60)
10 smart00503 SynN Syntaxin N-ter 98.5 1E-06 2.3E-11 65.7 9.5 84 11-96 32-117 (117)
11 smart00397 t_SNARE Helical reg 98.2 8.8E-07 1.9E-11 59.2 2.8 57 133-190 10-66 (66)
12 PF00804 Syntaxin: Syntaxin; 97.6 0.0004 8.7E-09 50.0 8.3 69 11-81 31-103 (103)
13 KOG0812|consensus 96.9 0.00071 1.5E-08 58.5 2.7 65 132-197 224-288 (311)
14 PF14523 Syntaxin_2: Syntaxin- 96.4 0.063 1.4E-06 39.0 10.0 39 58-96 61-99 (102)
15 COG5074 t-SNARE complex subuni 93.9 0.66 1.4E-05 39.5 9.5 90 107-196 107-238 (280)
16 cd00179 SynN Syntaxin N-termin 80.6 11 0.00023 28.9 7.4 31 71-108 98-128 (151)
17 KOG3894|consensus 77.1 9.4 0.0002 33.8 6.7 53 142-198 242-294 (316)
18 smart00503 SynN Syntaxin N-ter 44.6 1.2E+02 0.0025 21.8 12.1 24 104-127 93-116 (117)
19 PF09164 VitD-bind_III: Vitami 39.9 69 0.0015 21.9 4.1 29 121-153 12-40 (68)
20 KOG3065|consensus 36.2 48 0.001 28.9 3.7 30 160-189 242-271 (273)
21 PF10498 IFT57: Intra-flagella 32.2 3.8E+02 0.0083 24.2 13.4 23 68-90 266-288 (359)
22 KOG3065|consensus 27.8 62 0.0013 28.2 3.0 33 158-190 101-133 (273)
23 PF09738 DUF2051: Double stran 24.9 4.8E+02 0.011 23.0 11.0 62 40-101 83-147 (302)
24 TIGR00606 rad50 rad50. This fa 24.0 7E+02 0.015 26.4 10.4 28 142-172 1137-1165(1311)
25 PF05983 Med7: MED7 protein; 22.1 4E+02 0.0088 21.1 9.7 68 18-90 52-129 (162)
26 PF15205 PLAC9: Placenta-speci 21.7 1.7E+02 0.0036 20.2 3.6 25 164-188 25-49 (74)
27 TIGR02338 gimC_beta prefoldin, 20.6 3.4E+02 0.0075 19.7 7.4 15 76-90 4-18 (110)
No 1
>KOG0810|consensus
Probab=99.96 E-value=2.4e-28 Score=211.56 Aligned_cols=186 Identities=37% Similarity=0.496 Sum_probs=157.1
Q ss_pred chhhcccchhhhhHHHhhcccchHHHH----HHHHhHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 11 PQIIETRLIEQSIEQEEQSNKSSADLR----IRDTQLRMIEQSIEQEEQSNKSSADLRIRKTQHSTLSRKFVEVMTEYNR 86 (199)
Q Consensus 11 ~~~~~~~~~e~~~~~~~~~n~~~~dlr----~~~~~Lk~l~~~~~~~~~~~~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~ 86 (199)
.++|+.|.++.++++++.+ ..++++ ..+.+|+.|.+.+..++..+++++..|++++|+..|+.+|.++|..|+.
T Consensus 64 s~~l~~~~~~~~~k~~l~~--~~~~~~~~a~~Ik~kL~~~e~~~~~~~~~~~~~~~~r~rrtq~~~~~kkf~~~M~~f~~ 141 (297)
T KOG0810|consen 64 SKSLHSPNADKELKRKLES--LVDEIRRRARKIKTKLKALEKENEADETQNRSSAGLRTRRTQTSALSKKLKELMNEFNR 141 (297)
T ss_pred hhHhccccccHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999998864 334443 3447999999998887766688999999999999999999999999999
Q ss_pred HHHHHHHHhhhhhHHHHHHhHH------HHHHHHhhhhhhHHHHHH----------HHHHHHHHHHHhccCCCHHHHHHH
Q psy14608 87 TQTDYRERCKGRIQRQLEISKK------FVEVMTEYNRTQTDYRER----------CKGRIQRQLEITGRTTTNEELEAM 150 (199)
Q Consensus 87 ~Q~~~~~k~k~r~~rq~~i~~~------~~e~~~e~~~~~~~~~e~----------~k~~iqRq~eI~~~e~sieEl~~m 150 (199)
+|.+|+++|+++++||+.|+++ ..+.|.+.+..+.+.+.. +.+.-.|.-+|..++.++.||++|
T Consensus 142 ~~~~~r~~~k~~i~Rql~i~~~~~~~de~ie~~ie~g~~~~f~~~~i~~~~~~~~~l~Eiq~Rh~~ik~LEksi~ELhql 221 (297)
T KOG0810|consen 142 TQSKYREEYKERIQRQLFIVGGEETTDEEIEEMIESGGSEVFTQKAIQDRGQAKQTLAEIQERHDEIKKLEKSIRELHQL 221 (297)
