Query 032341
Match_columns 142
No_of_seqs 108 out of 506
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:49:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032341.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032341hhsearch_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 9.9E-40 2.1E-44 249.8 11.2 122 4-131 1-123 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 99.9 1.7E-25 3.8E-30 173.6 10.1 122 5-132 1-133 (216)
3 PF13774 Longin: Regulated-SNA 99.9 6.7E-24 1.4E-28 142.9 11.2 81 31-112 1-82 (83)
4 KOG0861 SNARE protein YKT6, sy 98.7 2.3E-07 5E-12 70.7 10.8 72 31-103 43-115 (198)
5 COG5143 SNC1 Synaptobrevin/VAM 98.6 1.9E-07 4E-12 72.1 7.9 111 5-116 2-120 (190)
6 PF04086 SRP-alpha_N: Signal r 95.4 0.014 2.9E-07 47.1 2.9 88 30-119 6-101 (279)
7 KOG0781 Signal recognition par 91.2 1.1 2.5E-05 39.6 7.7 87 7-95 4-96 (587)
8 KOG0938 Adaptor complexes medi 78.8 32 0.0007 29.4 10.0 85 7-94 5-93 (446)
9 PF04099 Sybindin: Sybindin-li 74.2 31 0.00068 25.1 9.8 86 32-119 45-141 (142)
10 PF01217 Clat_adaptor_s: Clath 68.8 39 0.00085 24.1 12.6 80 13-94 11-96 (141)
11 PF09426 Nyv1_N: Vacuolar R-SN 60.9 18 0.00039 26.7 4.2 56 32-87 47-110 (141)
12 PF03164 Mon1: Trafficking pro 49.0 1.1E+02 0.0023 26.4 7.7 63 28-90 37-100 (415)
13 KOG2740 Clathrin-associated pr 41.6 97 0.0021 26.8 6.2 45 51-95 53-97 (418)
14 PHA01811 hypothetical protein 39.4 36 0.00079 22.0 2.6 19 43-61 4-22 (78)
15 cd01617 DCX Ubiquitin-like dom 36.8 65 0.0014 21.0 3.7 49 25-73 25-78 (80)
16 PF03607 DCX: Doublecortin; I 30.4 66 0.0014 19.8 2.8 48 25-72 8-58 (60)
17 KOG4078 Putative mitochondrial 27.2 1.4E+02 0.0031 22.4 4.4 57 18-74 33-115 (173)
18 PHA02979 hypothetical protein; 26.2 1.1E+02 0.0023 22.2 3.4 33 43-75 59-91 (140)
19 KOG4131 Ngg1-interacting facto 23.9 49 0.0011 26.9 1.6 33 10-42 223-257 (272)
20 KOG0164 Myosin class I heavy c 20.2 1.1E+02 0.0024 28.9 3.2 46 80-126 735-785 (1001)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.9e-40 Score=249.75 Aligned_cols=122 Identities=60% Similarity=0.937 Sum_probs=114.4
Q ss_pred ceeEEEEEEcCCeEEEeeeCCCCCHHHHHHHHHhcCCCC-CCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 032341 4 KSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL 82 (142)
Q Consensus 4 m~I~Ya~VArg~~iLae~~~~~gnf~~~a~~iL~kl~~~-~~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL 82 (142)
|+|+||+||||++|||||++.+|||.++|++||+|||++ ++|+||..|+|+|||+.+||++||||+|++.+|++||+||
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 799999999999999999999999999999999999986 6799999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCCccCCCCCChhhHHHHHHHhhchhccccCCCCC
Q 032341 83 ERVKDEFVSKYGGGKAATAPANGLNKEFGYSVVILILKPMNRRFSCYSS 131 (142)
Q Consensus 83 ~eI~~~F~~~y~~~~~~~a~~ysl~~~F~~~l~~lm~~~~~~~~n~~~~ 131 (142)
++|+++|.++||. .+.+|.||+||+||+++| ++-|+.|.+++.
