Query 038670
Match_columns 259
No_of_seqs 155 out of 477
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 13:26:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038670hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0859 Synaptobrevin/VAMP-lik 100.0 5.4E-37 1.2E-41 267.7 11.0 117 6-127 1-119 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 99.9 5.2E-21 1.1E-25 169.5 12.7 117 7-129 1-130 (216)
3 PF13774 Longin: Regulated-SNA 99.8 1.1E-19 2.3E-24 138.0 10.8 79 33-117 1-82 (83)
4 COG5143 SNC1 Synaptobrevin/VAM 98.0 3.5E-05 7.5E-10 68.1 8.2 86 32-121 32-120 (190)
5 KOG0861 SNARE protein YKT6, sy 97.9 4.8E-05 1E-09 66.6 8.2 66 33-99 43-111 (198)
6 PF04086 SRP-alpha_N: Signal r 96.0 0.016 3.5E-07 52.9 6.1 94 31-128 5-101 (279)
7 KOG0781 Signal recognition par 89.3 2 4.4E-05 43.5 8.7 86 9-96 4-95 (587)
8 PF01217 Clat_adaptor_s: Clath 88.8 7.4 0.00016 31.9 10.5 80 15-96 11-96 (141)
9 PF04099 Sybindin: Sybindin-li 79.2 11 0.00023 31.6 7.5 75 45-124 65-141 (142)
10 KOG0938 Adaptor complexes medi 71.7 40 0.00086 33.1 10.0 84 10-96 6-93 (446)
11 PF04628 Sedlin_N: Sedlin, N-t 50.1 1.4E+02 0.003 24.3 9.4 109 12-124 1-131 (132)
12 PF11675 DUF3271: Protein of u 31.4 1.5E+02 0.0032 27.6 6.2 57 3-62 26-82 (249)
13 KOG0860 Synaptobrevin/VAMP-lik 29.7 7.5 0.00016 32.2 -2.2 21 237-257 81-101 (116)
14 PF03164 Mon1: Trafficking pro 26.9 2.8E+02 0.006 27.3 7.7 49 45-93 53-101 (415)
15 KOG2740 Clathrin-associated pr 25.0 2.2E+02 0.0047 28.3 6.4 38 59-96 59-96 (418)
16 cd01617 DCX Ubiquitin-like dom 23.9 1.1E+02 0.0024 22.9 3.5 52 25-76 23-79 (80)
17 PF09426 Nyv1_N: Vacuolar R-SN 23.8 1.6E+02 0.0034 25.2 4.6 81 34-130 47-135 (141)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.4e-37 Score=267.65 Aligned_cols=117 Identities=21% Similarity=0.387 Sum_probs=111.5
Q ss_pred ceeEEEEEEcCCeeEEeeeCCCCCHHHHHHHHHhcCCCC-CceEEEEeCCEEEEEEEeCCEEEEEEecCCCChhhHHHHH
Q 038670 6 NTVHYCSVSRGNRSLYVYSGGDHEIENLATLCLERTPPF-HKWYFETIGKRIYGFLIEDGYAYFMIADEGLGNRGALQFL 84 (259)
Q Consensus 6 ~~IlYA~VARg~tILAEys~~~gNf~~ia~~iL~Klp~~-~~k~s~~~g~y~FhyL~edgivYlcItd~s~~k~iaF~FL 84 (259)
++|+||+||||++|||||++.+|||.++|++||+|||++ ++|+||..|+|+|||+++||++||||+|++++|++||+||
T Consensus 1 m~iiYs~VARGTvvLaeft~~~gNf~sva~qiL~klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFL 80 (217)
T KOG0859|consen 1 MSIIYSFVARGTVILAEFTEFSGNFSSIAAQILQKLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFL 80 (217)
T ss_pred CceeEEEEecceEEEEeeeeccCCHHHHHHHHHHhCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHH
Confidence 479999999999999999999999999999999999987 7799999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhh-ccCCCCCCCCccccccccccHHHHHHHHHhhh
Q 038670 85 EHLRDEFKKVA-KKGSRGSFSGMNAIGVQEQLVPVIRRLITSLE 127 (259)
Q Consensus 85 eeIk~eF~~~y-~~~~~a~a~a~~~~~~~~eF~pvLq~lM~sln 127 (259)
|+|+++|.+.| ..+.+|.||+| |.||+++|++.|+.+-
T Consensus 81 e~Ik~~F~k~YG~~a~ta~Aysm-----N~EFs~vL~qqm~y~s 119 (217)
T KOG0859|consen 81 ERIKEDFKKRYGGGAHTAVAYSM-----NKEFSSVLKQQMQYCS 119 (217)
T ss_pred HHHHHHHHHHhccchhHHHHhHh-----HHHHHHHHHHHHHHHH