T ss_pred HHHHHHHHHHHHHHHHHhhhCCCcCChHHHHHHHHCCChHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999975 355666665444333322 333446788999999999999999
Q ss_pred HhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q psy14608 151 LDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKARR 199 (199)
Q Consensus 151 ~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~RK 199 (199)
|-|.+ .++..||||||+||+||++|.+||++|..++.+|+.||+++||
T Consensus 222 FlDMa-~LVe~QgEmvd~IE~nV~~A~~~V~~g~~~~~kAv~~qkkaRK 269 (297)
T KOG0810|consen 222 FLDMA-VLVESQGEMVDRIENNVENAVDYVEQGVDHLKKAVKYQKKARK 269 (297)
T ss_pred HHHHH-HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99976 4457779999999999999999999999999999999999997
No 2
>KOG0811|consensus
Probab=99.77 E-value=7.8e-18 Score=144.05 Aligned_cols=139 Identities=27% Similarity=0.376 Sum_probs=102.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHhHHH------HHHHH----hhh---hhh---HH
Q psy14608 60 SADLRIRKTQHSTLSRKFVEVMTEYNRTQTDYRERCK-GRIQRQLEISKKF------VEVMT----EYN---RTQ---TD 122 (199)
Q Consensus 60 s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q~~~~~k~k-~r~~rq~~i~~~~------~e~~~----e~~---~~~---~~ 122 (199)
+.+.+..+.+.+.|...|..++..|+.+|+...+..+ ...++-+..+..+ ...+. .+. +++ .+
T Consensus 87 ~~~~~~~k~~~~kL~~ef~~~l~efq~vQrk~ae~ek~~~~a~~s~~s~~~~~~~~~~~~~~~~~~~~~~q~e~~~q~~e 166 (269)
T KOG0811|consen 87 ESDLRQLKIQLDKLVDEFSAALKEFQKVQRKSAEREKIPMVARGSQNSQQLDEESPRVDELSNNGSQSQQQLEEQAQDNE 166 (269)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccccccccccchhhhhhhhhhhhhhccchhhhhHHHHHHhhhh
Confidence 5667899999999999999999999999999998886 2222211111111 11100 000 011 01
Q ss_pred HHHHHHHHH-HHHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q psy14608 123 YRERCKGRI-QRQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKARR 199 (199)
Q Consensus 123 ~~e~~k~~i-qRq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~RK 199 (199)
+-+-....| .|.-.|..++..|-|||+||.+++ .++++||++||+||+||++|.+||+.|+.+|.+|.+|++++||
T Consensus 167 ~~~~~~~~ieeR~q~I~~lE~dI~dvN~IFkdL~-~lV~eQG~~VDsIe~nve~a~~nveqg~~~L~kA~~yq~~~~k 243 (269)
T KOG0811|consen 167 ILEYQLDLIEEREQAIEQLEADIIDVNEIFKDLG-SLVHEQGELVDSIEANVENASVNVEQGTENLRKAAKYQRKARK 243 (269)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 111111223 377889999999999999999998 5668889999999999999999999999999999999999986
No 3
>KOG0809|consensus
Probab=99.66 E-value=9.2e-16 Score=131.10 Aligned_cols=141 Identities=21% Similarity=0.345 Sum_probs=108.5
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhHHH--------HHHHHh--hhhhh-HHHHHH
Q psy14608 58 KSSADLRIRKTQHSTLSRKFVEVMTEYNRTQTDYRERCKGRIQRQLEISKKF--------VEVMTE--YNRTQ-TDYRER 126 (199)
Q Consensus 58 ~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q~~~~~k~k~r~~rq~~i~~~~--------~e~~~e--~~~~~-~~~~e~ 126 (199)
+++.+.-+++|.+..|+..++++..+|+..|..|.++++.+-++....--.+ .+.... +++.+ ..+...
