Query 000514
Match_columns 1450
No_of_seqs 54 out of 56
Neff 3.2
Searched_HMMs 29240
Date Tue Mar 26 17:46:40 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000514.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_286-290//hhsearch_pdb/000514hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3r2d_A Protein NUSB, N utiliza 1.0 1 1 21.7 -1.1 117 1181-1333 10-127 (149)
2 1tzv_A NUSB protein, N utiliza 1.0 1 1 18.2 1.8 115 1181-1333 10-126 (142)
3 1lj8_A Mannitol dehydrogenase; 1.0 1 1 15.7 3.5 10 856-865 200-209 (493)
4 1x4p_A Putative splicing facto 1.0 1 1 15.3 -1.7 19 520-538 6-24 (66)
5 3tso_C RAB11 family-interactin 1.0 1 1 15.1 1.2 21 520-540 39-59 (75)
6 1eyv_A NUSB protein, N-utilizi 1.0 1 1 15.1 1.3 84 1214-1333 50-134 (156)
7 3h47_A Ca, capsid protein P24; 1.0 1 1 15.0 -2.4 11 409-419 42-52 (231)
8 2kpa_A ARNO(375-400); hydrolas 1.0 1 1 14.5 0.6 12 324-335 2-13 (26)
9 3gv2_A Ca, fusion protein cons 1.0 1 1 14.3 -1.8 107 204-314 85-221 (342)
10 2pyq_A Uncharacterized protein 1.0 1 1 14.2 3.8 39 282-332 62-103 (114)
No 1
>3r2d_A Protein NUSB, N utilization substance protein B; cross species NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB: 2jr0_A 3r2c_A* 4eya_A
Probab=1.00 E-value=1 Score=21.75 Aligned_cols=117 Identities=16% Similarity=0.132 Sum_probs=65.4
Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 79999983125898888930001003999988999779999999997411564446898888666666688899988778
Q 000514 1181 KLIVRILNVFDLSKIPFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTSQ 1260 (1450)
Q Consensus 1181 kLV~~ILg~Ld~~r~~LSEsF~~y~~~~~~~w~Pd~~Yy~~LI~RLVnnvl~~~~~~~~s~~~~~as~r~~~t~f~a~s~ 1260 (1450)
..+..+|-+.+.....+.+.+..+....+..-..|-.|+.+|+.+.+.+. .. .|.-. .+
T Consensus 10 ~~A~q~L~~~~~~~~~~~~~l~~~~~~~~~~~~~dr~~~~~lv~gvl~~~-~~----------lD~~i----~~------ 68 (149)
T 3r2d_A 10 DTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHI-EE----------IDSII----EK------ 68 (149)
T ss_dssp HHHHHHHHHHHHHCCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTH-HH----------HHHHH----HT------
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-HH----------HHHHH----HH------
T ss_conf 99999999998549999999999997532378899999999999999969-99----------99999----99------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHCCC-CCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 9999988668444347997303655430000001158-989899999998786604874335789986555435
Q 000514 1261 SGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSL-PVSASQIVSSLVQIVVNIQPTLIQTSNGPYGASNSV 1333 (1450)
Q Consensus 1261 ~~P~~fs~~DWRF~EfpNPgs~allvL~tACIELMaL-Pvsp~~Vv~aLIDVV~~~~s~~p~~~~~~~~~iNaI 1333 (1450)
+. .+|.+..++ |...+++ ..++-|++-+ .+|+..++|--|+++-+--. ....+.+|||
T Consensus 69 -----~l-~~w~~~rl~-~~~r~iL--rla~yEl~~~~~iP~~vaInEaVelaK~~~~------~~~~~fVNgV 127 (149)
T 3r2d_A 69 -----HL-KGWSIDRLG-YVERNAL--RLGVAELIFLKSKEPGRVFIDIVDLVKKYAD------EKAGKFVNGV 127 (149)
T ss_dssp -----TC----CGGGSC-HHHHHHH--HHHHHHHTTSCCSCHHHHHHHHHHHHHHHSC------HHHHHHHHHH
T ss_pred -----HH-CCCCCCCCC-HHHHHHH--HHHHHHHHHCCCCCCEEHHHHHHHHHHHHCC------CCCCCCCHHH
