Query psy1423
Match_columns 125
No_of_seqs 104 out of 404
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:43:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1423.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1423hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00509 TFS2N Domain in the 99.8 5.7E-19 1.2E-23 119.6 7.8 71 33-104 3-74 (75)
2 cd00183 TFIIS_I N-terminal dom 99.8 6E-19 1.3E-23 119.2 7.4 67 37-104 10-76 (76)
3 TIGR01385 TFSII transcription 99.7 2.6E-17 5.5E-22 136.2 8.7 71 35-106 8-78 (299)
4 PF08711 Med26: TFIIS helical 99.7 1.8E-16 3.9E-21 99.9 5.5 53 52-104 1-53 (53)
5 KOG1105|consensus 99.5 1.8E-14 3.8E-19 119.5 7.7 76 31-106 3-81 (296)
6 KOG2821|consensus 97.9 7.8E-06 1.7E-10 71.3 3.5 73 32-107 8-81 (433)
7 PF11467 LEDGF: Lens epitheliu 97.0 0.0019 4.1E-08 46.8 5.6 62 43-104 18-80 (106)
8 KOG1793|consensus 95.8 0.0092 2E-07 52.0 3.4 53 51-103 236-290 (417)
9 COG5139 Uncharacterized conser 95.3 0.019 4.2E-07 49.0 3.7 52 51-103 233-286 (397)
10 PLN02976 amine oxidase 89.5 0.9 1.9E-05 45.9 6.3 60 47-107 1300-1360(1713)
11 PF14726 RTTN_N: Rotatin, an a 76.5 6.5 0.00014 28.0 4.6 53 44-97 44-96 (98)
12 PF07149 Pes-10: Pes-10; Inte 76.2 9.5 0.00021 33.3 6.4 64 37-103 10-73 (370)
13 cd03561 VHS VHS domain family; 52.5 57 0.0012 23.5 5.8 75 31-105 35-116 (133)
14 smart00288 VHS Domain present 43.9 1.1E+02 0.0024 22.1 6.2 75 31-105 35-115 (133)
15 cd00197 VHS_ENTH_ANTH VHS, ENT 36.6 1.4E+02 0.003 20.5 5.7 66 31-100 35-114 (115)
16 cd03568 VHS_STAM VHS domain fa 30.9 1.8E+02 0.0039 21.5 5.6 73 31-104 35-113 (144)
17 PF10562 CaM_bdg_C0: Calmoduli 29.2 50 0.0011 18.9 1.8 17 87-103 12-28 (29)
18 PF04558 tRNA_synt_1c_R1: Glut 28.4 1.3E+02 0.0027 23.1 4.5 55 45-106 82-140 (164)
19 cd03569 VHS_Hrs_Vps27p VHS dom 27.3 2.4E+02 0.0051 20.8 5.7 68 31-104 39-117 (142)
20 KOG1087|consensus 26.6 1.6E+02 0.0035 26.4 5.4 70 31-105 36-116 (470)
21 PF00790 VHS: VHS domain; Int 22.5 2.4E+02 0.0052 20.3 4.9 69 31-103 40-120 (140)
22 COG1752 RssA Predicted esteras 20.5 1.4E+02 0.003 24.2 3.6 51 51-101 27-78 (306)
No 1
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.78 E-value=5.7e-19 Score=119.57 Aligned_cols=71 Identities=39% Similarity=0.638 Sum_probs=64.0
Q ss_pred HHHhhhHhhcCC-CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 33 KRTSGDNKLTGL-VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 33 El~~~lek~~~~-~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
++.+.++++.++ .+.+.|+++|+.|+.++||.++|++|+||++||+|||| +|++|+.+|+.||++||++|+
T Consensus 3 ~~~k~~~k~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh-~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 3 RAAKKLDKVANNGKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKH-KNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHHhc
Confidence 344577777664 56789999999999999999999999999999999999 899999999999999999985
No 2
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.78 E-value=6e-19 Score=119.23 Aligned_cols=67 Identities=39% Similarity=0.603 Sum_probs=62.0
Q ss_pred hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 37 ~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
.|++..++.+.+.++++|+.|+.+|||.++|++|+||+.||+|||| ++++|+.+|+.||++||++|+
T Consensus 10 ~l~~~~~~~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh-~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 10 KLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKH-SNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HhhccccCCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcC-CcHHHHHHHHHHHHHHHHhcC
Confidence 6666666678999999999999999999999999999999999999 789999999999999999874
