Query 032686
Match_columns 136
No_of_seqs 111 out of 516
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 04:39:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032686hhsearch_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 1.2E-41 2.6E-46 253.7 13.7 128 4-132 1-136 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 99.9 5.9E-27 1.3E-31 177.4 12.1 122 5-127 1-133 (216)
3 PF13774 Longin: Regulated-SNA 99.9 1.1E-24 2.3E-29 143.8 11.5 82 31-113 1-83 (83)
4 KOG0861 SNARE protein YKT6, sy 98.9 3.2E-08 7E-13 73.4 10.0 70 30-100 42-112 (198)
5 COG5143 SNC1 Synaptobrevin/VAM 98.8 2.6E-08 5.6E-13 74.9 8.9 111 5-116 2-120 (190)
6 PF04086 SRP-alpha_N: Signal r 95.9 0.0075 1.6E-07 47.6 3.4 92 30-123 6-105 (279)
7 KOG0781 Signal recognition par 92.3 0.97 2.1E-05 39.1 8.3 87 7-95 4-96 (587)
8 PF01217 Clat_adaptor_s: Clath 88.2 7.1 0.00015 27.4 8.9 49 46-94 48-96 (141)
9 KOG0938 Adaptor complexes medi 85.4 12 0.00027 31.1 9.6 87 7-95 5-94 (446)
10 PF03164 Mon1: Trafficking pro 77.1 13 0.00029 31.2 7.4 65 30-94 39-104 (415)
11 PF04099 Sybindin: Sybindin-li 77.0 24 0.00052 25.2 9.6 85 33-119 46-141 (142)
12 PF09426 Nyv1_N: Vacuolar R-SN 58.5 26 0.00056 25.2 4.6 78 32-122 47-132 (141)
13 PHA01811 hypothetical protein 49.8 20 0.00044 22.6 2.6 20 43-62 4-23 (78)
14 KOG4131 Ngg1-interacting facto 47.5 11 0.00025 29.8 1.5 33 10-42 223-257 (272)
15 KOG2740 Clathrin-associated pr 46.8 75 0.0016 26.8 6.1 44 52-95 54-97 (418)
16 PHA02979 hypothetical protein; 34.5 64 0.0014 22.7 3.4 32 44-75 60-91 (140)
17 cd01617 DCX Ubiquitin-like dom 29.4 1E+02 0.0022 19.6 3.6 49 25-73 25-78 (80)
18 PRK15364 pathogenicity island 27.9 8.6 0.00019 29.1 -1.9 90 28-124 77-172 (196)
19 PF06523 DUF1106: Protein of u 25.5 1.1E+02 0.0023 19.9 3.0 50 45-94 16-79 (91)
20 PF11675 DUF3271: Protein of u 23.7 2.6E+02 0.0057 22.1 5.5 55 3-60 28-82 (249)
21 PF03433 EspA: EspA-like secre 21.6 35 0.00076 25.9 0.3 91 26-123 75-170 (188)
22 cd02646 R3H_G-patch R3H domain 20.9 1.5E+02 0.0033 17.5 3.1 42 82-125 1-43 (58)
23 PF07897 DUF1675: Protein of u 20.0 1.1E+02 0.0023 24.7 2.8 26 50-75 238-263 (284)
24 PF03607 DCX: Doublecortin; I 20.0 1.6E+02 0.0034 17.6 3.0 48 25-72 8-58 (60)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-41 Score=253.69 Aligned_cols=128 Identities=59% Similarity=0.947 Sum_probs=119.3
Q ss_pred ceeEEEEEEcCCeEEEeeeCCCCCHHHHHHHHhccCCCC-CCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 032686 4 KSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL 82 (136)
Q Consensus 4 m~I~Ya~Iar~~~iLae~~~~~~nf~~~~~~iL~~l~~~-~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL 82 (136)
|+|+|++||||++|||||++.+|||..++.+||+|||++ ++|+||..|+|+|||+++||++||||+|++++|++||+||
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 789999999999999999999999999999999999997 6699999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCCcchhhHHHHHHHHHHhh-------HHHHHHhhhh
Q 032686 83 ERVKDEFVSKYGGGKAATAPANGLNKEFGTVLIILRRSAS-------LRRLRLRFQK 132 (136)
Q Consensus 83 ~eI~~~F~~~y~~~~~~~a~~y~~~~~F~~~i~~~m~~~~-------~~~~~~~~~~ 132 (136)
