Query psy15388
Match_columns 217
No_of_seqs 117 out of 857
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 19:41:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0859|consensus 100.0 8.6E-53 1.9E-57 336.3 2.9 192 2-203 3-196 (217)
2 KOG0862|consensus 100.0 3E-43 6.4E-48 286.5 8.3 193 1-193 1-195 (216)
3 KOG0861|consensus 100.0 8.1E-31 1.8E-35 206.3 7.1 149 35-188 42-193 (198)
4 COG5143 SNC1 Synaptobrevin/VAM 99.9 3.5E-26 7.7E-31 184.0 1.2 183 5-193 4-190 (190)
5 KOG0860|consensus 99.8 1.4E-23 2.9E-28 155.9 -7.6 74 130-203 26-100 (116)
6 PF13774 Longin: Regulated-SNA 99.8 2.9E-19 6.3E-24 127.6 5.8 81 36-117 1-82 (83)
7 PF00957 Synaptobrevin: Synapt 99.7 4.5E-21 9.8E-26 138.9 -9.9 72 132-203 2-74 (89)
8 COG5143 SNC1 Synaptobrevin/VAM 96.7 2.2E-05 4.7E-10 63.9 -7.5 72 134-205 95-167 (190)
9 PF09426 Nyv1_N: Vacuolar R-SN 96.1 0.0064 1.4E-07 46.6 3.4 58 36-93 46-110 (141)
10 PF04086 SRP-alpha_N: Signal r 92.9 0.18 3.9E-06 43.5 5.0 78 50-127 18-100 (279)
11 PF01217 Clat_adaptor_s: Clath 91.1 0.65 1.4E-05 35.8 5.7 95 1-100 1-96 (141)
12 PF04099 Sybindin: Sybindin-li 88.5 1.9 4.1E-05 33.6 6.5 86 38-124 46-141 (142)
13 COG5122 TRS23 Transport protei 76.5 17 0.00036 27.5 6.9 81 40-123 46-131 (134)
14 PF08923 MAPKK1_Int: Mitogen-a 72.4 40 0.00086 25.5 8.5 83 10-93 24-110 (119)
15 KOG0938|consensus 63.9 29 0.00062 31.3 6.8 48 53-100 46-93 (446)
16 PF03164 Mon1: Trafficking pro 61.3 47 0.001 30.5 8.1 84 13-100 21-104 (415)
17 KOG0781|consensus 58.1 30 0.00066 32.7 6.2 86 4-101 5-96 (587)
18 PF04628 Sedlin_N: Sedlin, N-t 56.5 22 0.00048 27.0 4.4 52 51-102 54-109 (132)
19 KOG3369|consensus 52.6 69 0.0015 26.1 6.6 82 40-124 110-196 (199)
20 KOG3368|consensus 37.8 1.9E+02 0.0041 22.5 6.7 55 37-93 45-102 (140)
21 PF03607 DCX: Doublecortin; I 36.6 83 0.0018 20.5 4.2 48 30-77 8-57 (60)
22 KOG1983|consensus 36.5 4.4 9.6E-05 41.4 -3.0 39 150-188 944-983 (993)
23 TIGR01478 STEVOR variant surfa 30.1 39 0.00084 29.6 2.1 25 131-155 101-125 (295)
24 PF07981 Plasmod_MYXSPDY: Plas 30.0 54 0.0012 16.0 1.7 16 190-205 1-16 (17)
25 COG2018 Uncharacterized distan 29.9 2.4E+02 0.0051 21.4 6.1 68 11-82 27-102 (119)
26 PF03259 Robl_LC7: Roadblock/L 29.3 1.4E+02 0.0031 20.1 4.7 63 11-73 23-88 (91)
27 PF04799 Fzo_mitofusin: fzo-li 27.1 16 0.00035 29.5 -0.7 44 136-179 112-156 (171)
28 PTZ00370 STEVOR; Provisional 26.7 48 0.001 29.0 2.1 39 117-155 86-124 (296)
29 PF05659 RPW8: Arabidopsis bro 23.7 65 0.0014 25.2 2.2 51 114-164 31-82 (147)
30 KOG3230|consensus 22.8 90 0.002 25.9 2.9 44 117-169 119-165 (224)
31 PHA03011 hypothetical protein; 22.3 1.3E+02 0.0028 22.2 3.4 54 115-170 62-115 (120)
32 PF04079 DUF387: Putative tran 22.0 2.2E+02 0.0047 22.6 4.9 79 80-160 25-121 (159)
33 PF02520 DUF148: Domain of unk 21.3 80 0.0017 23.1 2.2 28 132-159 35-62 (113)
34 PF10504 DUF2452: Protein of u 21.0 1.2E+02 0.0026 24.2 3.2 59 30-88 61-125 (159)
35 KOG0810|consensus 20.8 20 0.00043 31.6 -1.4 72 133-204 206-288 (297)
No 1
>KOG0859|consensus
Probab=100.00 E-value=8.6e-53 Score=336.30 Aligned_cols=192 Identities=20% Similarity=0.372 Sum_probs=180.6
Q ss_pred hhhhhHHHhhcCceeeeeeccccccccchhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEEeeccccch
Q psy15388 2 FLLTMIARVRDGLILSASMQDDEYSERSTLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLALCEKTFST 81 (217)
Q Consensus 2 I~~~~IaR~~D~l~L~~~~~~~~~~~~~~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~p~ 81 (217)
|+|+.|||| .++|++++. . .+||..++.++|+++|+..+.|+||++|+|+|||+++||++|+|+++.++++
T Consensus 3 iiYs~VARG--TvvLaeft~--~-----~gNf~sva~qiL~klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR 73 (217)
T KOG0859|consen 3 IIYSFVARG--TVILAEFTE--F-----SGNFSSIAAQILQKLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGR 73 (217)
T ss_pred eeEEEEecc--eEEEEeeee--c-----cCCHHHHHHHHHHhCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEeccccc
Confidence 899999998 588999984 2 3699999999999999866779999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhhhccCccceeccceeE-EeechHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHhh
Q psy15388 82 KVAYSYLESLSLEFHGQYGGQFEQCTRPYAF-VEFDSSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINATM 160 (217)
Q Consensus 82 ~~af~fL~ei~~~F~~~~~~~~~~~~~~~~~-~~F~~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~Rg 160 (217)
++||.||++|+++|.+.|+....++. +|++ .+|++.|++.|++|.+.|+.|++.+++.|++|||+||.+|||++|+||
T Consensus 74 ~ipfaFLe~Ik~~F~k~YG~~a~ta~-AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~evk~vM~eNIekvldRG 152 (217)
T KOG0859|consen 74 QIPFAFLERIKEDFKKRYGGGAHTAV-AYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTEVKGVMMENIEKVLDRG 152 (217)
T ss_pred cccHHHHHHHHHHHHHHhccchhHHH-HhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999998766664 7777 799999999999999999999999999999999999999999999999
Q ss_pred hHhhhcCccc-cccCCCcceeecCCCCCccCCCCCcceeeeecC
Q psy15388 161 NLVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGIPDQVRLFIGL 203 (217)
Q Consensus 161 ekLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~~~~~~~~~~~ 203 (217)
|+||.|+||| +|+++|..|++++++++|+|||+|.++.+++++
T Consensus 153 ekiELLVdKTenl~~~s~~fr~q~r~~~r~mw~~n~kl~~iv~~ 196 (217)
T KOG0859|consen 153 EKIELLVDKTENLRSKSFDFRTQGRKLRRKMWFQNMKLKLIVLG 196 (217)
T ss_pred CeEEeeechhhhhhhhhHHHHHHHHHHHHHHHHhccceehhhhh
Confidence 9999999999 999999999999999999999999999988764
No 2
>KOG0862|consensus
Probab=100.00 E-value=3e-43 Score=286.50 Aligned_cols=193 Identities=47% Similarity=0.753 Sum_probs=182.1
Q ss_pred ChhhhhHHHhhcCceeeeeeccccccccchhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEEeeccccc
Q psy15388 1 MFLLTMIARVRDGLILSASMQDDEYSERSTLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLALCEKTFS 80 (217)
Q Consensus 1 mI~~~~IaR~~D~l~L~~~~~~~~~~~~~~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~p 80 (217)