T Consensus 130 ~~~~e~~~~~n~~~~la~~LQ~~s~~fR~~Qs~YLK~l~~~ee~~~~~e~~~~~~~~~~dd~d~~~~~~qe~ql~~~e~~ 209 (305)
T KOG0809|consen 130 LSPSERLLRKNAQGYLALQLQTLSREFRGLQSKYLKRLRNREENSQEYEDSLDNTVDLPDDEDFSDRTFQEQQLMLFENN 209 (305)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhhcccchhhhccccccCcchhhhhhhhHHHHHHHHHhcc
Confidence 4567777888999999999999999999999999999998877744322111 111100 11111 112222
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q psy14608 127 CKGRIQRQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKARR 199 (199)
Q Consensus 127 ~k~~iqRq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~RK 199 (199)
-..-+.|.-||.....||-||++||.|++.+| .+||.+||+|+|||+++..+|+.|.++|.||..|||+++|
T Consensus 210 ~~~~~erE~EV~ql~~sI~dL~~if~DL~~lV-vdQGtvvDRIDyNvEqt~~~v~~a~keL~KAe~yQk~~~k 281 (305)
T KOG0809|consen 210 EEVVREREKEVTQLVESIYDLNQIFKDLSALV-VDQGTVVDRIDYNVEQTQVRVEDALKELHKAERYQKRNKK 281 (305)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhccchhheecchhhhhhhHHhHHHHHHHHHHHHhcCCc
Confidence 22245778899999999999999999987556 4559999999999999999999999999999999999986
No 4
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=99.61 E-value=1.6e-14 Score=113.20 Aligned_cols=117 Identities=50% Similarity=0.650 Sum_probs=89.1
Q ss_pred hhhcccchhhhhHHHhhcccch--HHHHHHHHhHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 12 QIIETRLIEQSIEQEEQSNKSS--ADLRIRDTQLRMIEQSIEQEEQSNKSSADLRIRKTQHSTLSRKFVEVMTEYNRTQT 89 (199)
Q Consensus 12 ~~~~~~~~e~~~~~~~~~n~~~--~dlr~~~~~Lk~l~~~~~~~~~~~~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q~ 89 (199)
.+++++.....+...++.-... .-.+..+..|+.|..........+ ++++.|++++|+..|+.+|.++|..|+.+|.
T Consensus 31 ~~~t~~~~~~~~~~~l~~~~~~~~~~~~~ik~~lk~l~~~~~~~~~~~-~s~~~r~~~~q~~~L~~~f~~~m~~fq~~Q~ 109 (151)
T cd00179 31 QLLTAPDADPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEALN-GSSVDRIRKTQHSGLSKKFVEVMTEFNKAQR 109 (151)
T ss_pred HHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566665444555544332111 111233367777766655433222 8899999999999999999999999999999
Q ss_pred HHHHHhhhhhHHHHHHhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHhcCCcccccc
Q psy14608 90 DYRERCKGRIQRQLEISKKFVEVMTEYNRTQTDYRERCKGRIQRQLEITGRTTTNEELEAMLDTGNPAVFTQ 161 (199)
Q Consensus 90 ~~~~k~k~r~~rq~~i~~~~~e~~~e~~~~~~~~~e~~k~~iqRq~eI~~~e~sieEl~~m~~~~~~~vf~q 161 (199)
. |++.|+.++.|++.|++|++|++||++|+++|+|.+|.+
T Consensus 110 ~--------------------------------~~~~~k~~i~Rq~~i~~~~~tdeei~~~~~~~~~~~~~~ 149 (151)
T cd00179 110 K--------------------------------YRERYKERIQRQLEITGGEATDEELEDMLESGNSEIFTS 149 (151)
T ss_pred H--------------------------------HHHHHHHHHHHHHHHcCCCCChHHHHHHHHcCChhhhcC
Confidence 9 888888999999999999999999999999998888876
No 5
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=99.48 E-value=8.9e-13 Score=109.73 Aligned_cols=134 Identities=24% Similarity=0.328 Sum_probs=109.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhHHH------HHHHHhhhhhh--HHHH----------HH
Q psy14608 65 IRKTQHSTLSRKFVEVMTEYNRTQTDYRERCKGRIQRQLEISKKF------VEVMTEYNRTQ--TDYR----------ER 126 (199)
Q Consensus 65 i~k~q~~~L~~~f~e~m~~yq~~Q~~~~~k~k~r~~rq~~i~~~~------~e~~~e~~~~~--~~~~----------e~ 126 (199)
-++.|.....++|.+++.+|+.++..|++-++.+..||+.|+++- .+.+.+-+..+ ++|- -.
