Query 001558
Match_columns 1053
No_of_seqs 60 out of 62
Neff 3.9
Searched_HMMs 29240
Date Tue Mar 26 17:44:49 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001558.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_854-858//hhsearch_pdb/001558hhsearch_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 19.8 1.1 104 623-756 10-114 (149)
2 3qx3_A DNA topoisomerase 2-bet 1.0 1 1 16.3 -1.2 78 739-853 463-542 (803)
3 3l4j_A DNA topoisomerase 2; to 1.0 1 1 16.2 -1.3 48 565-614 268-326 (757)
4 1yvw_A PRA-PH, phosphoribosyl- 1.0 1 1 16.1 -2.3 18 981-998 61-79 (115)
5 1y6x_A Phosphoribosyl-ATP pyro 1.0 1 1 16.1 -2.7 20 980-999 65-85 (93)
6 1tzv_A NUSB protein, N utiliza 1.0 1 1 16.0 3.5 102 623-756 10-113 (142)
7 2a7w_A PRA-PH, phosphoribosyl- 1.0 1 1 15.4 -2.1 18 981-998 62-80 (116)
8 2bid_A Protein (BID); programm 1.0 1 1 15.3 1.7 71 295-380 124-194 (197)
9 1yxb_A PRA-PH, phosphoribosyl- 1.0 1 1 14.8 -0.3 19 980-998 62-81 (98)
10 3oc3_A Helicase MOT1, MOT1; re 1.0 1 1 14.6 2.7 16 267-282 218-238 (800)
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=19.81 Aligned_cols=104 Identities=15% Similarity=0.144 Sum_probs=64.0
Q ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89999984215789989910332102899998999578999999998500344446898888654566788999988778
Q 001558 623 KLIVRILNVFDLSKIPFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTSQ 702 (1053)
Q Consensus 623 kLV~~Ilg~ld~~r~~lSesf~~yl~~~~~~~~P~~~Yf~~Li~rLv~~vlp~~~~~~~~~~~~d~s~~~~~~~fp~~s~ 702 (1053)
..++.+|-+.+.....+.+.+.++....+..-..+..|+.+|+.+...+. ...|.-...
T Consensus 10 ~~A~q~L~~~~~~~~~~~~~l~~~~~~~~~~~~~dr~~~~~lv~gvl~~~-----------~~lD~~i~~---------- 68 (149)
T 3r2d_A 10 DTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHI-----------EEIDSIIEK---------- 68 (149)
T ss_dssp HHHHHHHHHHHHHCCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHTH-----------HHHHHHHHT----------
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-----------HHHHHHHHH----------
T ss_conf 99999999998549999999999997532378899999999999999969-----------999999999----------
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHH
Q ss_conf 9999887778432347995202567675544524059-98978999888887660
Q 001558 703 SGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSL-PVSASQIVSSLVQIVVN 756 (1053)
Q Consensus 703 ~~~~~~~~~dwrF~E~~nP~~~al~~L~tacIELLsL-P~~p~~iv~aLidiv~~ 756 (1053)
+. .+|.+...+ |...+.+ -.++-|++-+ .+|+..++|--|+++-+
T Consensus 69 -----~l-~~w~~~rl~-~~~r~iL--rla~yEl~~~~~iP~~vaInEaVelaK~ 114 (149)
T 3r2d_A 69 -----HL-KGWSIDRLG-YVERNAL--RLGVAELIFLKSKEPGRVFIDIVDLVKK 114 (149)
T ss_dssp -----TC----CGGGSC-HHHHHHH--HHHHHHHTTSCCSCHHHHHHHHHHHHHH
T ss_pred -----HH-CCCCCCCCC-HHHHHHH--HHHHHHHHHCCCCCCEEHHHHHHHHHHH
T ss_conf -----83-279933158-9999999--9999999986899972129999999987
No 2
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain, coiled-coil domain, DNA and cleavage, nucleus; HET: DNA EVP; 2.16A {Homo sapiens} PDB: 4fm9_A*
Probab=1.00 E-value=1 Score=16.28 Aligned_cols=78 Identities=17% Similarity=0.273 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 998978999888887660375322357999898888898877889999-9988888998898876676666543466532
Q 001558 739 LPVSASQIVSSLVQIVVNIQPTLIQTSNGPYGASNSVGQGSVLPTSPS-GGSTDSLGASRSTPSVSGINTSSFVSRSGYT 817 (1053)
Q Consensus 739 LP~~p~~iv~aLidiv~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~ps-~~~~~~~~~~~~~~~~~~in~s~~~~~~~~~ 817 (1053)
.|+.+..|+++++.++-... .+|-.|+-+- +|.++..| .-.+..|.-+.