T Consensus 81 e~Ik~~F~k~YG~-~a~ta~AysmN~EFs~vL-----~qqm~y~s~~p~ 123 (217)
T KOG0859|consen 81 ERIKEDFKKRYGG-GAHTAVAYSMNKEFSSVL-----KQQMQYCSEHPE 123 (217)
T ss_pred HHHHHHHHHHhcc-chhHHHHhHhHHHHHHHH-----HHHHHHHHcCcc
Confidence 9999999999995 589999999999999999 556666666654
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=1.7e-25 Score=173.64 Aligned_cols=122 Identities=23% Similarity=0.426 Sum_probs=108.4
Q ss_pred eeEEEEEEc--CCeEEEeeeC---CCCCH----HHHHHHHHhcCCCC-CCeEEEEeCCeEEEEEEeCCEEEEEEecCCCC
Q 032341 5 SLIYAFVAR--GNVVLAEYTE---FSGNF----NSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSG 74 (142)
Q Consensus 5 ~I~Ya~VAr--g~~iLae~~~---~~gnf----~~~a~~iL~kl~~~-~~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~ 74 (142)
||++++|+| +++|||...+ .+|+. .+.++.+++++.+. +.+.|.+.|.|.|||++++||||+|+||+++|
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 789999999 6799998654 24443 67899999999886 88999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHhhcCCCCCC-ccCCCCCChhhHHHHHHHhhchhccccCCCCCc
Q 032341 75 RQIPMAFLERVKDEFVSKYGGGKAA-TAPANGLNKEFGYSVVILILKPMNRRFSCYSSL 132 (142)
Q Consensus 75 ~~~aF~FL~eI~~~F~~~y~~~~~~-~a~~ysl~~~F~~~l~~lm~~~~~~~~n~~~~~ 132 (142)
+++||+||++|.++|.+.|+.+... ..+||++ -+|.+.| |+.+++||+.++-
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~F-ieFD~~I-----Qk~Kk~ynd~r~~ 133 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAF-IEFDTFI-----QKTKKRYNDTRSQ 133 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCeeE-EehhHHH-----HHHHHHhcCcHHH
Confidence 9999999999999999999975554 6689999 5999999 8999999998753
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=99.91 E-value=6.7e-24 Score=142.94 Aligned_cols=81 Identities=33% Similarity=0.696 Sum_probs=74.8
Q ss_pred HHHHHHhcCCCCC-CeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCCCccCCCCCChh
Q 032341 31 IAYQCLQKLPASN-NKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKE 109 (142)
Q Consensus 31 ~a~~iL~kl~~~~-~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL~eI~~~F~~~y~~~~~~~a~~ysl~~~ 109 (142)
+|++||+++++.+ +|.+++.|+|.|||+++||++||||||+++|+++||.||++|+++|.++|+...+.++.||+| .+
T Consensus 1 ~a~~il~~i~~~~~~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~~~~~~~a~~~~~-~~ 79 (83)
T PF13774_consen 1 QARKILKRIPPNGNSKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYGGDQIKSASPYSF-KE 79 (83)
T ss_dssp HHHHHHHTS-TTSESEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTTTTTTTSTTTTT-HH
T ss_pred CHHHHHHhcCCCCCCeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcCcchhcccCCcch-hh
Confidence 5899999999655 899999999999999999999999999999999999999999999999999778999999999 89
Q ss_pred hHH
Q 032341 110 FGY 112 (142)
Q Consensus 110 F~~ 112 (142)
|++
T Consensus 80 F~~ 82 (83)
T PF13774_consen 80 FDS 82 (83)
T ss_dssp HHH
T ss_pred cCC
Confidence 986
No 4
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.71 E-value=2.3e-07 Score=70.73 Aligned_cols=72 Identities=17% Similarity=0.261 Sum_probs=62.5
Q ss_pred HHHHHHhcCCCCCCeEEEEeCCeEEEEEEeC-CEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCCCccCC
Q 032341 31 IAYQCLQKLPASNNKFTYNCDAHTFNYLVDN-GYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPA 103 (142)