||++++|+|+.||||||+++++++.+..++.++++.++.+++++.+.+++++|++.|.|.|||++++|+||+|+||..||
T Consensus 1 mi~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~Sietg~f~fHfli~~~Vcylvicd~~yP 80 (216)
T KOG0862|consen 1 MILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCSIETGPFVFHFLIESGVCYLVICDKSYP 80 (216)
T ss_pred CceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccccccCCeEEEEEecCCEEEEEEecCCCc
Confidence 89999999999999999999755556677799999999999999987799999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhhhccCccce-eccceeEEeechHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHh
Q psy15388 81 TKVAYSYLESLSLEFHGQYGGQFEQ-CTRPYAFVEFDSSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINAT 159 (217)
Q Consensus 81 ~~~af~fL~ei~~~F~~~~~~~~~~-~~~~~~~~~F~~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~R 159 (217)
+++||+||+++.++|.+.|+....+ +.+||+|.+|++.|++..++||+++.++++.++.+++.+|+.||.+||+++|+|
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~FieFD~~IQk~Kk~ynd~r~~~n~~~~n~el~~v~~im~~niedvl~r 160 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAFIEFDTFIQKTKKRYNDTRSQRNLLKLNQELQDVQRIMVENLEDVLQR 160 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCeeEEehhHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHhHHHHHhh
Confidence 9999999999999999999877665 889999999999999999999999889999999999999999999999999999
Q ss_pred hhHhhhcCccc-cccCCCcceeecCCCCCccCCCC
Q psy15388 160 MNLVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGI 193 (217)
Q Consensus 160 gekLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~ 193 (217)
||.|+.|..++ .|+..|...++.|+.++++-.|+
T Consensus 161 g~~l~~l~~~~s~l~~~s~~y~~~a~~in~~sl~~ 195 (216)
T KOG0862|consen 161 GEVLNALSSMASELSSESRKYPKTAKGINRKSLIR 195 (216)
T ss_pred chHHHhhhhhhhcccHHHHhhHHHHHHHHHHHHHH
Confidence 99999999999 99999999999999998765443
No 3
>KOG0861|consensus
Probab=99.97 E-value=8.1e-31 Score=206.26 Aligned_cols=149 Identities=15% Similarity=0.257 Sum_probs=132.1
Q ss_pred hHHHHHHHHhCCCCCCceeeeccceeee-eeeecceEEEEeeccccchhHHHHHHHHHHHHHhhhccC-ccceeccceeE
Q psy15388 35 NQAKQLFRKLNLNSPAKLSIETGNYFFH-YLIDRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQYGG-QFEQCTRPYAF 112 (217)
Q Consensus 35 ~~a~~il~~i~~~~~~k~s~~~~~~~~h-~l~~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~~-~~~~~~~~~~~ 112 (217)
.+++.+.+|.+| .+++++++++|.+| |...||+++|+++|.+||.|+||.+|.++.++|....+. .|. .. ..+-
T Consensus 42 F~sktvaeRt~~--g~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~-~~-~~~~ 117 (198)
T KOG0861|consen 42 FISKTVAERTGP--GQRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEFTTKVPATQWP-VG-ETAD 117 (198)
T ss_pred HHHHHHHHhcCc--ccccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHHhhcCcccccC-cC-CCcC
Confidence 478889999998 59999999999999 555679999999999999999999999999999776553 444 22 2222
Q ss_pred EeechHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc-cccCCCcceeecCCCCCc
Q psy15388 113 VEFDSSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI-DLTGIPDQVRLLGLPDKH 188 (217)
Q Consensus 113 ~~F~~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F~~~a~klkr 188 (217)
..| +.|..++.+|+||.++|+|.++|++|+|+|.||++.|+.+|+||||||+|++|| +|+.+|+.|+++|+|.++
T Consensus 118 ~~~-~~L~~~l~kyqdP~ead~l~kvQ~EldETKiiLhkTiesVL~RgEKLDdLV~KSe~Ls~qSKmfYKsAKK~Ns 193 (198)
T KOG0861|consen 118 LSY-PYLDTLLSKYQDPAEADPLLKVQNELDETKIILHKTIESVLERGEKLDDLVSKSENLSLQSKMFYKSAKKTNS 193 (198)
T ss_pred CCc-hhHHHHHHHhcChhhhChHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHhhhHHHHHHHHHHhhcCC
Confidence 444 679999999999999999999999999999999999999999999999999999 999999999999999876
No 4
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=99.91 E-value=3.5e-26 Score=183.97 Aligned_cols=183 Identities=25% Similarity=0.329 Sum_probs=148.6
Q ss_pred hhHHHhhcCceeeeeeccccccccc-hhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeee-cceEEEEeeccccchh
Q psy15388 5 TMIARVRDGLILSASMQDDEYSERS-TLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLID-RGVCFLALCEKTFSTK 82 (217)
Q Consensus 5 ~~IaR~~D~l~L~~~~~~~~~~~~~-~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~-~~i~~~~it~~~~p~~ 82 (217)
+.+-|. ++.|++..++. ++..+ .---+..+..+|.++.|....+.+++.++|.|||... +|++|+|+|+++||.+
T Consensus 4 ~~~~~~-~~~~~~~~~~~--~s~~~~~ff~~~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~ 80 (190)
T COG5143 4 ISLFRV-KGEPLRTLSDA--ESLSSFSFFHRSKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNK 80 (190)
T ss_pred EEEEee-cCCcceeeccc--cccCcccccccchHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchh
Confidence 344454 56666665532 21111 1124567888999999866678899999999998765 5999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccCc-cceeccceeEEeechHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHhhh
Q psy15388 83 VAYSYLESLSLEFHGQYGGQ-FEQCTRPYAFVEFDSSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINATMN 161 (217)
Q Consensus 83 ~af~fL~ei~~~F~~~~~~~-~~~~~~~~~~~~F~~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~Rge 161 (217)
+||++++++..+|....+.. +.....++.+..|++.+++ .|+++..+|++.+++.+++||+.+|.+||+++|.|||
T Consensus 81 la~~~~~~~~~~~~~s~~~~~~~d~~~~~~~~~~d~~~e~---~y~d~s~~D~~d~l~~el~e~K~~l~k~ie~~l~R~e 157 (190)
T COG5143 81 LAYGYLNSIATEFLKSSALEQLIDDTVGIMRVNIDKVIEK---GYRDPSIQDKLDQLQQELEETKRVLNKNIEKVLYRDE 157 (190)
T ss_pred hhhHHHHhhccHhhhhhhHhhcccCccchhhhhHHHHHHh---hcCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 99999999999998877643 3333334555677777766 3999999999999999999999999999999999999
Q ss_pred HhhhcCccc-cccCCCcceeecCCCCCccCCCC
Q psy15388 162 LVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGI 193 (217)
Q Consensus 162 kLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~ 193 (217)
+|+.|+++| .|..+|+.|+++|++.+..+||.