No 3
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=99.71 E-value=2.6e-17 Score=136.24 Aligned_cols=71 Identities=32% Similarity=0.532 Sum_probs=66.7
Q ss_pred HhhhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423 35 TSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY 106 (125)
Q Consensus 35 ~~~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~ 106 (125)
.+.|+++.++.+.+.++++|++|+.++||.|+|++|+||++||+|||| ++++|+.+|+.||++||++|..+
T Consensus 8 ~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh-~~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 8 AKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKH-PNEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred HHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcC-CcHHHHHHHHHHHHHHHHHHhhh
Confidence 338888888888899999999999999999999999999999999999 89999999999999999999775
No 4
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.66 E-value=1.8e-16 Score=99.94 Aligned_cols=53 Identities=45% Similarity=0.763 Sum_probs=48.3
Q ss_pred HHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 52 DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 52 ~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
++|+.|+.+|||.++|++|+||++||.|+||+++++|+++|+.||++||++|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 58999999999999999999999999999998899999999999999999874
No 5
>KOG1105|consensus
Probab=99.54 E-value=1.8e-14 Score=119.53 Aligned_cols=76 Identities=38% Similarity=0.537 Sum_probs=69.0
Q ss_pred hHHHHh---hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423 31 KKKRTS---GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY 106 (125)
Q Consensus 31 ~~El~~---~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~ 106 (125)
.+|+++ .++++.++.+.+.++++|.+|+++|||.++|++|+||+.||.+||+++|++|+++|+.||+.||++|...
T Consensus 3 ~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 3 EEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred cHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 345555 8899999899999999999999999999999999999999977777799999999999999999999863
No 6
>KOG2821|consensus
Probab=97.92 E-value=7.8e-06 Score=71.28 Aligned_cols=73 Identities=23% Similarity=0.216 Sum_probs=61.6
Q ss_pred HHHHhhhHhhcCC-CCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhhh
Q psy1423 32 KKRTSGDNKLTGL-VRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPYV 107 (125)
Q Consensus 32 ~El~~~lek~~~~-~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~~ 107 (125)
.+.++.++..+++ .++..++..|..|.++|++++.|.+|++|+.|+.||++ . .+..+|.+++..||++|-...
T Consensus 8 l~~Vr~lQ~~l~~~~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~-~--~~g~~~~Dl~~~WK~~v~~d~ 81 (433)
T KOG2821|consen 8 LGAVRKLQARLENRIDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKI-S--HVGKLAFDLVALWKDLVLVDF 81 (433)
T ss_pred HHHHHHHHHHHHhCccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHh-h--cccccccchHHHHHHhccccc
Confidence 4455544444443 48899999999999999999999999999999999999 2 799999999999999995444
No 7
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=97.02 E-value=0.0019 Score=46.77 Aligned_cols=62 Identities=18% Similarity=0.266 Sum_probs=51.1
Q ss_pred CCCCHHHHHHHHHHHhcCcCCHHHhh-cccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 43 GLVRQEQALDLLKALQTLNIDLNILT-KTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 43 ~~~~~~~il~~L~~L~~~~iT~elL~-~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
...+.+.|+++|..|..+++|.-+|+ -+.+--++.++|+.-.|..|.+.|..|..+-|.++-