Confidence 99999999999 45688999998 9999999999999764
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.85 E-value=5.2e-21 Score=169.52 Aligned_cols=117 Identities=18% Similarity=0.257 Sum_probs=103.8
Q ss_pred eeEEEEEEc--CCeeEEeeeC---CCCCH----HHHHHHHHhcCCCC-CceEEEEeCCEEEEEEEeCCEEEEEEecCCCC
Q 038670 7 TVHYCSVSR--GNRSLYVYSG---GDHEI----ENLATLCLERTPPF-HKWYFETIGKRIYGFLIEDGYAYFMIADEGLG 76 (259)
Q Consensus 7 ~IlYA~VAR--g~tILAEys~---~~gNf----~~ia~~iL~Klp~~-~~k~s~~~g~y~FhyL~edgivYlcItd~s~~ 76 (259)
||++++|+| +++|||+..+ .+++. .+.++.+++++.+. ++++|.+.|.|+|||+++.|||||||||.+||
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 689999999 7899998754 23443 57999999999987 99999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHhhccC---CCCCCCCccccccccccHHHHHHHHHhhhcc
Q 038670 77 NRGALQFLEHLRDEFKKVAKKG---SRGSFSGMNAIGVQEQLVPVIRRLITSLENV 129 (259)
Q Consensus 77 k~iaF~FLeeIk~eF~~~y~~~---~~a~a~a~~~~~~~~eF~pvLq~lM~sln~~ 129 (259)
+++||+|||+|.+||.+.|... ....||++ .+|+++||+.-++||.+
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~F------ieFD~~IQk~Kk~ynd~ 130 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAF------IEFDTFIQKTKKRYNDT 130 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCeeE------EehhHHHHHHHHHhcCc
Confidence 9999999999999999999543 36677776 79999999999999964
No 3
>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=99.82 E-value=1.1e-19 Score=138.00 Aligned_cols=79 Identities=28% Similarity=0.417 Sum_probs=69.9
Q ss_pred HHHHHHhcCCCCC-ceEEEEeCCEEEEEEEeCCEEEEEEecCCCChhhHHHHHHHHHHHHHHhhc--cCCCCCCCCcccc
Q 038670 33 LATLCLERTPPFH-KWYFETIGKRIYGFLIEDGYAYFMIADEGLGNRGALQFLEHLRDEFKKVAK--KGSRGSFSGMNAI 109 (259)
Q Consensus 33 ia~~iL~Klp~~~-~k~s~~~g~y~FhyL~edgivYlcItd~s~~k~iaF~FLeeIk~eF~~~y~--~~~~a~a~a~~~~ 109 (259)
+|++||+++++.+ .|.|++.++|+|||+++||++||||||+++|+++||.||++|+++|..+|+ ++..+.+|+|
T Consensus 1 ~a~~il~~i~~~~~~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~~~~~~~a~~~~~--- 77 (83)
T PF13774_consen 1 QARKILKRIPPNGNSKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYGGDQIKSASPYSF--- 77 (83)
T ss_dssp HHHHHHHTS-TTSESEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTTTTTTTSTTTTT---
T ss_pred CHHHHHHhcCCCCCCeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcCcchhcccCCcch---
Confidence 5899999999655 899999999999999999999999999999999999999999999999996 4577778776
Q ss_pred ccccccHH
Q 038670 110 GVQEQLVP 117 (259)
Q Consensus 110 ~~~~eF~p 117 (259)
.+|++
T Consensus 78 ---~~F~~ 82 (83)
T PF13774_consen 78 ---KEFDS 82 (83)
T ss_dssp ---HHHHH
T ss_pred ---hhcCC
Confidence 67775
No 4
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=97.95 E-value=3.5e-05 Score=68.07 Aligned_cols=86 Identities=19% Similarity=0.227 Sum_probs=65.9
Q ss_pred HHHHHHHhcCCCC-CceEEEEeCCEEEEEEEeC-CEEEEEEecCCCChhhHHHHHHHHHHHHHHhhc-cCCCCCCCCccc
Q 038670 32 NLATLCLERTPPF-HKWYFETIGKRIYGFLIED-GYAYFMIADEGLGNRGALQFLEHLRDEFKKVAK-KGSRGSFSGMNA 108 (259)
Q Consensus 32 ~ia~~iL~Klp~~-~~k~s~~~g~y~FhyL~ed-givYlcItd~s~~k~iaF~FLeeIk~eF~~~y~-~~~~a~a~a~~~ 108 (259)
..+..+|.++.+. .++.+.+.++|.|||+..+ |++|.|+|+..+|+++||.+|+++..+|..+.. ......+.+.
