Query psy5853
Match_columns 217
No_of_seqs 159 out of 651
Neff 7.4
Searched_HMMs 29240
Date Fri Aug 16 19:45:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5853.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/5853hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2efe_A Similarity to vacuolar 100.0 7.4E-50 2.5E-54 343.1 19.9 206 7-216 31-245 (267)
2 2ot3_A RAB5 GDP/GTP exchange f 100.0 2.5E-46 8.6E-51 322.2 18.4 204 7-216 37-249 (274)
3 2jxc_B Stonin-2, stoned B; end 61.2 2.3 7.9E-05 25.2 0.6 16 2-17 28-43 (45)
4 3tl4_X Glutaminyl-tRNA synthet 43.2 67 0.0023 25.2 6.6 64 144-212 33-97 (187)
5 2cos_A Serine/threonine protei 28.1 30 0.001 21.7 1.7 15 203-217 38-52 (54)
6 2bn5_B U1 small nuclear ribonu 23.7 28 0.00096 17.9 0.9 7 2-8 12-18 (26)
7 1a0a_A BHLH, protein (phosphat 20.4 44 0.0015 21.3 1.5 16 200-215 44-59 (63)
8 2es9_A Putative cytoplasmic pr 19.7 1.9E+02 0.0066 20.2 4.8 45 114-161 12-57 (115)
9 3iq2_A Sorting nexin-7; SNX7, 17.1 71 0.0024 23.3 2.3 42 2-45 70-113 (138)
10 3ggz_E Vacuolar protein-sortin 15.0 93 0.0032 16.8 1.7 17 77-93 12-28 (29)
No 1
>2efe_A Similarity to vacuolar protein sorting-associated VPS9; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_A 2efc_A* 2efh_A*
Probab=100.00 E-value=7.4e-50 Score=343.15 Aligned_cols=206 Identities=29% Similarity=0.479 Sum_probs=189.8
Q ss_pred CcccccccccCCCCcHHHHHHHHHHhhHh--HhhcCcccCCCCHHHHHHHHHHHHHHHHHHhHHhhcCCCCCCCchhhHH
Q psy5853 7 IKPDISNVTGQGGGTAEYRRRTYEFVDNN--RRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQV 84 (217)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~--~~~~~~~~~~~~~~~~~~~~~~lE~~V~~~iy~~if~~~~~~~~~~D~~ 84 (217)
|++++.+|.+.....++.++.+++|++.+ .+..|+.|+++++++++.+++++|||||++||+++|++... +.++|..
T Consensus 31 i~~Fi~~f~~~~~~~~e~~~~v~~f~~~~~~~l~~~~~~~~~~~~~~~~~~e~iEk~v~~~ly~~lf~~~~~-d~~~D~~ 109 (267)
T 2efe_A 31 IKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTE-EVIADEK 109 (267)
T ss_dssp HHHHHHTTTTSCCCHHHHHHHHHHHHHHHHHHHHSCGGGTTCCHHHHHHHHHHHHHHHHHHHHHHHSSCSHH-HHHHHHH
T ss_pred HHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHcCCchh-hHHHHHH
Confidence 56777888888888899999999999975 78899999999999999999999999999999999998753 7889999
Q ss_pred HHHHHHHh-hcccCCCCcccccCCCCCCCCChHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhc-----CCCCCCc
Q psy5853 85 LHEHVKNL-AKIITPNHKYLRIPKMFHSECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSL-----TSAVPAA 158 (217)
Q Consensus 85 l~~~i~~L-~~~i~p~~l~l~I~~~~~~~~~~~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~~-----~~~~~~A 158 (217)
|++||+.| +++ +|+| ||||+.+..+.+|..|+++|++|+.++||+|||.||++||+.|++.++. .+.++||
T Consensus 110 L~~ki~~l~~~i-~~~~--L~I~~~~~~~~~~~~A~~eL~ki~~~~sP~dKl~~l~~~~k~I~~~l~~~~~~~~~~~~~A 186 (267)
T 2efe_A 110 LFQKMSLVQQFI-SPEN--LDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGA 186 (267)
T ss_dssp HHHHHHHHTTTC-CGGG--GTCCGGGCCTTCSHHHHHHHHTGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCH
T ss_pred HHHHHHHHHccC-CHHH--cCCCCccCCcccHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHhhccccccCCCCh
Confidence 99999999 576 9998 7889888888899999999999999999999999999999999998863 2378999
Q ss_pred hhhhHHHHHHHHhcCCCChhhHHHHHHhhcc-CccCChhHHHHHHHHHHHHHHhccCCC