T Consensus 463 PphNl~Evi~a~~~ll~~~~------------------~~pd~P~~~gf~G~i~~tG------------rg~~~~rg~~~ 512 (803)
T 3qx3_A 463 PNYDAREIVNNVRRMLDGLD------------------PHPMLPNYKNFKGTIQELG------------QNQYAVSGEIF 512 (803)
T ss_dssp CCCCHHHHHHHHHHHHTTCC------------------CCCCCCCCTTCCSEEEEEE------------TTEEEEECEEE
T ss_pred CCCCHHHHHHHHHHHHCCCC------------------CCCCCCCCCCCCCEEEECC------------CCEEEEEEEEE
T ss_conf 99999999999999956999------------------8877770279753597369------------82799999999
Q ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHH-HHHHHC
Q ss_conf 100246799999999720993579999999-999860
Q 001558 818 CQQLSCLLIQACGLLLAQLPPDFHMQLYME-ASRIIK 853 (1053)
Q Consensus 818 ~~~~s~l~InAigLlLaaLP~~f~~~ly~e-~~~vi~ 853 (1053)
-. .--.++.+-||...|++.|.+ +.+-|.
T Consensus 513 ~~-------~~~~IvITELPy~~~t~~~k~~lle~i~ 542 (803)
T 3qx3_A 513 VV-------DRNTVEITELPVRTWTQVYKEQVLEPML 542 (803)
T ss_dssp EE-------ETTEEEEEECCTTCCHHHHHHHTHHHHH
T ss_pred EE-------CCCEEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf 95-------5977999978985656579999999987
No 3
>3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently linked comple supercoiling; HET: DNA PTR TSP; 2.48A {Saccharomyces cerevisiae} SCOP: e.11.1.1 PDB: 3l4k_A* 1bjt_A 1bgw_A 2rgr_A*
Probab=1.00 E-value=1 Score=16.19 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=27.9
Q ss_pred HHHHCCCH--------HHHHHHHHHCCC---HHHHHHHHHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf 86214736--------799999981594---114999998602122248763267888798
Q 001558 565 AARLLPVI--------PLIVYRLIENDA---MDSADRVLATYSSFLAYYPLRFSFVRDILA 614 (1053)
Q Consensus 565 clRlLPVi--------DivI~R~LE~~~---~k~le~LL~~~~~LYrYHd~PvTfly~tL~ 614 (1053)
+.|-||=+ -=|+|-+.|... .|++.-+=+..+. =+|| ---+=+|+++-
T Consensus 268 ~~RAlPdv~DGLKPvqRrILyam~~~~~~~~~K~A~ivG~V~~~-~~YH-HGD~siydaiV 326 (757)
T 3l4j_A 268 NIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSEC-TAYH-HGEQSLAQTII 326 (757)
T ss_dssp HHHHSCBTTTCCCHHHHHHHHHHHHTTTTSCEEHHHHHHHHHHH-TTCC-SCHHHHHHHHH
T ss_pred HHCCCCHHHCCCCCHHEEEEHHHHHHCCCCCCCEEEEEHHHHHH-CCCC-CCCHHHHHHHH
T ss_conf 43247614306875010310536640887676315651645210-1257-78067999999
No 4
>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=16.06 Aligned_cols=18 Identities=17% Similarity=0.314 Sum_probs=9.3
Q ss_pred HHHHHHHHEE-EEEECCCC
Q ss_conf 5566241002-47611587
Q 001558 981 ADLIDFLHHV-VHYEGQGG 998 (1053)
Q Consensus 981 d~IcDFlyHi-ym~~G~~~ 998 (1053)
.-++|++||. ++...+|.