|+|+++|.++||. .+.+|.+|+||+||+++|++.|+.++ +++++.|..+
T Consensus 81 e~Ik~~F~k~YG~-~a~ta~AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~e 136 (217)
T KOG0859|consen 81 ERIKEDFKKRYGG-GAHTAVAYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTE 136 (217)
T ss_pred HHHHHHHHHHhcc-chhHHHHhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHH
Confidence 9999999999995 58899999999999999999999775 4556665544
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=5.9e-27 Score=177.37 Aligned_cols=122 Identities=23% Similarity=0.413 Sum_probs=108.3
Q ss_pred eeEEEEEEc--CCeEEEeeeC---CCCCH----HHHHHHHhccCCCC-CCeEEEEeCCeEEEEEEeCCEEEEEEecCCCC
Q 032686 5 SLIYAFVAR--GNVVLAEYTE---FSGNF----NSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSG 74 (136)
Q Consensus 5 ~I~Ya~Iar--~~~iLae~~~---~~~nf----~~~~~~iL~~l~~~-~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~ 74 (136)
||++|+|+| +++|||+..+ .+|+. .+.++.+++++.+. +++.|.+.|+|+|||++++||||+||||++||
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 6799998765 23443 57899999999886 88999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHhhcCCCCCC-CCCCCCcchhhHHHHHHHHHHhhHHHHH
Q 032686 75 RQIPMAFLERVKDEFVSKYGGGKAA-TAPANGLNKEFGTVLIILRRSASLRRLR 127 (136)
Q Consensus 75 ~~~aF~FL~eI~~~F~~~y~~~~~~-~a~~y~~~~~F~~~i~~~m~~~~~~~~~ 127 (136)
+++||+|||+|+++|.+.|+.+... ..+||+|. +|+++|++..++||-.|.+
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~Fi-eFD~~IQk~Kk~ynd~r~~ 133 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAFI-EFDTFIQKTKKRYNDTRSQ 133 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCeeEE-ehhHHHHHHHHHhcCcHHH
Confidence 9999999999999999999976555 56999999 7999999999998877643
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=99.92 E-value=1.1e-24 Score=143.83 Aligned_cols=82 Identities=33% Similarity=0.702 Sum_probs=74.8
Q ss_pred HHHHHhccCCCCC-CeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCCCCCCCCCcchh
Q 032686 31 IAYQCLQKLPASN-NKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKE 109 (136)
Q Consensus 31 ~~~~iL~~l~~~~-~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~~~~~~a~~y~~~~~ 109 (136)
++++||++|++.+ +|.+++.|+|+|||+++||++||||||+++|+++||.||++|+++|.++|+..++.++.||+| .+
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 899999999999999999999999999999999999999999999999999778899999999 78
Q ss_pred hHHH
Q 032686 110 FGTV 113 (136)
Q Consensus 110 F~~~ 113 (136)
|++.
T Consensus 80 F~~~ 83 (83)
T PF13774_consen 80 FDSF 83 (83)
T ss_dssp HHHH
T ss_pred cCCC
Confidence 9873
No 4
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.86 E-value=3.2e-08 Score=73.43 Aligned_cols=70 Identities=17% Similarity=0.252 Sum_probs=61.3
Q ss_pred HHHHHHhccCCCCCCeEEEEeCCeEEEEEEeC-CEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCCCC
Q 032686 30 SIAYQCLQKLPASNNKFTYNCDAHTFNYLVDN-GYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAAT 100 (136)
Q Consensus 30 ~~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~~-gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~~~~~~ 100 (136)
-+++.+.++.+| ..+.+++.+.|..|..+.| |++++|++|.+||.+.||.+|++|.++|...-...+|..