T Consensus 97 ~k~aQae~~r~Kf~~~I~~yr~i~~~yree~~e~~rrQy~Ia~P~ATEdeve~aInd~nG~qvfsqalL~anr~geAkta 176 (280)
T COG5074 97 NKQAQAENVRQKFLKLIQDYRIIDSNYREEEKEQARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNANRRGEAKTA 176 (280)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhhhcCCccchHHHHHHhcccchHHHHHHHHHhcCccchHHHH
Confidence 357788889999999999999999999999999999999999852 22333433333 3332 11
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q psy14608 127 CKGRIQRQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKARR 199 (199)
Q Consensus 127 ~k~~iqRq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~RK 199 (199)
+++--.|..+|..++.++.||-++|.+.. ..+.+|.+++|.|..||+.+..+|++|+.++.+|.+|.|++||
T Consensus 177 L~Evq~Rh~~ikkiEkt~ael~qLfndm~-~~V~eq~e~Vd~I~~~~~~~~~n~~~g~~h~d~AvksaRaaRk 248 (280)
T COG5074 177 LAEVQARHQEIKKIEKTMAELTQLFNDME-ELVIEQQENVDVIDKNVEDAQENVEQGVGHTDKAVKSARAARK 248 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcchHHHHHhhHhhHHhhHHHhhhhHHHHHHHHHHHHh
Confidence 33344677889999999999999999876 4456679999999999999999999999999999999999986
No 6
>COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=99.38 E-value=4.7e-12 Score=107.70 Aligned_cols=68 Identities=24% Similarity=0.427 Sum_probs=63.3
Q ss_pred HHHHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q psy14608 131 IQRQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKARR 199 (199)
Q Consensus 131 iqRq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~RK 199 (199)
.+|.-+|.++..+|-||++||.|++ .++.+||++||+||+|+++|.+|++.|..+|.+|-.|||+++|
T Consensus 191 ~er~~eI~~l~~gI~Eln~IF~dL~-~lV~eQG~lVdrID~Ni~~t~~n~k~A~kEL~kA~~hqrrt~k 258 (283)
T COG5325 191 TERDEEIKNLARGIYELNEIFRDLG-SLVGEQGELVDRIDFNIENTSDNLKNANKELEKAPAHQRRTKK 258 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhhhhHHhhhhhhhhHHHHhhHHHHHHhHHHHhhhcc
Confidence 3678899999999999999999987 5668889999999999999999999999999999999999876
No 7
>KOG0810|consensus
Probab=99.00 E-value=5.7e-08 Score=84.71 Aligned_cols=95 Identities=40% Similarity=0.575 Sum_probs=79.5
Q ss_pred HHhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcc-CCCHHHHHHHHhcCCcccccch--------------------
Q psy14608 104 EISKKFVEVMTEYNRTQTDYRERCKGRIQRQLEITGR-TTTNEELEAMLDTGNPAVFTQG-------------------- 162 (199)
Q Consensus 104 ~i~~~~~e~~~e~~~~~~~~~e~~k~~iqRq~eI~~~-e~sieEl~~m~~~~~~~vf~qq-------------------- 162 (199)
.+.++|.+.|.+|+.++..|++.|+.+|+|||.|+++ .+++++|+.|+++|++.+|.+.
T Consensus 127 ~~~kkf~~~M~~f~~~~~~~r~~~k~~i~Rql~i~~~~~~~de~ie~~ie~g~~~~f~~~~i~~~~~~~~~l~Eiq~Rh~ 206 (297)
T KOG0810|consen 127 ALSKKLKELMNEFNRTQSKYREEYKERIQRQLFIVGGEETTDEEIEEMIESGGSEVFTQKAIQDRGQAKQTLAEIQERHD 206 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCcCChHHHHHHHHCCChHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 3445788999999999999999999999999999999 9999999999999999988652
Q ss_pred -------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q psy14608 163 -------------------GEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKAR 198 (199)
Q Consensus 163 -------------------Ge~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~R 198 (199)
-.+|..=-..|+....+|..|...+..|..+=++|+
T Consensus 207 ~ik~LEksi~ELhqlFlDMa~LVe~QgEmvd~IE~nV~~A~~~V~~g~~~~~kAv 261 (297)
T KOG0810|consen 207 EIKKLEKSIRELHQLFLDMAVLVESQGEMVDRIENNVENAVDYVEQGVDHLKKAV 261 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444455677788888889888888888776664
No 8
>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [, ]. Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure []. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related []. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; GO: 0005515 protein binding; PDB: 1URQ_B 3RL0_R 1HVV_B 1SFC_B 1N7S_B 3IPD_B 3C98_B 3HD7_F 3RK2_B 1KIL_B ....