T Consensus 158 kl~~lv~~ss~L~~~s~~~~k~akk~n~~~~~~ 190 (190)
T COG5143 158 KLDLLVDLSSILLLSSKMFPKSAKKSNLCCLIN 190 (190)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeC
Confidence 999999999 99999999999999999999984
No 5
>KOG0860|consensus
Probab=99.83 E-value=1.4e-23 Score=155.95 Aligned_cols=74 Identities=16% Similarity=0.222 Sum_probs=70.8
Q ss_pred hhhcccccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc-cccCCCcceeecCCCCCccCCCCCcceeeeecC
Q psy15388 130 RVRRNLNTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGIPDQVRLFIGL 203 (217)
Q Consensus 130 ~~~dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~~~~~~~~~~~ 203 (217)
+.++++.++|+||+||++||++||+|+|||||||++|++|| .|...|.+|++.|++|||+|||++-++.+++|+
T Consensus 26 ~~~~k~~~tq~QvdeVv~IMr~NV~KVlER~ekL~~L~drad~L~~~as~F~~~A~klkrk~wWkn~Km~~il~~ 100 (116)
T KOG0860|consen 26 TANDKLQQTQAQVDEVVDIMRENVEKVLERGEKLDELDDRADQLQAGASQFEKTAVKLKRKMWWKNCKMRIILGL 100 (116)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999999999 999999999999999999999999999888875
No 6
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=99.78 E-value=2.9e-19 Score=127.62 Aligned_cols=81 Identities=40% Similarity=0.892 Sum_probs=70.1
Q ss_pred HHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEEeeccccchhHHHHHHHHHHHHHhhhcc-CccceeccceeEEe
Q psy15388 36 QAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQYG-GQFEQCTRPYAFVE 114 (217)
Q Consensus 36 ~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~-~~~~~~~~~~~~~~ 114 (217)
+|+.||++++++.+.|.+++.++|.|||++++|++|+|||+++||.++||.||++|+++|.++|+ ..+.++. ++++.+
T Consensus 1 ~a~~il~~i~~~~~~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~~~~~~~a~-~~~~~~ 79 (83)
T PF13774_consen 1 QARKILKRIPPNGNSKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYGGDQIKSAS-PYSFKE 79 (83)
T ss_dssp HHHHHHHTS-TTSESEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTTTTTTTST-TTTTHH
T ss_pred CHHHHHHhcCCCCCCeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcCcchhcccC-Ccchhh
Confidence 58899999997545899999999999999999999999999999999999999999999999998 4666665 887766
Q ss_pred ech
Q psy15388 115 FDS 117 (217)
Q Consensus 115 F~~ 117 (217)
|++
T Consensus 80 F~~ 82 (83)
T PF13774_consen 80 FDS 82 (83)
T ss_dssp HHH
T ss_pred cCC
Confidence 654
No 7
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=99.73 E-value=4.5e-21 Score=138.85 Aligned_cols=72 Identities=17% Similarity=0.206 Sum_probs=68.8
Q ss_pred hcccccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc-cccCCCcceeecCCCCCccCCCCCcceeeeecC
Q psy15388 132 RRNLNTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGIPDQVRLFIGL 203 (217)
Q Consensus 132 ~dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~~~~~~~~~~~ 203 (217)
+|++.+++++|++|+++|.+||+++++|||+|++|++|| +|+..|..|+++|++++|+|||++.++.+++++
T Consensus 2 ~dkl~~i~~~v~~v~~im~~Ni~~ll~Rge~L~~L~~kt~~L~~~a~~F~k~a~~l~r~~~~~~~k~~~i~~~ 74 (89)
T PF00957_consen 2 NDKLEQIQEQVEEVKNIMRENIDKLLERGEKLEELEDKTEELSDNAKQFKKNAKKLKRKMWWRNYKLYIIIII 74 (89)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHh
Confidence 588999999999999999999999999999999999999 999999999999999999999999988877763
No 8
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=96.67 E-value=2.2e-05 Score=63.90 Aligned_cols=72 Identities=14% Similarity=0.157 Sum_probs=66.6
Q ss_pred ccccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc-cccCCCcceeecCCCCCccCCCCCcceeeeecCCC
Q psy15388 134 NLNTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI-DLTGIPDQVRLLGLPDKHTLSGIPDQVRLFIGLPD 205 (217)
Q Consensus 134 kl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F~~~a~klkr~m~~~~~~~~~~~~~~~ 205 (217)
+...++..++.++.+|..|+++.+++|++...+.|+. .|..+++.|++-+.+...+||||+.++...+++..
T Consensus 95 ~s~~~~~~~d~~~~~~~~~~d~~~e~~y~d~s~~D~~d~l~~el~e~K~~l~k~ie~~l~R~ekl~~lv~~ss 167 (190)
T COG5143 95 KSSALEQLIDDTVGIMRVNIDKVIEKGYRDPSIQDKLDQLQQELEETKRVLNKNIEKVLYRDEKLDLLVDLSS 167 (190)
T ss_pred hhhhHhhcccCccchhhhhHHHHHHhhcCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHH
Confidence 4567889999999999999999999999999999999 99999999999999999999999999988877643
No 9
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold []. Vacuolar v-SNARE is required for docking and is only involved in homotypic vacuole fusion. Nyv1 is required for Ca(2+) efflux from the vacuolar lumen, a required signal for subsequent membrane fusion events, by inhibiting vacuolar Ca(2+)-ATPase PMC1 and promoting Ca(2+) release when forming trans-SNARE assemblies during the docking step. In yeast, the N-terminal domain of Nyv1 is sufficient to direct the transport of Nyv1 to limiting membrane of the vacuole []. ; PDB: 2FZ0_A.