T Consensus 42 F~sktvaeRt~~-g~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~ 112 (198)
T KOG0861|consen 42 FISKTVAERTGP-GQRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEFTTKVPATQWPV 112 (198)
T ss_pred HHHHHHHHhcCc-ccccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHHhhcCcccccCc
Confidence 467888888887 5689999999999999976 999999999999999999999999999977666566763
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=98.83 E-value=2.6e-08 Score=74.93 Aligned_cols=111 Identities=17% Similarity=0.229 Sum_probs=81.7
Q ss_pred eeEEEEEEcCC--eEEEe-eeCCCCCH--HHHHHHHhccCCCC-CCeEEEEeCCeEEEEEEeC-CEEEEEEecCCCCccc
Q 032686 5 SLIYAFVARGN--VVLAE-YTEFSGNF--NSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDN-GYTYCVVADESSGRQI 77 (136)
Q Consensus 5 ~I~Ya~Iar~~--~iLae-~~~~~~nf--~~~~~~iL~~l~~~-~~k~s~~~~~~~fh~l~~~-gi~ylcitd~~~~~~~ 77 (136)
.+++..+..|. .+|++ ++..+..| ...+.++|..+.|. .++.+.+.++|.|||+..+ |++|.|+|+..+|+++
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 45555565553 34443 21112222 35677888877653 4578889999999999976 9999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCCCC-CCCCCCCcchhhHHHHHH
Q 032686 78 PMAFLERVKDEFVSKYGGGKA-ATAPANGLNKEFGTVLII 116 (136)
Q Consensus 78 aF~FL~eI~~~F~~~y~~~~~-~~a~~y~~~~~F~~~i~~ 116 (136)
||.+|+++..+|..+.+-..+ ....++.+. +|++++++
T Consensus 82 a~~~~~~~~~~~~~s~~~~~~~d~~~~~~~~-~~d~~~e~ 120 (190)
T COG5143 82 AYGYLNSIATEFLKSSALEQLIDDTVGIMRV-NIDKVIEK 120 (190)
T ss_pred hhHHHHhhccHhhhhhhHhhcccCccchhhh-hHHHHHHh
Confidence 999999999999988874433 334667775 79999988
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=95.95 E-value=0.0075 Score=47.59 Aligned_cols=92 Identities=22% Similarity=0.306 Sum_probs=53.6
Q ss_pred HHHHHHhccCCCCCCeEEEEeCCeEEEEEEeC--CEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCC----CC-CC
Q 032686 30 SIAYQCLQKLPASNNKFTYNCDAHTFNYLVDN--GYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKA----AT-AP 102 (136)
Q Consensus 30 ~~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~~--gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~~~~----~~-a~ 102 (136)
.+++.+|-.=. .+..+|.+|+|..+|...| |+||++|-..-..-...=.||++|+..|...|+.... .. ..
T Consensus 6 ~LI~~vlleeR--~~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~l~~~~~~~~~~ 83 (279)
T PF04086_consen 6 ALIRDVLLEER--SGNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQLKQLKPNTSIN 83 (279)
T ss_dssp HHHHHTGGG---------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHHHHSSSTHHHHT
T ss_pred HHHHHhheeec--cCCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHHhhccccccccc
Confidence 45555543311 2346688999999999976 4999999998888777779999999999999984211 11 11
Q ss_pred CC-CcchhhHHHHHHHHHHhhH
Q 032686 103 AN-GLNKEFGTVLIILRRSASL 123 (136)
Q Consensus 103 ~y-~~~~~F~~~i~~~m~~~~~ 123 (136)
.| .|...|..+|+++-.....