Q psy5853 159 DDLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NKMEGEIQYWWVQFCSAIEFIKTMDYK 216 (217)
Q Consensus 159 Dd~LPiliyviika~~~~l~s~i~yI~~f~~-~~~~gE~~Y~lt~l~aAv~fI~~l~~~ 216 (217)
|||||+||||||||+||+|+||++||++|++ +.+.||.|||||||+||++||++++.+
T Consensus 187 Dd~LP~Liyvvika~~~~L~s~l~yI~~f~~~~~l~gE~gY~lt~l~aA~~fI~~l~~~ 245 (267)
T 2efe_A 187 DEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAK 245 (267)
T ss_dssp HHHHHHHHHHHHHHCCTTHHHHHHHHHHHSCTTTSCHHHHHHHHHHHHHHHHHHTCCTT
T ss_pred hHHHHHHHHHHHhcCcccHHHHHHHHHHHcCccccCCHHHHHHHHHHHHHHHHHhCCHh
Confidence 9999999999999999999999999999996 677999999999999999999999976
No 2
>2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular traffic, protein transport; 2.10A {Homo sapiens} SCOP: a.222.1.1 PDB: 1txu_A
Probab=100.00 E-value=2.5e-46 Score=322.19 Aligned_cols=204 Identities=25% Similarity=0.456 Sum_probs=180.8
Q ss_pred Cccccccccc-CCCCcHHHHHHHHHHhhHh--HhhcCcccCCCCHHHHHHHHHHHHHHHHHHhHHhhcCCCCCCCchhhH
Q psy5853 7 IKPDISNVTG-QGGGTAEYRRRTYEFVDNN--RRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQ 83 (217)
Q Consensus 7 ~~~~~~~~~~-~~~~~~~~~~~~~~f~~~~--~~~~~~~~~~~~~~~~~~~~~~lE~~V~~~iy~~if~~~~~~~~~~D~ 83 (217)
|++|+.+|.+ +....++.++.+++|+... ++..+ |+. ++++++.+++++|+|||++||+.+|++..+.+..+|.
T Consensus 37 i~sFi~~f~~~~~~~~~e~~~~v~~f~~~~~~~l~~~--~~~-s~~~~~~~~~~iEk~v~~~ly~~lf~~~~~~~~~~D~ 113 (274)
T 2ot3_A 37 TKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTR--GKV-PPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDL 113 (274)
T ss_dssp HHHHHHHHHTTTTSCHHHHHHHHHHHHHHHHHHHHST--TCC-CHHHHHHHHHHHHHHHHHHHHHHHSSCTTSSHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHH--hcc-CHHHHHHHHHHHHHHHHHHHHHHHcCCchhhhHHHHH
Confidence 5778888875 4678899999999999875 56555 886 6789999999999999999999999998877889999
Q ss_pred HHHHHHHHhhcccCCCCcccccCCCCCC---CCChHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhcCC-CCCCch
Q psy5853 84 VLHEHVKNLAKIITPNHKYLRIPKMFHS---ECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS-AVPAAD 159 (217)
Q Consensus 84 ~l~~~i~~L~~~i~p~~l~l~I~~~~~~---~~~~~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~~~~-~~~~AD 159 (217)
.|+++|+.|+++ +|+| ||||..... ...|..|+++|++|+.++||+|||.||++||+.|++.++.++ .++|||
T Consensus 114 ~l~~ki~~L~~i-~~~~--L~I~~~~~~p~~~~~~~~A~~eL~~i~~~~sP~dKL~~l~~~~k~I~~~l~~~~~~~~~AD 190 (274)
T 2ot3_A 114 AIQKRIRALRWV-TPQM--LCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASAD 190 (274)
T ss_dssp HHHHHHHHTTTC-CTTT--TTCCCCTTSHHHHHHHHHHHHHHHHGGGCCSHHHHHHHHHHHHHHHHHHHHHHHSSCBCHH
T ss_pred HHHHHHHHHcCC-CHHH--cCCCcccCCchHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHHhcCCCCCCHH
Confidence 999999999998 9999 556654421 135899999999999999999999999999999999997654 689999
Q ss_pred hhhHHHHHHHHhcCCCChhhHHHHHHhhcc-Cc-cCChhHHHHHHHHHHHHHHhccCCC
Q psy5853 160 DLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NK-MEGEIQYWWVQFCSAIEFIKTMDYK 216 (217)
Q Consensus 160 d~LPiliyviika~~~~l~s~i~yI~~f~~-~~-~~gE~~Y~lt~l~aAv~fI~~l~~~ 216 (217)
||||+||||||||+||+|+||++||++|++ +. +.||.|||||||+||++||++++.+
T Consensus 191 d~LP~Liyvvika~~~~l~s~l~yI~~F~~~~~l~~GE~gY~lttl~aAv~fI~~l~~~ 249 (274)
T 2ot3_A 191 DFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQ 249 (274)