Probab=96.09 E-value=0.0064 Score=46.65 Aligned_cols=58 Identities=14% Similarity=0.148 Sum_probs=38.8
Q ss_pred HHHHHHHHhCCC---CCCceeee-ccceeeeeee---ecceEEEEeeccccchhHHHHHHHHHHH
Q psy15388 36 QAKQLFRKLNLN---SPAKLSIE-TGNYFFHYLI---DRGVCFLALCEKTFSTKVAYSYLESLSL 93 (217)
Q Consensus 36 ~a~~il~~i~~~---~~~k~s~~-~~~~~~h~l~---~~~i~~~~it~~~~p~~~af~fL~ei~~ 93 (217)
+-..+++++-|- +-.|+|.. .+||.++|.+ +++-+++|+|..+.|+-++...|.|++.
T Consensus 46 i~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~ 110 (141)
T PF09426_consen 46 IHDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKG 110 (141)
T ss_dssp HHHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTT
T ss_pred HhhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhcc
Confidence 444567777663 35566766 5899999988 3679999999999999999999999884
No 10
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=92.95 E-value=0.18 Score=43.49 Aligned_cols=78 Identities=22% Similarity=0.415 Sum_probs=45.0
Q ss_pred Cceeeeccceeeeeeeec--ceEEEEeeccccchhHHHHHHHHHHHHHhhhccCccceeccce---eEEeechHHHHHHH
Q psy15388 50 AKLSIETGNYFFHYLIDR--GVCFLALCEKTFSTKVAYSYLESLSLEFHGQYGGQFEQCTRPY---AFVEFDSSIKKLRK 124 (217)
Q Consensus 50 ~k~s~~~~~~~~h~l~~~--~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~~~~~~~~~~~---~~~~F~~~l~~l~~ 124 (217)
...+|.+++|.++|...+ +++||||=..-..-.-+=.||+.|+..|...|........... ....|+....+++.
T Consensus 18 ~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~l~~~~~~~~~~~~~~Fd~~F~~~l~ 97 (279)
T PF04086_consen 18 GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQLKQLKPNTSINEYFDFDEEFDQLLK 97 (279)
T ss_dssp ----------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHHHHSSSTHHHHT-----HHHHHHHHH
T ss_pred CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHHhhccccccccccchhHHHHHHHHHH
Confidence 456789999999998876 6999999888888777779999999999999975433111011 11256666666555
Q ss_pred Hhh
Q psy15388 125 SFT 127 (217)
Q Consensus 125 ~yn 127 (217)
...
T Consensus 98 ~~e 100 (279)
T PF04086_consen 98 ELE 100 (279)
T ss_dssp HHC
T ss_pred HHH
Confidence 543
No 11
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=91.09 E-value=0.65 Score=35.79 Aligned_cols=95 Identities=18% Similarity=0.213 Sum_probs=60.5
Q ss_pred ChhhhhHHHhhcCceeeeeeccccccccchhhhhhHHHHHHHHhCCCC-CCceeeeccceeeeeeeecceEEEEeecccc
Q psy15388 1 MFLLTMIARVRDGLILSASMQDDEYSERSTLEYQNQAKQLFRKLNLNS-PAKLSIETGNYFFHYLIDRGVCFLALCEKTF 79 (217)
Q Consensus 1 mI~~~~IaR~~D~l~L~~~~~~~~~~~~~~~~f~~~a~~il~~i~~~~-~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~ 79 (217)
||.+.+|.=......++-+... .. ...-+...+.+........ +.--.+.++++.+-|..-+++.++++++.+.
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~e 75 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRD-VS----EEERQKLFEKFIKKKSSRNSKQSPIFEHDNYRIVYKRYSDLYFVVVGDENE 75 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESST-ST----SHHHHHHHHHHHHHHHTSSSSSTSEEEETTEEEEEEEETTEEEEEEESSTS
T ss_pred CEEEEEEEcCCCCEEEehhcCC-cc----HHHHHHHHHHHHHHHHhcccccceeeecccceeeeEeeccEEEEEEeeccc
Confidence 6666666554333455555532 11 1222333444443333321 2233466788888888889999999999999
Q ss_pred chhHHHHHHHHHHHHHhhhcc
Q psy15388 80 STKVAYSYLESLSLEFHGQYG 100 (217)
Q Consensus 80 p~~~af~fL~ei~~~F~~~~~ 100 (217)
..-....||..+.+-+..-++
T Consensus 76 Nel~~~e~l~~~v~~l~~~~~ 96 (141)
T PF01217_consen 76 NELLLLEFLHRLVEVLDDYFG 96 (141)
T ss_dssp BHHHHHHHHHHHHHHHHHHHS
T ss_pred chHHHHHHHHHhhhhhhhhhc
Confidence 998999999998888877554
No 12
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=88.46 E-value=1.9 Score=33.58 Aligned_cols=86 Identities=20% Similarity=0.230 Sum_probs=44.2
Q ss_pred HHHHHHhCCC--------CCCceeeeccceeeeeee-ecceEEEEeeccccchhHHHHHHHHHHHHHhhhc-cCccceec
Q psy15388 38 KQLFRKLNLN--------SPAKLSIETGNYFFHYLI-DRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQY-GGQFEQCT 107 (217)
Q Consensus 38 ~~il~~i~~~--------~~~k~s~~~~~~~~h~l~-~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~-~~~~~~~~ 107 (217)
+.+..++.|. ..+-.+++.+.|.+|+.- -.|+-|+++||+..+. ..-.++..+.+.|..-. .++.-...
T Consensus 46 ~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV~KNPfy~~~ 124 (142)
T PF04099_consen 46 KAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCFETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYVVKNPFYSLE 124 (142)
T ss_dssp HHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHHHS-TTS-TT
T ss_pred HHHHHHhCCCCcccccccceeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHHhhCCCCCCC
Confidence 4567778772 234678888999999654 5899999999999863 23344555554444321 12211111
Q ss_pred cceeEEeechHHHHHHH
Q psy15388 108 RPYAFVEFDSSIKKLRK 124 (217)
Q Consensus 108 ~~~~~~~F~~~l~~l~~ 124 (217)
-|-....|+..|.++++
T Consensus 125 ~pI~~~lF~~~l~~~~~ 141 (142)
T PF04099_consen 125 MPIRCELFDTKLDQYVK 141 (142)
T ss_dssp S----HHHHHHHHHHHH
T ss_pred CcEehHHHHHHHHHHHh
Confidence 22222356666665543
No 13
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=76.54 E-value=17 Score=27.47 Aligned_cols=81 Identities=17% Similarity=0.324 Sum_probs=47.1
Q ss_pred HHHHhCC--CCCCceeeeccceeee-eeeecceEEEEeeccccchhHHHHHHHHHHHHHhhhcc--CccceeccceeEEe
Q psy15388 40 LFRKLNL--NSPAKLSIETGNYFFH-YLIDRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQYG--GQFEQCTRPYAFVE 114 (217)
Q Consensus 40 il~~i~~--~~~~k~s~~~~~~~~h-~l~~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~--~~~~~~~~~~~~~~ 114 (217)
|+.++.| ++.++.....+++..| |-+..|.-||.++.+. +...+|+ |+.+...|. +|. +..-+-.-|-....
