Query psy17710
Match_columns 75
No_of_seqs 65 out of 67
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 21:02:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17710hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1826|consensus 99.6 1.3E-15 2.7E-20 134.8 4.4 68 1-73 973-1040(2724)
2 PF01843 DIL: DIL domain; Int 72.7 8.1 0.00018 24.2 3.9 39 13-52 12-50 (105)
3 PF08203 RNA_polI_A14: Yeast R 44.8 11 0.00023 23.9 0.8 9 62-70 60-68 (76)
4 PF11108 Phage_glycop_gL: Vira 40.0 45 0.00098 22.4 3.3 40 14-53 61-100 (111)
5 PRK03907 fliE flagellar hook-b 38.1 29 0.00063 22.7 2.1 23 22-44 69-91 (97)
6 PRK01699 fliE flagellar hook-b 37.0 31 0.00067 22.6 2.1 23 22-44 71-93 (99)
7 PRK00732 fliE flagellar hook-b 36.5 32 0.00069 22.6 2.1 23 22-44 74-96 (102)
8 PRK00790 fliE flagellar hook-b 34.3 36 0.00078 22.6 2.1 22 23-44 82-103 (109)
9 PF10547 P22_AR_N: P22_AR N-te 31.3 16 0.00036 24.6 0.1 36 39-75 73-108 (120)
10 PRK00253 fliE flagellar hook-b 31.2 43 0.00094 22.0 2.1 23 22-44 80-102 (108)
11 cd06405 PB1_Mekk2_3 The PB1 do 30.1 23 0.00049 22.8 0.5 11 64-74 50-60 (79)
12 cd03568 VHS_STAM VHS domain fa 28.9 97 0.0021 21.0 3.5 35 11-51 80-114 (144)
13 PRK01482 fliE flagellar hook-b 28.7 51 0.0011 22.0 2.1 23 22-44 81-103 (108)
14 TIGR00205 fliE flagellar hook- 28.4 52 0.0011 21.8 2.1 23 22-44 81-103 (108)
15 PRK12728 fliE flagellar hook-b 27.9 54 0.0012 21.4 2.1 23 22-44 74-96 (102)
16 PF02049 FliE: Flagellar hook- 27.3 57 0.0012 20.5 2.1 23 22-44 68-90 (96)
17 PRK12729 fliE flagellar hook-b 27.0 55 0.0012 22.6 2.1 23 22-44 100-122 (127)
18 PF00790 VHS: VHS domain; Int 26.8 1.1E+02 0.0024 20.1 3.5 18 34-51 105-122 (140)
19 PF14922 FWWh: Protein of unkn 26.2 70 0.0015 22.3 2.5 19 34-52 135-153 (161)
20 cd03569 VHS_Hrs_Vps27p VHS dom 24.1 1.3E+02 0.0029 20.1 3.5 23 29-51 96-118 (142)
21 COG5606 Uncharacterized conser 23.4 92 0.002 20.5 2.5 22 27-48 18-39 (91)
22 smart00288 VHS Domain present 23.1 1.7E+02 0.0037 19.2 3.9 36 11-51 80-115 (133)
23 PF08514 STAG: STAG domain ; 22.4 1.3E+02 0.0029 19.6 3.2 42 6-52 16-57 (118)
24 PF08236 SRI: SRI (Set2 Rpb1 i 22.1 1.2E+02 0.0025 19.0 2.7 41 29-74 4-44 (88)
25 TIGR02837 spore_II_R stage II 21.6 1E+02 0.0022 22.2 2.6 20 32-51 58-77 (168)
26 cd03561 VHS VHS domain family; 21.4 1.6E+02 0.0035 19.2 3.4 23 30-52 95-117 (133)
27 PF11081 DUF2890: Protein of u 21.3 1.4E+02 0.003 21.9 3.3 39 4-44 120-158 (187)
28 COG1677 FliE Flagellar hook-ba 20.9 88 0.0019 20.5 2.1 23 22-44 77-99 (105)
No 1
>KOG1826|consensus
Probab=99.57 E-value=1.3e-15 Score=134.84 Aligned_cols=68 Identities=38% Similarity=0.561 Sum_probs=61.7
Q ss_pred CcchhhHHHHHHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCCCCCCCCCCCCchhhhhhhhhhh