T Consensus 32 ~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~la~~~~~~~~~~~~~s~~~~~~~d~~~~~-- 109 (190)
T COG5143 32 SKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNKLAYGYLNSIATEFLKSSALEQLIDDTVGI-- 109 (190)
T ss_pred chHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchhhhhHHHHhhccHhhhhhhHhhcccCccch--
Confidence 4677777777763 4477889999999999986 999999999999999999999999999988872 2212222221
Q ss_pred cccccccHHHHHH
Q 038670 109 IGVQEQLVPVIRR 121 (259)
Q Consensus 109 ~~~~~eF~pvLq~ 121 (259)
.-.+|++++++
T Consensus 110 --~~~~~d~~~e~ 120 (190)
T COG5143 110 --MRVNIDKVIEK 120 (190)
T ss_pred --hhhhHHHHHHh
Confidence 12578888777
No 5
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.91 E-value=4.8e-05 Score=66.57 Aligned_cols=66 Identities=21% Similarity=0.250 Sum_probs=57.1
Q ss_pred HHHHHHhcCCCCCceEEEEeCCEEEEEEEeC-CEEEEEEecCCCChhhHHHHHHHHHHHHHHhh--ccCC
Q 038670 33 LATLCLERTPPFHKWYFETIGKRIYGFLIED-GYAYFMIADEGLGNRGALQFLEHLRDEFKKVA--KKGS 99 (259)
Q Consensus 33 ia~~iL~Klp~~~~k~s~~~g~y~FhyL~ed-givYlcItd~s~~k~iaF~FLeeIk~eF~~~y--~~~~ 99 (259)
+++.+.++.++. .+.+++.++|..|..+.+ |+++++++|..||-+.||.+|++|.++|.... .+|.
T Consensus 43 ~sktvaeRt~~g-~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~ 111 (198)
T KOG0861|consen 43 ISKTVAERTGPG-QRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEFTTKVPATQWP 111 (198)
T ss_pred HHHHHHHhcCcc-cccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHHhhcCcccccC
Confidence 778888999884 578899999999988875 99999999999999999999999999995554 3454
No 6
>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=95.96 E-value=0.016 Score=52.93 Aligned_cols=94 Identities=15% Similarity=0.120 Sum_probs=53.0
Q ss_pred HHHHHHHHhcCCCCCceEEEEeCCEEEEEEEeC--CEEEEEEecCCCChhhHHHHHHHHHHHHHHhhccC-CCCCCCCcc
Q 038670 31 ENLATLCLERTPPFHKWYFETIGKRIYGFLIED--GYAYFMIADEGLGNRGALQFLEHLRDEFKKVAKKG-SRGSFSGMN 107 (259)
Q Consensus 31 ~~ia~~iL~Klp~~~~k~s~~~g~y~FhyL~ed--givYlcItd~s~~k~iaF~FLeeIk~eF~~~y~~~-~~a~a~a~~ 107 (259)
..+++.||=.=. -.-.+|++++|+..|..++ +++|++|-..-+.-.-.=.||+.|+..|...|... ........