Probab=98.89 E-value=1.4e-09 Score=73.24 Aligned_cols=60 Identities=32% Similarity=0.433 Sum_probs=52.3
Q ss_pred HHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 135 LEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQS 195 (199)
Q Consensus 135 ~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qk 195 (199)
-.|..++.++.+|++||.+.+ ..+..||++||+|+.||+.|..++..|..+|.+|.+|+|
T Consensus 4 ~~l~~l~~~i~~l~~~~~~i~-~ev~~Q~~~ld~i~~~vd~~~~~l~~~~~~l~ka~~~~k 63 (63)
T PF05739_consen 4 EELDELEQSIQELKQMFQDIG-EEVEEQNEMLDRIEDNVDRANENLKKGNKKLKKALKYQK 63 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344555788899999999976 445777999999999999999999999999999999986
No 9
>cd00193 t_SNARE Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent
Probab=98.53 E-value=5.8e-08 Score=64.02 Aligned_cols=56 Identities=29% Similarity=0.321 Sum_probs=48.0
Q ss_pred HHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 134 QLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKA 190 (199)
Q Consensus 134 q~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA 190 (199)
..++..+..++.+|+.||.+.+. .+..||++||+|++||+.+..++..|...|.+|
T Consensus 5 ~~~l~~l~~~i~~l~~l~~~i~~-~v~~Q~~~ld~i~~~~~~~~~~~~~~~~~l~ka 60 (60)
T cd00193 5 DEELEQLEASIGELKQIFLDLGT-EVEEQGELLDRIEDNVDNADVNVKRANKRLKKA 60 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34556668899999999999764 446679999999999999999999999999876
No 10
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=98.51 E-value=1e-06 Score=65.70 Aligned_cols=84 Identities=26% Similarity=0.359 Sum_probs=55.8
Q ss_pred chhhcccchhhhhHHHhhcc--cchHHHHHHHHhHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 11 PQIIETRLIEQSIEQEEQSN--KSSADLRIRDTQLRMIEQSIEQEEQSNKSSADLRIRKTQHSTLSRKFVEVMTEYNRTQ 88 (199)
Q Consensus 11 ~~~~~~~~~e~~~~~~~~~n--~~~~dlr~~~~~Lk~l~~~~~~~~~~~~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q 88 (199)
..+++++..+..+..++... .+..-.+..+..|+.|......... .++++.|++++|+..|+..|.++|.+||.+|
T Consensus 32 ~~~l~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~--~~~~~~r~~~~q~~~L~~~f~~~m~~fq~~Q 109 (117)
T smart00503 32 EELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRA--SGSASDRTRKAQTEKLRKKFKEVMNEFQRLQ 109 (117)
T ss_pred HHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcc--cCCHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566665445554444321 1111113333677777665543222 2577899999999999999999999999999
Q ss_pred HHHHHHhh
Q psy14608 89 TDYRERCK 96 (199)
Q Consensus 89 ~~~~~k~k 96 (199)
..|+++||
T Consensus 110 ~~~~~~~k 117 (117)
T smart00503 110 RKYREREK 117 (117)
T ss_pred HHHHHHcC
Confidence 99888775
No 11
>smart00397 t_SNARE Helical region found in SNAREs. All alpha-helical motifs that form twisted and parallel four-helix bundles in target soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor proteins. This motif found in "Q-SNAREs".
Probab=98.22 E-value=8.8e-07 Score=59.20 Aligned_cols=57 Identities=28% Similarity=0.324 Sum_probs=48.5
Q ss_pred HHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 133 RQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKA 190 (199)
Q Consensus 133 Rq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA 190 (199)
|...|..+..++.+++.||.+.+ ..+.+||++||+|++|++.+..++..|...|.+|
T Consensus 10 ~~~~l~~l~~~i~~l~~l~~~i~-~~v~~Q~~~ld~i~~~~d~~~~~~~~~~~~l~~~ 66 (66)
T smart00397 10 RDEELEQLEKSIGELKQIFLDMG-TELEEQGEQLDRIEDNVDDADVNLKKANKRLKKA 66 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcC
Confidence 34456666889999999999876 4457779999999999999999999999999875
No 12
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=97.64 E-value=0.0004 Score=50.04 Aligned_cols=69 Identities=28% Similarity=0.429 Sum_probs=48.3
Q ss_pred chhhcccchhhhhHHHhhcccchHHH----HHHHHhHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHHH
Q psy14608 11 PQIIETRLIEQSIEQEEQSNKSSADL----RIRDTQLRMIEQSIEQEEQSNKSSADLRIRKTQHSTLSRKFVEVM 81 (199)
Q Consensus 11 ~~~~~~~~~e~~~~~~~~~n~~~~dl----r~~~~~Lk~l~~~~~~~~~~~~~s~e~Ri~k~q~~~L~~~f~e~m 81 (199)
..+|++|..+...+.+.+. ...++ ..-..+|+.|...+......++++++.|++++|+..|+.+|+++|
T Consensus 31 ~~~l~~~~~d~~~~~el~~--l~~~i~~~~~~~~~~lk~l~~~~~~~~~~~~~~~~~ri~~nq~~~L~~kf~~~m 103 (103)
T PF00804_consen 31 KKILSSPDQDSELKRELDE--LTDEIKQLFQKIKKRLKQLSKDNEDSEGEEPSSNEVRIRKNQVQALSKKFQEVM 103 (103)
T ss_dssp HHHHTSSSHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHCTT--SHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhcCCCCcchhHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhhhcccCCCcHHHHHHHHHHHHHHHHHHHHC
Confidence 3567777755455554432 33333 334478888888877556678899999999999999999999987
No 13
>KOG0812|consensus
Probab=96.86 E-value=0.00071 Score=58.51 Aligned_cols=65 Identities=18% Similarity=0.220 Sum_probs=54.4
Q ss_pred HHHHHHhccCCCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14608 132 QRQLEITGRTTTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKA 197 (199)