Q psy17710 1 MTVHAVHIKTKLCNLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSANQVTIPPTPGESFVSISRDLLKF 73 (75)
Q Consensus 1 ~t~~slRiKik~CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~~~~~~~~~~d~~~rlqrDLD~a 73 (75)
|||..+|||+|+|||+|+||.|||+|+|++|++|||+|+||+++|+|+.+...+ .++ ..++-||||||
T Consensus 973 i~V~~irvrskLcqL~Evmi~rredLtf~~em~f~nkl~e~L~d~vmgt~~~aa----l~~-~~~~~rdlDQa 1040 (2724)
T KOG1826|consen 973 ITVKFIRVRSKLCQLAEVMISRREDLTFPLEMGFVNKLFESLYDSVMGTEYLAA----LNF-HERNIRDLDQA 1040 (2724)
T ss_pred hhhhhhhHHHHHHHHHHHHHhhhhhchhHHHHHHHHHHHHHHHHhhcchhHHHh----hhh-HHHHhhhHHHH
Confidence 689999999999999999999999999999999999999999999999665532 344 88999999998
No 2
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=72.75 E-value=8.1 Score=24.23 Aligned_cols=39 Identities=18% Similarity=0.416 Sum_probs=31.7
Q ss_pred HHHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCCC
Q psy17710 13 CNLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSANQ 52 (75)
Q Consensus 13 CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~~ 52 (75)
|.+.+.+|.+++..+....+++|-. |..|.+|.......
T Consensus 12 ~~~fN~ll~~~~~~~~~~g~qi~~n-ls~l~~W~~~~~l~ 50 (105)
T PF01843_consen 12 ASLFNSLLLRRKYCSWSKGVQIRYN-LSELEDWARSHGLE 50 (105)
T ss_dssp HHHHHHHHCHSS-B-HHHHHHHHHH-HHHHHHCCCCTTST
T ss_pred HHHHHHHHCCCCccccccHHHHHHH-HHHHHHHHHhcccc
Confidence 6788999999999999999999965 57999999866554
No 3
>PF08203 RNA_polI_A14: Yeast RNA polymerase I subunit RPA14; InterPro: IPR013239 Saccharomyces cerevisiae RNA polymerase I (Pol I) is a complex consisting of 14 subunits. Subunit RPA14 forms part of a Pol I subcomplex consisting of RPA14 and and RPA43. The RPA14 and RPA43 heterodimer is proposed to play a role in the recruitment of Pol I to the promoter []. ; PDB: 2RF4_F.
Probab=44.81 E-value=11 Score=23.93 Aligned_cols=9 Identities=44% Similarity=0.663 Sum_probs=7.9
Q ss_pred chhhhhhhh
Q psy17710 62 SFVSISRDL 70 (75)
Q Consensus 62 ~~~rlqrDL 70 (75)
+++|+||||
T Consensus 60 QLKRiQRdl 68 (76)
T PF08203_consen 60 QLKRIQRDL 68 (76)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHhh
Confidence 489999998
No 4
>PF11108 Phage_glycop_gL: Viral glycoprotein L; InterPro: IPR020175 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH [].; PDB: 3PHF_N.
Probab=40.01 E-value=45 Score=22.43 Aligned_cols=40 Identities=10% Similarity=0.090 Sum_probs=32.4
Q ss_pred HHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCCCC
Q psy17710 14 NLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSANQV 53 (75)
Q Consensus 14 qL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~~~ 53 (75)
..+.+|++|-+.=+-..|.+|.|.|..+..++.+..+...