T Consensus 61 ~E~ADLlYHllVlL~~~gv 79 (115)
T 1yvw_A 61 KEMVDVFYHCFVLLAEKNI 79 (115)
T ss_dssp HHHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHHHCCC
T ss_conf 9999999999999998699
No 5
>1y6x_A Phosphoribosyl-ATP pyrophosphatase; helical bundle, histidine, hydrolase, ST genomics, PSI, protein structure initiative; 1.25A {Mycobacterium tuberculosis} SCOP: a.204.1.4 PDB: 3c90_X
Probab=1.00 E-value=1 Score=16.06 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=13.6
Q ss_pred HHHHHHHHHEE-EEEECCCCC
Q ss_conf 35566241002-476115877
Q 001558 980 IADLIDFLHHV-VHYEGQGGP 999 (1053)
Q Consensus 980 id~IcDFlyHi-ym~~G~~~~ 999 (1053)
+.-++|++||. ++...+|..
T Consensus 65 ~~E~ADLlYHllVlL~~~gv~ 85 (93)
T 1y6x_A 65 AEEISQLLYWTQVLMISRGLS 85 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHTCC
T ss_pred HHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999999999999986999
No 6
>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=16.00 Aligned_cols=102 Identities=10% Similarity=0.105 Sum_probs=61.9
Q ss_pred HHHHHHHHHCCCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 899999842157899-8991033210289999899957899999999850034444689888865456678899998877
Q 001558 623 KLIVRILNVFDLSKI-PFSESFPQHISSSNPVMCPPLDYFATLLLGLVNNVIPALNYNSKSGSTMDASLRAPHNKSPMTS 701 (1053)
Q Consensus 623 kLV~~Ilg~ld~~r~-~lSesf~~yl~~~~~~~~P~~~Yf~~Li~rLv~~vlp~~~~~~~~~~~~d~s~~~~~~~fp~~s 701 (1053)
..+..++-+.+.... ...+...++.. .. .-..|..|+.+|+.+...+. ...|.-.. +
T Consensus 10 ~~A~~~L~~~~~~~~~~~~~~l~~~~~-~~-l~~~d~~~~~~Lv~gvl~~~-----------~~lD~~I~----~----- 67 (142)
T 1tzv_A 10 LAVFKALFQHEFRRDEDLEQILEEILD-ET-YDKKAKEDARRYIRGIKENL-----------SMIDDLIS----R----- 67 (142)
T ss_dssp HHHHHHHHHHTTCTTSCHHHHHHHHCC-TT-SCHHHHHHHHHHHHHHHHTH-----------HHHHHHHH----T-----
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH-HC-CCHHHHHHHHHHHHHHHHHH-----------HHHHHHHH----H-----
T ss_conf 999999999985599989999999988-55-78889999999999999979-----------99999999----8-----
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHH
Q ss_conf 899998877784323479952025676755445240599-8978999888887660
Q 001558 702 QSGPSNVSEGRKEFYQNQDPGTYTQLVLETAVIEILSLP-VSASQIVSSLVQIVVN 756 (1053)
Q Consensus 702 ~~~~~~~~~~dwrF~E~~nP~~~al~~L~tacIELLsLP-~~p~~iv~aLidiv~~ 756 (1053)
+. ..|.+...+ |...+.+ -.++-|++-++ +|+..++|--|+++-+
T Consensus 68 ------~l-~~w~l~rl~-~~~r~iL--rla~yEl~~~~~iP~~vaInEaVelaK~ 113 (142)
T 1tzv_A 68 ------YL-EKWSLNRLS-VVDRNVL--RLATYELLFEKDIPIEVTIDEAIEIAKR 113 (142)
T ss_dssp ------TC-SSSCGGGSC-HHHHHHH--HHHHHHHHHCTTSCHHHHHHHHHHHHHH
T ss_pred ------HC-CCCCHHHCC-HHHHHHH--HHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf ------72-799967778-9999999--9999999866799940489999999999
No 7
>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=15.39 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=10.0
Q ss_pred HHHHHHHHEE-EEEECCCC
Q ss_conf 5566241002-47611587
Q 001558 981 ADLIDFLHHV-VHYEGQGG 998 (1053)
Q Consensus 981 d~IcDFlyHi-ym~~G~~~ 998 (1053)
.-++|++||+ ++...+|.
