Query 000338
Match_columns 1639
No_of_seqs 60 out of 62
Neff 3.2
Searched_HMMs 29240
Date Tue Mar 26 16:34:30 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000338.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_117-121//hhsearch_pdb/000338hhsearch_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 18.7 -1.2 104 1209-1342 10-114 (149)
2 3oc3_A Helicase MOT1, MOT1; re 1.0 1 1 15.7 3.0 29 544-572 54-82 (800)
3 3h47_A Ca, capsid protein P24; 1.0 1 1 15.1 -2.2 13 436-448 41-53 (231)
4 1tzv_A NUSB protein, N utiliza 1.0 1 1 14.9 1.4 102 1209-1342 10-113 (142)
5 1x4p_A Putative splicing facto 1.0 1 1 14.6 -1.1 18 548-565 6-23 (66)
6 3gv2_A Ca, fusion protein cons 1.0 1 1 14.5 -1.7 60 409-469 12-73 (342)
7 2kpa_A ARNO(375-400); hydrolas 1.0 1 1 14.2 0.6 12 352-363 2-13 (26)
8 2a7w_A PRA-PH, phosphoribosyl- 1.0 1 1 14.1 -2.8 16 1569-1584 64-80 (116)
9 2pyq_A Uncharacterized protein 1.0 1 1 14.0 3.8 44 309-363 61-106 (114)
10 1yvw_A PRA-PH, phosphoribosyl- 1.0 1 1 14.0 -2.8 14 1569-1582 63-77 (115)
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=18.71 Aligned_cols=104 Identities=15% Similarity=0.140 Sum_probs=61.4
Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 79999983114689888930001004999988999568999999998600444446898888665565788999988778
Q 000338 1209 KLIVRILNVFDLSKIPFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTSQ 1288 (1639)
Q Consensus 1209 kLV~~ILg~Ld~~r~plSEsF~~y~~~~~~~~~P~~~Yy~~LI~RLvnnvlp~~~~~~~~~~~~dgs~~~~~~~~p~~s~ 1288 (1639)
.++..++-+.+.....+.+.+.++....+..-..|-.|+.+|+.+.+.+. ...|....
T Consensus 10 ~~A~q~L~~~~~~~~~~~~~l~~~~~~~~~~~~~dr~~~~~lv~gvl~~~-----------~~lD~~i~----------- 67 (149)
T 3r2d_A 10 DTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHI-----------EEIDSIIE----------- 67 (149)
T ss_dssp HHHHHHHHHHHHHCCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTH-----------HHHHHHHH-----------
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-----------HHHHHHHH-----------
T ss_conf 99999999998549999999999997532378899999999999999969-----------99999999-----------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHCCEEECCCC-CCCHHHHHHHHHHHHHC
Q ss_conf 9999888889421237997303666530010010158-88978999888876440
Q 000338 1289 SGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSL-PVSASQIVSSLVQIVVN 1342 (1639)
Q Consensus 1289 ~~p~~~s~~DwrF~EfpnPga~al~vL~tacIELLsL-Pvsp~~Vv~aLIdvvv~ 1342 (1639)
.+. .+|.+..++ |...+++. .++-|++-+ .+|+..++|--|+++-+
T Consensus 68 ----~~l-~~w~~~rl~-~~~r~iLr--la~yEl~~~~~iP~~vaInEaVelaK~ 114 (149)
T 3r2d_A 68 ----KHL-KGWSIDRLG-YVERNALR--LGVAELIFLKSKEPGRVFIDIVDLVKK 114 (149)
T ss_dssp ----TTC----CGGGSC-HHHHHHHH--HHHHHHTTSCCSCHHHHHHHHHHHHHH
T ss_pred ----HHH-CCCCCCCCC-HHHHHHHH--HHHHHHHHCCCCCCEEHHHHHHHHHHH
T ss_conf ----983-279933158-99999999--999999986899972129999999987
No 2
>3oc3_A Helicase MOT1, MOT1; regulation of transcription, hydrolase-transc complex; HET: MES; 3.10A {Encephalitozoon cuniculi}
Probab=1.00 E-value=1 Score=15.66 Aligned_cols=29 Identities=28% Similarity=0.322 Sum_probs=17.8
Q ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCCCH
Q ss_conf 02666799899999752059854333204
Q 000338 544 SGCIDFVDFVDKLVSRLQDGDNHILRTNH 572 (1639)
Q Consensus 544 ~~~~df~~fi~kL~~r~~~gd~~~~~~nh 572 (1639)
+.+.||--||.|-+-|+--|.+.+-|.|-
T Consensus 54 ~ey~df~~~i~~~~y~ll~~~~~~~r~~g 82 (800)
T 3oc3_A 54 KEYVDFTPYILKQTYRLLCGQASEDRRNG 82 (800)
T ss_dssp HHHCCCCSSCCHHHHHHHTCSCHHHHHHH
T ss_pred HHHHCCHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 88735024999999999818763002326
No 3
>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=15.11 Aligned_cols=13 Identities=31% Similarity=0.235 Sum_probs=4.6
Q ss_pred CCCCCCCCHHHHH
Q ss_conf 4448876502333
Q 000338 436 SVLGEPLHGEDLA 448 (1639)
Q Consensus 436 ~~~ge~l~ge~~a 448 (1639)
++|-|-+.-+|+.