T Consensus 61 SFllAvl~rl~~~~~~~~~~lln~L~~~~~~F~~~f~~~t 100 (111)
T PF11108_consen 61 SFLLAVLDRLPSNTPPEDLELLNHLQRLKDSFLEKFSAVT 100 (111)
T ss_dssp HHHHHHHHGGGGG--THHHHHHHHHHHHHTTSGGGGGGS-
T ss_pred HHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 4578999999777779999999999999999988877753
No 5
>PRK03907 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=38.06 E-value=29 Score=22.67 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=19.6
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|+--+.+|||+||.--|
T Consensus 69 ~kA~ls~q~~vqVRNKlveAYqE 91 (97)
T PRK03907 69 GKAETSMKLMLEVRNKAISAYKE 91 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999997655
No 6
>PRK01699 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=36.96 E-value=31 Score=22.56 Aligned_cols=23 Identities=9% Similarity=0.322 Sum_probs=19.6
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.|..++|.=-+.+|||++|---|
T Consensus 71 ~kA~lslq~~vqVRNK~veAYqE 93 (99)
T PRK01699 71 KKAESQMKTAALVRDNLIENYKS 93 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999997655
No 7
>PRK00732 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=36.48 E-value=32 Score=22.58 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=19.8
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..|+|.-=+.+|||++|---|
T Consensus 74 ~kA~lslq~~vqVRNKlveAYqE 96 (102)
T PRK00732 74 AETDVAVSTLVSVRDRVIQAYEE 96 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999997655
No 8
>PRK00790 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=34.30 E-value=36 Score=22.62 Aligned_cols=22 Identities=18% Similarity=0.501 Sum_probs=18.5
Q ss_pred cccchhhhHHHHHHHHHHHHHH
Q psy17710 23 RDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 23 kd~l~~r~e~~~RNkLle~i~e 44 (75)
+..++|+==+.+|||++|---|
T Consensus 82 kA~lslq~~vqVRNKlVeAYqE 103 (109)
T PRK00790 82 QAEQALQTAVAIRDKVVEAYLE 103 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999997655
No 9
>PF10547 P22_AR_N: P22_AR N-terminal domain; InterPro: IPR018875 The antirepressor protein, ANT, prevents the prophage p22 c2 repressor protein from binding to its operators; it also inhibits the action of other prophage repressor proteins, including those of phages lambda and 434. The synthesis of antirepressor is negatively regulated by the protein products of the two other immi genes, mnt and arc.
Probab=31.28 E-value=16 Score=24.57 Aligned_cols=36 Identities=14% Similarity=0.374 Sum_probs=25.5
Q ss_pred HHHHHHHhcCcCCCCCCCCCCCCchhhhhhhhhhhhC
Q psy17710 39 VDYLMDWVLGSANQVTIPPTPGESFVSISRDLLKFIW 75 (75)
Q Consensus 39 le~i~eW~~~~s~~~~~~~~~~d~~~rlqrDLD~a~~ 75 (75)
|++|..|+...+...+ .+.-.|-+..+|++-+.|+|
T Consensus 73 l~~L~~WL~~I~p~kV-~pelr~kvi~YQ~Ec~~vL~ 108 (120)
T PF10547_consen 73 LRKLPGWLFTINPNKV-KPELREKVIAYQEECDDVLW 108 (120)
T ss_pred HHHHHHHHhhCChhhc-CHHHHHHHHHHHHHHHHHHH
Confidence 6899999998766544 22222348889999888775
No 10
>PRK00253 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=31.22 E-value=43 Score=22.01 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=19.0
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|.-=+.+|||+||---|
T Consensus 80 ~kA~lslq~~~qVRNKlv~AYqE 102 (108)
T PRK00253 80 QKASVSFQAGIQVRNKLVAAYQE 102 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999997654
No 11
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=30.10 E-value=23 Score=22.81 Aligned_cols=11 Identities=27% Similarity=0.268 Sum_probs=8.6
Q ss_pred hhhhhhhhhhh
Q psy17710 64 VSISRDLLKFI 74 (75)
Q Consensus 64 ~rlqrDLD~a~ 74 (75)
-+=|-|||+||
T Consensus 50 l~~Q~DLDkAi 60 (79)
T cd06405 50 LKNQEDLDRAI 60 (79)
T ss_pred ccCHHHHHHHH
Confidence 34578999997
No 12
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=28.87 E-value=97 Score=20.96 Aligned_cols=35 Identities=14% Similarity=0.315 Sum_probs=26.1
Q ss_pred HHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCC
Q psy17710 11 KLCNLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSAN 51 (75)
Q Consensus 11 k~CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~ 51 (75)
.|.+-+..+..++ -...+++++++.|-+|...+..