T Consensus 84 ~~~~Fd~~F~~~l~~~e~~~~~ 105 (279)
T PF04086_consen 84 EYFDFDEEFDQLLKELEARSKS 105 (279)
T ss_dssp -----HHHHHHHHHHHCCCTT-
T ss_pred cchhHHHHHHHHHHHHHHHhcc
Confidence 23 7888888888887654443
No 7
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.34 E-value=0.97 Score=39.15 Aligned_cols=87 Identities=22% Similarity=0.315 Sum_probs=65.5
Q ss_pred EEEEEEcCCeEEEeeeCCCCCHHH----HHHHHhccCCCCCCeEEEEeCCeEEEEEEe--CCEEEEEEecCCCCcccHHH
Q 032686 7 IYAFVARGNVVLAEYTEFSGNFNS----IAYQCLQKLPASNNKFTYNCDAHTFNYLVD--NGYTYCVVADESSGRQIPMA 80 (136)
Q Consensus 7 ~Ya~Iar~~~iLae~~~~~~nf~~----~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~--~gi~ylcitd~~~~~~~aF~ 80 (136)
+++...+|++||+-|.+...||.. ..+.+|-.= ..+-.++..+.|+..|--+ -+++|+|+-.+-.--..+-.
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~e--r~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv~~ 81 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSE--RGGVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYVDK 81 (587)
T ss_pred eeeeecCCcEEEEEecccchhccchHHHHHHHHHHHh--hcCcccCchhheeEeeeecCCccEEEEEEEeccchhhhHHH
Confidence 678889999999999887666643 445544331 1222336677888888775 46999999998888888889
Q ss_pred HHHHHHHHHHhhcCC
Q 032686 81 FLERVKDEFVSKYGG 95 (136)
Q Consensus 81 FL~eI~~~F~~~y~~ 95 (136)
+|+++.+-|...|.+
T Consensus 82 ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 82 LLNDVLNLFREKYDT 96 (587)
T ss_pred HHHHHHHHHHHHhcc
Confidence 999999999999964
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=88.19 E-value=7.1 Score=27.42 Aligned_cols=49 Identities=20% Similarity=0.352 Sum_probs=43.4
Q ss_pred EEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcC
Q 032686 46 FTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYG 94 (136)
Q Consensus 46 ~s~~~~~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~ 94 (136)
-....+++.+=|..-+++.++++++.+..--....||..+-+-+..-++
T Consensus 48 ~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v~~l~~~~~ 96 (141)
T PF01217_consen 48 PIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLVEVLDDYFG 96 (141)
T ss_dssp SEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHHHHHHHHHS
T ss_pred eeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhhhhhhhhhc
Confidence 3456789999999999999999999999888899999999999988876
No 9
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.42 E-value=12 Score=31.13 Aligned_cols=87 Identities=11% Similarity=0.256 Sum_probs=64.1
Q ss_pred EEEEEEcCCeEEEee-e-CCCCCHHHHHHH-HhccCCCCCCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHH
Q 032686 7 IYAFVARGNVVLAEY-T-EFSGNFNSIAYQ-CLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLE 83 (136)
Q Consensus 7 ~Ya~Iar~~~iLae~-~-~~~~nf~~~~~~-iL~~l~~~~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL~ 83 (136)
+|-.=.||++.++-. . +..+|..++.+- ++....-.. -..+.|+-.|||+..+++--.+||..+....+.|.||.
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d~r~--PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~ 82 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLDVRS--PVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLY 82 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccccCC--CeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHH
Confidence 344456899988863 2 345666665543 333321111 22357899999999999999999999999999999999
Q ss_pred HHHHHHHhhcCC
Q 032686 84 RVKDEFVSKYGG 95 (136)
Q Consensus 84 eI~~~F~~~y~~ 95 (136)
.+.+-+.+-||.
T Consensus 83 kl~avm~aYfgk 94 (446)
T KOG0938|consen 83 KLDAVMNAYFGK 94 (446)
T ss_pred HHHHHHHHHhcc
Confidence 999999988883
No 10
>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=77.07 E-value=13 Score=31.21 Aligned_cols=65 Identities=8% Similarity=0.092 Sum_probs=48.6
Q ss_pred HHHHHHhccCCC-CCCeEEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcC
Q 032686 30 SIAYQCLQKLPA-SNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYG 94 (136)
Q Consensus 30 ~~~~~iL~~l~~-~~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~ 94 (136)
.+.+.++.-... ++.-.++..|+..|.|+.+++++|+||+...-+...--.-|+-+........+
T Consensus 39 g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils~lt 104 (415)
T PF03164_consen 39 GVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILSILT 104 (415)
T ss_pred HHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHHhcc
Confidence 444555554432 34556778899999999999999999999998877777888887766665443
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=77.02 E-value=24 Score=25.17 Aligned_cols=85 Identities=13% Similarity=0.094 Sum_probs=48.3
Q ss_pred HHHhccCCC---------CCCeEEEEeCCeEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCC-CCCCCC
Q 032686 33 YQCLQKLPA---------SNNKFTYNCDAHTFNYLV-DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGG-GKAATA 101 (136)
Q Consensus 33 ~~iL~~l~~---------~~~k~s~~~~~~~fh~l~-~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~-~~~~~a 101 (136)
+.+..+|.| ..+..+++.+.|..|++- --|+-|+++||.+.+. ..=.++..+.+-|...--. .-....