T Consensus 41 ~alse~~tp~D~n 53 (231)
T 3h47_A 41 SALSCGATPQDLN 53 (231)
T ss_dssp HHHTTTCCHHHHH
T ss_pred HHHHCCCCHHHHH
T ss_conf 9860799879999
No 4
>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=14.90 Aligned_cols=102 Identities=10% Similarity=0.091 Sum_probs=59.6
Q ss_pred HHHHHHHHHCCCCCC-CCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 799999831146898-8893000100499998899956899999999860044444689888866556578899998877
Q 000338 1209 KLIVRILNVFDLSKI-PFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTS 1287 (1639)
Q Consensus 1209 kLV~~ILg~Ld~~r~-plSEsF~~y~~~~~~~~~P~~~Yy~~LI~RLvnnvlp~~~~~~~~~~~~dgs~~~~~~~~p~~s 1287 (1639)
..+..++-+.+.... ...+....+.. ...-..|..|+..|+.+...+. ...|.-..
T Consensus 10 ~~A~~~L~~~~~~~~~~~~~~l~~~~~--~~l~~~d~~~~~~Lv~gvl~~~-----------~~lD~~I~---------- 66 (142)
T 1tzv_A 10 LAVFKALFQHEFRRDEDLEQILEEILD--ETYDKKAKEDARRYIRGIKENL-----------SMIDDLIS---------- 66 (142)
T ss_dssp HHHHHHHHHHTTCTTSCHHHHHHHHCC--TTSCHHHHHHHHHHHHHHHHTH-----------HHHHHHHH----------
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHH-----------HHHHHHHH----------
T ss_conf 999999999985599989999999988--5578889999999999999979-----------99999999----------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCEEECCCCC-CCHHHHHHHHHHHHHC
Q ss_conf 899998888894212379973036665300100101588-8978999888876440
Q 000338 1288 QSGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSLP-VSASQIVSSLVQIVVN 1342 (1639)
Q Consensus 1288 ~~~p~~~s~~DwrF~EfpnPga~al~vL~tacIELLsLP-vsp~~Vv~aLIdvvv~ 1342 (1639)
.+. ..|.+...+ |.-.+++. .++-|++-++ +|+..++|--|+++-+
T Consensus 67 -----~~l-~~w~l~rl~-~~~r~iLr--la~yEl~~~~~iP~~vaInEaVelaK~ 113 (142)
T 1tzv_A 67 -----RYL-EKWSLNRLS-VVDRNVLR--LATYELLFEKDIPIEVTIDEAIEIAKR 113 (142)
T ss_dssp -----TTC-SSSCGGGSC-HHHHHHHH--HHHHHHHHCTTSCHHHHHHHHHHHHHH
T ss_pred -----HHC-CCCCHHHCC-HHHHHHHH--HHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf -----872-799967778-99999999--999999866799940489999999999
No 5
>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=14.55 Aligned_cols=18 Identities=33% Similarity=0.460 Sum_probs=10.5
Q ss_pred CHHHHHHHHHHHHCCCCC
Q ss_conf 679989999975205985
Q 000338 548 DFVDFVDKLVSRLQDGDN 565 (1639)
Q Consensus 548 df~~fi~kL~~r~~~gd~ 565 (1639)
+-+++||||+.+.++|.+
T Consensus 6 ~~~~~ieKLa~fVaeGgp 23 (66)
T 1x4p_A 6 SGVGTIDQLVKRVIEGSL 23 (66)
T ss_dssp CSSHHHHHHHHHHHHTCS
T ss_pred HHHHHHHHHHHHHHCCCC
T ss_conf 699999999999984697
No 6
>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=14.49 Aligned_cols=60 Identities=27% Similarity=0.304 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 2222456765302001244335654--774448876502333100379720899999999986
Q 000338 409 HRILSQTTPNISVEAAGNLRYSPIT--YPSVLGEPLHGEDLATSIQRGSLDWERAMRCIRHAI 469 (1639)
Q Consensus 409 ~~~~~~~~~~~~~~~~~~lr~s~~t--y~~~~ge~l~ge~~a~~~~~~~~~~e~a~rc~~~~~ 469 (1639)
|+-+|+.+-|.=++.+..--+||-+ +-++|-|.+.-+|+.+-..- .-++--|+--++..+