T Consensus 80 ~Fl~eL~kl~~~~------~~~~Vk~kil~li~~W~~~f~~ 114 (144)
T cd03568 80 DFTQELKKLINDR------VHPTVKEKLREVVKQWADEFKN 114 (144)
T ss_pred HHHHHHHHHhccc------CCHHHHHHHHHHHHHHHHHhCC
Confidence 4555555556665 4679999999999999887664
No 13
>PRK01482 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=28.74 E-value=51 Score=21.97 Aligned_cols=23 Identities=4% Similarity=0.151 Sum_probs=19.5
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|.--+.+|||+||.--|
T Consensus 81 qkA~lslql~vqVRNKlVeAYqE 103 (108)
T PRK01482 81 AKANMNLSIAKAVVERSIKAYQD 103 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999997655
No 14
>TIGR00205 fliE flagellar hook-basal body complex protein FliE. fliE is a component of the flagellar hook-basal body complex located possibly at (MS-ring)-rod junction.
Probab=28.43 E-value=52 Score=21.76 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=19.2
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|.--+.+|||++|.--|
T Consensus 81 ~kA~lslq~~vqVRNKlveAYqE 103 (108)
T TIGR00205 81 QKASMSMSILKEVRNKAVKAYQE 103 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999997654
No 15
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=27.85 E-value=54 Score=21.37 Aligned_cols=23 Identities=17% Similarity=0.456 Sum_probs=19.1
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|.-=+.+|||+|+.--|
T Consensus 74 ~kA~lslq~~vqVRNKlv~AYqE 96 (102)
T PRK12728 74 QKASISLQLTVQIRNKVVEAYQE 96 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999997655
No 16
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein []. All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella []. The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined []. The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar []. Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis []. From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits []. FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway []. On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures [].; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum
Probab=27.30 E-value=57 Score=20.52 Aligned_cols=23 Identities=22% Similarity=0.418 Sum_probs=19.1
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
-+..++|.==+.+|||+++-.-|
T Consensus 68 ~kA~lslq~~vqVRnK~v~AYqE 90 (96)
T PF02049_consen 68 QKASLSLQLAVQVRNKAVEAYQE 90 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999997655
No 17
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=26.98 E-value=55 Score=22.55 Aligned_cols=23 Identities=9% Similarity=0.154 Sum_probs=19.7
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.+..++|.==+.+|||+||.--|
T Consensus 100 qKAslSlql~vQVRNKvVeAYqE 122 (127)
T PRK12729 100 EKARVALTFTKTIADGVVRAYRE 122 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999997655
No 18
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=26.76 E-value=1.1e+02 Score=20.07 Aligned_cols=18 Identities=17% Similarity=0.549 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhcCcCC
Q psy17710 34 FRNKLVDYLMDWVLGSAN 51 (75)
Q Consensus 34 ~RNkLle~i~eW~~~~s~ 51 (75)
+|+++++.|.+|-..+..
T Consensus 105 Vk~k~l~ll~~W~~~f~~ 122 (140)
T PF00790_consen 105 VKEKILELLQEWAEAFKS 122 (140)
T ss_dssp HHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHCC
Confidence 999999999999987744
No 19
>PF14922 FWWh: Protein of unknown function
Probab=26.24 E-value=70 Score=22.33 Aligned_cols=19 Identities=21% Similarity=0.585 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhcCcCCC
Q psy17710 34 FRNKLVDYLMDWVLGSANQ 52 (75)
Q Consensus 34 ~RNkLle~i~eW~~~~s~~ 52 (75)
||..|.+.+.+|++|.-..
