Query 030884
Match_columns 170
No_of_seqs 144 out of 337
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:02:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030884hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3487 TRAPP 20 K subunit [In 100.0 6.3E-38 1.4E-42 240.5 6.7 118 1-128 1-128 (139)
2 PF04628 Sedlin_N: Sedlin, N-t 100.0 1.2E-36 2.6E-41 234.2 8.9 122 7-150 1-130 (132)
3 KOG3444 Uncharacterized conser 100.0 5.2E-35 1.1E-39 219.1 9.6 116 1-117 1-118 (121)
4 COG5603 TRS20 Subunit of TRAPP 100.0 1.3E-32 2.7E-37 209.1 7.8 116 1-126 1-125 (136)
5 PF04099 Sybindin: Sybindin-li 98.5 1.6E-06 3.4E-11 67.9 10.5 128 2-147 1-137 (142)
6 KOG3369 Transport protein part 98.1 7.8E-06 1.7E-10 66.7 5.8 94 33-151 103-196 (199)
7 COG5122 TRS23 Transport protei 97.5 0.00036 7.9E-09 53.6 6.9 116 4-145 5-126 (134)
8 KOG3368 Transport protein part 97.0 0.014 3.1E-07 45.8 11.0 112 3-133 4-123 (140)
9 KOG3487 TRAPP 20 K subunit [In 51.2 4.8 0.0001 31.6 -0.1 40 107-153 97-136 (139)
10 PF01217 Clat_adaptor_s: Clath 46.8 1.2E+02 0.0027 22.7 9.5 73 1-87 1-73 (141)
11 PF04099 Sybindin: Sybindin-li 29.5 18 0.00038 28.1 -0.0 9 118-126 125-133 (142)
12 cd03483 MutL_Trans_MLH1 MutL_T 28.5 1.1E+02 0.0025 22.8 4.3 49 66-115 30-83 (127)
13 PF01119 DNA_mis_repair: DNA m 28.4 65 0.0014 23.7 2.9 50 65-115 20-75 (119)
14 PF15205 PLAC9: Placenta-speci 27.1 40 0.00086 23.8 1.4 19 28-46 18-36 (74)
15 KOG4497 Uncharacterized conser 24.5 58 0.0013 29.9 2.3 53 29-86 168-220 (447)
16 COG1507 Uncharacterized conser 21.1 60 0.0013 26.3 1.5 18 91-109 81-98 (167)
No 1
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.3e-38 Score=240.53 Aligned_cols=118 Identities=26% Similarity=0.420 Sum_probs=106.8
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCc-------ccchhh-hHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEE
Q 030884 1 MIACVAVVGHQNNPLYIQSFTEA-------DDALKL-HHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYG 72 (170)
Q Consensus 1 Mi~~~aIIG~~d~PLy~~~f~~~-------~~~l~~-qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~Vyg 72 (170)
|.+|+||||+.|+|+||.+++.. ++..++ |||+|||||+|||.+|. +++||||.+|+|+++.|+|
T Consensus 1 m~~yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~HAaLdiVde~~W~-------~snmYLktVDkfne~~VSA 73 (139)
T KOG3487|consen 1 MTAYFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIVHAALDIVDELQWT-------TSNMYLKTVDKFNELFVSA 73 (139)
T ss_pred CceEEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHH-------HHhhHHHHHHhhcceeEEE
Confidence 78999999999999999999954 234677 99999999999999997 3799999999999999999
Q ss_pred EEecCceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhccc--ccCcccccccccC
Q 030884 73 YLTNTKVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAW--KKDNIQNICRESK 128 (170)
Q Consensus 73 yvT~t~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF--~~~~i~np~f~~~ 128 (170)
|+|++++||+++|..+ .|++||+||+| |||+|+|++|||| .+|+|++|.||.+
T Consensus 74 yvTas~i~f~mlh~~~--~~~~ik~Ffqe-v~elyik~lmnpFy~~~dpirs~afd~k 128 (139)
T KOG3487|consen 74 YVTASHIRFIMLHINR--ADDNIKLFFQE-VHELYIKTLMNPFYEINDPIRSPAFDHK 128 (139)
