Query psy9417
Match_columns 161
No_of_seqs 126 out of 159
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 18:38:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9417.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9417hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0132|consensus 100.0 9.9E-35 2.1E-39 273.7 6.7 107 55-161 2-109 (894)
2 KOG0132|consensus 99.9 7.9E-27 1.7E-31 220.5 7.9 86 1-86 10-100 (894)
3 cd03562 CID CID (CTD-Interacti 99.9 9.4E-22 2E-26 145.2 8.3 94 58-159 2-96 (114)
4 KOG2071|consensus 99.7 3.5E-18 7.7E-23 158.4 7.2 92 55-156 4-95 (579)
5 smart00582 RPR domain present 99.7 1E-16 2.3E-21 118.7 9.6 87 59-152 1-87 (121)
6 cd03562 CID CID (CTD-Interacti 99.0 2.6E-09 5.7E-14 78.8 7.8 53 12-64 16-68 (114)
7 smart00582 RPR domain present 98.7 5.2E-08 1.1E-12 72.1 7.5 54 11-64 10-63 (121)
8 PF04818 CTD_bind: RNA polymer 98.6 1.3E-08 2.9E-13 68.8 1.1 46 112-159 1-47 (64)
9 cd00197 VHS_ENTH_ANTH VHS, ENT 98.0 2.5E-05 5.3E-10 57.6 6.5 69 73-147 15-83 (115)
10 KOG2669|consensus 97.5 0.00054 1.2E-08 60.9 8.7 90 60-157 9-99 (325)
11 PF12243 CTK3: CTD kinase subu 97.1 0.005 1.1E-07 48.7 9.1 91 57-152 7-97 (139)
12 KOG2071|consensus 96.3 0.004 8.6E-08 59.1 3.9 58 11-68 18-75 (579)
13 PF00790 VHS: VHS domain; Int 95.5 0.027 5.9E-07 43.3 4.7 75 75-150 22-96 (140)
14 cd03561 VHS VHS domain family; 94.7 0.041 8.9E-07 42.0 3.8 57 75-131 17-73 (133)
15 KOG0151|consensus 94.5 0.12 2.6E-06 50.8 7.1 88 60-152 436-525 (877)
16 cd03572 ENTH_epsin_related ENT 88.2 2.9 6.2E-05 32.5 7.2 58 72-129 15-72 (122)
17 smart00288 VHS Domain present 86.8 0.72 1.6E-05 35.4 3.1 57 75-131 17-73 (133)
18 PF01417 ENTH: ENTH domain; I 86.2 2.4 5.3E-05 31.7 5.7 56 73-129 18-76 (125)
19 cd00197 VHS_ENTH_ANTH VHS, ENT 76.3 3.2 7E-05 30.3 3.1 55 9-63 13-67 (115)
20 cd03569 VHS_Hrs_Vps27p VHS dom 67.6 6.3 0.00014 30.8 3.1 60 90-150 36-95 (142)
21 cd03568 VHS_STAM VHS domain fa 65.8 10 0.00023 29.7 4.1 55 77-131 19-73 (144)
22 cd03567 VHS_GGA VHS domain fam 63.9 13 0.00027 29.2 4.2 56 93-149 36-91 (139)
23 KOG2669|consensus 58.0 75 0.0016 28.7 8.5 88 18-105 21-130 (325)
24 PF12309 KBP_C: KIF-1 binding 48.2 31 0.00067 31.2 4.5 87 8-105 250-344 (371)
25 cd03565 VHS_Tom1 VHS domain fa 47.2 28 0.00061 27.1 3.6 53 79-131 22-75 (141)
26 KOG2221|consensus 46.3 27 0.00058 30.7 3.6 51 15-69 192-242 (267)
27 PF04100 Vps53_N: Vps53-like, 42.4 2.6E+02 0.0056 25.3 10.7 117 25-153 108-235 (383)
28 KOG1087|consensus 42.1 31 0.00067 32.5 3.7 51 80-130 23-73 (470)
29 cd03561 VHS VHS domain family; 38.5 98 0.0021 23.4 5.4 56 32-88 36-91 (133)
30 PF08767 CRM1_C: CRM1 C termin 35.0 2.7E+02 0.0058 24.3 8.2 25 105-129 81-106 (319)
31 PLN00047 photosystem II biogen 34.9 3.3E+02 0.0072 24.3 10.3 121 30-151 76-205 (283)
32 KOG1818|consensus 34.6 61 0.0013 31.8 4.5 72 79-155 29-100 (634)
33 cd03569 VHS_Hrs_Vps27p VHS dom 30.2 1.8E+02 0.0039 22.5 5.8 53 75-127 82-136 (142)
34 PF14747 DUF4473: Domain of un 27.8 1.5E+02 0.0032 21.0 4.5 49 58-111 9-71 (82)
35 KOG1829|consensus 26.8 1.4E+02 0.0031 29.0 5.5 70 23-92 426-503 (580)
36 PF09894 DUF2121: Uncharacteri 24.7 1.6E+02 0.0035 24.9 4.8 46 32-78 127-172 (194)
37 PF13324 GCIP: Grap2 and cycli 24.7 4.3E+02 0.0093 22.3 11.2 137 9-158 113-253 (275)
38 PF03392 OS-D: Insect pheromon 23.3 78 0.0017 23.3 2.4 40 92-131 40-79 (95)
39 PF01602 Adaptin_N: Adaptin N 23.2 3.2E+02 0.0068 24.2 6.7 91 56-158 340-430 (526)
40 KOG2148|consensus 20.6 86 0.0019 31.5 2.8 37 27-67 827-863 (867)
41 PF09585 Lin0512_fam: Conserve 20.3 58 0.0012 25.3 1.3 12 18-29 16-27 (113)
No 1
>KOG0132|consensus
Probab=100.00 E-value=9.9e-35 Score=273.74 Aligned_cols=107 Identities=54% Similarity=0.874 Sum_probs=104.6
Q ss_pred HHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc-cc
Q psy9417 55 YVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK-YK 133 (161)
Q Consensus 55 yvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~-~k 133 (161)
.+|.+|+.||+||.++|+||||+||..||++|++|++.|+|||+.||+||+||+|+||||+|||||||||+++||++ +|
T Consensus 2 e~v~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~k 81 (894)
T KOG0132|consen 2 DAVKEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEK 81 (894)
T ss_pred hHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred CccHHhhHHHHHHHHhhhhcCCCcccCC
Q psy9417 134 DVYAPRFARNLYRTFGYVFQCPDEDRKK 161 (161)
Q Consensus 134 d~Y~~rF~~nl~~tf~~~~~c~~~dk~k 161 (161)
|+|++||.+|+..||+++|+|+.+||++
T Consensus 82 d~F~prf~~n~~~tf~~L~~c~~edks~ 109 (894)
T KOG0132|consen 82 DVFGPRFSKNFTGTFQNLYECPQEDKSD 109 (894)
T ss_pred cccCCccchhHHHHHHHHHhcCHHHHHH
Confidence 9999999999999999999999999864
No 2
>KOG0132|consensus
Probab=99.93 E-value=7.9e-27 Score=220.54 Aligned_cols=86 Identities=48% Similarity=0.594 Sum_probs=73.7