T Consensus 46 I~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kFV~~~~k~-t~na~~q-l~kiY~lYs-dYV~knPfys~EMPI~c~l 122 (134)
T COG5122 46 ILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEKR-TVNALFQ-LQKIYSLYS-DYVTKNPFYSPEMPIQCSL 122 (134)
T ss_pred hhhhcccCCCCCceEEEEeccEEEEEEEecCCcEEEEEecCC-chhHHHH-HHHHHHHHH-HHhhcCCCCCcccceehhh
Confidence 5555555 5567888888899888 5556899999999544 3334555 444444443 232 11111112333456
Q ss_pred echHHHHHH
Q psy15388 115 FDSSIKKLR 123 (217)
Q Consensus 115 F~~~l~~l~ 123 (217)
|++-+++..
T Consensus 123 Fde~lkrm~ 131 (134)
T COG5122 123 FDEHLKRMF 131 (134)
T ss_pred hhHHHHHHh
Confidence 777776654
No 14
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=72.35 E-value=40 Score=25.49 Aligned_cols=83 Identities=16% Similarity=0.114 Sum_probs=47.3
Q ss_pred hhcCceeeeeeccccccccc----hhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEEeeccccchhHHH
Q psy15388 10 VRDGLILSASMQDDEYSERS----TLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLALCEKTFSTKVAY 85 (217)
Q Consensus 10 ~~D~l~L~~~~~~~~~~~~~----~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~p~~~af 85 (217)
..||+|++...+.+.....- ...|...+++ +.|+.-+++......+++|.+.-.....+....+|+++...-.-.
T Consensus 24 DrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~Q-~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~aN~G~il 102 (119)
T PF08923_consen 24 DRDGVPIAKVSSDSAPESAMRPSLLSTFAMAIDQ-ASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSNANTGLIL 102 (119)
T ss_dssp ETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHHH-HTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETTS-HHHHH
T ss_pred CCCCcEEEEecCCCCcchhhhhHHHHHHHHHhhc-ccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCCCCHHHHH
Confidence 36899998876431111111 1224444443 556665555556667888866544567888888888888777666
Q ss_pred HHHHHHHH
Q psy15388 86 SYLESLSL 93 (217)
Q Consensus 86 ~fL~ei~~ 93 (217)
.+-+++..
T Consensus 103 ~l~~~L~~ 110 (119)
T PF08923_consen 103 SLEEELAP 110 (119)
T ss_dssp HHHHHHHH
T ss_pred HhHHHHHH
Confidence 66666554
No 15
>KOG0938|consensus
Probab=63.92 E-value=29 Score=31.27 Aligned_cols=48 Identities=15% Similarity=0.365 Sum_probs=42.2
Q ss_pred eeeccceeeeeeeecceEEEEeeccccchhHHHHHHHHHHHHHhhhcc
Q psy15388 53 SIETGNYFFHYLIDRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQYG 100 (217)
Q Consensus 53 s~~~~~~~~h~l~~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~ 100 (217)
..+.++-+|||+..+++-.++||..+......|.||.++-+.+..-|+
T Consensus 46 V~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~kl~avm~aYfg 93 (446)
T KOG0938|consen 46 VLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLYKLDAVMNAYFG 93 (446)
T ss_pred eeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHHHHHHHHHHHhc
Confidence 445788899999999999999999999999999999999988876555
No 16
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=61.29 E-value=47 Score=30.53 Aligned_cols=84 Identities=13% Similarity=0.082 Sum_probs=61.6
Q ss_pred CceeeeeeccccccccchhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEEeeccccchhHHHHHHHHHH
Q psy15388 13 GLILSASMQDDEYSERSTLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLALCEKTFSTKVAYSYLESLS 92 (217)
Q Consensus 13 ~l~L~~~~~~~~~~~~~~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~it~~~~p~~~af~fL~ei~ 92 (217)
|-|..+.. + .+.....+-.+.+.++.-+....+.=.++..++..|.|+..+.+.+|||+...-|...-..-|+-+.
T Consensus 21 GKPIysr~-G---~e~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly 96 (415)
T PF03164_consen 21 GKPIYSRY-G---DEDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLY 96 (415)
T ss_pred CceeEEec-C---ChHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHH
Confidence 56665543 2 2233557888888888877653344558888999999999999999999999998877777777777
Q ss_pred HHHhhhcc
Q psy15388 93 LEFHGQYG 100 (217)
Q Consensus 93 ~~F~~~~~ 100 (217)
....+..+
T Consensus 97 ~qils~lt 104 (415)
T PF03164_consen 97 SQILSILT 104 (415)
T ss_pred HHHHHhcc
Confidence 66665443
No 17
>KOG0781|consensus
Probab=58.07 E-value=30 Score=32.67 Aligned_cols=86 Identities=14% Similarity=0.240 Sum_probs=58.1
Q ss_pred hhhHHHhhcCceeeeeeccccccccchhhhhh----HHHHHHHHhCCCCCCceeeeccceeeeeeeec--ceEEEEeecc
Q psy15388 4 LTMIARVRDGLILSASMQDDEYSERSTLEYQN----QAKQLFRKLNLNSPAKLSIETGNYFFHYLIDR--GVCFLALCEK 77 (217)
Q Consensus 4 ~~~IaR~~D~l~L~~~~~~~~~~~~~~~~f~~----~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~--~i~~~~it~~ 77 (217)
|+++-|+ |++|-.|+.. . .+|+. .++.+|-.=. .+-.+++.+.|+.-|--++ +++|+|+-.+
T Consensus 5 faIFtkg--G~vLw~~~~~---~----~~~~~~in~lI~~~ll~er---~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqk 72 (587)
T KOG0781|consen 5 FAIFTKG--GLVLWCYQEV---G----DNLKGPINALIRSVLLSER---GGVNSFTFEAYTLKYQLDNQYSLVFVVVFQK 72 (587)
T ss_pred eeeecCC--cEEEEEeccc---c----hhccchHHHHHHHHHHHhh---cCcccCchhheeEeeeecCCccEEEEEEEec
Confidence 4555565 9999998743 1 13333 3333332211 1223377888888886654 6999999888
Q ss_pred ccchhHHHHHHHHHHHHHhhhccC
Q psy15388 78 TFSTKVAYSYLESLSLEFHGQYGG 101 (217)
Q Consensus 78 ~~p~~~af~fL~ei~~~F~~~~~~ 101 (217)
-..-.-+=.||+++.+.|...|..