Q Consensus 31 ~a~~iL~kl~~~~~k~t~~~~~~~fh~L~~~-gi~ylcvtd~~~~~~~aF~FL~eI~~~F~~~y~~~~~~~a~~ 103 (142)
+++.+.++.+| ..+.+++.+.|..|..+.+ |++++|++|.+||.+.||.+|++|.++|...-...+|....+
T Consensus 43 ~sktvaeRt~~-g~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~~~~ 115 (198)
T KOG0861|consen 43 ISKTVAERTGP-GQRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEFTTKVPATQWPVGET 115 (198)
T ss_pred HHHHHHHhcCc-ccccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHHhhcCcccccCcCCC
Confidence 67889999987 5678899999999999976 999999999999999999999999999977766677774433
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=98.61 E-value=1.9e-07 Score=72.06 Aligned_cols=111 Identities=16% Similarity=0.213 Sum_probs=79.9
Q ss_pred eeEEEEEEcCC--eEEEe-eeCCCCCH--HHHHHHHHhcCCCC-CCeEEEEeCCeEEEEEEeC-CEEEEEEecCCCCccc
Q 032341 5 SLIYAFVARGN--VVLAE-YTEFSGNF--NSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDN-GYTYCVVADESSGRQI 77 (142)
Q Consensus 5 ~I~Ya~VArg~--~iLae-~~~~~gnf--~~~a~~iL~kl~~~-~~k~t~~~~~~~fh~L~~~-gi~ylcvtd~~~~~~~ 77 (142)
.+++..+..|. .+|++ ++..+..| ...++.+|.++.|. .++.+.+.++|.|||+..+ |++|.|+|+.++|+++
T Consensus 2 ~s~~~~~~~~~~~~~~~~~~s~~~~~ff~~~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~l 81 (190)
T COG5143 2 ASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNKL 81 (190)
T ss_pred ceEEEEeecCCcceeeccccccCcccccccchHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchhh
Confidence 45565565553 34443 21112222 45788888888663 4567888999999999976 9999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCc-cCCCCCChhhHHHHHH
Q 032341 78 PMAFLERVKDEFVSKYGGGKAAT-APANGLNKEFGYSVVI 116 (142)
Q Consensus 78 aF~FL~eI~~~F~~~y~~~~~~~-a~~ysl~~~F~~~l~~ 116 (142)
|+.+|+++..+|..+.....+.. ..++.+ .+|.+.+++
T Consensus 82 a~~~~~~~~~~~~~s~~~~~~~d~~~~~~~-~~~d~~~e~ 120 (190)
T COG5143 82 AYGYLNSIATEFLKSSALEQLIDDTVGIMR-VNIDKVIEK 120 (190)
T ss_pred hhHHHHhhccHhhhhhhHhhcccCccchhh-hhHHHHHHh
Confidence 99999999999988876444333 345556 588888854
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=95.38 E-value=0.014 Score=47.07 Aligned_cols=88 Identities=22% Similarity=0.270 Sum_probs=51.1
Q ss_pred HHHHHHHhcCCCCCCeEEEEeCCeEEEEEEeC--CEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCC----Cc-c-
Q 032341 30 SIAYQCLQKLPASNNKFTYNCDAHTFNYLVDN--GYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKA----AT-A- 101 (142)
Q Consensus 30 ~~a~~iL~kl~~~~~k~t~~~~~~~fh~L~~~--gi~ylcvtd~~~~~~~aF~FL~eI~~~F~~~y~~~~~----~~-a- 101 (142)
.+++.+|-.=.. ...+|.+|+|..+|...| |++|++|-.+-..-.-.=.||++|+..|...|+.... .. .
T Consensus 6 ~LI~~vlleeR~--~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~l~~~~~~~~~~ 83 (279)
T PF04086_consen 6 ALIRDVLLEERS--GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQLKQLKPNTSIN 83 (279)
T ss_dssp HHHHHTGGG---------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHHHHSSSTHHHHT
T ss_pred HHHHHhheeecc--CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHHhhccccccccc
Confidence 445555433222 345678899999999976 5999999998888766669999999999999984211 11 1
Q ss_pred CCCCCChhhHHHHHHHhh
Q 032341 102 PANGLNKEFGYSVVILIL 119 (142)
Q Consensus 102 ~~ysl~~~F~~~l~~lm~ 119 (142)
....|+..|...|+++-.