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 445566655 135788899999999998 5899999999999863 3344556666555431100 011112
Q ss_pred CCCCcchhhHHHHHHHHH
Q 032686 102 PANGLNKEFGTVLIILRR 119 (136)
Q Consensus 102 ~~y~~~~~F~~~i~~~m~ 119 (136)
.|-- +..|+..|.++++
T Consensus 125 ~pI~-~~lF~~~l~~~~~ 141 (142)
T PF04099_consen 125 MPIR-CELFDTKLDQYVK 141 (142)
T ss_dssp S-----HHHHHHHHHHHH
T ss_pred CcEe-hHHHHHHHHHHHh
Confidence 3332 4578888888765
No 12
>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=58.45 E-value=26 Score=25.25 Aligned_cols=78 Identities=13% Similarity=0.169 Sum_probs=45.7
Q ss_pred HHHHhccCCCC-C---CeEEEE-eCCeEEEEEE---eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCCCCCCCCCC
Q 032686 32 AYQCLQKLPAS-N---NKFTYN-CDAHTFNYLV---DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPA 103 (136)
Q Consensus 32 ~~~iL~~l~~~-~---~k~s~~-~~~~~fh~l~---~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~~~~~~a~~ 103 (136)
-..+|+++-|- . .|+|.. .|+|==.|-. +++-+|+|.+..+.|+-+|-.-|.|++.. ...
T Consensus 47 ~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~~-----~~~------- 114 (141)
T PF09426_consen 47 HDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKGL-----ENN------- 114 (141)
T ss_dssp HHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTTS-----S---------
T ss_pred hhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhccc-----cCC-------
Confidence 34457777552 2 244443 5888877777 57899999999999999999999998742 110
Q ss_pred CCcchhhHHHHHHHHHHhh
Q 032686 104 NGLNKEFGTVLIILRRSAS 122 (136)
Q Consensus 104 y~~~~~F~~~i~~~m~~~~ 122 (136)
.-+.+.+.-+.+.++.|-
T Consensus 115 -~~D~~L~~~v~~IlD~FH 132 (141)
T PF09426_consen 115 -DTDEELSAHVGNILDEFH 132 (141)
T ss_dssp --STTSHHHHHHHHHHHHH
T ss_pred -CCHHHHHHHHHHHHHHHH
Confidence 113456666666666553
No 13
>PHA01811 hypothetical protein
Probab=49.83 E-value=20 Score=22.56 Aligned_cols=20 Identities=20% Similarity=0.381 Sum_probs=16.0
Q ss_pred CCeEEEEeCCeEEEEEEeCC
Q 032686 43 NNKFTYNCDAHTFNYLVDNG 62 (136)
Q Consensus 43 ~~k~s~~~~~~~fh~l~~~g 62 (136)
+.-++....+|++|||-+++
T Consensus 4 ddivtlrvkgyi~hyldd~n 23 (78)
T PHA01811 4 DDIVTLRVKGYILHYLDDDN 23 (78)
T ss_pred ccEEEEEEeeEEEEEEcCch
Confidence 45678889999999997653
No 14
>KOG4131 consensus Ngg1-interacting factor 3 protein NIF3L1 [General function prediction only]
Probab=47.54 E-value=11 Score=29.79 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=24.3
Q ss_pred EEEcCC-eEEEeeeCCCCCH-HHHHHHHhccCCCC
Q 032686 10 FVARGN-VVLAEYTEFSGNF-NSIAYQCLQKLPAS 42 (136)
Q Consensus 10 ~Iar~~-~iLae~~~~~~nf-~~~~~~iL~~l~~~ 42 (136)
+.+.|. +|||||+..+..| .++..++.+.++.+
T Consensus 223 ~~~~g~sVilc~HSNtERgfL~d~~~kl~~~l~~~ 257 (272)
T KOG4131|consen 223 AAANGISVILCEHSNTERGFLSDLCDKLASSLEEE 257 (272)
T ss_pred HHHcCCeEEEecCCCccchhHHHHHHHHHhhCCcc
Confidence 456775 9999999887776 45677777777654
No 15
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.82 E-value=75 Score=26.79 Aligned_cols=44 Identities=23% Similarity=0.429 Sum_probs=33.8
Q ss_pred CeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhcCC
Q 032686 52 AHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGG 95 (136)
Q Consensus 52 ~~~fh~l~~~gi~ylcitd~~~~~~~aF~FL~eI~~~F~~~y~~ 95 (136)
.|.+--+.++++.|+.++..+.|.=.++.||.+|-+-|..-||.