Q Consensus 132 qRq~eI~~~e~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~ 197 (199)
+|--.+.+++.+|-||-.||..+++ ++.+|||++-+|+.||+.+..+++.|..+|.|--..=.++
T Consensus 224 ~R~~~~q~IEstIsElG~IF~QLA~-mVseQ~E~i~RID~nv~ds~lnI~gA~~ellKy~e~vSSN 288 (311)
T KOG0812|consen 224 ERAKTMQNIESTISELGGIFQQLAS-MVSEQEETIQRIDDNVDDSDLNIEGAHSELLKYFERVSSN 288 (311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHhccc
Confidence 4555777899999999999999874 5588899999999999999999999999998755443333
No 14
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=96.38 E-value=0.063 Score=38.97 Aligned_cols=39 Identities=33% Similarity=0.525 Sum_probs=31.9
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14608 58 KSSADLRIRKTQHSTLSRKFVEVMTEYNRTQTDYRERCK 96 (199)
Q Consensus 58 ~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q~~~~~k~k 96 (199)
......+..+.+.+.|+..|..++.+|+.+|..|.++.+
T Consensus 61 ~~~~~~~~~k~~~~KL~~df~~~l~~fq~~q~~~~~~~k 99 (102)
T PF14523_consen 61 SDRSNDRQQKLQREKLSRDFKEALQEFQKAQRRYAEKEK 99 (102)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345667888999999999999999999999999887665
No 15
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=93.86 E-value=0.66 Score=39.47 Aligned_cols=90 Identities=24% Similarity=0.420 Sum_probs=70.6
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHhc-CCcccccc------------------h-----
Q psy14608 107 KKFVEVMTEYNRTQTDYRERCKGRIQRQLEITGRTTTNEELEAMLDT-GNPAVFTQ------------------G----- 162 (199)
Q Consensus 107 ~~~~e~~~e~~~~~~~~~e~~k~~iqRq~eI~~~e~sieEl~~m~~~-~~~~vf~q------------------q----- 162 (199)
++|.+.+..|-.++.-|++..+++..|||.|..|++|++|++..+.+ +|..||.+ |
T Consensus 107 ~Kf~~~I~~yr~i~~~yree~~e~~rrQy~Ia~P~ATEdeve~aInd~nG~qvfsqalL~anr~geAktaL~Evq~Rh~~ 186 (280)
T COG5074 107 QKFLKLIQDYRIIDSNYREEEKEQARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNANRRGEAKTALAEVQARHQE 186 (280)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHhhhhcCCccchHHHHHHhcccchHHHHHHHHHhcCccchHHHHHHHHHHHHHH
Confidence 46778888888888889999999999999999999999999999965 44578853 1
Q ss_pred ------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy14608 163 ------------------GEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSK 196 (199)
Q Consensus 163 ------------------Ge~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk 196 (199)
.+++--=+.||+...++|..|..++..+..|--+
T Consensus 187 ikkiEkt~ael~qLfndm~~~V~eq~e~Vd~I~~~~~~~~~n~~~g~~h~d~ 238 (280)
T COG5074 187 IKKIEKTMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQENVEQGVGHTDK 238 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHhhHhhHHhhHHHhhhhHHH
Confidence 3333333457888888888888888888776543
No 16
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=80.56 E-value=11 Score=28.93 Aligned_cols=31 Identities=39% Similarity=0.551 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhHH
Q psy14608 71 STLSRKFVEVMTEYNRTQTDYRERCKGRIQRQLEISKK 108 (199)
Q Consensus 71 ~~L~~~f~e~m~~yq~~Q~~~~~k~k~r~~rq~~i~~~ 108 (199)
..+...|+.+=..|.. +|+.++.||++|+++
T Consensus 98 ~~~m~~fq~~Q~~~~~-------~~k~~i~Rq~~i~~~ 128 (151)
T cd00179 98 VEVMTEFNKAQRKYRE-------RYKERIQRQLEITGG 128 (151)
T ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHcCC
Confidence 3556678888888885 678899999999874
No 17
>KOG3894|consensus
Probab=77.09 E-value=9.4 Score=33.77 Aligned_cols=53 Identities=19% Similarity=0.240 Sum_probs=41.6
Q ss_pred CCHHHHHHHHhcCCcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q psy14608 142 TTNEELEAMLDTGNPAVFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKALKYQSKAR 198 (199)
Q Consensus 142 ~sieEl~~m~~~~~~~vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA~~~qkk~R 198 (199)
+.|.-|+.+|-. .| .+|..-||.|-.++-.|..++..|+..|++|.....+.|
T Consensus 242 vEI~~Lq~ifse---hv-l~Q~~~Id~I~d~~~~~teNIk~gNe~irka~~~~~~~r 294 (316)
T KOG3894|consen 242 VEISALQDIFSE---HV-LQQDQNIDLIHDLQSGATENIKDGNEEIRKAKRNNGGLR 294 (316)
T ss_pred HHHHHHHHHHHH---HH-HHHHHHHHHHHHhcccchhhhhhhHHHHHHHHHhcccch
Confidence 344556666654 34 455889999999999999999999999999998766554
No 18
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=44.59 E-value=1.2e+02 Score=21.80 Aligned_cols=24 Identities=54% Similarity=0.845 Sum_probs=19.9
Q ss_pred HHhHHHHHHHHhhhhhhHHHHHHH
Q psy14608 104 EISKKFVEVMTEYNRTQTDYRERC 127 (199)
Q Consensus 104 ~i~~~~~e~~~e~~~~~~~~~e~~ 127 (199)
.+...|.+.|.+|+.++..|++.|
T Consensus 93 ~L~~~f~~~m~~fq~~Q~~~~~~~ 116 (117)
T smart00503 93 KLRKKFKEVMNEFQRLQRKYRERE 116 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHc
Confidence 666778899999999998888765
No 19
>PF09164 VitD-bind_III: Vitamin D binding protein, domain III; InterPro: IPR015247 This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin []. ; PDB: 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A.