T ss_conf -----83-279933158-9999999--9999999986899972129999999987488------8766552497
No 2
>1tzv_A NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A 1tzw_A 1tzx_A*
Probab=1.00 E-value=1 Score=18.18 Aligned_cols=115 Identities=9% Similarity=0.093 Sum_probs=65.9
Q ss_pred HHHHHHHHHCCCCCC-CCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 799999831258988-8893000100399998899977999999999741156444689888866666668889998877
Q 000514 1181 KLIVRILNVFDLSKI-PFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTS 1259 (1450)
Q Consensus 1181 kLV~~ILg~Ld~~r~-~LSEsF~~y~~~~~~~w~Pd~~Yy~~LI~RLVnnvl~~~~~~~~s~~~~~as~r~~~t~f~a~s 1259 (1450)
..+..++-+.+.... ...+....+.. .+ .-..|..|+.+|+.+.+.+. .. .|.-. .+
T Consensus 10 ~~A~~~L~~~~~~~~~~~~~~l~~~~~-~~-l~~~d~~~~~~Lv~gvl~~~-~~----------lD~~I----~~----- 67 (142)
T 1tzv_A 10 LAVFKALFQHEFRRDEDLEQILEEILD-ET-YDKKAKEDARRYIRGIKENL-SM----------IDDLI----SR----- 67 (142)
T ss_dssp HHHHHHHHHHTTCTTSCHHHHHHHHCC-TT-SCHHHHHHHHHHHHHHHHTH-HH----------HHHHH----HT-----
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH-HC-CCHHHHHHHHHHHHHHHHHH-HH----------HHHHH----HH-----
T ss_conf 999999999985599989999999988-55-78889999999999999979-99----------99999----98-----
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHCCCC-CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 899999886684443479973036554300000011589-89899999998786604874335789986555435
Q 000514 1260 QSGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSLP-VSASQIVSSLVQIVVNIQPTLIQTSNGPYGASNSV 1333 (1450)
Q Consensus 1260 ~~~P~~fs~~DWRF~EfpNPgs~allvL~tACIELMaLP-vsp~~Vv~aLIDVV~~~~s~~p~~~~~~~~~iNaI 1333 (1450)
+. .+|.+..++ |.-.+++ ..|+-|++-++ +|+..++|--|+++-+-- ....++.+|||
T Consensus 68 ------~l-~~w~l~rl~-~~~r~iL--rla~yEl~~~~~iP~~vaInEaVelaK~~~------~~~~~~fVNgV 126 (142)
T 1tzv_A 68 ------YL-EKWSLNRLS-VVDRNVL--RLATYELLFEKDIPIEVTIDEAIEIAKRYG------TENSGKFVNGI 126 (142)
T ss_dssp ------TC-SSSCGGGSC-HHHHHHH--HHHHHHHHHCTTSCHHHHHHHHHHHHHHHS------CHHHHHHHHHH
T ss_pred ------HC-CCCCHHHCC-HHHHHHH--HHHHHHHHHCCCCCCHHHHHHHHHHHHHHC------CCCCHHHHHHH
T ss_conf ------72-799967778-9999999--999999986679994048999999999977------88612669999
No 3
>1lj8_A Mannitol dehydrogenase; oxidoreductase, NAD, long-chain dehydrogenase; HET: NAD; 1.70A {Pseudomonas fluorescens} SCOP: a.100.1.9 c.2.1.6 PDB: 1m2w_A*
Probab=1.00 E-value=1 Score=15.69 Aligned_cols=10 Identities=30% Similarity=0.554 Sum_probs=3.5
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q 000514 856 RITVIALAII 865 (1450)
Q Consensus 856 R~LILTLARs 865 (1450)
|..|+.+|+.
T Consensus 200 r~~V~~~a~~ 209 (493)
T 1lj8_A 200 RKALLAFAAL 209 (493)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
T ss_conf 9999999985
No 4
>1x4p_A Putative splicing factor, arginine/serine-rich 14; SURP domain, SFRS14 protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.217.1.1
Probab=1.00 E-value=1 Score=15.27 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=12.0
Q ss_pred CHHHHHHHHHHHHCCCCCC
Q ss_conf 2999999998651169854
Q 000514 520 DFVDFVDKLVSRLQDGDNH 538 (1450)
Q Consensus 520 d~~~fi~~l~~r~~~gd~~ 538 (1450)
+-++.|+||+...++|.+.