T Consensus 18 ~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 18 DNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp TEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 67889999999999999999998876 567888999999988889999999999999999994
No 8
>KOG1793|consensus
Probab=95.77 E-value=0.0092 Score=52.05 Aligned_cols=53 Identities=36% Similarity=0.478 Sum_probs=46.9
Q ss_pred HHHHHHHhcCcCCH-HHhhcccchhhhhhhhcCC-CcHHHHHHHHHHHHHHHHhh
Q psy1423 51 LDLLKALQTLNIDL-NILTKTHIGMTVNNLRKSS-KDDEVINLAKTLIKNWKKFI 103 (125)
Q Consensus 51 l~~L~~L~~~~iT~-elL~~T~IGk~VnkLRKhs-~d~~I~~lAk~LV~kWKk~v 103 (125)
..+|.-|..+||-. |.|+..+||++|-=|-||- ...+++.+|..||..|-.-+
T Consensus 236 ~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI 290 (417)
T KOG1793|consen 236 KSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI 290 (417)
T ss_pred HHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence 56788888999988 9999999999999999983 44789999999999998776
No 9
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=95.31 E-value=0.019 Score=49.01 Aligned_cols=52 Identities=33% Similarity=0.521 Sum_probs=44.0
Q ss_pred HHHHHHHhcCcCCHHHhhcccchhhhh--hhhcCCCcHHHHHHHHHHHHHHHHhh
Q psy1423 51 LDLLKALQTLNIDLNILTKTHIGMTVN--NLRKSSKDDEVINLAKTLIKNWKKFI 103 (125)
Q Consensus 51 l~~L~~L~~~~iT~elL~~T~IGk~Vn--kLRKhs~d~~I~~lAk~LV~kWKk~v 103 (125)
-.+|..|..+||-.|.|++.+||+.|. .+.|. +.++|+.+|+.||..|-.-+
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk-~e~~v~r~A~~LV~eWtrpI 286 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKK-EEKEVRRSAKALVQEWTRPI 286 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCc-ccHHHHHHHHHHHHHhhccc
Confidence 456777889999999999999998774 44555 77899999999999998765
No 10
>PLN02976 amine oxidase
Probab=89.47 E-value=0.9 Score=45.92 Aligned_cols=60 Identities=18% Similarity=0.272 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHhcCcCCHHHhhcccchhhhh-hhhcCCCcHHHHHHHHHHHHHHHHhhhhhh
Q psy1423 47 QEQALDLLKALQTLNIDLNILTKTHIGMTVN-NLRKSSKDDEVINLAKTLIKNWKKFIRPYV 107 (125)
Q Consensus 47 ~~~il~~L~~L~~~~iT~elL~~T~IGk~Vn-kLRKhs~d~~I~~lAk~LV~kWKk~v~~~~ 107 (125)
++-+..+|+-|=.++..+..++..+||++|. ++.-| .+.+|..+|+.|+..|-+.+..+.
T Consensus 1300 ~~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h-~~~~~r~~a~~~~~~w~~~~~~~~ 1360 (1713)
T PLN02976 1300 TQLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVH-TSRDIRAIASQLVSVWLEVFRREK 1360 (1713)
T ss_pred HHHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhc-ccHHHHHHHHHHHHHHHHHHHHhh
Confidence 4445566777777888888999999999985 67888 788999999999999999996554
No 11
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=76.49 E-value=6.5 Score=27.96 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=44.7
Q ss_pred CCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHH
Q psy1423 44 LVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIK 97 (125)
Q Consensus 44 ~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~ 97 (125)
-..++.++++|.+|-+-|....+|+.-+.-...++||++ -++..+.....|++
T Consensus 44 ~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~-~~~~~~~~id~il~ 96 (98)
T PF14726_consen 44 VPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPN-VEPNLQAEIDEILD 96 (98)
T ss_pred CccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhc-CCHHHHHHHHHHHh
Confidence 356789999999999999999999998877889999998 67777777666654
No 12
>PF07149 Pes-10: Pes-10; InterPro: IPR009819 This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=76.24 E-value=9.5 Score=33.25 Aligned_cols=64 Identities=13% Similarity=0.230 Sum_probs=49.2
Q ss_pred hhHhhcCCCCHHHHHHHHHHHhcCcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhh
Q psy1423 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103 (125)