T ss_pred EEccCcEEEEEEeecc--ccccHHHHHHH-HHHHHHHHHhCcccccCCccccHHHHHH
Confidence 9999999999999986 69999999997 9999999999999 4578888877654
No 2
>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=100.00 E-value=1.2e-36 Score=234.24 Aligned_cols=122 Identities=36% Similarity=0.597 Sum_probs=95.1
Q ss_pred EEcCCCCeeEEEcCCCcccch------hhhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEecCceE
Q 030884 7 VVGHQNNPLYIQSFTEADDAL------KLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (170)
Q Consensus 7 IIG~~d~PLy~~~f~~~~~~l------~~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT~t~iK 80 (170)
|||++|+|||++++++.+++. .+||++|+|||+|||++|+ +++++|||+|+++++++||||+|+||+|
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~------~~~~~yLg~l~~~~~~~vygyvT~t~~K 74 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWK------SSSDMYLGLLDPFEDYKVYGYVTNTGIK 74 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHC------SSSCSEEEEEEEETTEEEEEEETTT--E
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhh------cccccccCceehhhhHHHHhhhccCcee
Confidence 799999999999999874332 2799999999999999997 1368999999999999999999999999
Q ss_pred EEEEEc--CCCCCchhhhhhhhhhhhhhhhhhhhcccccCcccccccccCCCCcchhhhhhHHHhhcccccc
Q 030884 81 FILVTT--DLDVRDADVRNEVPCCIYRCRFKPISRAWKKDNIQNICRESKHHSQVIWVEFSWLIAAGVRLNL 150 (170)
Q Consensus 81 fVll~~--~~~~~d~~Ik~fF~e~V~elYvk~l~NPF~~~~i~np~f~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (170)
|||+++ ....+|++||+||++ +|++|++++||||+. +++ +| .|.-|++.||-.+
T Consensus 75 fvl~~~~~~~~~~d~~ik~fF~~-vh~~Y~~~~~NPF~~---------~~~---~I---~S~~Fd~~v~~l~ 130 (132)
T PF04628_consen 75 FVLVHDMSDNSIRDEDIKQFFKE-VHELYVKALCNPFYQ---------PGT---PI---KSPKFDSRVRALA 130 (132)
T ss_dssp EEEEECGGG-S--HHHHHHHHHH-HHHHHHHHHTSTTCG---------CT----HH---HHHHHHHHHHHHH
T ss_pred EEEEEecccCCcchHHHHHHHHH-HHHHHHHHccCCCCC---------CCC---Cc---CCHHHHHHHHHHh
Confidence 999998 334799999999997 999999999999964 222 55 5667777776544
No 3
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.2e-35 Score=219.10 Aligned_cols=116 Identities=50% Similarity=0.794 Sum_probs=110.4
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCcccchhhhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEecCceE
Q 030884 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (170)
Q Consensus 1 Mi~~~aIIG~~d~PLy~~~f~~~~~~l~~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT~t~iK 80 (170)
|++|+|++|++|+|+|+..+++.++++++|+.+|+|||+|||+....+|+..++++.|||+|++.++++||||+|||++|
T Consensus 1 m~v~~av~g~kn~~lyi~s~t~~e~~L~~~y~v~~sLDVieekvn~~gkg~~tsne~fLGLLy~ted~kvYgfvtNTkVK 80 (121)
T KOG3444|consen 1 MLVCLAVAGPKNEPLYIESITPKEKELKLHYQVHLSLDVIEEKVNDPGKGERTSNELFLGLLYPTEDYKVYGFVTNTKVK 80 (121)
T ss_pred CEEEEEEEcCCCCccEEEecCcHHHHHHhHhhhhhhHHHHHHHhcCcccCccchhhhhhcccccccceeEEEEEeccEEE
Confidence 89999999999999999999988899999999999999999999888888888899999999999999999999999999
Q ss_pred EEEEEcCCC--CCchhhhhhhhhhhhhhhhhhhhccccc
Q 030884 81 FILVTTDLD--VRDADVRNEVPCCIYRCRFKPISRAWKK 117 (170)
Q Consensus 81 fVll~~~~~--~~d~~Ik~fF~e~V~elYvk~l~NPF~~ 117 (170)
||+++++++ .+|++||++|+. .|-+|.+.+||||+.