T Consensus 5 n~LI~~vlleeR--~~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~l~~~~~~~~- 81 (279)
T PF04086_consen 5 NALIRDVLLEER--SGNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQLKQLKPNTS- 81 (279)
T ss_dssp HHHHHHTGGG---------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHHHHSSSTHHH-
T ss_pred HHHHHHhheeec--cCCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHHhhccccccc-
Confidence 345555443211 1345689999999999986 69999999888887777779999999999999432 11111110
Q ss_pred ccccccccHHHHHHHHHhhhc
Q 038670 108 AIGVQEQLVPVIRRLITSLEN 128 (259)
Q Consensus 108 ~~~~~~eF~pvLq~lM~sln~ 128 (259)
+..+.+|+.++.+++..++.
T Consensus 82 -~~~~~~Fd~~F~~~l~~~e~ 101 (279)
T PF04086_consen 82 -INEYFDFDEEFDQLLKELEA 101 (279)
T ss_dssp -HT-----HHHHHHHHHHHCC
T ss_pred -cccchhHHHHHHHHHHHHHH
Confidence 00123888888888888774
No 7
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.27 E-value=2 Score=43.50 Aligned_cols=86 Identities=10% Similarity=0.158 Sum_probs=65.3
Q ss_pred EEEEEEcCCeeEEeeeCCCCCH----HHHHHHHHhcCCCCCceEEEEeCCEEEEEEEeC--CEEEEEEecCCCChhhHHH
Q 038670 9 HYCSVSRGNRSLYVYSGGDHEI----ENLATLCLERTPPFHKWYFETIGKRIYGFLIED--GYAYFMIADEGLGNRGALQ 82 (259)
Q Consensus 9 lYA~VARg~tILAEys~~~gNf----~~ia~~iL~Klp~~~~k~s~~~g~y~FhyL~ed--givYlcItd~s~~k~iaF~ 82 (259)
+++.+.+|+.||..|.+..-|| ..+++.+|-.-.. +-.+++.+.|+..|-.++ +++|+|+..+-..-.-+-.
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er~--~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv~~ 81 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSERG--GVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYVDK 81 (587)
T ss_pred eeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhhc--CcccCchhheeEeeeecCCccEEEEEEEeccchhhhHHH
Confidence 4788899999999998655554 3455554433111 122378889999888875 6999999998888888888
Q ss_pred HHHHHHHHHHHhhc
Q 038670 83 FLEHLRDEFKKVAK 96 (259)
Q Consensus 83 FLeeIk~eF~~~y~ 96 (259)
||+++.+.|...|.
T Consensus 82 ll~~v~~~f~e~~~ 95 (587)
T KOG0781|consen 82 LLNDVLNLFREKYD 95 (587)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999999994
No 8
>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=88.76 E-value=7.4 Score=31.86 Aligned_cols=80 Identities=16% Similarity=0.136 Sum_probs=56.9
Q ss_pred cCCeeEEeeeC-CC-CC----HHHHHHHHHhcCCCCCceEEEEeCCEEEEEEEeCCEEEEEEecCCCChhhHHHHHHHHH
Q 038670 15 RGNRSLYVYSG-GD-HE----IENLATLCLERTPPFHKWYFETIGKRIYGFLIEDGYAYFMIADEGLGNRGALQFLEHLR 88 (259)
Q Consensus 15 Rg~tILAEys~-~~-gN----f~~ia~~iL~Klp~~~~k~s~~~g~y~FhyL~edgivYlcItd~s~~k~iaF~FLeeIk 88 (259)
+|.++++.|-. .+ .. |+.+...+..+-+ ..--...++++.|-|..-+++.|+++++.+..--..+.||..+-
T Consensus 11 ~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v 88 (141)
T PF01217_consen 11 QGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNS--KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLV 88 (141)