T Consensus 73 i~~L~yv~~ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 73 ILTLTYVDKLLNDVLNLFREKYDT 96 (587)
T ss_pred cchhhhHHHHHHHHHHHHHHHhcc
Confidence 777777789999999999998853
No 18
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=56.48 E-value=22 Score=27.04 Aligned_cols=52 Identities=10% Similarity=0.194 Sum_probs=35.1
Q ss_pred ceeeeccceeee-eeeecceEEEEeec---cccchhHHHHHHHHHHHHHhhhccCc
Q psy15388 51 KLSIETGNYFFH-YLIDRGVCFLALCE---KTFSTKVAYSYLESLSLEFHGQYGGQ 102 (217)
Q Consensus 51 k~s~~~~~~~~h-~l~~~~i~~~~it~---~~~p~~~af~fL~ei~~~F~~~~~~~ 102 (217)
+..+..++|.++ |++..++=|+.+++ ........-.|+.++.+.|....-++
T Consensus 54 g~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~~~~NP 109 (132)
T PF04628_consen 54 GLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVKALCNP 109 (132)
T ss_dssp EEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHHHHTST
T ss_pred CceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHHHccCC
Confidence 445556787666 88888999998888 45566667889999998888765443
No 19
>KOG3369|consensus
Probab=52.58 E-value=69 Score=26.08 Aligned_cols=82 Identities=22% Similarity=0.273 Sum_probs=50.9
Q ss_pred HHHHhCCC--CCCceeeeccceeee-eeeecceEEEEeeccccchhHHHHHHHHHHHHHhhhcc--CccceeccceeEEe
Q psy15388 40 LFRKLNLN--SPAKLSIETGNYFFH-YLIDRGVCFLALCEKTFSTKVAYSYLESLSLEFHGQYG--GQFEQCTRPYAFVE 114 (217)
Q Consensus 40 il~~i~~~--~~~k~s~~~~~~~~h-~l~~~~i~~~~it~~~~p~~~af~fL~ei~~~F~~~~~--~~~~~~~~~~~~~~ 114 (217)
|..++.|- +.+....+.+.+..| |-+-.|+-|++||++.. ..|=.+|..+...|. .|. +..-+..=|-....
T Consensus 110 I~~qlsp~~ksSGie~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYs-DyvlKNPfYSlEMPIRc~l 186 (199)
T KOG3369|consen 110 ISTQLSPEPKSSGIEVLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYS-DYVLKNPFYSLEMPIRCEL 186 (199)
T ss_pred eeeccCCCCCCCceEEEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHH-HHhhcCCccCcccceeHHH
Confidence 55566652 234556677888777 55568999999999877 456678888877664 453 21111111233346
Q ss_pred echHHHHHHH
Q psy15388 115 FDSSIKKLRK 124 (217)
Q Consensus 115 F~~~l~~l~~ 124 (217)
|+..|+.+++
T Consensus 187 FDe~lk~~le 196 (199)
T KOG3369|consen 187 FDEKLKFLLE 196 (199)
T ss_pred hhHHHHHHHh
Confidence 7777776654
No 20
>KOG3368|consensus
Probab=37.84 E-value=1.9e+02 Score=22.46 Aligned_cols=55 Identities=20% Similarity=0.257 Sum_probs=41.5
Q ss_pred HHHHHHHhCCC--CCCceeeeccceeeeeee-ecceEEEEeeccccchhHHHHHHHHHHH
Q psy15388 37 AKQLFRKLNLN--SPAKLSIETGNYFFHYLI-DRGVCFLALCEKTFSTKVAYSYLESLSL 93 (217)
Q Consensus 37 a~~il~~i~~~--~~~k~s~~~~~~~~h~l~-~~~i~~~~it~~~~p~~~af~fL~ei~~ 93 (217)
.+.+..++.|+ .++-.++..+.|-.||.. -.|+-+|.+||+.... .-..|+.|..
T Consensus 45 lkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 45 LKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred HHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 56678899986 466778889999999765 4899999999987754 1244555555
No 21
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=36.64 E-value=83 Score=20.45 Aligned_cols=48 Identities=13% Similarity=0.116 Sum_probs=35.3
Q ss_pred hhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeee--ecceEEEEeecc
Q psy15388 30 TLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLI--DRGVCFLALCEK 77 (217)
Q Consensus 30 ~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~--~~~i~~~~it~~ 77 (217)
..+|..+...+-+++.....-+..|+.+|.-++-+. .+|-.|+|....
T Consensus 8 ~~s~e~lL~~it~~v~l~~gVr~lyt~~G~~V~~l~~l~dg~~yVa~g~e 57 (60)
T PF03607_consen 8 FRSFEQLLDEITEKVQLPSGVRKLYTLDGKRVKSLDELEDGGSYVASGRE 57 (60)
T ss_dssp HSSHHHHHHHHHHSSSSTTS-SEEEETTSSEESSGGGS-TTEEEEEESSS
T ss_pred hcCHHHHHHHHHhhcCCCcccceEECCCCCEeCCHHHHCCCCEEEEEcCC
Confidence 457888888898988875557888998887776554 378889988544
No 22
>KOG1983|consensus
Probab=36.50 E-value=4.4 Score=41.38 Aligned_cols=39 Identities=8% Similarity=0.032 Sum_probs=33.2
Q ss_pred hhchhhHHHhhhHhhhcCccc-cccCCCcceeecCCCCCc
Q psy15388 150 VQNIDDINATMNLVLGLGNQI-DLTGIPDQVRLLGLPDKH 188 (217)
Q Consensus 150 ~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F~~~a~klkr 188 (217)
..--+.+.+|||+|+.++++| +|++.|.+|-..|.++--
T Consensus 944 ~~a~~~l~e~~erL~~~e~~t~~~~~sa~~~s~~a~e~~~ 983 (993)
T KOG1983|consen 944 SGALQPLNERGERLSRLEERTAEMANSAKQFSSTAHELTG 983 (993)
T ss_pred hhcchhhHhhccccchHHHHHHHhhccHHHHHHHHHHHHh
Confidence 334557899999999999999 999999999988887643
No 23
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=30.08 E-value=39 Score=29.56 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=14.6
Q ss_pred hhcccccchhhhhHHHHHHhhchhh
Q psy15388 131 VRRNLNTLNTELQDVQRIMVQNIDD 155 (217)
Q Consensus 131 ~~dkl~~i~~~l~evk~iM~~NIdk 155 (217)
..+..++++.|+-|.-+-|..|=..