T Consensus 12 h~plsPrtl~awvk~veek~f~pevip~f~alse~~tp~Din~mln~-vgg~q~~~q~lk~~i 73 (342)
T 3gv2_A 12 HQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNT-VGGHQAAMQMLKETI 73 (342)
T ss_dssp ECCCCHHHHHHHHHHHHHHCSCTTHHHHHHHHTTTCCHHHHHHHHTT-CCSCHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHH-CCHHHHHHHHHHHHH
T ss_conf 67899305999999998527991033689971489986999999984-431466899999999
No 7
>2kpa_A ARNO(375-400); hydrolase; NMR {Synthetic} PDB: 2kpb_A
Probab=1.00 E-value=1 Score=14.15 Aligned_cols=12 Identities=42% Similarity=0.750 Sum_probs=8.0
Q ss_pred CCCCHHHHHHCC
Q ss_conf 654169986202
Q 000338 352 CRVPFYELLRTG 363 (1639)
Q Consensus 352 ~rvpfy~ll~~~ 363 (1639)
.+.|||++|...
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 8
>2a7w_A PRA-PH, phosphoribosyl-ATP pyrophosphatase; structural genomics, PSI, protein structure initiative; 2.80A {Chromobacterium violaceum} SCOP: a.204.1.4
Probab=1.00 E-value=1 Score=14.07 Aligned_cols=16 Identities=25% Similarity=0.287 Sum_probs=7.0
Q ss_pred HHHHHCEE-EEEECCCC
Q ss_conf 55130104-67720587
Q 000338 1569 LIDFLHHV-VHYEGQGG 1584 (1639)
Q Consensus 1569 ICDFLYHI-YMFVG~g~ 1584 (1639)
++|++||+ ++.+-+|.
T Consensus 64 ~ADLlYHllVlL~~~gv 80 (116)
T 2a7w_A 64 VADLWFHTMVLLTYHGL 80 (116)
T ss_dssp HHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHCCC
T ss_conf 99999999999998699
No 9
>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=14.04 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=26.2
Q ss_pred HHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH--HCCCCCCCCHHHHHHCC
Q ss_conf 71001124877567864410157999999889998887--53997654169986202
Q 000338 309 VTWDQKQQGIDESDGKSWRLDKALIEWLHSCLDVIWLL--VDEDRCRVPFYELLRTG 363 (1639)
Q Consensus 309 ~~wd~~~~g~~~~~~~~~~~~~~~~~w~~~cl~viw~l--v~e~~~rvpfy~ll~~~ 363 (1639)
.||=++..|.+|++ .++.+ +. .|+=.. -+-+|+|+.||-||--.
T Consensus 61 ~nfl~KKLGl~d~~----~ld~a----I~---~V~e~mgks~rnK~R~~~YYllak~ 106 (114)
T 2pyq_A 61 KNFLMKKLGLADSE----SLMGG----IQ---SVIETYGRSERNKYRAVVYYMLTKH 106 (114)
T ss_dssp HHTTTTTSCCCSSH----HHHHH----HH---HHHHHHCTTCSCCBHHHHHHHHHHH
T ss_pred HHHHHHHCCCCCCH----HHHHH----HH---HHHHHHHCCCCCCCEEHHHHHHHHH
T ss_conf 82899970899857----69999----99---9999983256776301038899998
No 10
>1yvw_A PRA-PH, phosphoribosyl-ATP pyrophosphatase; helix bundle, histidine biosynthesis, structural genomics, PSI, protein structure initiative; 2.60A {Bacillus cereus} SCOP: a.204.1.4
Probab=1.00 E-value=1 Score=13.97 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=5.6
Q ss_pred HHHHHCEE-EEEECC
Q ss_conf 55130104-677205
Q 000338 1569 LIDFLHHV-VHYEGQ 1582 (1639)
Q Consensus 1569 ICDFLYHI-YMFVG~ 1582 (1639)
+.|++||+ ++.+-+
T Consensus 63 ~ADLlYHllVlL~~~ 77 (115)
T 1yvw_A 63 MVDVFYHCFVLLAEK 77 (115)
T ss_dssp HHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHC
T ss_conf 999999999999986
Done!