T Consensus 81 FIlvvdssd~avreteiRsv~r~-~h~l~td~~~npfy~ 118 (121)
T KOG3444|consen 81 FILVVDSSDYAVRETEIRSVFRI-LHLLYTDLSCNPFYL 118 (121)
T ss_pred EEEEEcCCcceehhHHHHHHHHH-HHHHHHHheecceec
Confidence 999998754 899999999995 999999999999975
No 4
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=99.97 E-value=1.3e-32 Score=209.11 Aligned_cols=116 Identities=18% Similarity=0.348 Sum_probs=100.0
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCccc------chhh-hHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEE
Q 030884 1 MIACVAVVGHQNNPLYIQSFTEADD------ALKL-HHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGY 73 (170)
Q Consensus 1 Mi~~~aIIG~~d~PLy~~~f~~~~~------~l~~-qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~Vygy 73 (170)
|-.++||||++|+|+|+.++++.++ -.++ ||++|+|||+++.++|+. +..|+|+||.+.++.++||
T Consensus 1 M~~y~aIIg~KdnpVYe~e~~~~n~~~d~~~~~~ln~fiihaSlDiv~~lqwsv-------N~~Y~~~~d~f~~l~IsAY 73 (136)
T COG5603 1 MGEYLAIIGEKDNPVYEREYDPINKTSDGEYCRLLNQFIIHASLDIVVWLQWSV-------NTSYFDCLDSFGDLRISAY 73 (136)
T ss_pred CCceEEEEecCCCceeeeeecCcCcccCHHHHHHHhHHhhhhhHHHHHHHHHHh-------hhHHHHHHHhhCCeEEEEE
Confidence 7789999999999999999995421 1345 999999999999999973 6899999999999999999
Q ss_pred EecCceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhccccc--Ccccccccc
Q 030884 74 LTNTKVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAWKK--DNIQNICRE 126 (170)
Q Consensus 74 vT~t~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF~~--~~i~np~f~ 126 (170)
++++|+||+++|+.. .++++|+||+| |||+|+|++||||+. ++|.+|.||
T Consensus 74 i~pSgmkf~~iH~n~--s~~N~rsF~qe-vHely~ktLmspfy~~~~pirsqafd 125 (136)
T COG5603 74 IMPSGMKFLFIHQNQ--SRKNARSFLQE-VHELYAKTLMSPFYEPDEPIRSQAFD 125 (136)
T ss_pred EccCCceEEEEeccc--hhhhHHHHHHH-HHHHHHHHhhCcccCCCccccchhhh
Confidence 999999999999875 78999999997 999999988888843 455554443
No 5
>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=98.50 E-value=1.6e-06 Score=67.85 Aligned_cols=128 Identities=15% Similarity=0.181 Sum_probs=71.1
Q ss_pred EEEEEEEcCCCCeeEEEcCCCcc---------cchhhhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEE
Q 030884 2 IACVAVVGHQNNPLYIQSFTEAD---------DALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYG 72 (170)
Q Consensus 2 i~~~aIIG~~d~PLy~~~f~~~~---------~~l~~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~Vyg 72 (170)
|..+=|+++...-||-+++.... ++.++=+=.--||--+-.++.......+..+...+. ...++.++++-
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~-~~~T~~yklh~ 79 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFE-SFETDTYKLHC 79 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEE-EEEESS-EEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEE-EEEeCCEEEEE
Confidence 45678999999999999998642 223332333345666666654311110000111222 24468999999
Q ss_pred EEecCceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhcccccCcccccccccCCCCcchhhhhhHHHhhccc
Q 030884 73 YLTNTKVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAWKKDNIQNICRESKHHSQVIWVEFSWLIAAGVR 147 (170)
Q Consensus 73 yvT~t~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF~~~~i~np~f~~~~~~~~~~~~~~~~~~~~~~ 147 (170)
|.|.||+|||++++.. .++....+.+ .+|++|++.+ +.||+|+++. || .+.||+.++.