T Consensus 101 d~e~~~klEKel~e~~~~~fg~e~~ 125 (295)
T TIGR01478 101 GAEPMSTIEKELLEKYEEMFGDESH 125 (295)
T ss_pred CcchhhHHHHHHHHHHHHHhCCccc
Confidence 3444566666666666666555554
No 24
>PF07981 Plasmod_MYXSPDY: Plasmodium repeat_MYXSPDY; InterPro: IPR012598 This repeat is found in two hypothetical Plasmodium proteins.
Probab=29.96 E-value=54 Score=15.99 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=11.4
Q ss_pred CCCCCcceeeeecCCC
Q psy15388 190 LSGIPDQVRLFIGLPD 205 (217)
Q Consensus 190 m~~~~~~~~~~~~~~~ 205 (217)
|+.-|+.---||+|||
T Consensus 1 mY~SPdytL~~v~Lpd 16 (17)
T PF07981_consen 1 MYFSPDYTLRLVQLPD 16 (17)
T ss_pred CccCCCceEEEEecCC
Confidence 4555666677888887
No 25
>COG2018 Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only]
Probab=29.94 E-value=2.4e+02 Score=21.43 Aligned_cols=68 Identities=15% Similarity=0.171 Sum_probs=42.7
Q ss_pred hcCceeeeeeccccccccchhhhhhH-------HHHHHHHhCCCCCCceeeecc-ceeeeeeeecceEEEEeeccccchh
Q psy15388 11 RDGLILSASMQDDEYSERSTLEYQNQ-------AKQLFRKLNLNSPAKLSIETG-NYFFHYLIDRGVCFLALCEKTFSTK 82 (217)
Q Consensus 11 ~D~l~L~~~~~~~~~~~~~~~~f~~~-------a~~il~~i~~~~~~k~s~~~~-~~~~h~l~~~~i~~~~it~~~~p~~ 82 (217)
.||||.+++... +....-+..+ +..+.+++..+.....+++.. ++.+-|-..++.++++++++...--
T Consensus 27 ~DGL~ia~~~p~----~~d~e~vaA~~a~~~g~~er~~~~l~~g~leqi~I~g~~g~i~l~~~g~~~il~~~a~~~~nLG 102 (119)
T COG2018 27 KDGLPIAAELPG----NVDAEIVAAMAATALGLAERAADELGGGELEQIMIEGKKGKILLYDAGDDAILVVLADEGTNLG 102 (119)
T ss_pred cCCceEeecCCC----cccHHHHHHHHHHHHHHhHHHHHHhCCCCceEEEEeccccEEEEEEcCCceEEEEEcCCCCcch
Confidence 589999887743 1111123333 344555666544455566644 6777777778999999999876543
No 26
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=29.34 E-value=1.4e+02 Score=20.08 Aligned_cols=63 Identities=22% Similarity=0.237 Sum_probs=33.8
Q ss_pred hcCceeeeeeccccccc---cchhhhhhHHHHHHHHhCCCCCCceeeeccceeeeeeeecceEEEE
Q psy15388 11 RDGLILSASMQDDEYSE---RSTLEYQNQAKQLFRKLNLNSPAKLSIETGNYFFHYLIDRGVCFLA 73 (217)
Q Consensus 11 ~D~l~L~~~~~~~~~~~---~~~~~f~~~a~~il~~i~~~~~~k~s~~~~~~~~h~l~~~~i~~~~ 73 (217)
.||+|+++..-++.... .-...+-..++.+.+.+..+.-....++.++..+.....++..++|
T Consensus 23 ~dG~~i~~~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~~L~ 88 (91)
T PF03259_consen 23 KDGLVIASSGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFYLLV 88 (91)
T ss_dssp TTSEEEEETSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCEEEE
T ss_pred CCCCEEEEecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCEEEE
Confidence 48999988221111110 0123344566677777875444556677776666655545544444
No 27
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=27.14 E-value=16 Score=29.51 Aligned_cols=44 Identities=7% Similarity=0.174 Sum_probs=38.1
Q ss_pred ccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc-cccCCCcce
Q psy15388 136 NTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI-DLTGIPDQV 179 (217)
Q Consensus 136 ~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt-~L~~~S~~F 179 (217)
..+..++++++.-|.+.|+++-..-++||.+..++ .|.+.|..+
T Consensus 112 ~rL~~~Vd~~~~eL~~eI~~L~~~i~~le~~~~~~k~LrnKa~~L 156 (171)
T PF04799_consen 112 ARLCQQVDQTKNELEDEIKQLEKEIQRLEEIQSKSKTLRNKANWL 156 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999999999999988 887765543
No 28
>PTZ00370 STEVOR; Provisional
Probab=26.68 E-value=48 Score=29.03 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=20.8
Q ss_pred hHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhh
Q psy15388 117 SSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDD 155 (217)
Q Consensus 117 ~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdk 155 (217)
..+++...++.+....+..++++.|+-|.=+.|..|=..