Q ss_pred CcccccCCCCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhhc-C----CCCCc
Q psy9417 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINS-T----KPPIS 75 (161)
Q Consensus 1 ~l~~~~~~~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~-~----k~~iS 75 (161)
||.||+|+||+||++||..|||+||||||+||||||+|||||+||||+||||||||||++++...+-+. . .+..|
T Consensus 10 eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F~prf~ 89 (894)
T KOG0132|consen 10 ELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVFGPRFS 89 (894)
T ss_pred HHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccccccCCccc
Confidence 799999999999999999999999999999999999999999999999999999999999998866554 1 23455
Q ss_pred HHHHHHHHHHH
Q psy9417 76 KAKITGIVKLA 86 (161)
Q Consensus 76 rskI~~LT~lA 86 (161)
+..+..+..++
T Consensus 90 ~n~~~tf~~L~ 100 (894)
T KOG0132|consen 90 KNFTGTFQNLY 100 (894)
T ss_pred hhHHHHHHHHH
Confidence 55555444443
No 3
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=99.86 E-value=9.4e-22 Score=145.20 Aligned_cols=94 Identities=29% Similarity=0.425 Sum_probs=85.2
Q ss_pred HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417 58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA 137 (161)
Q Consensus 58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~ 137 (161)
.+|...|++|..++ +|++.|++||.+|++|.++++.||+.++++|++|+|++||++|||+|||+||++++ |.
T Consensus 2 ~~~~~~l~~L~~~~--~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~------~~ 73 (114)
T cd03562 2 FDYNALLEKLTFNK--NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRK------YK 73 (114)
T ss_pred ccHHHHHHHHHcCc--ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccc------hH
Confidence 57888899998865 89999999999999999999999999999999999999999999999999999987 55
Q ss_pred HhhHHHHHHHHhhhh-cCCCccc
Q psy9417 138 PRFARNLYRTFGYVF-QCPDEDR 159 (161)
Q Consensus 138 ~rF~~nl~~tf~~~~-~c~~~dk 159 (161)
..|+..+.++|.+++ +|+++.|
T Consensus 74 ~~~~~~~~~~f~~~~~~~~~~~r 96 (114)
T cd03562 74 EFFSEFLVPLFLDAYEKVDEKTR 96 (114)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHH
Confidence 888888899999888 5666554
No 4
>KOG2071|consensus
Probab=99.73 E-value=3.5e-18 Score=158.42 Aligned_cols=92 Identities=29% Similarity=0.436 Sum_probs=85.3
Q ss_pred HHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccC
Q psy9417 55 YVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKD 134 (161)
Q Consensus 55 yvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd 134 (161)
-+..+|...|++|+. ||++.|++||.+|.||..+++.||..||+||.||+|..||+++|++|||++|+|.+
T Consensus 4 ~~~~dy~s~ledltf----nskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~p----- 74 (579)
T KOG2071|consen 4 DACRDYQSSLEDLTF----NSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSP----- 74 (579)
T ss_pred HhHHHHHHHHHHHhc----CCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCc-----
Confidence 456789999999984 88999999999999999999999999999999999999999999999999999998
Q ss_pred ccHHhhHHHHHHHHhhhhcCCC
Q psy9417 135 VYAPRFARNLYRTFGYVFQCPD 156 (161)
Q Consensus 135 ~Y~~rF~~nl~~tf~~~~~c~~ 156 (161)
|+-.|++||+.||+++|.--+
T Consensus 75 -y~~~fs~~l~a~f~~~~~~vd 95 (579)
T KOG2071|consen 75 -YTTAFSRNLVATFICAFTKVD 95 (579)
T ss_pred -chhhhhhhHHHHHHHHHhhcc
Confidence 779999999999999996543
No 5
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=99.70 E-value=1e-16 Score=118.69 Aligned_cols=87 Identities=25% Similarity=0.397 Sum_probs=74.6
Q ss_pred hhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHH
Q psy9417 59 EWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAP 138 (161)
Q Consensus 59 ef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~ 138 (161)
+|++.|++|. +|++.|+++|..|++|.+++++||+.+++++++++|++||+.|||+|+|++|++.+++ ..|..
T Consensus 1 ~f~~~L~~L~-----~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~--~~f~~ 73 (121)
T smart00582 1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYG--SEFGD 73 (121)
T ss_pred ChHHHHHhcc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccH--HHHHH
Confidence 4788899986 7999999999999999999999999999999999999999999999999999998854 23445
Q ss_pred hhHHHHHHHHhhhh
Q psy9417 139 RFARNLYRTFGYVF 152 (161)
Q Consensus 139 rF~~nl~~tf~~~~ 152 (161)
-|.+.+..+|.+++
T Consensus 74 ~~~~~~~~~~~~~~ 87 (121)
T smart00582 74 ELGPVFQDALRDVL 87 (121)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555666665
No 6
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=98.97 E-value=2.6e-09 Score=78.76 Aligned_cols=53 Identities=32% Similarity=0.474 Sum_probs=50.8
Q ss_pred chHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHh
Q psy9417 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQEL 64 (161)
Q Consensus 12 ~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL 64 (161)
.|+..|+.+|.-|+.+.++++++|+.++++|.+|.|+.|+|+|||+|+.....