T Consensus 80 ~eT~TGlKFvl~td~~--~~~~~~~l~~-~~~~lY~dyV--------~KNPfy~~~~---pI---~~~lF~~~l~ 137 (142)
T PF04099_consen 80 FETPTGLKFVLITDPN--VPSLRDELLR-IYYELYVDYV--------VKNPFYSLEM---PI---RCELFDTKLD 137 (142)
T ss_dssp EE-TTS-EEEEEE-TT--CCHCHHHHHH-HHHHHHHHHH--------HS-TTS-TTS----------HHHHHHHH
T ss_pred EEcCcCcEEEEEecCC--CccHHHHHHH-HHHHHHHHHH--------hhCCCCCCCC---cE---ehHHHHHHHH
Confidence 9999999999999874 3344555666 4999998843 3455566654 67 7888887765
No 6
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.07 E-value=7.8e-06 Score=66.73 Aligned_cols=94 Identities=16% Similarity=0.148 Sum_probs=70.9
Q ss_pred HHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEecCceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhh
Q 030884 33 VHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPIS 112 (170)
Q Consensus 33 ~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT~t~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~ 112 (170)
..-+|+.|.++....++++ + + .+-.++.+....|.|-||+|||++.+. .-..+.+++++ +||+|.+-
T Consensus 103 ~fhsl~aI~~qlsp~~ksS---G---i-e~LetdtF~l~~~QTlTG~KFVvis~~---~~~~aD~lLrK-iYelYsDy-- 169 (199)
T KOG3369|consen 103 SFHSLFAISTQLSPEPKSS---G---I-EVLETDTFTLHIFQTLTGTKFVVIAEP---GTQGADSLLRK-IYELYSDY-- 169 (199)
T ss_pred hhcchhheeeccCCCCCCC---c---e-EEEEeccEEEEEEEccCCcEEEEEecC---CchhHHHHHHH-HHHHHHHH--
Confidence 3457888888877654432 1 1 133467899999999999999999987 44789999997 99999873
Q ss_pred cccccCcccccccccCCCCcchhhhhhHHHhhccccccc
Q 030884 113 RAWKKDNIQNICRESKHHSQVIWVEFSWLIAAGVRLNLL 151 (170)
Q Consensus 113 NPF~~~~i~np~f~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (170)
.+.||||.+.= || -+.|||.++...+.