T ss_dssp TSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSS--SSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHH
T ss_pred CCCEEEehhcCCccHHHHHHHHHHHHHHHHhccc--ccceeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhh
Confidence 46688888742 22 12 2233333333321 11335778999999999999999999999998889999999999
Q ss_pred HHHHHhhc
Q 038670 89 DEFKKVAK 96 (259)
Q Consensus 89 ~eF~~~y~ 96 (259)
+-+...++
T Consensus 89 ~~l~~~~~ 96 (141)
T PF01217_consen 89 EVLDDYFG 96 (141)
T ss_dssp HHHHHHHS
T ss_pred hhhhhhhc
Confidence 99988764
No 9
>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=79.16 E-value=11 Score=31.57 Aligned_cols=75 Identities=9% Similarity=0.105 Sum_probs=43.5
Q ss_pred CceEEEEeCCEEEEEEEe-CCEEEEEEecCCCChhhHHHHHHHHHHHHHHhhccCCCCCCCCc-cccccccccHHHHHHH
Q 038670 45 HKWYFETIGKRIYGFLIE-DGYAYFMIADEGLGNRGALQFLEHLRDEFKKVAKKGSRGSFSGM-NAIGVQEQLVPVIRRL 122 (259)
Q Consensus 45 ~~k~s~~~g~y~FhyL~e-dgivYlcItd~s~~k~iaF~FLeeIk~eF~~~y~~~~~a~a~a~-~~~~~~~eF~pvLq~l 122 (259)
.+-.+++.+.|..||+-- -|+-|+++||...+. ..=.+|..+.+-|...- -..+.|.+ ... -+..|+..|.++
T Consensus 65 ~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV---~KNPfy~~~~pI-~~~lF~~~l~~~ 139 (142)
T PF04099_consen 65 SGFESFETDTYKLHCFETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYV---VKNPFYSLEMPI-RCELFDTKLDQY 139 (142)
T ss_dssp -SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHH---HS-TTS-TTS-----HHHHHHHHHH
T ss_pred eeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHH---hhCCCCCCCCcE-ehHHHHHHHHHH
Confidence 456789999999999885 799999999999863 33334555555554322 12222322 111 267899998888
Q ss_pred HH
Q 038670 123 IT 124 (259)
Q Consensus 123 M~ 124 (259)
++
T Consensus 140 ~~ 141 (142)
T PF04099_consen 140 VK 141 (142)
T ss_dssp HH
T ss_pred Hh
Confidence 76
No 10
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.75 E-value=40 Score=33.10 Aligned_cols=84 Identities=12% Similarity=0.123 Sum_probs=64.5
Q ss_pred EEEEEcCCeeEEee--eCCCCCHHHHHHH-HHhcCCCCCceE-EEEeCCEEEEEEEeCCEEEEEEecCCCChhhHHHHHH
Q 038670 10 YCSVSRGNRSLYVY--SGGDHEIENLATL-CLERTPPFHKWY-FETIGKRIYGFLIEDGYAYFMIADEGLGNRGALQFLE 85 (259)
Q Consensus 10 YA~VARg~tILAEy--s~~~gNf~~ia~~-iL~Klp~~~~k~-s~~~g~y~FhyL~edgivYlcItd~s~~k~iaF~FLe 85 (259)
|-.=.||.++++.. .+..+|..++.+- ++..+ +.+. ..++|.-+|||+..+.+-..+|+.....-...|.||.
T Consensus 6 fi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~---d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~ 82 (446)
T KOG0938|consen 6 FIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNL---DVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLY 82 (446)
T ss_pred EEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcc---ccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHH
Confidence 44456899998875 3566777776663 44442 2232 5688999999999999988999998889999999999
Q ss_pred HHHHHHHHhhc
Q 038670 86 HLRDEFKKVAK 96 (259)
Q Consensus 86 eIk~eF~~~y~ 96 (259)
.+-+-|.+-|.