T Consensus 54 ~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~ 97 (418)
T KOG2740|consen 54 HHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGG 97 (418)
T ss_pred ceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcc
Confidence 33333345667777777777888889999999999999988884
No 16
>PHA02979 hypothetical protein; Provisional
Probab=34.51 E-value=64 Score=22.68 Aligned_cols=32 Identities=9% Similarity=0.223 Sum_probs=25.4
Q ss_pred CeEEEEeCCeEEEEEEeCCEEEEEEecCCCCc
Q 032686 44 NKFTYNCDAHTFNYLVDNGYTYCVVADESSGR 75 (136)
Q Consensus 44 ~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~~ 75 (136)
-+.....++|.|-.=....+.-+|+|.+++|-
T Consensus 60 i~LimD~ndYs~e~gN~SnfiiiCI~Sdd~GL 91 (140)
T PHA02979 60 IKLIMDANDYSFETGNSSNFIIICICSDDCGL 91 (140)
T ss_pred eeeEEecccceEEeCCcccEEEEEEecccccE
Confidence 35666777888877667889999999999864
No 17
>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=29.37 E-value=1e+02 Score=19.61 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHhccCCC--CCCeEEEEeCC-eEEEEEE--eCCEEEEEEecCCC
Q 032686 25 SGNFNSIAYQCLQKLPA--SNNKFTYNCDA-HTFNYLV--DNGYTYCVVADESS 73 (136)
Q Consensus 25 ~~nf~~~~~~iL~~l~~--~~~k~s~~~~~-~~fh~l~--~~gi~ylcitd~~~ 73 (136)
-.+|+.+...+=+++.+ ..-+..|+.++ ....-+- ++|-.|+|.-.+.+
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 47899998888888874 44467777776 6665554 68999999877655
No 18
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=27.91 E-value=8.6 Score=29.08 Aligned_cols=90 Identities=10% Similarity=0.063 Sum_probs=58.5
Q ss_pred HHHHHHHHhccCCCCCCeEEEEeCCeEEEEEEeCCEEEEEEecCCC------CcccHHHHHHHHHHHHHhhcCCCCCCCC
Q 032686 28 FNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESS------GRQIPMAFLERVKDEFVSKYGGGKAATA 101 (136)
Q Consensus 28 f~~~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~------~~~~aF~FL~eI~~~F~~~y~~~~~~~a 101 (136)
+...+..++..+...+.+.+-..-+-++.|+.++||+.=-+++.+| +..+--.=|+.|+..+....+
T Consensus 77 mAN~VDevIA~v~k~ddK~k~~LPddVI~YmrdNgI~VdG~sid~Yl~k~~~~~~LdkG~LqAVKAALd~~sn------- 149 (196)
T PRK15364 77 KSNEMDEVIAKAAKGDAKTKEEVPEDVIKYMRDNGILIDGMTIDDYMAKYGDHGKLDKGGLQAIKAALDNDAN------- 149 (196)
T ss_pred HHHHHHHHHHHHhcCCCcccccCCHHHHHHHHHcCceecccchHHHHhccCCccCCChhhHHHHHHHHHhhcc-------
Confidence 3445566777776556665555667778888888888766665443 223444567778877766544
Q ss_pred CCCCcchhhHHHHHHHHHHhhHH
Q 032686 102 PANGLNKEFGTVLIILRRSASLR 124 (136)
Q Consensus 102 ~~y~~~~~F~~~i~~~m~~~~~~ 124 (136)
+.-.+..+=.-.|+++|+.||..