T Consensus 84 ~~~~Fd~~F~~~l~~~e~ 101 (279)
T PF04086_consen 84 EYFDFDEEFDQLLKELEA 101 (279)
T ss_dssp -----HHHHHHHHHHHCC
T ss_pred cchhHHHHHHHHHHHHHH
Confidence 123788888888876643
No 7
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.22 E-value=1.1 Score=39.65 Aligned_cols=87 Identities=22% Similarity=0.313 Sum_probs=64.1
Q ss_pred EEEEEEcCCeEEEeeeCCCCCHHH----HHHHHHhcCCCCCCeEEEEeCCeEEEEEEe--CCEEEEEEecCCCCcccHHH
Q 032341 7 IYAFVARGNVVLAEYTEFSGNFNS----IAYQCLQKLPASNNKFTYNCDAHTFNYLVD--NGYTYCVVADESSGRQIPMA 80 (142)
Q Consensus 7 ~Ya~VArg~~iLae~~~~~gnf~~----~a~~iL~kl~~~~~k~t~~~~~~~fh~L~~--~gi~ylcvtd~~~~~~~aF~ 80 (142)
.++...+|+.||+-|.+.+.||.. +.+.+|-.-.. +--+++.+.|...|=-+ -+++|+|+-.+-.--..+-.
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 578889999999999877666644 44444433211 11225667777777665 47999999998888778889
Q ss_pred HHHHHHHHHHhhcCC
Q 032341 81 FLERVKDEFVSKYGG 95 (142)
Q Consensus 81 FL~eI~~~F~~~y~~ 95 (142)
+|+++.+.|...|..
T Consensus 82 ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 82 LLNDVLNLFREKYDT 96 (587)
T ss_pred HHHHHHHHHHHHhcc
Confidence 999999999999963
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=78.81 E-value=32 Score=29.44 Aligned_cols=85 Identities=13% Similarity=0.293 Sum_probs=64.0
Q ss_pred EEEEEEcCCeEEEee-e-CCCCCHHHHHH-HHHhcCCCCCCe-EEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 032341 7 IYAFVARGNVVLAEY-T-EFSGNFNSIAY-QCLQKLPASNNK-FTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL 82 (142)
Q Consensus 7 ~Ya~VArg~~iLae~-~-~~~gnf~~~a~-~iL~kl~~~~~k-~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL 82 (142)
+|-.=.||.++++.. . +..++..++-+ .++... +-+ -..+.|+-.|||+..+++--.+||.........|.||
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~---d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl 81 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNL---DVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFL 81 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcc---ccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHH
Confidence 344457899988864 2 34667666554 344332 211 2335799999999999999999999999999999999
Q ss_pred HHHHHHHHhhcC
Q 032341 83 ERVKDEFVSKYG 94 (142)
Q Consensus 83 ~eI~~~F~~~y~ 94 (142)
..+-+-+..-+|
T Consensus 82 ~kl~avm~aYfg 93 (446)
T KOG0938|consen 82 YKLDAVMNAYFG 93 (446)
T ss_pred HHHHHHHHHHhc
Confidence 999999988887
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=74.21 E-value=31 Score=25.12 Aligned_cols=86 Identities=10% Similarity=0.082 Sum_probs=47.6
Q ss_pred HHHHHhcCCC---------CCCeEEEEeCCeEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCC-CCCc
Q 032341 32 AYQCLQKLPA---------SNNKFTYNCDAHTFNYLV-DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGG-KAAT 100 (142)
Q Consensus 32 a~~iL~kl~~---------~~~k~t~~~~~~~fh~L~-~~gi~ylcvtd~~~~~~~aF~FL~eI~~~F~~~y~~~-~~~~ 100 (142)
.+.+..+|.| ..+-.+++-+.|-.|++- -.|+-|+++||...+. ..=.+|..+.+-|...--.+ -...