T ss_dssp HHHHHHHHHHHHHCCTTHHHHHHHHHHHSCTTTTTSSHHHHHHHHHHHHHHHHHHCCTG
T ss_pred HHHHHHHHHHHHcCcchHHHHHHHHHHHcCcccccCCHHHHHHHHHHHHHHHHHhCCHH
Confidence 999999999999999999999999999997 44 4899999999999999999999875
No 3
>2jxc_B Stonin-2, stoned B; endocytosis, calcium, chromosomal rearrangement, cytoplasm, membrane, phosphorylation, polymorphism, proto-oncogene; NMR {Homo sapiens}
Probab=61.25 E-value=2.3 Score=25.21 Aligned_cols=16 Identities=38% Similarity=0.488 Sum_probs=12.3
Q ss_pred CCCCCCcccccccccC
Q psy5853 2 VLPPPIKPDISNVTGQ 17 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~ 17 (217)
|+||||-++=.-|+.+
T Consensus 28 vqPSPINPFsafFeE~ 43 (45)
T 2jxc_B 28 VQPSPINPFSAFFEEQ 43 (45)
T ss_dssp CCCCTTCSCTTHHHHC
T ss_pred CCCCCCChHHHhhhhh
Confidence 7999999886666544
No 4
>3tl4_X Glutaminyl-tRNA synthetase; glutamine, appended domain, hinge, tRNA LIG amidotransferase, ligase; 2.30A {Saccharomyces cerevisiae}
Probab=43.22 E-value=67 Score=25.21 Aligned_cols=64 Identities=14% Similarity=0.130 Sum_probs=42.1
Q ss_pred HHHHHhhcCCCCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhc-cCccCChhHHHHHHHHHHHHHHhc
Q psy5853 144 TILNLLSLTSAVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFY-ANKMEGEIQYWWVQFCSAIEFIKT 212 (217)
Q Consensus 144 ~I~~~i~~~~~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~-~~~~~gE~~Y~lt~l~aAv~fI~~ 212 (217)
.+...+...+...+.|.=.-.|+|.+...-++.-..+..|+-+|. ++++.+.. ++.+|+.|+..
T Consensus 33 ~L~~~i~ea~~~~~~dk~~g~LLy~latk~k~~~~~~r~~l~~~I~~gklkt~~-----Qv~AAl~yl~~ 97 (187)
T 3tl4_X 33 SLYKLIKETPSDYQWNKSTRALVHNLASFVKGTDLPKSELIVNGIINGDLKTSL-----QVDAAFKYVKA 97 (187)
T ss_dssp HHHHHHHTSCTTCCCCHHHHHHHHHHHHHHTTCCCTTHHHHHHHHHTTSCCSHH-----HHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCHHHHHHHHHHHHhccCccchhHHHHHHHHHhccCCcHH-----HHHHHHHHHHh
Confidence 334444444334456888888888888654455555667777776 46666544 68899999975
No 5
>2cos_A Serine/threonine protein kinase LATS2; UBA domain, structure genomics, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.5.2.1
Probab=28.12 E-value=30 Score=21.70 Aligned_cols=15 Identities=27% Similarity=0.392 Sum_probs=12.5
Q ss_pred HHHHHHHHhccCCCC
Q psy5853 203 FCSAIEFIKTMDYKE 217 (217)
Q Consensus 203 l~aAv~fI~~l~~~~ 217 (217)
+++|++||..+.+.+
T Consensus 38 le~AmewL~k~~~~~ 52 (54)
T 2cos_A 38 IEAALEYISKMSGPS 52 (54)
T ss_dssp HHHHHHHHHHHSCSC
T ss_pred HHHHHHHHHHhcCCC
Confidence 889999999888753
No 6
>2bn5_B U1 small nuclear ribonucleoprotein 70 kDa; nuclear protein, splicing, protein-protein interaction, structure, proline-rich peptide; NMR {Drosophila melanogaster}
Probab=23.72 E-value=28 Score=17.87 Aligned_cols=7 Identities=71% Similarity=1.227 Sum_probs=5.2
Q ss_pred CCCCCCc
Q psy5853 2 VLPPPIK 8 (217)
Q Consensus 2 ~~~~p~~ 8 (217)
|+|+||-
T Consensus 12 vppppi~ 18 (26)
T 2bn5_B 12 VPPPPIL 18 (26)
T ss_dssp CCCCSCC
T ss_pred CCCCCcc
Confidence 6788874
No 7
>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1
Probab=20.38 E-value=44 Score=21.31 Aligned_cols=16 Identities=13% Similarity=0.206 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHhccCC
Q psy5853 200 WVQFCSAIEFIKTMDY 215 (217)
Q Consensus 200 lt~l~aAv~fI~~l~~ 215 (217)
.+.|+.|++||+.|..