T Consensus 150 r~TD~vsQsQLqiQk~~QtyN~~ 172 (196)
T PRK15364 150 RNTDLMSQGQITIQKMSQELNAV 172 (196)
T ss_pred ccchhhhHHHHHHHHHHHHHHHH
Confidence 22234455677899999998863
No 19
>PF06523 DUF1106: Protein of unknown function (DUF1106); InterPro: IPR009490 This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=25.50 E-value=1.1e+02 Score=19.90 Aligned_cols=50 Identities=12% Similarity=0.282 Sum_probs=29.0
Q ss_pred eEEEEeCCeEEEEEE------------eCCEEEEEEecCCCCcccHHHHH--HHHHHHHHhhcC
Q 032686 45 KFTYNCDAHTFNYLV------------DNGYTYCVVADESSGRQIPMAFL--ERVKDEFVSKYG 94 (136)
Q Consensus 45 k~s~~~~~~~fh~l~------------~~gi~ylcitd~~~~~~~aF~FL--~eI~~~F~~~y~ 94 (136)
+..++.+.+.|..++ .+|++|+.|.-..-.++..|.|= +-|-++...-|+
T Consensus 16 rryfeq~e~sfsiicgrlrgiv~t~kcs~g~iylsi~v~pnn~~hi~ly~kk~yi~dklkeifp 79 (91)
T PF06523_consen 16 RRYFEQGEHSFSIICGRLRGIVLTIKCSNGIIYLSIKVNPNNSNHIFLYHKKNYIFDKLKEIFP 79 (91)
T ss_pred eehhhccCeeEEEEeeceeeEEEEEEecCcEEEEEEEeCCCCcceEEEEecchhHHHHHHHhCC
Confidence 444455555555543 59999999987776666554221 223344444444
No 20
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=23.70 E-value=2.6e+02 Score=22.11 Aligned_cols=55 Identities=16% Similarity=0.318 Sum_probs=35.9
Q ss_pred cceeEEEEEEcCCeEEEeeeCCCCCHHHHHHHHhccCCCCCCeEEEEeCCeEEEEEEe
Q 032686 3 QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60 (136)
Q Consensus 3 ~m~I~Ya~Iar~~~iLae~~~~~~nf~~~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~ 60 (136)
+.+|-|..||.-+..+......-..+-.+.-.+|..=+. +.+..|+-|+ ||+++-
T Consensus 28 pk~i~y~sv~qpt~~f~~~~k~h~~YLdiIN~il~~eSe-N~Kyayeg~n--YHwvIT 82 (249)
T PF11675_consen 28 PKPIAYISVAQPTATFEHDEKKHTKYLDIINDILRDESE-NIKYAYEGGN--YHWVIT 82 (249)
T ss_pred CCceeEEeccCceEEEeecCccchhHHHHHHHHHhcccc-ccceeeeCCc--eEEEEE
Confidence 568999999998877776543334456777777776443 3456666555 455553
No 21
>PF03433 EspA: EspA-like secreted protein ; InterPro: IPR005095 EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [, ].; PDB: 1XOU_A.