T Consensus 45 l~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV~KNPfy~~ 123 (142)
T PF04099_consen 45 LKAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCFETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYVVKNPFYSL 123 (142)
T ss_dssp HHHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHHHS-TTS-T
T ss_pred HHHHHHHhCCCCcccccccceeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHHhhCCCCCC
Confidence 4666777766 134677888999999988 4899999999999863 33345555555554321110 1111
Q ss_pred cCCCCCChhhHHHHHHHhh
Q 032341 101 APANGLNKEFGYSVVILIL 119 (142)
Q Consensus 101 a~~ysl~~~F~~~l~~lm~ 119 (142)
..|-- +..|...|.+++.
T Consensus 124 ~~pI~-~~lF~~~l~~~~~ 141 (142)
T PF04099_consen 124 EMPIR-CELFDTKLDQYVK 141 (142)
T ss_dssp TS-----HHHHHHHHHHHH
T ss_pred CCcEe-hHHHHHHHHHHHh
Confidence 12222 4567777766653
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=68.83 E-value=39 Score=24.06 Aligned_cols=80 Identities=19% Similarity=0.316 Sum_probs=55.7
Q ss_pred cCCeEEEeeeCC-CCC-----HHHHHHHHHhcCCCCCCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHH
Q 032341 13 RGNVVLAEYTEF-SGN-----FNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVK 86 (142)
Q Consensus 13 rg~~iLae~~~~-~gn-----f~~~a~~iL~kl~~~~~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL~eI~ 86 (142)
+|+++++-|-.. +.. ++...+.+..+-+. .--....+++.+=|..-+++.++++++.+..--....||..+-
T Consensus 11 ~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v 88 (141)
T PF01217_consen 11 QGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSK--QSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLV 88 (141)
T ss_dssp TSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSS--STSEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHH
T ss_pred CCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccc--cceeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhh
Confidence 366888876432 111 23333333333211 1233557899999988999999999999999888999999999
Q ss_pred HHHHhhcC
Q 032341 87 DEFVSKYG 94 (142)
Q Consensus 87 ~~F~~~y~ 94 (142)
+-+..-++
T Consensus 89 ~~l~~~~~ 96 (141)
T PF01217_consen 89 EVLDDYFG 96 (141)
T ss_dssp HHHHHHHS
T ss_pred hhhhhhhc
Confidence 99988776
No 11
>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=60.86 E-value=18 Score=26.70 Aligned_cols=56 Identities=18% Similarity=0.275 Sum_probs=35.9
Q ss_pred HHHHHhcCCCC--C--CeEEEE-eCCeEEEEEE---eCCEEEEEEecCCCCcccHHHHHHHHHH
Q 032341 32 AYQCLQKLPAS--N--NKFTYN-CDAHTFNYLV---DNGYTYCVVADESSGRQIPMAFLERVKD 87 (142)
Q Consensus 32 a~~iL~kl~~~--~--~k~t~~-~~~~~fh~L~---~~gi~ylcvtd~~~~~~~aF~FL~eI~~ 87 (142)
-.-+|+|+-|- + .|++.. .|+|==.|-. +++-+|+|.+..+.|+-+|-.-|.|++.
T Consensus 47 ~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~ 110 (141)
T PF09426_consen 47 HDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKG 110 (141)
T ss_dssp HHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTT
T ss_pred hhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhcc
Confidence 34566666542 2 244444 5888888877 5789999999999999999999999874
No 12
>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=49.04 E-value=1.1e+02 Score=26.41 Aligned_cols=63 Identities=6% Similarity=0.100 Sum_probs=46.3
Q ss_pred HHHHHHHHHhcCCC-CCCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHH
Q 032341 28 FNSIAYQCLQKLPA-SNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFV 90 (142)
Q Consensus 28 f~~~a~~iL~kl~~-~~~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL~eI~~~F~ 90 (142)
+-.+.+.++.-... .+.-.++..|+..|.|+..+.++|+||+...-+...--.-|+-|.....
T Consensus 37 ~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qil 100 (415)
T PF03164_consen 37 LMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQIL 100 (415)
T ss_pred HHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHH
Confidence 33455666665533 3455677889999999999999999999999887666667776665444
No 13
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.64 E-value=97 Score=26.76 Aligned_cols=45 Identities=22% Similarity=0.414 Sum_probs=36.2
Q ss_pred CCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCC
Q 032341 51 DAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGG 95 (142)
Q Consensus 51 ~~~~fh~L~~~gi~ylcvtd~~~~~~~aF~FL~eI~~~F~~~y~~ 95 (142)
..|.+.-+.++++.|++++.-+.+.-.++.||..|-+-|..-||.