Q Consensus 37 ~lek~~~~~~~~~il~~L~~L~~~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v 103 (125)
-|.+.+...+.+-|..+++.|...++|.++|.+..+--.|.+ |+|+-+-+.--...+..||..-
T Consensus 10 lLAriI~tg~d~~IT~ai~qL~~~~~s~~ilDk~NlP~LI~~---~ap~N~aA~~L~~~~~~~K~~q 73 (370)
T PF07149_consen 10 LLARIIKTGNDEMITKAINQLPNHPVSVEILDKCNLPYLIDR---YAPNNEAAQSLARIHRQWKNIQ 73 (370)
T ss_pred HHHHHHHhCchHhHHHHHHhCCCCCCcHHHHHHcCchHHHHH---hCCCcHHHHHHHHHHHHHHHHH
Confidence 455555555668999999999999999999999999998874 4444455555556678999874
No 13
>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=52.50 E-value=57 Score=23.46 Aligned_cols=75 Identities=20% Similarity=0.129 Sum_probs=42.0
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcCcCCH------HHhhcccchhhhhhhhcC-CCcHHHHHHHHHHHHHHHHhh
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDL------NILTKTHIGMTVNNLRKS-SKDDEVINLAKTLIKNWKKFI 103 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~~iT~------elL~~T~IGk~VnkLRKh-s~d~~I~~lAk~LV~kWKk~v 103 (125)
..+..+.|.+-....++...+-+|.-|+.+.-+. ++-...-.-..++-+... ..++.|+..+..++..|...+
T Consensus 35 ~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f 114 (133)
T cd03561 35 PKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAWSESF 114 (133)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 4566666666665566666666666655422221 111111111111112221 257899999999999999987
Q ss_pred hh
Q psy1423 104 RP 105 (125)
Q Consensus 104 ~~ 105 (125)
..
T Consensus 115 ~~ 116 (133)
T cd03561 115 GG 116 (133)
T ss_pred cC
Confidence 54
No 14
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=43.95 E-value=1.1e+02 Score=22.10 Aligned_cols=75 Identities=17% Similarity=0.111 Sum_probs=43.0
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcCcCC------HHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNID------LNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~~iT------~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
..+..+.|.+-+...++...+-+|.-|+.+.-+ .++-...=+-..++-+..+...+.|++.+..++..|...+.
T Consensus 35 ~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~~f~ 114 (133)
T smart00288 35 PKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQEWADAFK 114 (133)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 566777666666667777666666666642222 11111111111222223332344599999999999999885
Q ss_pred h
Q psy1423 105 P 105 (125)
Q Consensus 105 ~ 105 (125)
.
T Consensus 115 ~ 115 (133)
T smart00288 115 N 115 (133)
T ss_pred C
Confidence 4
No 15
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. 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 is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=36.62 E-value=1.4e+02 Score=20.47 Aligned_cols=66 Identities=15% Similarity=0.166 Sum_probs=37.4
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcC------cCCHHHhhcccchhhhhhh-h-------cCCCcHHHHHHHHHHH
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTL------NIDLNILTKTHIGMTVNNL-R-------KSSKDDEVINLAKTLI 96 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~------~iT~elL~~T~IGk~VnkL-R-------Khs~d~~I~~lAk~LV 96 (125)
..++.+.|.+-+...+...++..|.-|+.+ ++..++-... ..+.+ + ....+..|+..++.|+
T Consensus 35 ~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~~----~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~ 110 (115)
T cd00197 35 PKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASND----FAVELLKFDKSKLLGDDVSTNVREKAIELV 110 (115)
T ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHHhH----HHHHHHHhhccccccCCCChHHHHHHHHHH
Confidence 345666666656666777666666666532 2222222221 22222 1 1124688999999999
Q ss_pred HHHH
Q psy1423 97 KNWK 100 (125)
Q Consensus 97 ~kWK 100 (125)
..|.