T Consensus 16 ~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~ 68 (114)
T cd03562 16 NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNV 68 (114)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHc
Confidence 59999999999999999999999999999999999999999999999988764
No 7
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=98.72 E-value=5.2e-08 Score=72.07 Aligned_cols=54 Identities=30% Similarity=0.325 Sum_probs=51.3
Q ss_pred CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHh
Q psy9417 11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQEL 64 (161)
Q Consensus 11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL 64 (161)
..||..|+++|.-|+.+.++++++|+.+++.+.+|.|+.|++.|||+|+....-
T Consensus 10 ~~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~ 63 (121)
T smart00582 10 NNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNS 63 (121)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHH
Confidence 389999999999999999999999999999999999999999999999987755
No 8
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=98.60 E-value=1.3e-08 Score=68.78 Aligned_cols=46 Identities=28% Similarity=0.474 Sum_probs=40.0
Q ss_pred cchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhhhhcC-CCccc
Q psy9417 112 KLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQC-PDEDR 159 (161)
Q Consensus 112 KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~~~~c-~~~dk 159 (161)
||+.|||+|+|++|++.+ ..|.|++.|++.|..+|.+++++ +++++
T Consensus 1 KL~~lYl~ndI~q~sk~k--~~~~f~~~F~~~l~~~~~~~~~~~~~~~~ 47 (64)
T PF04818_consen 1 KLALLYLANDILQNSKRK--NPDEFAPAFSPVLPDAFAHAYKNVDPEVR 47 (64)
T ss_dssp HHHHHHHHHHHHHHHHHH--TTHCHHHHHHCCHHHHHHHHCCCS-HHHH
T ss_pred CcceeehHHHHHHHhhhc--ChHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence 799999999999999876 45789999999999999999988 55544
No 9
>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=97.97 E-value=2.5e-05 Score=57.65 Aligned_cols=69 Identities=17% Similarity=0.125 Sum_probs=59.9
Q ss_pred CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHH
Q psy9417 73 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRT 147 (161)
Q Consensus 73 ~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~t 147 (161)
+-+.+.|..|+.+.-++...++.++..|.++|....|...+.+|+++|++++|.+.+| ...|+.+.+-.
T Consensus 15 ~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f------~~~i~~~~~~~ 83 (115)
T cd00197 15 GPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERF------HQEVASNDFAV 83 (115)
T ss_pred CCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHH------HHHHHHhHHHH
Confidence 6788999999999988878899999999999999999999999999999999999874 45666654433
No 10
>KOG2669|consensus
Probab=97.50 E-value=0.00054 Score=60.94 Aligned_cols=90 Identities=12% Similarity=0.207 Sum_probs=77.7
Q ss_pred hHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHh
Q psy9417 60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPR 139 (161)
Q Consensus 60 f~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~r 139 (161)
|...|..|. +|...|+++..-.+.|-+++..||+.=.+.+++....+||..||++.-++-|++.+ .+.|.+-
T Consensus 9 l~~kL~~L~-----~TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk---~~ef~~e 80 (325)
T KOG2669|consen 9 LEKKLAELS-----NTQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRK---GPEFVDE 80 (325)
T ss_pred HHHHHHhcc-----chHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhc---CchhHHH
Confidence 444455553 68899999999999999999999999999999999999999999999999999433 4679999
Q ss_pred hHHHHHHHHhhhh-cCCCc
Q psy9417 140 FARNLYRTFGYVF-QCPDE 157 (161)
Q Consensus 140 F~~nl~~tf~~~~-~c~~~ 157 (161)
|.+-+.+-|.+++ +|+.+
T Consensus 81 f~~v~~~a~~~i~~~~~~~ 99 (325)
T KOG2669|consen 81 FWPVVLKAFAHIVEETDVK 99 (325)
T ss_pred HHHHHHHHHHHHHHhcchh
Confidence 9999999999998 55554
No 11
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=97.09 E-value=0.005 Score=48.73 Aligned_cols=91 Identities=21% Similarity=0.230 Sum_probs=77.1
Q ss_pred HHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCcc
Q psy9417 57 IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVY 136 (161)
Q Consensus 57 IDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y 136 (161)
=-.|.+-|+.|. .|...|+..|..|++|......+..+|-..+.+..=.-|...+|.||++|-.+...-+....|
T Consensus 7 r~~F~~~L~~L~-----aS~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Y 81 (139)
T PF12243_consen 7 RMQFTQLLRRLN-----ASQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPY 81 (139)
T ss_pred HHHHHHHHHHcc-----hhHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchh
Confidence 334555566654 477889999999999999999999999999999988889999999999999988776567899
Q ss_pred HHhhHHHHHHHHhhhh
Q psy9417 137 APRFARNLYRTFGYVF 152 (161)
Q Consensus 137 ~~rF~~nl~~tf~~~~ 152 (161)
...-.++|..+...+.
T Consensus 82 v~~l~~dL~~Iv~~V~ 97 (139)
T PF12243_consen 82 VSMLQRDLPRIVDAVA 97 (139)
T ss_pred HHHHHHHHHHHHHHhC
Confidence 9999999999887764
No 12
>KOG2071|consensus
Probab=96.31 E-value=0.004 Score=59.14 Aligned_cols=58 Identities=28% Similarity=0.322 Sum_probs=53.2
Q ss_pred CchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhh
Q psy9417 11 PISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN 68 (161)
Q Consensus 11 ~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~ 68 (161)
.=||-.|+-.|..|..-+.+=+-+|..+|.-|+||.|-.|||++|++|++..-+.+=+
T Consensus 18 fnskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~py 75 (579)
T KOG2071|consen 18 FNSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSPY 75 (579)
T ss_pred cCCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCcc
Confidence 5688899999999999999999999999999999999999999999999988775533
No 13
>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=95.46 E-value=0.027 Score=43.27 Aligned_cols=75 Identities=17% Similarity=0.222 Sum_probs=57.4
Q ss_pred cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhh
Q psy9417 75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGY 150 (161)
Q Consensus 75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~ 150 (161)
.=+.|-.|.+..-.+....+.++..|.++++...|..-+.+|.|+|++++|.|.++. .-+=..+|...|.+++..