T Consensus 83 kl~avm~aYfg 93 (446)
T KOG0938|consen 83 KLDAVMNAYFG 93 (446)
T ss_pred HHHHHHHHHhc
Confidence 99999987663
No 11
>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=50.10 E-value=1.4e+02 Score=24.33 Aligned_cols=109 Identities=15% Similarity=0.288 Sum_probs=57.1
Q ss_pred EEEcCCeeEEeee--CCC-CC-------HHHHHH---HHHhcC-CC-CCc---eEEEEeCC-EEEEEEEeCCEEEEEEec
Q 038670 12 SVSRGNRSLYVYS--GGD-HE-------IENLAT---LCLERT-PP-FHK---WYFETIGK-RIYGFLIEDGYAYFMIAD 72 (259)
Q Consensus 12 ~VARg~tILAEys--~~~-gN-------f~~ia~---~iL~Kl-p~-~~~---k~s~~~g~-y~FhyL~edgivYlcItd 72 (259)
.|.+.+.+|.+.+ ... .. +.-++. .+++.. .. ... +..+..++ .+|.|+.-.++-|+.+++
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 3788899998875 222 22 333332 333322 12 111 23455555 578888888899988888
Q ss_pred ---CCCChhhHHHHHHHHHHHHHHhhccCCCCCCCCccccccccccHHHHHHHHH
Q 038670 73 ---EGLGNRGALQFLEHLRDEFKKVAKKGSRGSFSGMNAIGVQEQLVPVIRRLIT 124 (259)
Q Consensus 73 ---~s~~k~iaF~FLeeIk~eF~~~y~~~~~a~a~a~~~~~~~~eF~pvLq~lM~ 124 (259)
....-...=.|+.+|++.+.+.. ..+.|.+...=-...|+..++++++
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~----~NPF~~~~~~I~S~~Fd~~v~~l~~ 131 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKAL----CNPFYQPGTPIKSPKFDSRVRALAK 131 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHH----TSTTCGCT-HHHHHHHHHHHHHHHH
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHc----cCCCCCCCCCcCCHHHHHHHHHHhc
Confidence 44555666778888888887765 2233322111012477777777764
No 12
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=31.42 E-value=1.5e+02 Score=27.62 Aligned_cols=57 Identities=12% Similarity=0.076 Sum_probs=42.7
Q ss_pred CccceeEEEEEEcCCeeEEeeeCCCCCHHHHHHHHHhcCCCCCceEEEEeCCEEEEEEEe
Q 038670 3 SIQNTVHYCSVSRGNRSLYVYSGGDHEIENLATLCLERTPPFHKWYFETIGKRIYGFLIE 62 (259)
Q Consensus 3 s~~~~IlYA~VARg~tILAEys~~~gNf~~ia~~iL~Klp~~~~k~s~~~g~y~FhyL~e 62 (259)
++|.+|-|+.||.-+..+.......-.+-.+.-.+|.+-+.+ .++.|+-++| |.++-
T Consensus 26 ~~pk~i~y~sv~qpt~~f~~~~k~h~~YLdiIN~il~~eSeN-~Kyayeg~nY--HwvIT 82 (249)
T PF11675_consen 26 NNPKPIAYISVAQPTATFEHDEKKHTKYLDIINDILRDESEN-IKYAYEGGNY--HWVIT 82 (249)
T ss_pred CCCCceeEEeccCceEEEeecCccchhHHHHHHHHHhccccc-cceeeeCCce--EEEEE
Confidence 578999999999987777776666566778888888876654 5777777765 44444
No 13
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.69 E-value=7.5 Score=32.17 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=15.6
Q ss_pred chhHHHHHHHhhheeeeeecc
Q 038670 237 PQCIQKKWWRQVGLFSSLMLL 257 (259)
Q Consensus 237 ~q~~~~~w~~~v~ivl~~d~~ 257 (259)
.+-.|++||+.+++.++|=++
T Consensus 81 ~klkrk~wWkn~Km~~il~~v 101 (116)
T KOG0860|consen 81 VKLKRKMWWKNCKMRIILGLV 101 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 556788999999987665443
No 14
>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=26.91 E-value=2.8e+02 Score=27.26 Aligned_cols=49 Identities=12% Similarity=0.080 Sum_probs=39.7
Q ss_pred CceEEEEeCCEEEEEEEeCCEEEEEEecCCCChhhHHHHHHHHHHHHHH
Q 038670 45 HKWYFETIGKRIYGFLIEDGYAYFMIADEGLGNRGALQFLEHLRDEFKK 93 (259)
Q Consensus 45 ~~k~s~~~g~y~FhyL~edgivYlcItd~s~~k~iaF~FLeeIk~eF~~ 93 (259)
+.-.++..|+..|.|+..+.++|+||+...-+...--.-|+-|......