T Consensus 111 ~~w~ 114 (115)
T cd00197 111 QLWA 114 (115)
T ss_pred HHHh
Confidence 9996
No 16
>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=30.88 E-value=1.8e+02 Score=21.54 Aligned_cols=73 Identities=11% Similarity=0.095 Sum_probs=41.6
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcCcCC------HHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhh
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNID------LNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIR 104 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~~iT------~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~ 104 (125)
..+..+.|.|-+...++...+-+|.-|+.+.-+ .++-..-=+...++-+.+. .+..|+.....||..|...+.
T Consensus 35 ~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~-~~~~Vk~kil~li~~W~~~f~ 113 (144)
T cd03568 35 AKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDR-VHPTVKEKLREVVKQWADEFK 113 (144)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhccc-CCHHHHHHHHHHHHHHHHHhC
Confidence 456666666666666677666666666532111 1111111111122222232 568999999999999998875
No 17
>PF10562 CaM_bdg_C0: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; InterPro: IPR018882 This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue [].
Probab=29.23 E-value=50 Score=18.91 Aligned_cols=17 Identities=24% Similarity=0.554 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHhh
Q psy1423 87 EVINLAKTLIKNWKKFI 103 (125)
Q Consensus 87 ~I~~lAk~LV~kWKk~v 103 (125)
.--.+|+..+++|+..+
T Consensus 12 k~~elAr~a~dkWR~~i 28 (29)
T PF10562_consen 12 KQLELARHAADKWRGNI 28 (29)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 45678999999999865
No 18
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=28.45 E-value=1.3e+02 Score=23.10 Aligned_cols=55 Identities=20% Similarity=0.169 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhc---CcCCHH-HhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHHHHhhhhh
Q psy1423 45 VRQEQALDLLKALQT---LNIDLN-ILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRPY 106 (125)
Q Consensus 45 ~~~~~il~~L~~L~~---~~iT~e-lL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kWKk~v~~~ 106 (125)
.+...+-.+|+.|.. -+++.+ .-+..+||+.| ..++|.......|.+=|..+.++
T Consensus 82 kt~~Ql~AA~~Yl~~~~~~~~d~~~Fe~~cGVGV~V-------T~E~I~~~V~~~i~~~k~~i~~~ 140 (164)
T PF04558_consen 82 KTNLQLDAALKYLKSNPSEPIDVAEFEKACGVGVVV-------TPEQIEAAVEKYIEENKEEILEK 140 (164)
T ss_dssp -SHHHHHHHHHHHHHHGG-G--HHHHHHTTTTT-----------HHHHHHHHHHHHHHTHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCCCCCCCHHHHHHHcCCCeEE-------CHHHHHHHHHHHHHHhHHHHHHH
Confidence 355666666666665 355654 44589999998 56789999988888777766544
No 19
>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=27.32 E-value=2.4e+02 Score=20.78 Aligned_cols=68 Identities=18% Similarity=0.151 Sum_probs=40.5
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcC-----------cCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHH
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTL-----------NIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNW 99 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~-----------~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kW 99 (125)
..+..+.|.+-+...++...+-+|.-|+.+ ..+.+.|.+ +-+.+. ++ .++.|++.+-.||..|
T Consensus 39 ~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~--l~~l~~---~~-~~~~Vk~kil~li~~W 112 (142)
T cd03569 39 PKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDE--LKDLIK---TT-KNEEVRQKILELIQAW 112 (142)
T ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHH--HHHHHc---cc-CCHHHHHHHHHHHHHH
Confidence 456666666665556666555555555421 123333322 112222 23 6789999999999999
Q ss_pred HHhhh
Q psy1423 100 KKFIR 104 (125)
Q Consensus 100 Kk~v~ 104 (125)
...+.