T Consensus 22 Dw~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~-~ev~~~~fl~~l~~l~~~ 96 (140)
T PF00790_consen 22 DWSLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFH-REVASKEFLDELVKLIKS 96 (140)
T ss_dssp -HHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHH-HHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHH-HHHhHHHHHHHHHHHHcc
Confidence 345667777777777778999999999999999999999999999999999998865 011123466666665543
No 14
>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=94.73 E-value=0.041 Score=42.00 Aligned_cols=57 Identities=14% Similarity=0.095 Sum_probs=47.8
Q ss_pred cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417 75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK 131 (161)
Q Consensus 75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~ 131 (161)
.-+-|-.|.++.-..-...+..++.|.++|+...|.--+.+|.++|++++|.|+++.
T Consensus 17 D~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~ 73 (133)
T cd03561 17 DWALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFH 73 (133)
T ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHH
Confidence 345566666666656667899999999999999999999999999999999998754
No 15
>KOG0151|consensus
Probab=94.49 E-value=0.12 Score=50.81 Aligned_cols=88 Identities=16% Similarity=0.229 Sum_probs=69.5
Q ss_pred hHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHH--HhhcCCCCcchhHHHHHHHHHHHhhhhcccCccH
Q psy9417 60 WNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKF--IWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYA 137 (161)
Q Consensus 60 f~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~--I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~ 137 (161)
|..-|++|+ --|+.|..+.--|++|.+.+-.||.+|..- +...+-.-|+.-||+|.-|.-|.-..-..--.|.
T Consensus 436 lE~liR~LT-----pEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR 510 (877)
T KOG0151|consen 436 LEDLIRGLT-----PEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYR 510 (877)
T ss_pred HHHHHHhcC-----cccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHH
Confidence 444445554 357789999999999999999999999864 4778888999999999999988865533334577
Q ss_pred HhhHHHHHHHHhhhh
Q psy9417 138 PRFARNLYRTFGYVF 152 (161)
Q Consensus 138 ~rF~~nl~~tf~~~~ 152 (161)
.-|-..|..+|.+++
T Consensus 511 ~~FEa~L~~Ifd~l~ 525 (877)
T KOG0151|consen 511 KSFEATLEDIFDDLN 525 (877)
T ss_pred HHHHHHHHHHHHHHH
Confidence 888888888887765
No 16
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. 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. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=88.16 E-value=2.9 Score=32.47 Aligned_cols=58 Identities=17% Similarity=0.170 Sum_probs=53.7
Q ss_pred CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhh
Q psy9417 72 PPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQ 129 (161)
Q Consensus 72 ~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~ 129 (161)
.|-++....+|+.+..++......|++.|-+.+++..|.-|+-+|=|||-+|++....
T Consensus 15 ~p~pgy~~~Eia~~t~~s~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~~ 72 (122)
T cd03572 15 EPTPGYLYEEIAKLTRKSVGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNSD 72 (122)
T ss_pred CCCchHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCHH
Confidence 3889999999999999998889999999999999999999999999999999998654
No 17
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=86.80 E-value=0.72 Score=35.35 Aligned_cols=57 Identities=19% Similarity=0.153 Sum_probs=45.6
Q ss_pred cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417 75 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK 131 (161)
Q Consensus 75 SrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~ 131 (161)
.-+.|-.+.++.-......+..+..|-+.++.-.|.--+-+|-++|++++|.|.++.
T Consensus 17 dw~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~ 73 (133)
T smart00288 17 DWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFH 73 (133)
T ss_pred CHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHH
Confidence 334455555555555556788899999999999999999999999999999998754
No 18
>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....
Probab=86.24 E-value=2.4 Score=31.68 Aligned_cols=56 Identities=7% Similarity=0.046 Sum_probs=45.1
Q ss_pred CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHH---hhcCCCCcchhHHHHHHHHHHHhhh
Q psy9417 73 PISKAKITGIVKLALKATHYYKYVVQSVEKFI---WKCKSQYKLPGLYVIDAIIHQARLQ 129 (161)
Q Consensus 73 ~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I---~k~~p~~KL~~LYVIDSIvRn~~~~ 129 (161)
|.++..+..|+...-+. ..+..|+..|-+.+ ....+.+++-+|.+|+-+++|....
T Consensus 18 gp~~~~l~eIa~~t~~~-~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~~ 76 (125)
T PF01417_consen 18 GPPGKLLAEIAQLTYNS-KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSER 76 (125)
T ss_dssp S--HHHHHHHHHHTTSC-HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-HH
T ss_pred CcCHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCHH
Confidence 67777777777776555 89999999999999 7777788999999999999998654
No 19
>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=76.25 E-value=3.2 Score=30.29 Aligned_cols=55 Identities=16% Similarity=0.030 Sum_probs=44.5
Q ss_pred CCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHH
Q psy9417 9 KPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQE 63 (161)
Q Consensus 9 ~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~e 63 (161)
.+.-+..-|.+|+...-.--...+.++..+.|.|+.+.|...+.+|+++|....-
T Consensus 13 ~~~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN 67 (115)
T cd00197 13 NMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKN 67 (115)
T ss_pred CCCCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHH
Confidence 3455677888888877554466789999999999999999999999999986553
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=67.55 E-value=6.3 Score=30.75 Aligned_cols=60 Identities=15% Similarity=0.265 Sum_probs=44.1
Q ss_pred hHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhh
Q psy9417 90 THYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGY 150 (161)
Q Consensus 90 ik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~ 150 (161)
-...+..+..|.+.++.--|..=+-+|-++|++++|.|.++. .-+=...|...|..++..
T Consensus 36 ~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh-~evas~~fl~~l~~l~~~ 95 (142)
T cd03569 36 DVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFH-DEVASREFMDELKDLIKT 95 (142)
T ss_pred CCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHH-HHHhhHHHHHHHHHHHcc
Confidence 345778889999999998899999999999999999988754 111124455555555543
No 21
>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=65.79 E-value=10 Score=29.68 Aligned_cols=55 Identities=15% Similarity=0.144 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417 77 AKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK 131 (161)
Q Consensus 77 skI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~ 131 (161)
+-|-.+....-.+-...+..+.+|-+.+...-|.-=+-+|-++|++++|.|..+.
T Consensus 19 ~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh 73 (144)
T cd03568 19 GLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFH 73 (144)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHH
Confidence 3455555555555566888899999999988899999999999999999998754
No 22
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=63.93 E-value=13 Score=29.20 Aligned_cols=56 Identities=20% Similarity=0.239 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHh
Q psy9417 93 YKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFG 149 (161)
Q Consensus 93 ~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~ 149 (161)
.+..+..|.+.++.-.|.-=|-+|-++|++++|.|+++. .-+=...|...|.+++.