T Consensus 135 FK~~l~~~~~~w~sGi~p~ 153 (161)
T PF14922_consen 135 FKSNLYNTCSEWISGIKPS 153 (161)
T ss_pred HHHHHHHHHHHHHcCCccC
Confidence 9999999999999987664
No 20
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=24.13 E-value=1.3e+02 Score=20.14 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=19.2
Q ss_pred hhHHHHHHHHHHHHHHHhcCcCC
Q psy17710 29 RREMSFRNKLVDYLMDWVLGSAN 51 (75)
Q Consensus 29 r~e~~~RNkLle~i~eW~~~~s~ 51 (75)
.-..++|+++++.|.+|...+..
T Consensus 96 ~~~~~Vk~kil~li~~W~~~f~~ 118 (142)
T cd03569 96 TKNEEVRQKILELIQAWALAFRN 118 (142)
T ss_pred cCCHHHHHHHHHHHHHHHHHhCC
Confidence 45678999999999999876654
No 21
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=23.44 E-value=92 Score=20.50 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=18.4
Q ss_pred hhhhHHHHHHHHHHHHHHHhcC
Q psy17710 27 AFRREMSFRNKLVDYLMDWVLG 48 (75)
Q Consensus 27 ~~r~e~~~RNkLle~i~eW~~~ 48 (75)
.--.++++|-+|.+.|..|+--
T Consensus 18 e~a~~m~ir~~l~~~i~~~i~q 39 (91)
T COG5606 18 EAAENMKIRSALMMAIKQWIEQ 39 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999863
No 22
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=23.13 E-value=1.7e+02 Score=19.17 Aligned_cols=36 Identities=11% Similarity=0.383 Sum_probs=24.3
Q ss_pred HHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCC
Q psy17710 11 KLCNLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSAN 51 (75)
Q Consensus 11 k~CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~ 51 (75)
+|.+-+..+...+.... .+|+++++.|.+|...+..
T Consensus 80 ~fl~~L~~l~~~~~~~~-----~Vk~kil~li~~W~~~f~~ 115 (133)
T smart00288 80 EFLNELVKLIKPKYPLP-----LVKKRILELIQEWADAFKN 115 (133)
T ss_pred HHHHHHHHHHcCCCCcH-----HHHHHHHHHHHHHHHHHcC
Confidence 35554555555544321 2999999999999887755
No 23
>PF08514 STAG: STAG domain ; InterPro: IPR013721 STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe (Fission yeast) mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version [].
Probab=22.41 E-value=1.3e+02 Score=19.64 Aligned_cols=42 Identities=12% Similarity=0.512 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHHHcccccchhhhHHHHHHHHHHHHHHHhcCcCCC
Q psy17710 6 VHIKTKLCNLIEAMMRRRDDLAFRREMSFRNKLVDYLMDWVLGSANQ 52 (75)
Q Consensus 6 lRiKik~CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~eW~~~~s~~ 52 (75)
=..+-.||.+++.++..=. .++-+-.-|+|.|..|+..-|..
T Consensus 16 k~Fr~~~~~F~~~lv~~~~-----~~~Lyd~~l~~~l~~wl~~lS~S 57 (118)
T PF08514_consen 16 KKFRKNFCEFFDQLVEQCH-----SSILYDDYLMDNLISWLTALSSS 57 (118)
T ss_pred HHHHHHHHHHHHHHHHHhc-----ccccccHHHHHHHHHHHHHhccC
Confidence 3567788999888887543 33344448999999999977664
No 24
>PF08236 SRI: SRI (Set2 Rpb1 interacting) domain; InterPro: IPR013257 The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. ; GO: 0018024 histone-lysine N-methyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0034968 histone lysine methylation, 0005694 chromosome; PDB: 2A7O_A 2C5Z_A.