T Consensus 113 ~~~f~ 117 (142)
T cd03569 113 ALAFR 117 (142)
T ss_pred HHHhC
Confidence 98874
No 20
>KOG1087|consensus
Probab=26.58 E-value=1.6e+02 Score=26.43 Aligned_cols=70 Identities=19% Similarity=0.173 Sum_probs=47.7
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhc-----------CcCCHHHhhcccchhhhhhhhcCCCcHHHHHHHHHHHHHH
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQT-----------LNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNW 99 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~-----------~~iT~elL~~T~IGk~VnkLRKhs~d~~I~~lAk~LV~kW 99 (125)
..|+.+.|.|-+...+....+-+|.-|+. -....++|.+ -|...+++..+..|+..+=.||..|
T Consensus 36 ~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~fh~~Va~k~fL~e-----mVk~~k~~~~~~~Vr~kiL~LI~~W 110 (470)
T KOG1087|consen 36 PKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSFHLQVASKEFLNE-----MVKRPKNKPRDLKVREKILELIDTW 110 (470)
T ss_pred cHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH-----HHhccccCCcchhHHHHHHHHHHHH
Confidence 34777777777765555555555555552 2234455555 5666677646778999999999999
Q ss_pred HHhhhh
Q psy1423 100 KKFIRP 105 (125)
Q Consensus 100 Kk~v~~ 105 (125)
...+..
T Consensus 111 ~~af~~ 116 (470)
T KOG1087|consen 111 QQAFCG 116 (470)
T ss_pred HHHccC
Confidence 999865
No 21
>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=22.46 E-value=2.4e+02 Score=20.28 Aligned_cols=69 Identities=20% Similarity=0.206 Sum_probs=41.2
Q ss_pred hHHHHhhhHhhcCCCCHHHHHHHHHHHhcCcCCH------HHhhcccchhhhhhhhc----CCCcHH--HHHHHHHHHHH
Q psy1423 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDL------NILTKTHIGMTVNNLRK----SSKDDE--VINLAKTLIKN 98 (125)
Q Consensus 31 ~~El~~~lek~~~~~~~~~il~~L~~L~~~~iT~------elL~~T~IGk~VnkLRK----hs~d~~--I~~lAk~LV~k 98 (125)
..|..+.|.+-+...++...+-+|.-|+.+.-+- ++-.. ..++.|.+ ....+. |+..+..+|..
T Consensus 40 ~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~----~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~ 115 (140)
T PF00790_consen 40 AKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASK----EFLDELVKLIKSKKTDPETPVKEKILELLQE 115 (140)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSH----HHHHHHHHHHHHTTTHHHSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHH----HHHHHHHHHHccCCCCchhHHHHHHHHHHHH
Confidence 4566666666666677777766666666422221 11111 12333332 323343 99999999999
Q ss_pred HHHhh
Q psy1423 99 WKKFI 103 (125)
Q Consensus 99 WKk~v 103 (125)
|...+
T Consensus 116 W~~~f 120 (140)
T PF00790_consen 116 WAEAF 120 (140)
T ss_dssp HHHHT
T ss_pred HHHHH
Confidence 99988
No 22
>COG1752 RssA Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]
Probab=20.54 E-value=1.4e+02 Score=24.23 Aligned_cols=51 Identities=27% Similarity=0.480 Sum_probs=41.8
Q ss_pred HHHHHHHhcCcCCHHHhhcccchhhhhhh-hcCCCcHHHHHHHHHHHHHHHH
Q psy1423 51 LDLLKALQTLNIDLNILTKTHIGMTVNNL-RKSSKDDEVINLAKTLIKNWKK 101 (125)
Q Consensus 51 l~~L~~L~~~~iT~elL~~T~IGk~VnkL-RKhs~d~~I~~lAk~LV~kWKk 101 (125)
+-+|+.|...-+..+.+-.|.+|-.|.-+ -.+...+++...+..+...|..
T Consensus 27 iGVl~aL~e~gi~~~~iaGtS~GAiva~l~A~g~~~~~~~~~~~~l~~~~~~ 78 (306)
T COG1752 27 IGVLKALEEAGIPIDVIAGTSAGAIVAALYAAGMDEDELELAAQRLTARWDN 78 (306)
T ss_pred HHHHHHHHHcCCCccEEEecCHHHHHHHHHHcCCChhHHHHHHHHHHhhhcc
Confidence 56777777777888899999999999888 3343566899999999999986
Done!