T Consensus 36 ~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh-~evas~~Fl~el~kl~~ 91 (139)
T cd03567 36 PQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFH-SEVGKFRFLNELIKLVS 91 (139)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHH-HHHHhHHHHHHHHHHhc
Confidence 556777788888877788889999999999999998754 11112345555555553
No 23
>KOG2669|consensus
Probab=57.99 E-value=75 Score=28.74 Aligned_cols=88 Identities=18% Similarity=0.144 Sum_probs=57.7
Q ss_pred hhHHHHHHHHhhhh---HHHHHHHHHHHHhccCCCCCchHHHHHhhHH-------------------HhhhhhcCCCCCc
Q psy9417 18 TGIVKLALKATHYY---KYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQ-------------------ELLSINSTKPPIS 75 (161)
Q Consensus 18 ~~it~~a~~~~~~~---k~vv~~vek~i~k~~~~~~~~~lyvIDef~~-------------------eL~sL~~~k~~iS 75 (161)
++|+..+.--|.++ .-||+.-++-..+-...-|+++||++.+.++ .+.+.....+.--
T Consensus 21 eSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk~~ef~~ef~~v~~~a~~~i~~~~~~~~ 100 (325)
T KOG2669|consen 21 ESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRKGPEFVDEFWPVVLKAFAHIVEETDVKC 100 (325)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhcCchhHHHHHHHHHHHHHHHHHhcchhh
Confidence 45555555555554 5589999999999999999999999876222 2233333322111
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Q psy9417 76 KAKITGIVKLALKATHYYKYVVQSVEKFIW 105 (161)
Q Consensus 76 rskI~~LT~lA~enik~~k~IV~~Ie~~I~ 105 (161)
+..|..|.++..+=--|-+.++..++.-+.
T Consensus 101 k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~ 130 (325)
T KOG2669|consen 101 KKKLGRLINIWEERNVFSPESLVDLEESLG 130 (325)
T ss_pred hHHHHHHHHHHHHhccCCHHHHHHHHHHhc
Confidence 488899999988844455555566666555
No 24
>PF12309 KBP_C: KIF-1 binding protein C terminal; InterPro: IPR022083 This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 365 and 621 amino acids in length. There is a conserved LLP sequence motif. KBP is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein.
Probab=48.16 E-value=31 Score=31.15 Aligned_cols=87 Identities=26% Similarity=0.336 Sum_probs=57.4
Q ss_pred CCCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCC-CCCchHHHHHhhHHHhhhhhcC-------CCCCcHHHH
Q psy9417 8 TKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQ-YKLPGLYVIGEWNQELLSINST-------KPPISKAKI 79 (161)
Q Consensus 8 ~~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~-~~~~~lyvIDef~~eL~sL~~~-------k~~iSrskI 79 (161)
..+|.+. .+..|...+.+||++|.+.+++.+ .|+ -++|.-.-.|++..-|.+.... -++..+.++
T Consensus 250 ~~~~~~~-~~~kin~l~~~ai~~y~~fl~s~~------~~~~~~~~~~~~~d~~~~~l~a~f~~arl~~K~~~~~~~~~~ 322 (371)
T PF12309_consen 250 NEPPDDH-ALKKINQLCSKAIKYYQKFLDSYK------SPDSGKLPEKLDEDELRPYLYAYFHIARLYSKLITSDPKEQL 322 (371)
T ss_pred CCCCChH-HHHHHHHHHHHHHHHHHHHHHHHc------CCccccCCCCCcHHHHHHHHHHHHHHHHHHccccCCChHHHH
Confidence 3444444 466689999999999999999988 566 6777776556655544333221 124555566
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHh
Q psy9417 80 TGIVKLALKATHYYKYVVQSVEKFIW 105 (161)
Q Consensus 80 ~~LT~lA~enik~~k~IV~~Ie~~I~ 105 (161)
..|+. ...+|+.||+..++|-.
T Consensus 323 ~~l~~----sl~~y~~vv~y~~~~~~ 344 (371)
T PF12309_consen 323 ENLEK----SLEYYKWVVDYCEKHPE 344 (371)
T ss_pred HHHHH----HHHHHHHHHHHHHhChh
Confidence 66553 56789999987777654
No 25
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=47.16 E-value=28 Score=27.05 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHhh-cCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417 79 ITGIVKLALKATHYYKYVVQSVEKFIWK-CKSQYKLPGLYVIDAIIHQARLQFK 131 (161)
Q Consensus 79 I~~LT~lA~enik~~k~IV~~Ie~~I~k-~~p~~KL~~LYVIDSIvRn~~~~~~ 131 (161)
|-.+.+.--..-...+..+.+|.+.++. ..|..=+-+|-++|++++|.|+.+.
T Consensus 22 ileicD~In~~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh 75 (141)
T cd03565 22 NMEICDIINETEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFH 75 (141)
T ss_pred HHHHHHHHhCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHH
Confidence 4444444433334577888899999964 2344457789999999999997744
No 26
>KOG2221|consensus
Probab=46.29 E-value=27 Score=30.69 Aligned_cols=51 Identities=24% Similarity=0.248 Sum_probs=34.6
Q ss_pred HHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhhc
Q psy9417 15 AKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINS 69 (161)
Q Consensus 15 ~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~ 69 (161)
++|...----|+|-+.+--.||+.||+ .|.|.++||.+|..=-..|.+|.-
T Consensus 192 apiaa~llmhmp~rdaf~~~vqiceky----lqgy~~sgleaiq~dg~il~~Llk 242 (267)
T KOG2221|consen 192 APIAAVLLMHMPARDAFWCFVQICEKY----LQGYYSSGLEAIQNDGGILEGLLK 242 (267)
T ss_pred chHHHHHHhcccHHHHHHHHHHHHHHH----cccccccchhhhhcccHHHHHHHH
Confidence 444444444455555455556666665 589999999999988888887764
No 27
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=42.43 E-value=2.6e+02 Score=25.25 Aligned_cols=117 Identities=15% Similarity=0.154 Sum_probs=59.1
Q ss_pred HHHhhhhHHHHHHH---HHHHHhccCCCCCchHHHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHH-hhHHHHHHHHHH
Q psy9417 25 LKATHYYKYVVQSV---EKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALK-ATHYYKYVVQSV 100 (161)
Q Consensus 25 ~~~~~~~k~vv~~v---ek~i~k~~~~~~~~~lyvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~e-nik~~k~IV~~I 100 (161)
|.+.+...=.|.+| +..+.+..-.-=++-|.+|.++..-.+... |=++|+.|..--.. --+....|..-.