Probab=22.06 E-value=1.2e+02 Score=18.97 Aligned_cols=41 Identities=17% Similarity=0.345 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHHHHHHHhcCcCCCCCCCCCCCCchhhhhhhhhhhh
Q psy17710 29 RREMSFRNKLVDYLMDWVLGSANQVTIPPTPGESFVSISRDLLKFI 74 (75)
Q Consensus 29 r~e~~~RNkLle~i~eW~~~~s~~~~~~~~~~d~~~rlqrDLD~a~ 74 (75)
+++-.||+.+-.++..-+.....+ ...+| +..+-|+|-+++
T Consensus 4 ~~~~~~~~~l~~~V~~~l~~y~~~----~~~dd-fK~~ar~lt~~l 44 (88)
T PF08236_consen 4 KQEKKFRKTLAKHVVNLLNKYRKK----LSKDD-FKHLARKLTHKL 44 (88)
T ss_dssp HHHHHHHHHHHHHHHHHHCTTTTT------HHH-HHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHcccc----CCHHH-HHHHHHHHHHHH
Confidence 457789999999999988877665 22344 999999987764
No 25
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=21.55 E-value=1e+02 Score=22.17 Aligned_cols=20 Identities=15% Similarity=0.504 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhcCcCC
Q psy17710 32 MSFRNKLVDYLMDWVLGSAN 51 (75)
Q Consensus 32 ~~~RNkLle~i~eW~~~~s~ 51 (75)
.++|+.+++++.+|+.+...
T Consensus 58 l~VRD~Vl~~~~~~~~~~~s 77 (168)
T TIGR02837 58 LKVRDAVLKEIRPWLSGLKS 77 (168)
T ss_pred HHHHHHHHHHHHHHhccCCC
Confidence 46899999999999986543
No 26
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=21.35 E-value=1.6e+02 Score=19.16 Aligned_cols=23 Identities=13% Similarity=0.381 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHHHHHHhcCcCCC
Q psy17710 30 REMSFRNKLVDYLMDWVLGSANQ 52 (75)
Q Consensus 30 ~e~~~RNkLle~i~eW~~~~s~~ 52 (75)
-+..+|+++++.|.+|...+...
T Consensus 95 ~~~~Vk~kil~ll~~W~~~f~~~ 117 (133)
T cd03561 95 YDPKVREKALELILAWSESFGGH 117 (133)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCC
Confidence 47889999999999999866653
No 27
>PF11081 DUF2890: Protein of unknown function (DUF2890); InterPro: IPR021304 This entry contains the 33kDa and 22kDa phosphoproteins from vertebrate adenoviruses.
Probab=21.29 E-value=1.4e+02 Score=21.86 Aligned_cols=39 Identities=10% Similarity=0.252 Sum_probs=28.7
Q ss_pred hhhHHHHHHHHHHHHHHcccccchhhhHHHHHHHHHHHHHH
Q psy17710 4 HAVHIKTKLCNLIEAMMRRRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 4 ~slRiKik~CqL~e~vm~rkd~l~~r~e~~~RNkLle~i~e 44 (75)
+.-+.|.++|+-+.+++...-.- .++.++||+-|.-++-
T Consensus 120 swr~lR~~I~~tLyaifqqsrG~--~~~~kikNRtlrSlTR 158 (187)
T PF11081_consen 120 SWRELRNRIFPTLYAIFQQSRGN--EQELKIKNRTLRSLTR 158 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCC--ccccchhhHHHHHHHH
Confidence 34567888888888888763322 7788999988887764
No 28
>COG1677 FliE Flagellar hook-basal body protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.86 E-value=88 Score=20.50 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=18.4
Q ss_pred ccccchhhhHHHHHHHHHHHHHH
Q psy17710 22 RRDDLAFRREMSFRNKLVDYLMD 44 (75)
Q Consensus 22 rkd~l~~r~e~~~RNkLle~i~e 44 (75)
.|..++|.=-+.+|||+++..-|
T Consensus 77 ~KAs~sLq~ai~VRnKlV~AYqE 99 (105)
T COG1677 77 QKASVSLQTAIQVRNKLVSAYQE 99 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667888889999999987655
Done!