T Consensus 6 ~~~~~ieKLa~fVaeGgpe 24 (66)
T 1x4p_A 6 SGVGTIDQLVKRVIEGSLS 24 (66)
T ss_dssp CSSHHHHHHHHHHHHTCSC
T ss_pred HHHHHHHHHHHHHHCCCCC
T ss_conf 6999999999999846974
No 5
>3tso_C RAB11 family-interacting protein 2; RAS GTPase fold (RAB25), vesicle trafficking, endosome, PROT transport; HET: GNP; 1.80A {Homo sapiens} PDB: 2k6s_A
Probab=1.00 E-value=1 Score=15.09 Aligned_cols=21 Identities=29% Similarity=0.640 Sum_probs=8.1
Q ss_pred CHHHHHHHHHHHHCCCCCCCC
Q ss_conf 299999999865116985422
Q 000514 520 DFVDFVDKLVSRLQDGDNHIL 540 (1450)
Q Consensus 520 d~~~fi~~l~~r~~~gd~~~~ 540 (1450)
|++||||.|-.|.-+-.+.|+
T Consensus 39 eLEdYID~LLvRVME~~P~iL 59 (75)
T 3tso_C 39 ELEDYIDNLLVRVMEETPSIL 59 (75)
T ss_dssp HHHHHHHHHHHHHHHHCGGGG
T ss_pred HHHHHHHHHHHHHHHHCCHHH
T ss_conf 999999999999997484886
No 6
>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} SCOP: a.79.1.1
Probab=1.00 E-value=1 Score=15.07 Aligned_cols=84 Identities=18% Similarity=0.193 Sum_probs=56.4
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHH
Q ss_conf 99779999999997411564446898888666666688899988778999998866844434799730365543000000
Q 000514 1214 PPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTSQSGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIE 1293 (1450)
Q Consensus 1214 Pd~~Yy~~LI~RLVnnvl~~~~~~~~s~~~~~as~r~~~t~f~a~s~~~P~~fs~~DWRF~EfpNPgs~allvL~tACIE 1293 (1450)
.+..|+.+|+.+.+.+. .. .|.-. .+ +. .+|.+..++ |.-.+++ ..++-|
T Consensus 50 ~~~~~~~~lv~gvl~~~-~~----------lD~~i----~~-----------~l-~~w~l~rl~-~~~r~iL--rla~ye 99 (156)
T 1eyv_A 50 RLHPYTAAVARGVSEHA-AH----------IDDLI----TA-----------HL-RGWTLDRLP-AVDRAIL--RVSVWE 99 (156)
T ss_dssp CCCHHHHHHHHHHHHTH-HH----------HHHHH----HT-----------TS-TTCCGGGSC-HHHHHHH--HHHHHH
T ss_pred HHHHHHHHHHHHHHHHH-HH----------HHHHH----HH-----------HH-CCCCHHHCC-HHHHHHH--HHHHHH
T ss_conf 79999999999999969-99----------99999----99-----------80-689923379-9999999--999999
Q ss_pred HCCCC-CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 11589-89899999998786604874335789986555435
Q 000514 1294 ILSLP-VSASQIVSSLVQIVVNIQPTLIQTSNGPYGASNSV 1333 (1450)
Q Consensus 1294 LMaLP-vsp~~Vv~aLIDVV~~~~s~~p~~~~~~~~~iNaI 1333 (1450)
++-++ +|+..++|--|+++-+. . ....++.+|||
T Consensus 100 l~~~~~iP~~v~InEaVelak~~-~-----~~~~~~fVNgV 134 (156)
T 1eyv_A 100 LLHAADVPEPVVVDEAVQLAKEL-S-----TDDSPGFVNGV 134 (156)
T ss_dssp HHHCTTSCHHHHHHHHHHHHHHH-S-----CTTHHHHHHHH
T ss_pred HHHCCCCCCHHHHHHHHHHHHHH-C-----CCCCCCCHHHH
T ss_conf 98767999613799999999985-8-----77643136999
No 7
>3h47_A Ca, capsid protein P24; hexamer, engineered disulfide bonds, viral protein; 1.90A {Human immunodeficiency virus type 1} PDB: 3h4e_A 2lf4_A 3mge_A 3p05_A 3p0a_A 3dik_A 3nte_A 1e6j_P
Probab=1.00 E-value=1 Score=14.97 Aligned_cols=11 Identities=27% Similarity=0.220 Sum_probs=3.5
Q ss_pred CCCCCCCHHHH
Q ss_conf 44887650233
Q 000514 409 VLGEPLHGEDL 419 (1450)
Q Consensus 409 ~~ge~l~ge~~ 419 (1450)
+|-|-+.-+|+
T Consensus 42 alse~~tp~D~ 52 (231)
T 3h47_A 42 ALSCGATPQDL 52 (231)
T ss_dssp HHTTTCCHHHH
T ss_pred HHHCCCCHHHH
T ss_conf 86079987999
No 8
>2kpa_A ARNO(375-400); hydrolase; NMR {Synthetic} PDB: 2kpb_A
Probab=1.00 E-value=1 Score=14.54 Aligned_cols=12 Identities=42% Similarity=0.750 Sum_probs=8.2
Q ss_pred CCCCHHHHHHCC
Q ss_conf 654169986202
Q 000514 324 CRVPFYELLRTG 335 (1450)
Q Consensus 324 ~rvpfy~ll~~~ 335 (1450)
.+.|||++|...