T Consensus 108 IT~LkrL~MLv~a~~qL~~~~~~r~Y~e~a~~L~av~~L~~~F~~yk------si~~I~~L~~~i~~l~~~L~~qI~~df 181 (383)
T PF04100_consen 108 ITTLKRLQMLVTAVEQLKELAKKRQYKEIASLLQAVKELLEHFKPYK------SIPQIAELSKRIDQLQNELKEQIFEDF 181 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHccc------CcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444 555554332222333445554443333332 33566666544332 122355666666
Q ss_pred HHHHhhcC-------CCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhhhhc
Q psy9417 101 EKFIWKCK-------SQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQ 153 (161)
Q Consensus 101 e~~I~k~~-------p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~~~~ 153 (161)
+..+..-. ...--.+..|+|++-..+++. ....|......-+..+|.
T Consensus 182 ~~~f~~~~~~~~~~~~~~l~~aC~vvd~L~~~~r~~------li~wf~~~qL~eY~~iF~ 235 (383)
T PF04100_consen 182 EELFGSQGDESPGQSSQQLSDACLVVDALGPDVREE------LIDWFCNKQLKEYRRIFR 235 (383)
T ss_pred HHHhccCCcccccchHhHHHHHHHHHHHcCchHHHH------HHHHHHHHHHHHHHHHHc
Confidence 66551111 233447889999998888766 335555555555555553
No 28
>KOG1087|consensus
Probab=42.09 E-value=31 Score=32.51 Aligned_cols=51 Identities=18% Similarity=0.184 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhh
Q psy9417 80 TGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQF 130 (161)
Q Consensus 80 ~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~ 130 (161)
-.|.++.=......+.+|..|.+.|...-|.--+-+|+|+|-+|+|.|+.|
T Consensus 23 leIcD~IN~~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~f 73 (470)
T KOG1087|consen 23 LEICDLINSTEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSF 73 (470)
T ss_pred HHHHHHHhcCccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHH
Confidence 333333333334466889999999999999999999999999999999763
No 29
>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=38.52 E-value=98 Score=23.37 Aligned_cols=56 Identities=16% Similarity=0.068 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHH
Q psy9417 32 KYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALK 88 (161)
Q Consensus 32 k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~~k~~iSrskI~~LT~lA~e 88 (161)
+-+++.+.|.|+...|.--+.+|.++|....--......- ..|+.....|.+++..
T Consensus 36 k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~-i~s~~fl~~l~~l~~~ 91 (133)
T cd03561 36 KEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQ-VADKEFLLELVKIAKN 91 (133)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHH-HhhHHHHHHHHHHhCC
Confidence 3445556677777777777777777777666443321110 2344555555555543
No 30
>PF08767 CRM1_C: CRM1 C terminal; InterPro: IPR014877 CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat []. ; PDB: 3M1I_C 3GB8_A 1W9C_A 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D.
Probab=35.02 E-value=2.7e+02 Score=24.31 Aligned_cols=25 Identities=16% Similarity=0.143 Sum_probs=17.5
Q ss_pred hhcCCCCcch-hHHHHHHHHHHHhhh
Q psy9417 105 WKCKSQYKLP-GLYVIDAIIHQARLQ 129 (161)
Q Consensus 105 ~k~~p~~KL~-~LYVIDSIvRn~~~~ 129 (161)
+++.|..|-| +|.++-+||++.++.
T Consensus 81 ~~~~p~~r~~evL~l~~~ii~kl~~~ 106 (319)
T PF08767_consen 81 QNSVPDAREPEVLSLMATIINKLGEL 106 (319)
T ss_dssp HHS-GGGS-HHHHHHHHHHHHHHGGG
T ss_pred hcCCccccChhHHHHHHHHHHHHHHh
Confidence 4577777776 578888888888764
No 31
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=34.91 E-value=3.3e+02 Score=24.29 Aligned_cols=121 Identities=17% Similarity=0.205 Sum_probs=79.6
Q ss_pred hhHHHHH--HHHHHHHhccCCCCCchHHHHHhhHHHhhhhhcC-CCCCcHHHHHH-HHHHHHHhhHHHHHHHHHHHHHHh
Q psy9417 30 YYKYVVQ--SVEKFIWKCKSQYKLPGLYVIGEWNQELLSINST-KPPISKAKITG-IVKLALKATHYYKYVVQSVEKFIW 105 (161)
Q Consensus 30 ~~k~vv~--~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~~-k~~iSrskI~~-LT~lA~enik~~k~IV~~Ie~~I~ 105 (161)
.|+.||| .||..+..=.-+|+-..+|.+- |+..++.|... .|.--+..|-+ |...-.++.+.|....+.++.+.+
T Consensus 76 iYrrvvdELLVElHLLs~n~~F~yDplFALG-lVtvfd~fm~GY~Pee~~~~IF~Alc~a~g~Dp~qyr~dA~~l~~~A~ 154 (283)
T PLN00047 76 IYSTVLQELLVQQHLMRYKKTYRYDPVFALG-FVTVYDQLMEGYPSDEDRDAIFKAYIKALGEDPEQYRKDAAKLEEWAR 154 (283)
T ss_pred HHHHHHHHHHHHHHHHHhccCceeCchhhhh-hHHHHHHHHccCCChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh
Confidence 4788888 5899999999999988888653 45555555543 34555666644 333334477888888888888887
Q ss_pred hcCCCCcchhHH---HHHHHHHHHhhh--hcccCccHHhhHHHHHHHHhhh
Q psy9417 106 KCKSQYKLPGLY---VIDAIIHQARLQ--FKYKDVYAPRFARNLYRTFGYV 151 (161)
Q Consensus 106 k~~p~~KL~~LY---VIDSIvRn~~~~--~~~kd~Y~~rF~~nl~~tf~~~ 151 (161)
...++.=+..+. .++++..+.-.. -+++-.|-+.|+.-|+.+++.+
T Consensus 155 ~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YSRlfAIGLf~LLe~a 205 (283)
T PLN00047 155 SQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYSRFFAIGLFRLLELA 205 (283)
T ss_pred cCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHhc
Confidence 666554333332 244544453211 2245579999999999988764