T Consensus 53 p~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~ 97 (418)
T KOG2740|consen 53 PHHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGG 97 (418)
T ss_pred CceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcc
Confidence 344444556778888888888889999999999999999888873
No 14
>PHA01811 hypothetical protein
Probab=39.37 E-value=36 Score=22.04 Aligned_cols=19 Identities=21% Similarity=0.394 Sum_probs=15.3
Q ss_pred CCeEEEEeCCeEEEEEEeC
Q 032341 43 NNKFTYNCDAHTFNYLVDN 61 (142)
Q Consensus 43 ~~k~t~~~~~~~fh~L~~~ 61 (142)
+.-++....+|++|||-++
T Consensus 4 ddivtlrvkgyi~hyldd~ 22 (78)
T PHA01811 4 DDIVTLRVKGYILHYLDDD 22 (78)
T ss_pred ccEEEEEEeeEEEEEEcCc
Confidence 3457888899999999765
No 15
>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=36.77 E-value=65 Score=21.01 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHhcCCC--CCCeEEEEeCC-eEEEEEE--eCCEEEEEEecCCC
Q 032341 25 SGNFNSIAYQCLQKLPA--SNNKFTYNCDA-HTFNYLV--DNGYTYCVVADESS 73 (142)
Q Consensus 25 ~gnf~~~a~~iL~kl~~--~~~k~t~~~~~-~~fh~L~--~~gi~ylcvtd~~~ 73 (142)
-.+|+++...+=+++.+ .+-+..|+.++ ....-+. ++|-.|+|...+.+
T Consensus 25 ~~sfd~lL~~lt~~l~l~~~~Vr~lyt~~g~~~v~~~~~l~~g~~yVa~g~e~f 78 (80)
T cd01617 25 FKSFDALLDDLTEKVQLDPGAVRKLYTLDGGHRVSLLDELEDGGVYVASGREPF 78 (80)
T ss_pred hCCHHHHHHHHHHHhCCCCCcEEEEEcCCCCeEeccHHHhcCCCEEEEECCCCC
Confidence 46899999998888874 45577777766 7766655 58999999876654
No 16
>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=30.38 E-value=66 Score=19.80 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHhcCCC-CCCeEEEEeCCeEEEEEE--eCCEEEEEEecCC
Q 032341 25 SGNFNSIAYQCLQKLPA-SNNKFTYNCDAHTFNYLV--DNGYTYCVVADES 72 (142)
Q Consensus 25 ~gnf~~~a~~iL~kl~~-~~~k~t~~~~~~~fh~L~--~~gi~ylcvtd~~ 72 (142)
..+|+++...+=+++.. ..-+.-|+.++.-.+-+. ++|-.|+|...+.
T Consensus 8 ~~s~e~lL~~it~~v~l~~gVr~lyt~~G~~V~~l~~l~dg~~yVa~g~e~ 58 (60)
T PF03607_consen 8 FRSFEQLLDEITEKVQLPSGVRKLYTLDGKRVKSLDELEDGGSYVASGREP 58 (60)
T ss_dssp HSSHHHHHHHHHHSSSSTTS-SEEEETTSSEESSGGGS-TTEEEEEESSSS
T ss_pred hcCHHHHHHHHHhhcCCCcccceEECCCCCEeCCHHHHCCCCEEEEEcCCc
Confidence 46788998888888864 335777888876665555 4899999986554
No 17
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=27.20 E-value=1.4e+02 Score=22.35 Aligned_cols=57 Identities=19% Similarity=0.251 Sum_probs=36.8
Q ss_pred EEeeeCCCCCHHHHHHHHHhcCCCC--------------CCeEEEE-------eCCeEEEEEEeC-----CEEEEEEecC
Q 032341 18 LAEYTEFSGNFNSIAYQCLQKLPAS--------------NNKFTYN-------CDAHTFNYLVDN-----GYTYCVVADE 71 (142)
Q Consensus 18 Lae~~~~~gnf~~~a~~iL~kl~~~--------------~~k~t~~-------~~~~~fh~L~~~-----gi~ylcvtd~ 71 (142)
+.|-....|+|+.+..+.+.++.|. +++.+.- .-+.+||.+-+| |.-|=|||..