T Consensus 44 a~iL~~Ai~YIk~Lq~ 59 (63)
T 1a0a_A 44 ATTVEAACRYIRHLQQ 59 (63)
T ss_dssp THHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4578899999988753
No 8
>2es9_A Putative cytoplasmic protein; structural genomics, PSI, protein structure initiative, NORT structural genomics consortium, NESG; 2.00A {Salmonella typhimurium} SCOP: a.247.1.1 PDB: 2jn8_A
Probab=19.74 E-value=1.9e+02 Score=20.16 Aligned_cols=45 Identities=16% Similarity=0.106 Sum_probs=36.0
Q ss_pred ChHHHHHHHhcccC-CCCHHHHHHHHHHHHHHHHHHhhcCCCCCCchhh
Q psy5853 114 PWPAAQAEISSISS-YKTAHDKVQCVYRTLNTILNLLSLTSAVPAADDL 161 (217)
Q Consensus 114 ~~~~a~~~L~~i~~-~~sP~dKl~~i~~~~k~I~~~i~~~~~~~~ADd~ 161 (217)
.+++|...+..||. ..+|..+=. .+.|.|+..++..+.+.+|||.
T Consensus 12 vIdKALDFI~~M~tSas~P~sMdE---STAKGifKyL~elGvPas~~dv 57 (115)
T 2es9_A 12 AIEKALDFIGGMNTSASVPHSMDE---STAKGILKYLHDLGVPVSPEVV 57 (115)
T ss_dssp HHHHHHHHHHTSCTTCSSCCHHHH---HHHHHHHHHHHHTTCCCCHHHH
T ss_pred HHHHHHHHhcccccCCCCCCccch---HHHHHHHHHHHHcCCCCCHHHH
Confidence 36889999999984 677766543 6789999999988888999984
No 9
>3iq2_A Sorting nexin-7; SNX7, PHOX, protein signalling, SGC, structur genomics consortium, protein transport, transport; 1.70A {Homo sapiens}
Probab=17.09 E-value=71 Score=23.32 Aligned_cols=42 Identities=12% Similarity=0.099 Sum_probs=18.4
Q ss_pred CCCCCCcccccccccC--CCCcHHHHHHHHHHhhHhHhhcCcccCC
Q psy5853 2 VLPPPIKPDISNVTGQ--GGGTAEYRRRTYEFVDNNRRDYRSGYSD 45 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~--~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 45 (217)
|||-|-|..+.+..+. ..-.++=++.++.||.. +..|+.+++
T Consensus 70 iP~lP~K~~~~~~~~~~~~~fie~Rr~~Le~fL~~--l~~~p~l~~ 113 (138)
T 3iq2_A 70 IPPLPEKFIVKGMVERFNDDFIETRRKALHKFLNR--IADHPTLTF 113 (138)
T ss_dssp CCCCCCCC----CCGGGCHHHHHHHHHHHHHHHHH--HHHSTTGGG
T ss_pred cCCCCcchhhccccccCCHHHHHHHHHHHHHHHHH--HHcCHhhhc
Confidence 5666777665432111 11123334445666643 556666654
No 10
>3ggz_E Vacuolar protein-sorting-associated protein 46; novel MIM binding mode, phosphoprotein, coiled coil, endosome, membrane; 3.80A {Saccharomyces cerevisiae}
Probab=15.00 E-value=93 Score=16.84 Aligned_cols=17 Identities=18% Similarity=0.306 Sum_probs=13.1
Q ss_pred CCchhhHHHHHHHHHhh
Q psy5853 77 GDISRDQVLHEHVKNLA 93 (217)
Q Consensus 77 ~~~~~D~~l~~~i~~L~ 93 (217)
...+++..|.+|++.|+
T Consensus 12 ~~eekEDkLAqRLRALR 28 (29)
T 3ggz_E 12 VDDEKEDKLAQRLRALR 28 (29)
T ss_pred ccchhhHHHHHHHHHHc
Confidence 34567788999999875
Done!