T Consensus 86 e~~~k~~~K~k~~~d~e~k~klEKel~e~~ee~fg~~~~ 124 (296)
T PTZ00370 86 EVVEKNGTKYTGGNDAEPMSTLEKELLETYEEMFGDESD 124 (296)
T ss_pred HHHHhcCCccccccCcchhHHHHHHHHHHHHHHhcCccc
Confidence 333333333433334455666677766666666665555
No 29
>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=23.66 E-value=65 Score=25.20 Aligned_cols=51 Identities=16% Similarity=0.359 Sum_probs=32.0
Q ss_pred eechHHHHHHHHhhhh-hhhcccccchhhhhHHHHHHhhchhhHHHhhhHhh
Q psy15388 114 EFDSSIKKLRKSFTDT-RVRRNLNTLNTELQDVQRIMVQNIDDINATMNLVL 164 (217)
Q Consensus 114 ~F~~~l~~l~~~yn~~-~~~dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd 164 (217)
.|.+.++++...-+.- |....|.+++.+++.-+.-..+-+..+|++|+.|=
T Consensus 31 ~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~g~~LV 82 (147)
T PF05659_consen 31 SFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEKGKELV 82 (147)
T ss_pred hhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHHHHHHH
Confidence 3555666655444332 55666777777777775556666777788886553
No 30
>KOG3230|consensus
Probab=22.80 E-value=90 Score=25.88 Aligned_cols=44 Identities=23% Similarity=0.230 Sum_probs=27.9
Q ss_pred hHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHhh---hHhhhcCcc
Q psy15388 117 SSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINATM---NLVLGLGNQ 169 (217)
Q Consensus 117 ~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~Rg---ekLd~L~~k 169 (217)
|.++++|.+|.. -...++.+.++|.++||..|+.. |--|+|+.+
T Consensus 119 pq~qkIm~eFek---------Qse~Mdm~~Emm~daIDdal~~~edEEEtd~lvnq 165 (224)
T KOG3230|consen 119 PQIQKIMQEFEK---------QSEIMDMKEEMMDDAIDDALGDDEDEEETDDLVNQ 165 (224)
T ss_pred HHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHH
Confidence 445555555543 23567788999999999999532 334444443
No 31
>PHA03011 hypothetical protein; Provisional
Probab=22.31 E-value=1.3e+02 Score=22.20 Aligned_cols=54 Identities=19% Similarity=0.292 Sum_probs=41.1
Q ss_pred echHHHHHHHHhhhhhhhcccccchhhhhHHHHHHhhchhhHHHhhhHhhhcCccc
Q psy15388 115 FDSSIKKLRKSFTDTRVRRNLNTLNTELQDVQRIMVQNIDDINATMNLVLGLGNQI 170 (217)
Q Consensus 115 F~~~l~~l~~~yn~~~~~dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~~kt 170 (217)
....+.+++-+||. -.|...-+..++.+...+..+|.|.+.-=...+|-|-+.-
T Consensus 62 i~e~ldeL~~qYN~--L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~ni 115 (120)
T PHA03011 62 IIEILDELIAQYNE--LLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENI 115 (120)
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHH
Confidence 34567778888886 3577788889999999999999998887666666665444
No 32
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=22.02 E-value=2.2e+02 Score=22.57 Aligned_cols=79 Identities=16% Similarity=0.245 Sum_probs=40.7
Q ss_pred chhHHHHHHHHHHHHHhhhc-cCccceeccceeEE---eechHHHHHHHHhhhhh-h------------hcccccchhhh
Q psy15388 80 STKVAYSYLESLSLEFHGQY-GGQFEQCTRPYAFV---EFDSSIKKLRKSFTDTR-V------------RRNLNTLNTEL 142 (217)
Q Consensus 80 p~~~af~fL~ei~~~F~~~~-~~~~~~~~~~~~~~---~F~~~l~~l~~~yn~~~-~------------~dkl~~i~~~l 142 (217)
+....-..|+++.++|...- +-.+......|.+. +|.+.++++...-...+ . ... -.+.+|
T Consensus 25 ~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~LS~aalEtLAiIAY~QP--iTr~eI 102 (159)
T PF04079_consen 25 SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPKLSQAALETLAIIAYKQP--ITRAEI 102 (159)
T ss_dssp -HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHHHHHHHHHHHHHHHHH-S--EEHHHH
T ss_pred CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCCCCHHHHHHHHHHHhcCC--cCHHHH
Confidence 34455667888888774421 11222222334442 55566665554411100 0 111 257889
Q ss_pred hHHHHHHhhc-hhhHHHhh
Q psy15388 143 QDVQRIMVQN-IDDINATM 160 (217)
Q Consensus 143 ~evk~iM~~N-IdkiL~Rg 160 (217)
++++++=.++ |+.+++||
T Consensus 103 e~IRGv~s~~~i~~L~e~g 121 (159)
T PF04079_consen 103 EEIRGVNSDSVIKTLLERG 121 (159)
T ss_dssp HHHHTS--HCHHHHHHHTT
T ss_pred HHHcCCChHHHHHHHHHCC
Confidence 9999987666 67777776
No 33
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=21.34 E-value=80 Score=23.13 Aligned_cols=28 Identities=11% Similarity=0.266 Sum_probs=16.9
Q ss_pred hcccccchhhhhHHHHHHhhchhhHHHh
Q psy15388 132 RRNLNTLNTELQDVQRIMVQNIDDINAT 159 (217)
Q Consensus 132 ~dkl~~i~~~l~evk~iM~~NIdkiL~R 159 (217)
.+.+.+...++..-+.-+.+|+..++.+
T Consensus 35 ~~~~~~f~~~~~~~~~~~~~~~~~vi~~ 62 (113)
T PF02520_consen 35 QDQYNEFKAQVQAQKEEVRKNVTAVISN 62 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666666666666666554
No 34
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=20.99 E-value=1.2e+02 Score=24.21 Aligned_cols=59 Identities=20% Similarity=0.348 Sum_probs=38.2
Q ss_pred hhhhhhHHHHHHHHhCCC---CCCceeeec-cceeee-eeeecceEEEEeecc-ccchhHHHHHH
Q psy15388 30 TLEYQNQAKQLFRKLNLN---SPAKLSIET-GNYFFH-YLIDRGVCFLALCEK-TFSTKVAYSYL 88 (217)
Q Consensus 30 ~~~f~~~a~~il~~i~~~---~~~k~s~~~-~~~~~h-~l~~~~i~~~~it~~-~~p~~~af~fL 88 (217)
+...++.|+.|+++...+ ...+|+|.- -|.+|| |..++|-.|+-+..+ +.+.+.++.||
T Consensus 61 i~~Lq~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~~G~~ylSmisP~EWg~~~p~~fl 125 (159)
T PF10504_consen 61 IRFLQEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRENGQDYLSMISPEEWGGSCPHEFL 125 (159)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECCCCCEEEEeeCHHHhCCCCCcCEE
Confidence 345677888889877753 366788774 477777 777788777666555 44544444333
No 35
>KOG0810|consensus
Probab=20.79 E-value=20 Score=31.57 Aligned_cols=72 Identities=8% Similarity=0.021 Sum_probs=43.6
Q ss_pred cccccchhhhhHHHHHHhhchhhHHHhhhHhhhcC----------ccc-cccCCCcceeecCCCCCccCCCCCcceeeee
Q psy15388 133 RNLNTLNTELQDVQRIMVQNIDDINATMNLVLGLG----------NQI-DLTGIPDQVRLLGLPDKHTLSGIPDQVRLFI 201 (217)
Q Consensus 133 dkl~~i~~~l~evk~iM~~NIdkiL~RgekLd~L~----------~kt-~L~~~S~~F~~~a~klkr~m~~~~~~~~~~~ 201 (217)
+.+.+++..|.|+.++-.+==-.+-..||-+|.++ ++. +=...|..++++|||.++..|.-.-.+.+++
T Consensus 206 ~~ik~LEksi~ELhqlFlDMa~LVe~QgEmvd~IE~nV~~A~~~V~~g~~~~~kAv~~qkkaRK~k~i~ii~~iii~~v~ 285 (297)
T KOG0810|consen 206 DEIKKLEKSIRELHQLFLDMAVLVESQGEMVDRIENNVENAVDYVEQGVDHLKKAVKYQKKARKWKIIIIIILIIIIVVL 285 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhceeeeehHHHHHHHHH
Confidence 55778888888888775555455555666655554 333 3334567788888887775554444444444
Q ss_pred cCC
Q psy15388 202 GLP 204 (217)
Q Consensus 202 ~~~ 204 (217)
-++
T Consensus 286 v~~ 288 (297)
T KOG0810|consen 286 VVV 288 (297)
T ss_pred hhh
Confidence 333
Done!