T Consensus 170 ------vlKNPfYSlEM---PI---Rc~lFDe~lk~~le 196 (199)
T KOG3369|consen 170 ------VLKNPFYSLEM---PI---RCELFDEKLKFLLE 196 (199)
T ss_pred ------hhcCCccCccc---ce---eHHHhhHHHHHHHh
Confidence 45678887777 77 78899988765543
No 7
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=97.53 E-value=0.00036 Score=53.60 Aligned_cols=116 Identities=16% Similarity=0.177 Sum_probs=72.2
Q ss_pred EEEEEcCCCCeeEEEcCCCcccchhh--hHHHHhhhhhhhhhhcCCCCCCCCCccccccc----ccccCCeEEEEEEecC
Q 030884 4 CVAVVGHQNNPLYIQSFTEADDALKL--HHIVHCSLDVVDERVNNPKKSGPTLNETFLGL----LYPTENYKVYGYLTNT 77 (170)
Q Consensus 4 ~~aIIG~~d~PLy~~~f~~~~~~l~~--qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~----Ld~~e~~~VygyvT~t 77 (170)
-+-||++...-+|-++|++.+.++.- ..++-++|-=|-....+. -+|-|. +-.+..+.+.=|.|-|
T Consensus 5 ~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~--------~p~~gssg~~~l~~~~f~m~I~qT~T 76 (134)
T COG5122 5 QFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQT--------IPLPGSSGRLVLYFRNFVMTIFQTTT 76 (134)
T ss_pred EEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhc--------ccCCCCCceEEEEeccEEEEEEEecC
Confidence 57799999999999999887554433 234444555444443321 112222 2236788899999999
Q ss_pred ceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhcccccCcccccccccCCCCcchhhhhhHHHhhc
Q 030884 78 KVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAWKKDNIQNICRESKHHSQVIWVEFSWLIAAG 145 (170)
Q Consensus 78 ~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF~~~~i~np~f~~~~~~~~~~~~~~~~~~~~ 145 (170)
|+|||++.+.+ .-+..-+ .|+ +|++|.+-++ .||||.+.- || -++|||.-
T Consensus 77 G~kFV~~~~k~--t~na~~q-l~k-iY~lYsdYV~--------knPfys~EM---PI---~c~lFde~ 126 (134)
T COG5122 77 GTKFVFVAEKR--TVNALFQ-LQK-IYSLYSDYVT--------KNPFYSPEM---PI---QCSLFDEH 126 (134)
T ss_pred CcEEEEEecCC--chhHHHH-HHH-HHHHHHHHhh--------cCCCCCccc---ce---ehhhhhHH
Confidence 99999999764 2222222 565 8999887443 355555444 45 55666643
No 8
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.04 E-value=0.014 Score=45.75 Aligned_cols=112 Identities=21% Similarity=0.295 Sum_probs=79.9
Q ss_pred EEEEEEcCCCCeeEEEcCCCc-------ccchhhhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEe
Q 030884 3 ACVAVVGHQNNPLYIQSFTEA-------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLT 75 (170)
Q Consensus 3 ~~~aIIG~~d~PLy~~~f~~~-------~~~l~~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT 75 (170)
.-+=|-+++.+=||-++-... +++.++=|=.-.||--+-+++... +.++.++ =+++..|++.=|.|
T Consensus 4 y~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~-----d~k~~f~--sy~Ts~YklhfyeT 76 (140)
T KOG3368|consen 4 YNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPG-----DVKDGFL--SYKTSKYKLHFYET 76 (140)
T ss_pred EEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCC-----CcccCee--EEeeceeEEEEEEc
Confidence 346677888888888776543 344667666667787777777532 2244444 35678999999999
Q ss_pred cCceEEEEEEcCCCCCchhhhhhhhhhhhh-hhhhhhhcccccCcccccccccCCCCcc
Q 030884 76 NTKVKFILVTTDLDVRDADVRNEVPCCIYR-CRFKPISRAWKKDNIQNICRESKHHSQV 133 (170)