T Consensus 53 d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils 101 (415)
T PF03164_consen 53 DELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILS 101 (415)
T ss_pred CcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHH
Confidence 4555788999999999999999999999888876667777777655443
No 15
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.04 E-value=2.2e+02 Score=28.31 Aligned_cols=38 Identities=11% Similarity=0.067 Sum_probs=29.3
Q ss_pred EEEeCCEEEEEEecCCCChhhHHHHHHHHHHHHHHhhc
Q 038670 59 FLIEDGYAYFMIADEGLGNRGALQFLEHLRDEFKKVAK 96 (259)
Q Consensus 59 yL~edgivYlcItd~s~~k~iaF~FLeeIk~eF~~~y~ 96 (259)
-+.++++.|+.++....+--.++.||.+|-+-|...|.
T Consensus 59 sv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg 96 (418)
T KOG2740|consen 59 SVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFG 96 (418)
T ss_pred eeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhc
Confidence 33456666666667777888999999999999988773
No 16
>cd01617 DCX Ubiquitin-like domain of DCX. DCX The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein. Doublecortin is expressed in migrating neurons. Mutations in the gene encoding doublecortin cause lissencephaly in males and 'double-cortex syndrome' in females.
Probab=23.88 E-value=1.1e+02 Score=22.94 Aligned_cols=52 Identities=17% Similarity=0.059 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHhcCCC--CCceEEEEeCC-EEEEEEE--eCCEEEEEEecCCCC
Q 038670 25 GGDHEIENLATLCLERTPP--FHKWYFETIGK-RIYGFLI--EDGYAYFMIADEGLG 76 (259)
Q Consensus 25 ~~~gNf~~ia~~iL~Klp~--~~~k~s~~~g~-y~FhyL~--edgivYlcItd~s~~ 76 (259)
..-.+|+++...+=+++.. ..-+..|+.++ ....-+- ++|-+|+|...+.+.
T Consensus 23 ~~~~sfd~lL~~lt~~l~l~~~~Vr~lyt~~g~~~v~~~~~l~~g~~yVa~g~e~fk 79 (80)
T cd01617 23 RRFKSFDALLDDLTEKVQLDPGAVRKLYTLDGGHRVSLLDELEDGGVYVASGREPFK 79 (80)
T ss_pred hhhCCHHHHHHHHHHHhCCCCCcEEEEEcCCCCeEeccHHHhcCCCEEEEECCCCCC
Confidence 3457999999999998884 56677888887 5544433 389999998877654
No 17
>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=23.75 E-value=1.6e+02 Score=25.24 Aligned_cols=81 Identities=10% Similarity=0.137 Sum_probs=49.6
Q ss_pred HHHHHhcCCCC----CceEE-EEeCCEEEEEEE---eCCEEEEEEecCCCChhhHHHHHHHHHHHHHHhhccCCCCCCCC
Q 038670 34 ATLCLERTPPF----HKWYF-ETIGKRIYGFLI---EDGYAYFMIADEGLGNRGALQFLEHLRDEFKKVAKKGSRGSFSG 105 (259)
Q Consensus 34 a~~iL~Klp~~----~~k~s-~~~g~y~FhyL~---edgivYlcItd~s~~k~iaF~FLeeIk~eF~~~y~~~~~a~a~a 105 (259)
-..+|+|+-|- -.|+| .-+++|-=.|-. +++-+|+|.+..+.|+=+|..-|.|++.. ... .
T Consensus 47 ~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~~-----~~~-----~- 115 (141)
T PF09426_consen 47 HDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKGL-----ENN-----D- 115 (141)
T ss_dssp HHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTTS-----S---------
T ss_pred hhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhccc-----cCC-----C-
Confidence 34456666652 23444 446888777776 46799999999999999999999998742 110 1
Q ss_pred ccccccccccHHHHHHHHHhhhccc
Q 038670 106 MNAIGVQEQLVPVIRRLITSLENVS 130 (259)
Q Consensus 106 ~~~~~~~~eF~pvLq~lM~sln~~~ 130 (259)
-++++..-+..+++.|-.++
T Consensus 116 -----~D~~L~~~v~~IlD~FH~EL 135 (141)
T PF09426_consen 116 -----TDEELSAHVGNILDEFHEEL 135 (141)
T ss_dssp -----STTSHHHHHHHHHHHHHHHH
T ss_pred -----CHHHHHHHHHHHHHHHHHHH
Confidence 15677778888888776555
Done!