Probab=39.87 E-value=69 Score=21.94 Aligned_cols=29 Identities=28% Similarity=0.578 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCHHHHHHHHhc
Q psy14608 121 TDYRERCKGRIQRQLEITGRTTTNEELEAMLDT 153 (199)
Q Consensus 121 ~~~~e~~k~~iqRq~eI~~~e~sieEl~~m~~~ 153 (199)
++|+.++.+++...+ |+++..+|.+|++.
T Consensus 12 tEyKKrL~e~l~~k~----P~at~~~l~~lve~ 40 (68)
T PF09164_consen 12 TEYKKRLAERLRAKL----PDATPTELKELVEK 40 (68)
T ss_dssp HHHHHHHHHHHHHH-----TTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHC----CCCCHHHHHHHHHH
Confidence 568877776654444 89999999999975
No 20
>KOG3065|consensus
Probab=36.24 E-value=48 Score=28.89 Aligned_cols=30 Identities=33% Similarity=0.349 Sum_probs=26.3
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 160 TQGGEMIDRIEYHVEHAVDYVQTATQDTKK 189 (199)
Q Consensus 160 ~qqGe~iD~IE~NVe~a~~~v~~g~~eL~k 189 (199)
..|-+.||+|+++|+.....|..++.-+++
T Consensus 242 e~Qn~~Ld~I~~k~d~~d~~v~~~n~R~~k 271 (273)
T KOG3065|consen 242 ESQNERLDRIEDKVDRLDLRVDKANKRAKK 271 (273)
T ss_pred HHHhHHHhHHHHHHHhhhhHHHHHHHHHHh
Confidence 567999999999999999999998877654
No 21
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=32.23 E-value=3.8e+02 Score=24.19 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 68 TQHSTLSRKFVEVMTEYNRTQTD 90 (199)
Q Consensus 68 ~q~~~L~~~f~e~m~~yq~~Q~~ 90 (199)
+|+..|...|..+..++..++..
T Consensus 266 ~qle~l~~eYr~~~~~ls~~~~~ 288 (359)
T PF10498_consen 266 NQLEPLIQEYRSAQDELSEVQEK 288 (359)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444433333
No 22
>KOG3065|consensus
Probab=27.79 E-value=62 Score=28.19 Aligned_cols=33 Identities=15% Similarity=0.324 Sum_probs=28.2
Q ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 158 VFTQGGEMIDRIEYHVEHAVDYVQTATQDTKKA 190 (199)
Q Consensus 158 vf~qqGe~iD~IE~NVe~a~~~v~~g~~eL~kA 190 (199)
.+.+||+.|++||.|+.........|..+|..-
T Consensus 101 ~L~~Q~eQL~rte~~lD~i~~d~~~~er~l~~l 133 (273)
T KOG3065|consen 101 MLSEQGEQLERTEKNLDDIKVDLKRAERNLTEL 133 (273)
T ss_pred HHHHhHHHHHhHHhhhhhhHHHHHHHHHHHHHH
Confidence 346779999999999999999999998887643
No 23
>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.