T Consensus 33 ~~e~~ts~Ggfa~a~dr~~~~vtp~q~~~~nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~r 112 (173)
T KOG4078|consen 33 AKELKTSAGGFASAIDRFLDKVTPLQEAQPNQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKR 112 (173)
T ss_pred hhcccccccchHHHHHHHhccCCCcccCCchhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcC
Confidence 3444455689998888888888541 1222221 136789987654 7789999987
Q ss_pred CCC
Q 032341 72 SSG 74 (142)
Q Consensus 72 ~~~ 74 (142)
---
T Consensus 113 P~~ 115 (173)
T KOG4078|consen 113 PAL 115 (173)
T ss_pred cCc
Confidence 543
No 18
>PHA02979 hypothetical protein; Provisional
Probab=26.20 E-value=1.1e+02 Score=22.20 Aligned_cols=33 Identities=9% Similarity=0.228 Sum_probs=26.6
Q ss_pred CCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCc
Q 032341 43 NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGR 75 (142)
Q Consensus 43 ~~k~t~~~~~~~fh~L~~~gi~ylcvtd~~~~~ 75 (142)
+-+...+.++|.|-.=....+.-+|+|.+++|-
T Consensus 59 hi~LimD~ndYs~e~gN~SnfiiiCI~Sdd~GL 91 (140)
T PHA02979 59 HIKLIMDANDYSFETGNSSNFIIICICSDDCGL 91 (140)
T ss_pred heeeEEecccceEEeCCcccEEEEEEecccccE
Confidence 346777778898877667889999999999874
No 19
>KOG4131 consensus Ngg1-interacting factor 3 protein NIF3L1 [General function prediction only]
Probab=23.91 E-value=49 Score=26.94 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=24.6
Q ss_pred EEEcCC-eEEEeeeCCCCCH-HHHHHHHHhcCCCC
Q 032341 10 FVARGN-VVLAEYTEFSGNF-NSIAYQCLQKLPAS 42 (142)
Q Consensus 10 ~VArg~-~iLae~~~~~gnf-~~~a~~iL~kl~~~ 42 (142)
+.+.|. +|||||++...-| .++..++.+.++.+
T Consensus 223 ~~~~g~sVilc~HSNtERgfL~d~~~kl~~~l~~~ 257 (272)
T KOG4131|consen 223 AAANGISVILCEHSNTERGFLSDLCDKLASSLEEE 257 (272)
T ss_pred HHHcCCeEEEecCCCccchhHHHHHHHHHhhCCcc
Confidence 456774 9999999877665 66778888777654
No 20
>KOG0164 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=20.19 E-value=1.1e+02 Score=28.88 Aligned_cols=46 Identities=20% Similarity=0.317 Sum_probs=34.4
Q ss_pred HHHHHHHHHHH-----hhcCCCCCCccCCCCCChhhHHHHHHHhhchhcccc
Q 032341 80 AFLERVKDEFV-----SKYGGGKAATAPANGLNKEFGYSVVILILKPMNRRF 126 (142)
Q Consensus 80 ~FL~eI~~~F~-----~~y~~~~~~~a~~ysl~~~F~~~l~~lm~~~~~~~~ 126 (142)
+++.+|+.+|. ..|+....+-++|+.+ .+|...|++|..+|.-+++
T Consensus 735 s~v~el~~~~rg~k~~r~ygk~~~WP~pP~~L-r~~~~~L~~lf~rwra~~~ 785 (1001)
T KOG0164|consen 735 SYVQELQRRFRGAKQMRDYGKSIRWPAPPLVL-REFEELLRELFIRWRAWQI 785 (1001)
T ss_pred HHHHHHHHHHHhhhhccccCCCCCCCCCchHH-HHHHHHHHHHHHHHHHHHH
Confidence 56777777776 3466555566788888 6999999999998877654
Done!