T Consensus 2 s~dPFYdml~~R 13 (26)
T 2kpa_A 2 SVDPFYEMLAAR 13 (26)
T ss_dssp CSHHHHHHHTCT
T ss_pred CCCHHHHHHHHH
T ss_conf 856089999999
No 9
>3gv2_A Ca, fusion protein consisting of capsid protein P24, carbon dioxide-concentrating mechanism...; hexameric retroviral capsid; 7.00A {Human immunodeficiency virus type 1}
Probab=1.00 E-value=1 Score=14.30 Aligned_cols=107 Identities=17% Similarity=0.288 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC----CCCCCCCCHHHH-------
Q ss_conf 863333321101356654578777887642212455541122232224678865200----136654408999-------
Q 000514 204 PAQSAIETSVCAAMSPVKSSDVSCTGQQFTTRVNSSVRDNAISSLRQLCCKIILTGL----EFSLKPVTHADI------- 272 (1450)
Q Consensus 204 p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~l~~l~c~i~l~~l----e~~lkp~t~~~i------- 272 (1450)
|.+-| |..-..+-.-+++||.+.+++.-.....-.+...| -.|..+-+-|+.|| .. .+|+.+.+|
T Consensus 85 P~~~g--p~~~gq~r~p~gsdi~G~tst~qeQ~~~~~~~~~~-pvg~iy~~Wii~~l~ki~~m-~~P~s~~~IkQGPkEP 160 (342)
T 3gv2_A 85 PVHAG--PIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPI-PVGEIYKRWIILGLNKIVRM-YSPTSILDIRQGPKEP 160 (342)
T ss_dssp CCCCS--CCCTTCCCCCCHHHHTTSSCCHHHHHHHHHSSSCC-CHHHHHHHHHHHHHHHHHTT-TCSSCGGGCCCCTTCC
T ss_pred CCCCC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCC-CHHHHHHHHHHHHHHHCCCC-CCCCCHHHHCCCCCCC
T ss_conf 87788--89974346986454456677889998623479962-19999999999998740354-3554221212589996
Q ss_pred HHHHHHHHH-------------HCCCCCCCCCCCC------CCCCCCHHHHHHHHHHHHHH
Q ss_conf 999999987-------------1001124877567------86441015799999988999
Q 000514 273 FYHMLNWLV-------------TWDQKQQGIDESD------GKSWRLDKALIEWLHSCLDV 314 (1450)
Q Consensus 273 ~~~~~~w~~-------------~wd~~~~g~~~~~------~~~~~~~~~~~~w~~~cl~v 314 (1450)
|--++..+. +|..++.-++... ++.++++..|-|+++.|-+|
T Consensus 161 f~DfVdRl~kal~~e~~~~~vK~~mt~tL~~qNANp~Ck~ilk~lg~~a~Lee~~~aCq~V 221 (342)
T 3gv2_A 161 FRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221 (342)
T ss_dssp HHHHHHHHHHHHHHTTCCHHHHHHHHHTHHHHTSCHHHHHHHHHHCTTCCHHHHHHHTC--
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHCCCC
T ss_conf 8999999999887531651112455663665406887899885358999989999874456
No 10
>2pyq_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, unknown function; HET: MSE; 1.50A {Jannaschia SP} SCOP: a.279.1.1
Probab=1.00 E-value=1 Score=14.21 Aligned_cols=39 Identities=21% Similarity=0.334 Sum_probs=0.0
Q ss_pred HCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH---CCCCCCCCHHHHH
Q ss_conf 10011248775678644101579999998899988875---3997654169986
Q 000514 282 TWDQKQQGIDESDGKSWRLDKALIEWLHSCLDVIWLLV---DEDRCRVPFYELL 332 (1450)
Q Consensus 282 ~wd~~~~g~~~~~~~~~~~~~~~~~w~~~cl~viw~lv---~e~~~rvpfy~ll 332 (1450)
||=++..|.+|+ .=+..-.+-.---. +-+|+|+.||-||
T Consensus 62 nfl~KKLGl~d~------------~~ld~aI~~V~e~mgks~rnK~R~~~YYll 103 (114)
T 2pyq_A 62 NFLMKKLGLADS------------ESLMGGIQSVIETYGRSERNKYRAVVYYML 103 (114)
T ss_dssp HTTTTTSCCCSS------------HHHHHHHHHHHHHHCTTCSCCBHHHHHHHH
T ss_pred HHHHHHCCCCCC------------HHHHHHHHHHHHHHHCCCCCCCEEHHHHHH
T ss_conf 289997089985------------769999999999983256776301038899
Done!