Probab=24.86 E-value=4.8e+02 Score=22.99 Aligned_cols=62 Identities=19% Similarity=0.251 Sum_probs=46.1
Q ss_pred HHhHHHHHHHHHH-HhhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh--hhHH
Q psy14608 40 DTQLRMIEQSIEQ-EEQSNKSSADLRIRKTQHSTLSRKFVEVMTEYNRTQTDYRERCKG--RIQR 101 (199)
Q Consensus 40 ~~~Lk~l~~~~~~-~~~~~~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~Q~~~~~k~k~--r~~r 101 (199)
+..|..+...+.. ...+..-..+..--.-|+..|...+-+.=..|..+++.|.+||+. |..+
T Consensus 83 k~~l~evEekyrkAMv~naQLDNek~~l~yqvd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~ 147 (302)
T PF09738_consen 83 KDSLAEVEEKYRKAMVSNAQLDNEKSALMYQVDLLKDKLEELEETLAQLQREYREKIRELERQKR 147 (302)
T ss_pred HHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3778777777776 333333334555567899999999999999999999999998885 4444
No 24
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.00 E-value=7e+02 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.324 Sum_probs=21.4
Q ss_pred CCHHHHHHHHhcCCc-ccccchhhhHHHHHHH
Q psy14608 142 TTNEELEAMLDTGNP-AVFTQGGEMIDRIEYH 172 (199)
Q Consensus 142 ~sieEl~~m~~~~~~-~vf~qqGe~iD~IE~N 172 (199)
.-++|||.++.++ | .+|. |..+|+|..+
T Consensus 1137 ~~~~~~n~~~~~~-w~~~~~--~~~~~~i~~~ 1165 (1311)
T TIGR00606 1137 MKMEEINKIIRDL-WRSTYR--GQDIEYIEIR 1165 (1311)
T ss_pred HHHHHHHHHHHHH-HHHHcC--ccHHHHhhcC
Confidence 4568899999887 5 4444 9999999983
No 25
>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=22.08 E-value=4e+02 Score=21.07 Aligned_cols=68 Identities=21% Similarity=0.240 Sum_probs=35.3
Q ss_pred chhhhhHH--H-hhcccchHHHHHHHHhHHHHHHHHHH-H---h---hcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 18 LIEQSIEQ--E-EQSNKSSADLRIRDTQLRMIEQSIEQ-E---E---QSNKSSADLRIRKTQHSTLSRKFVEVMTEYNRT 87 (199)
Q Consensus 18 ~~e~~~~~--~-~~~n~~~~dlr~~~~~Lk~l~~~~~~-~---~---~~~~~s~e~Ri~k~q~~~L~~~f~e~m~~yq~~ 87 (199)
+.++.|.+ + .+....+.|.+ ..|+.|...+.- + . ..+++..+. +-.....|...+.-++++|+-.
T Consensus 52 L~~~gi~qLy~~~~~~~~~~d~~---~eLkkL~~sll~nfleLl~~l~~~P~~~~~--ki~~i~~L~~NmhhllNeyRPh 126 (162)
T PF05983_consen 52 LESQGIRQLYPPDDDPSPSVDRK---KELKKLNKSLLLNFLELLDILSKNPSQYER--KIEDIRLLFINMHHLLNEYRPH 126 (162)
T ss_dssp ------------------HHHHH---HHHHHHHHHHHHHHHHHTTSS---CCCHHH--HHHHHHHHHHHHHHHHHHTHHH
T ss_pred chhccccccCCCccccCCCchHH---HHHHHHHHHHHHHHHHHHHHHHhCCccHHH--HHHHHHHHHHHHHHHHHHhCHH
Confidence 44555555 1 12223445555 677777776664 2 1 224455555 4456788888999999999998
Q ss_pred HHH
Q psy14608 88 QTD 90 (199)
Q Consensus 88 Q~~ 90 (199)
|..
T Consensus 127 QAR 129 (162)
T PF05983_consen 127 QAR 129 (162)
T ss_dssp HHH
T ss_pred HHH
Confidence 877
No 26
>PF15205 PLAC9: Placenta-specific protein 9
Probab=21.67 E-value=1.7e+02 Score=20.25 Aligned_cols=25 Identities=24% Similarity=0.308 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Q psy14608 164 EMIDRIEYHVEHAVDYVQTATQDTK 188 (199)
Q Consensus 164 e~iD~IE~NVe~a~~~v~~g~~eL~ 188 (199)
.-+|.||.-|++|+++.+.-.+-|-
T Consensus 25 ~RLdviEe~veKTVEhLeaEvk~LL 49 (74)
T PF15205_consen 25 SRLDVIEETVEKTVEHLEAEVKGLL 49 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3469999999999999887665553
No 27
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=20.64 E-value=3.4e+02 Score=19.72 Aligned_cols=15 Identities=7% Similarity=0.204 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHH
Q psy14608 76 KFVEVMTEYNRTQTD 90 (199)
Q Consensus 76 ~f~e~m~~yq~~Q~~ 90 (199)
.+.+.+..|+..|..
T Consensus 4 ~~q~~~~~~q~~q~~ 18 (110)
T TIGR02338 4 QVQNQLAQLQQLQQQ 18 (110)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456667777777666
Done!