T Consensus 62 ~E~ADLlYHllVlL~~~gv 80 (116)
T 2a7w_A 62 REVADLWFHTMVLLTYHGL 80 (116)
T ss_dssp HHHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHHHCCC
T ss_conf 9999999999999998699
No 8
>2bid_A Protein (BID); programmed cell death, apoptosis regulation and amplification; NMR {Homo sapiens} SCOP: f.1.4.1
Probab=1.00 E-value=1 Score=15.29 Aligned_cols=71 Identities=25% Similarity=0.243 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHH
Q ss_conf 67899999999998752654402454499999999860888884355402938899997004788874155399999999
Q 001558 295 TLNRITVIALAIIIKTRGIADADHVLYLQTMLEQIMATSQHTWSEKTLRYFPSLLRDALIGRIDKRGLTIQAWQQAETTV 374 (1053)
Q Consensus 295 eLNR~lIltlAr~iKitGi~d~~~~~~~~~~L~~im~~tph~Ws~kTL~~FP~~L~~~~~~~~d~~~~~~~~~qql~~tV 374 (1053)
+-+|.|--++-..+.+-.. |.++. |.+|---| -..+|.-.+-|+.||+.|...++..| |++.+-|
T Consensus 124 drr~~LAaaleql~Qt~P~-DmeqE---KtmLvlam-----LLAKKVa~htPSLLrdVF~TTVnfIn------qNl~aYv 188 (197)
T 2bid_A 124 DRNRDLATALEQLLQAYPR-DMEKE---KTMLVLAL-----LLAKKVASHTPSLLRDVFHTTVNFIN------QNLRTYV 188 (197)
T ss_dssp HHHHHHHHHHHHHHTTSCC-SSCSH---HHHHHHHH-----HHHHHHHHHCTTCHHHHHHHHHHHHH------TTTHHHH
T ss_pred HHHHHHHHHHHHHHHHCCC-CHHHH---HHHHHHHH-----HHHHHHHHCCHHHHHHHHHHHHHHHH------HHHHHHH
T ss_conf 8987899999999987798-37689---99999999-----99999986084999999999899998------8899999
Q ss_pred HHHHHH
Q ss_conf 999850
Q 001558 375 INQCTQ 380 (1053)
Q Consensus 375 ~~e~~~ 380 (1053)
.+-.|+
T Consensus 189 r~L~Rn 194 (197)
T 2bid_A 189 RSLARN 194 (197)
T ss_dssp HHHHHT
T ss_pred HHHHHC
T ss_conf 999851
No 9
>1yxb_A PRA-PH, phosphoribosyl-ATP pyrophosphatase; structural genomics, PSI, protein structure initiative; 2.60A {Streptomyces coelicolor} SCOP: a.204.1.4
Probab=1.00 E-value=1 Score=14.77 Aligned_cols=19 Identities=26% Similarity=0.371 Sum_probs=11.5
Q ss_pred HHHHHHHHHEE-EEEECCCC
Q ss_conf 35566241002-47611587
Q 001558 980 IADLIDFLHHV-VHYEGQGG 998 (1053)
Q Consensus 980 id~IcDFlyHi-ym~~G~~~ 998 (1053)
+.-++|++||. ++...+|.
T Consensus 62 ~~E~ADLlYHllVlL~~~gv 81 (98)
T 1yxb_A 62 AEEISQLLYHVQVMMVARGI 81 (98)
T ss_dssp HHHHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999999999998699
No 10
>3oc3_A Helicase MOT1, MOT1; regulation of transcription, hydrolase-transc complex; HET: MES; 3.10A {Encephalitozoon cuniculi}
Probab=1.00 E-value=1 Score=14.56 Aligned_cols=16 Identities=19% Similarity=0.167 Sum_probs=7.1
Q ss_pred HHHHHHHHHH-----HCCCCC
Q ss_conf 9999999521-----000123
Q 001558 267 NLCMNLILSQ-----RDFFSL 282 (1053)
Q Consensus 267 ~~~LrlI~sl-----~s~~~~ 282 (1053)
.++.|+++-+ |||.+.
T Consensus 218 DLAvRLLCVLALDRFGDYVSD 238 (800)
T 3oc3_A 218 KLFSKIYEILVTDKFNDFVDD 238 (800)
T ss_dssp THHHHHHHHHHHBCCBBCSSS
T ss_pred HHHHHHHHHHHHCCCCCCCCC
T ss_conf 899999999996020254568
Done!