No 32
>KOG1818|consensus
Probab=34.58 E-value=61 Score=31.81 Aligned_cols=72 Identities=14% Similarity=0.074 Sum_probs=54.7
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhhhhcCC
Q psy9417 79 ITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCP 155 (161)
Q Consensus 79 I~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~~~~c~ 155 (161)
|-.++.+-..-.--.|.-++.+++.|..+.|.-+++.|=+.|.-|||.|+. +...-+.+....+|.++++|+
T Consensus 29 ~~e~~d~ir~~~~~~k~slr~~~~~i~h~np~~~~~~~~~~d~cvkn~G~g-----v~~ei~tre~m~~~~~~l~~~ 100 (634)
T KOG1818|consen 29 ILEISDMIRSGGVPPKPSLRGIKKRIDHENPNVQLFTLKLTDHCVKNCGHG-----VHCEIATREFMDLLKSLLESQ 100 (634)
T ss_pred hhhHHHHHHhcCCCCchhHHHHHHHHhccCCCcccchhhhHHHHHhcCCcc-----hhHHHHHHHHHHHHHhhhccc
Confidence 333344333322335566788889999999999999999999999999984 566777788888888888877
No 33
>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=30.22 E-value=1.8e+02 Score=22.54 Aligned_cols=53 Identities=8% Similarity=0.108 Sum_probs=24.7
Q ss_pred cHHHHHHHHHHHHHhh--HHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHh
Q psy9417 75 SKAKITGIVKLALKAT--HYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQAR 127 (161)
Q Consensus 75 SrskI~~LT~lA~eni--k~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~ 127 (161)
|+..++.|.+++..+. +=-+.+...|..+-..-+.+.+++.++-+=.-.|+-|
T Consensus 82 s~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~f~~~~~l~~i~~~y~~L~~~G 136 (142)
T cd03569 82 SREFMDELKDLIKTTKNEEVRQKILELIQAWALAFRNKPQLKYVVDTYQILKAEG 136 (142)
T ss_pred hHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHcC
Confidence 4444444444443311 1123455555555555555555555555444444444
No 34
>PF14747 DUF4473: Domain of unknown function (DUF4473)
Probab=27.76 E-value=1.5e+02 Score=21.00 Aligned_cols=49 Identities=31% Similarity=0.344 Sum_probs=33.6
Q ss_pred HhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHH----------HH----HHHHHHHHHhhcCCCC
Q psy9417 58 GEWNQELLSINSTKPPISKAKITGIVKLALKATHYY----------KY----VVQSVEKFIWKCKSQY 111 (161)
Q Consensus 58 Def~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~----------k~----IV~~Ie~~I~k~~p~~ 111 (161)
++..++|.+ .|+|..-|..|++++.+.-..+ +. +..-++.||+..+++.
T Consensus 9 ee~kaEL~a-----AGmS~~aidgi~~i~~~~~~~~~~~~~~~e~~~~~~~~~~~e~~~fikt~s~~D 71 (82)
T PF14747_consen 9 EEAKAELVA-----AGMSEKAIDGIVKIAEKFKSQFAKAKGNKEAAKKFFEKYKAEVDAFIKTQSEED 71 (82)
T ss_pred HHHHHHHHH-----cCCCHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHCCHHH
Confidence 444555544 3899999999999999854443 33 3346678888877654
No 35
>KOG1829|consensus
Probab=26.77 E-value=1.4e+02 Score=28.99 Aligned_cols=70 Identities=16% Similarity=0.188 Sum_probs=47.4
Q ss_pred HHHHHhhhhHHHHHHHHHHHHhccCC--CCCchHHHHHhhHHH------hhhhhcCCCCCcHHHHHHHHHHHHHhhHH
Q psy9417 23 LALKATHYYKYVVQSVEKFIWKCKSQ--YKLPGLYVIGEWNQE------LLSINSTKPPISKAKITGIVKLALKATHY 92 (161)
Q Consensus 23 ~a~~~~~~~k~vv~~vek~i~k~~~~--~~~~~lyvIDef~~e------L~sL~~~k~~iSrskI~~LT~lA~enik~ 92 (161)
.|+.+++.-.--.+.+|.|+.-|... -.++...++..+..+ |.+|.+..++.=-..++.+++.+.++|.+
T Consensus 426 ~~L~~v~~lR~qL~~m~~~l~~Cr~a~~~~~~~~~~~~~yL~e~~~~~Sl~DL~~i~~g~L~~~l~~~~k~~~~HV~~ 503 (580)
T KOG1829|consen 426 KALAEVKELRQQLQHIEGYLKTCRFASLKLLRQRLAVRRYLTESPHLFSLKDLQDIQDGALLRLLNELTKLSSKHVKE 503 (580)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcchhhhhhhhhhhhhhhccCchhhhhhhHHHhhcccHHHHHHHHHHHhhhhhhh
Confidence 35555555555678899999999988 567777777776653 33444434455556777777777777665
No 36
>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. They do show distant similarity to NTPases and to nucleic acid binding enzymes.
Probab=24.70 E-value=1.6e+02 Score=24.90 Aligned_cols=46 Identities=17% Similarity=0.151 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhhcCCCCCcHHH
Q psy9417 32 KYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAK 78 (161)
Q Consensus 32 k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~~~k~~iSrsk 78 (161)
|++=+.+|++|++=-+ -+.+..++-+-|...++......|.+|+.-
T Consensus 127 k~~K~ia~~~lkk~~~-~k~~l~~i~~i~~~i~~~~a~~tpsvS~~~ 172 (194)
T PF09894_consen 127 KFTKEIANKELKKYWK-PKMSLKDIENIFEKIMEEVASKTPSVSKEY 172 (194)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHHHhhcCCCccCcE
Confidence 5667889999999888 778888899999999988877777787753
No 37
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=24.66 E-value=4.3e+02 Score=22.32 Aligned_cols=137 Identities=8% Similarity=0.080 Sum_probs=62.0
Q ss_pred CCCchHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhhh-cCCCCCc---HHHHHHHHH
Q psy9417 9 KPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSIN-STKPPIS---KAKITGIVK 84 (161)
Q Consensus 9 ~~~~s~~~~~~it~~a~~~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL~-~~k~~iS---rskI~~LT~ 84 (161)
-..++++-...|.+....-...-|-++.-+|.+...|..+---....=...-..+..+.- +.-.-.| +..+.....