Probab=21.59 E-value=35 Score=25.88 Aligned_cols=91 Identities=12% Similarity=0.107 Sum_probs=13.5
Q ss_pred CCHHHHHHHHhccCCCCCCeEEEEeCCeEEEEEEeCCEEEEEEecCCCC-----cccHHHHHHHHHHHHHhhcCCCCCCC
Q 032686 26 GNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSG-----RQIPMAFLERVKDEFVSKYGGGKAAT 100 (136)
Q Consensus 26 ~nf~~~~~~iL~~l~~~~~k~s~~~~~~~fh~l~~~gi~ylcitd~~~~-----~~~aF~FL~eI~~~F~~~y~~~~~~~ 100 (136)
.+....+..++.++++.+.+.+-...+=++-|+.++||..=-++..+|= ..+--.-|+.|+..+-...+
T Consensus 75 Q~maN~vDevIA~~~k~~dk~k~~lp~dVi~Ym~~ngI~VdG~si~~Yl~~n~~~~LdkG~LqaVKaAld~~sn------ 148 (188)
T PF03433_consen 75 QDMANRVDEVIAEVAKSDDKAKAPLPDDVIDYMRDNGIKVDGKSIDDYLKKNGSGGLDKGQLQAVKAALDNESN------ 148 (188)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHhccCCCccccccCCHHHHHHHHHcCCeecCeeccchhhhhhhccCCchhHHHHHHHHHhhhc------
Confidence 3445566777888877666666666788899999999887555555542 23334455556555543322
Q ss_pred CCCCCcchhhHHHHHHHHHHhhH
Q 032686 101 APANGLNKEFGTVLIILRRSASL 123 (136)
Q Consensus 101 a~~y~~~~~F~~~i~~~m~~~~~ 123 (136)
+.-.+..+=.-.|+++|+.||.
T Consensus 149 -r~TD~vsq~QLqlQk~~qt~n~ 170 (188)
T PF03433_consen 149 -RATDFVSQSQLQLQKMMQTYNV 170 (188)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHH
T ss_pred -cccchhhHHHHHHHHHHHHHHH
Confidence 1222344456678899998875
No 22
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=20.86 E-value=1.5e+02 Score=17.52 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=25.4
Q ss_pred HHHHHHHHHhhcCCC-CCCCCCCCCcchhhHHHHHHHHHHhhHHH
Q 032686 82 LERVKDEFVSKYGGG-KAATAPANGLNKEFGTVLIILRRSASLRR 125 (136)
Q Consensus 82 L~eI~~~F~~~y~~~-~~~~a~~y~~~~~F~~~i~~~m~~~~~~~ 125 (136)
+++|++++..--... ..-..+| |+..--.+|+++-+.|++.+
T Consensus 1 ~~~i~~~i~~F~~~~~~~~~fpp--m~~~~R~~vH~lA~~~~L~S 43 (58)
T cd02646 1 IEDIKDEIEAFLLDSRDSLSFPP--MDKHGRKTIHKLANCYNLKS 43 (58)
T ss_pred ChHHHHHHHHHHhCCCceEecCC--CCHHHHHHHHHHHHHcCCcc
Confidence 356676665443322 2223355 66667788999998887654
No 23
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=20.04 E-value=1.1e+02 Score=24.75 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=22.2
Q ss_pred eCCeEEEEEEeCCEEEEEEecCCCCc
Q 032686 50 CDAHTFNYLVDNGYTYCVVADESSGR 75 (136)
Q Consensus 50 ~~~~~fh~l~~~gi~ylcitd~~~~~ 75 (136)
.++++|-|-..+.+..+|+|.-++-.
T Consensus 238 i~g~ly~y~~~~~v~i~c~chg~~~~ 263 (284)
T PF07897_consen 238 IEGFLYKYGKGEEVRIVCVCHGSFLS 263 (284)
T ss_pred eeEEEEEecCCCeEEEEEEecCCCCC
Confidence 47899999778899999999988743
No 24
>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=20.01 E-value=1.6e+02 Score=17.61 Aligned_cols=48 Identities=17% Similarity=0.265 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHhccCCCC-CCeEEEEeCCeEEEEEE--eCCEEEEEEecCC
Q 032686 25 SGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLV--DNGYTYCVVADES 72 (136)
Q Consensus 25 ~~nf~~~~~~iL~~l~~~-~~k~s~~~~~~~fh~l~--~~gi~ylcitd~~ 72 (136)
..+|+++...+=+++... .-+.-|+.++.-.+=+- ++|-.|+|...+.
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 367888888888888643 34677777776555544 5888899986654
Done!