Q Consensus 76 ~t~iKfVll~~~~~~~d~~Ik~fF~e~V~e-lYvk~l~NPF~~~~i~np~f~~~~~~~~ 133 (170)
+||+|||+.++. +-.++|...+. +|. +|++.+ ..||.+..+-.+|+
T Consensus 77 ptglk~vl~Tdp---k~~~ir~vLq~-IYs~lyVE~V--------vknpl~~~~~~~~i 123 (140)
T KOG3368|consen 77 PTGLKFVLNTDP---KAGSIRDVLQY-IYSHLYVEYV--------VKNPLYTYDPGSPI 123 (140)
T ss_pred CCCcEEEEecCC---CcccHHHHHHH-HHHHHHHHHH--------HcCcccccCCCCcc
Confidence 999999999976 67789999997 888 898843 33666665444443
No 9
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.15 E-value=4.8 Score=31.65 Aligned_cols=40 Identities=20% Similarity=0.052 Sum_probs=29.1
Q ss_pred hhhhhhcccccCcccccccccCCCCcchhhhhhHHHhhccccccccc
Q 030884 107 RFKPISRAWKKDNIQNICRESKHHSQVIWVEFSWLIAAGVRLNLLNL 153 (170)
Q Consensus 107 Yvk~l~NPF~~~~i~np~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (170)
+...+..-+++ .++||||++++ || -|.-|++-||.-+++-
T Consensus 97 Ffqev~elyik-~lmnpFy~~~d---pi---rs~afd~kv~~~~rkh 136 (139)
T KOG3487|consen 97 FFQEVHELYIK-TLMNPFYEIND---PI---RSPAFDHKVRGLARKH 136 (139)
T ss_pred HHHHHHHHHHH-HHhCcccccCC---cc---ccHHHHHHHHHHHHHH
Confidence 34444445566 89999999999 77 7788888888766554
No 10
>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=46.81 E-value=1.2e+02 Score=22.73 Aligned_cols=73 Identities=10% Similarity=0.296 Sum_probs=43.3
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCcccchhhhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEecCceE
Q 030884 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (170)
Q Consensus 1 Mi~~~aIIG~~d~PLy~~~f~~~~~~l~~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT~t~iK 80 (170)
|+.++-|.+++.++++.+-+...+...+ +-+..... ...... . ++. ..+...++ ..+-|...+++-
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~-~~~~~~~~----~~~~~~--~----~~~--~~i~~~~~-~~~vy~~~~dl~ 66 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEER-QKLFEKFI----KKKSSR--N----SKQ--SPIFEHDN-YRIVYKRYSDLY 66 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHH-HHHHHHHH----HHHHTS--S----SSS--TSEEEETT-EEEEEEEETTEE
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHH-HHHHHHHH----HHHHhc--c----ccc--ceeeeccc-ceeeeEeeccEE
Confidence 8999999999999999999965433221 21222111 111111 0 011 22233444 444777888999
Q ss_pred EEEEEcC
Q 030884 81 FILVTTD 87 (170)
Q Consensus 81 fVll~~~ 87 (170)
|+++.+.
T Consensus 67 ~~~v~~~ 73 (141)
T PF01217_consen 67 FVVVGDE 73 (141)
T ss_dssp EEEEESS
T ss_pred EEEEeec
Confidence 9999975
No 11
>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=29.54 E-value=18 Score=28.09 Aligned_cols=9 Identities=11% Similarity=-0.178 Sum_probs=2.2
Q ss_pred Ccccccccc
Q 030884 118 DNIQNICRE 126 (170)
Q Consensus 118 ~~i~np~f~ 126 (170)
.+|.++.||
T Consensus 125 ~pI~~~lF~ 133 (142)
T PF04099_consen 125 MPIRCELFD 133 (142)
T ss_dssp S----HHHH
T ss_pred CcEehHHHH
Confidence 445554444
No 12
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=28.52 E-value=1.1e+02 Score=22.83 Aligned_cols=49 Identities=22% Similarity=0.374 Sum_probs=35.1
Q ss_pred CCeEEEEEEec-----CceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhccc
Q 030884 66 ENYKVYGYLTN-----TKVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAW 115 (170)
Q Consensus 66 e~~~VygyvT~-----t~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF 115 (170)
+++++.||++. ++-+..+.++.+++++..+....++ .|+-|+..-.-||
T Consensus 30 ~~~~i~G~is~p~~~~~~~~q~~fVNgR~V~~~~l~~aI~~-~Y~~~l~~~~~P~ 83 (127)
T cd03483 30 LGFKVKGLISNANYSKKKIIFILFINNRLVECSALRRAIEN-VYANYLPKGAHPF 83 (127)
T ss_pred CcEEEEEEEcCchhcCCCceEEEEEcCCEecCHHHHHHHHH-HHHHhCcCCCccE
Confidence 46999999853 3455677778888888888887775 7777665445566
No 13
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=28.37 E-value=65 Score=23.68 Aligned_cols=50 Identities=14% Similarity=0.305 Sum_probs=33.0
Q ss_pred cCCeEEEEEEecC------ceEEEEEEcCCCCCchhhhhhhhhhhhhhhhhhhhccc
Q 030884 65 TENYKVYGYLTNT------KVKFILVTTDLDVRDADVRNEVPCCIYRCRFKPISRAW 115 (170)
Q Consensus 65 ~e~~~VygyvT~t------~iKfVll~~~~~~~d~~Ik~fF~e~V~elYvk~l~NPF 115 (170)
.+++.+.||++.. +-...+-++.+++++..+....++ .|+-+...-..|+
T Consensus 20 ~~~~~i~G~is~p~~~~~~~~~q~ifVN~R~V~~~~l~~~I~~-~y~~~~~~~~~P~ 75 (119)
T PF01119_consen 20 DEDFSIEGYISKPDVSRSSRDRQFIFVNGRPVENKALSKAINE-AYRERLPKGRYPI 75 (119)
T ss_dssp ECCEEEEEEEE-SSCSBSSCTCEEEEETTEEE--HHHHHHHHH-HHHCTTCTTSB-E
T ss_pred CCCEEEEEEEECchhccCCCCcEEEEeCCCeEeChHHHHHHHH-HHhhcccCCCCce
Confidence 4679999999843 345666677777888888888775 7775555566666
No 14
>PF15205 PLAC9: Placenta-specific protein 9
Probab=27.08 E-value=40 Score=23.81 Aligned_cols=19 Identities=42% Similarity=0.665 Sum_probs=15.6
Q ss_pred hhhHHHHhhhhhhhhhhcC
Q 030884 28 KLHHIVHCSLDVVDERVNN 46 (170)
Q Consensus 28 ~~qfi~haSLDiiEe~~~~ 46 (170)
+-|+-+|.-||++||++-+
T Consensus 18 drhmav~~RLdviEe~veK 36 (74)
T PF15205_consen 18 DRHMAVHSRLDVIEETVEK 36 (74)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3477899999999998854
No 15
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=24.48 E-value=58 Score=29.86 Aligned_cols=53 Identities=21% Similarity=0.250 Sum_probs=40.5
Q ss_pred hhHHHHhhhhhhhhhhcCCCCCCCCCcccccccccccCCeEEEEEEecCceEEEEEEc
Q 030884 29 LHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFILVTT 86 (170)
Q Consensus 29 ~qfi~haSLDiiEe~~~~~~k~~~~s~~~YLG~Ld~~e~~~VygyvT~t~iKfVll~~ 86 (170)
.+.+-|..+|-+|-.--.+. .++..|...|..=+++||+|--.+|+|++---+
T Consensus 168 W~ll~~f~~dT~DltgieWs-----Pdg~~laVwd~~Leykv~aYe~~lG~k~v~wsP 220 (447)
T KOG4497|consen 168 WILLKEFKLDTIDLTGIEWS-----PDGNWLAVWDNVLEYKVYAYERGLGLKFVEWSP 220 (447)
T ss_pred HHHHHhcCCCcccccCceEC-----CCCcEEEEecchhhheeeeeeeccceeEEEecc
Confidence 35667888888886543321 256789999999999999999999999986544
No 16
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=21.11 E-value=60 Score=26.26 Aligned_cols=18 Identities=17% Similarity=0.148 Sum_probs=16.9
Q ss_pred Cchhhhhhhhhhhhhhhhh
Q 030884 91 RDADVRNEVPCCIYRCRFK 109 (170)
Q Consensus 91 ~d~~Ik~fF~e~V~elYvk 109 (170)
.|++++++|++ .||-|+|
T Consensus 81 ~d~eL~~~~~r-aHe~~lk 98 (167)
T COG1507 81 QDEELRAFYRR-AHESYLK 98 (167)
T ss_pred ccHHHHHHHHH-HHHHHHH
Confidence 78999999996 9999998
Done!