T Consensus 113 l~~lp~~n~~av~~~~~~~~~lvkDa~~El~E~~~~~~~~~~~d~~~d~~~~ddd~~~~~~~~d~~~seee~~~~~~~~~ 192 (275)
T PF13324_consen 113 LKKLPKDNKVAVLRRLKQSRDLVKDALEELEEWDEEPSLDDSEDEFSDEEDDDDDEDDDDFGDDEDLSEEEMELAKAVLG 192 (275)
T ss_dssp TTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--------------------------TTS--HHHHHHHHHHHH
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCccccccccccccccccccccccCCHHHHHHHHHHHH
Confidence 344555555667776666677777888888888888822211111100000001110100 0000122 233444444
Q ss_pred HHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCccHHhhHHHHHHHHhhhhcCCCcc
Q psy9417 85 LALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDED 158 (161)
Q Consensus 85 lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~Y~~rF~~nl~~tf~~~~~c~~~d 158 (161)
+.......-+.++..|.+..+.-.|..+-...=-+|+++...+ .++..+..+-..+| ||.|
T Consensus 193 l~~~~~~~lk~~~~~i~~~~k~~~~~~~~~~v~~Ld~L~~~~~-----------~i~~~VDel~~slY--pP~d 253 (275)
T PF13324_consen 193 LLKASLAVLKKLLRAITKLLKSEKPSDSPEQVAQLDKLLDLCQ-----------EISPSVDELASSLY--PPQD 253 (275)
T ss_dssp HHHHHHHHHHHHHHHHHHH---------TT-HHHHHHHHHHHH-----------HHHHHHHHHHHHHS--SS--
T ss_pred HHHHHHHHHHHHHHHHHhcccccccccChhhHHHHHHHHHHHH-----------HhhhHHHHHHHHhc--CCCC
Confidence 4444444455555555555544446666666777898888874 47788888888888 5443
No 38
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=23.28 E-value=78 Score=23.34 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhc
Q psy9417 92 YYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK 131 (161)
Q Consensus 92 ~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~ 131 (161)
.-..+-.+|++-+.+|.|.+|-.+-=||+-+.++.-+.|.
T Consensus 40 lK~~ipeal~t~C~KCt~kQK~~~~kv~~~l~~~~P~~w~ 79 (95)
T PF03392_consen 40 LKKVIPEALKTNCAKCTPKQKENARKVIKFLKKNYPDEWE 79 (95)
T ss_dssp HHHHHHHHHHCTTTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccccCCCHHHHHHHHHHHHHHHHcCHHHHH
Confidence 3446677888889999999999999999998888766543
No 39
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 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 N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=23.21 E-value=3.2e+02 Score=24.21 Aligned_cols=91 Identities=13% Similarity=0.099 Sum_probs=0.0
Q ss_pred HHHhhHHHhhhhhcCCCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHhhhhcccCc
Q psy9417 56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDV 135 (161)
Q Consensus 56 vIDef~~eL~sL~~~k~~iSrskI~~LT~lA~enik~~k~IV~~Ie~~I~k~~p~~KL~~LYVIDSIvRn~~~~~~~kd~ 135 (161)
+++++...+.+..+.. +.+.-|..|..+|.++...++..++.+.+.+....+...--.+..+-.++++....
T Consensus 340 Il~eL~~~l~~~~d~~--~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~~~~~~~~~~~~~i~~ll~~~~~~------ 411 (526)
T PF01602_consen 340 ILDELLKYLSELSDPD--FRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEISGDYVSNEIINVIRDLLSNNPEL------ 411 (526)
T ss_dssp HHHHHHHHHHHC--HH--HHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHCTGGGCHCHHHHHHHHHHHHSTTT------
T ss_pred HHHHHHHHHHhccchh--hhhhHHHHHHHHHhccCchHHHHHHHHHHhhhhccccccchHHHHHHHHhhcChhh------
Q ss_pred cHHhhHHHHHHHHhhhhcCCCcc
Q psy9417 136 YAPRFARNLYRTFGYVFQCPDED 158 (161)
Q Consensus 136 Y~~rF~~nl~~tf~~~~~c~~~d 158 (161)
...-+..++..+..+...+
T Consensus 412 ----~~~~l~~L~~~l~~~~~~~ 430 (526)
T PF01602_consen 412 ----REKILKKLIELLEDISSPE 430 (526)
T ss_dssp ----HHHHHHHHHHHHTSSSSHH
T ss_pred ----hHHHHHHHHHHHHHhhHHH
No 40
>KOG2148|consensus
Probab=20.60 E-value=86 Score=31.53 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=29.5
Q ss_pred HhhhhHHHHHHHHHHHHhccCCCCCchHHHHHhhHHHhhhh
Q psy9417 27 ATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSI 67 (161)
Q Consensus 27 ~~~~~k~vv~~vek~i~k~~~~~~~~~lyvIDef~~eL~sL 67 (161)
-|++|+| .|++|.||-|--++|+-.-|+++.+-.+++
T Consensus 827 Fi~qy~~----f~~lIakcYpgs~v~le~~iq~iLaffS~I 863 (867)
T KOG2148|consen 827 FIDQYES----FEQLIAKCYPGSNVPLEFEIQDILAFFSEI 863 (867)
T ss_pred HHHHHHH----HHHHHHHhcCCCCCceeeeHHHHHHHHHHH
Confidence 4677776 478999999999999999888876655554
No 41
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=20.31 E-value=58 Score=25.27 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=10.3
Q ss_pred hhHHHHHHHHhh
Q psy9417 18 TGIVKLALKATH 29 (161)
Q Consensus 18 ~~it~~a~~~~~ 29 (161)
+|.||||.+|++
T Consensus 16 qD~TkAA~RAv~ 27 (113)
T PF09585_consen 16 QDYTKAAVRAVR 27 (113)
T ss_pred CcHHHHHHHHHH
Confidence 589999999975
Done!