Query 029683
Match_columns 189
No_of_seqs 142 out of 340
Neff 5.1
Searched_HMMs 29240
Date Tue Mar 26 18:20:06 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/029683.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_2304-2308//hhsearch_pdb/029683hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_E DNA-directed RNA polyme 1.0 1 1 384.5 7.9 167 22-189 4-176 (210)
2 1dzf_A DNA-directed RNA polyme 1.0 1 1 383.8 10.3 167 22-189 5-181 (215)
3 1eik_A RNA polymerase subunit 1.0 1 1 113.3 3.6 42 148-189 1-42 (77)
4 1hmj_A RPB5, protein (subunit 1.0 1 1 108.3 2.5 40 150-189 1-40 (78)
5 4ayb_H DNA-directed RNA polyme 1.0 1 1 107.2 3.0 45 145-189 4-48 (84)
6 4f0q_A Restriction endonucleas 1.0 1 1 19.3 2.9 55 91-148 360-414 (456)
7 1y88_A Hypothetical protein AF 1.0 1 1 17.1 4.5 127 34-176 22-160 (199)
8 2i7u_A Four-alpha-helix bundle 1.0 1 1 16.5 -0.0 10 2-11 29-38 (62)
9 2lz1_A Nuclear factor erythroi 1.0 1 1 15.7 -0.1 24 163-186 42-65 (90)
10 2jmk_A Hypothetical protein TA 1.0 1 1 15.7 5.6 57 56-115 46-106 (111)
No 1
>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=1.00 E-value=1 Score=384.49 Aligned_cols=167 Identities=25% Similarity=0.405 Sum_probs=162.9
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCC---CCCCCCEEEECCCCCC-CCCEEEEECCCCCCC
Q ss_conf 966799999999989998449998679100037977899882999---9987507980288999-981899944998643
Q 029683 22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK---CDLESLRLCLPLRSNP-SKKMLVVYLGTEEIR 97 (189)
Q Consensus 22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~eF~~~f~~~---~~r~~L~~~~~~~~dp-~~~i~VfF~~~~kvg 97 (189)
++.|++||||+|||++|||+||||.|+++|+++|+++|+++|++. |+|++|+|++.+.+|| +++|+|||+++++||
T Consensus 4 ~~~e~~rl~rirrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~~~~~r~~l~~~~~~~~dp~~~~i~VfF~~~~~vg 83 (210)
T 3h0g_E 4 EEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEFAKEPSVG 83 (210)
T ss_dssp CTHHHHHHHGGGSSSSSTTTTTTEECCTTTTSCCHHHHHHHSCCSSSSCCCSSCCCEEEESSCSSCCCEEEECCCSSSCC
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCHHHHHHHHCCCCCCCCCHHEEEEEECCCCCCCCEEEEEECCCCCCC
T ss_conf 06888999999999999951899846987870799999998633678987021699977589976674999978998648
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHCCCC--CEEEEEEECCCEECCCCCEECCCCCCCCHHHHHHHHHH
Q ss_conf 6589999999842168666999975899998898601148--11784340310010454201175110597899999987
Q 029683 98 TQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKK 175 (189)
Q Consensus 98 vk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ak~~i~~~~--~~iE~F~e~ELl~nit~H~lVP~H~~l~~eE~~~lL~~ 175 (189)
+|+||.|++++ .++|++++|||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+||+++||++
T Consensus 84 vk~Ir~~~~~~-~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~lL~~ 162 (210)
T 3h0g_E 84 IKEMRTFVHTL-GDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDR 162 (210)
T ss_dssp TTTTGGGTHHH-HHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHHHHH
T ss_pred HHHHHHHHHHH-HHCCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEEEEHHEEEECCCCCCCCCEEECCHHHHHHHHHH
T ss_conf 68999999999-88698669999888899799999997186757999740471676223544675787378999999998
Q ss_pred CCCCCCCCCCCCCC
Q ss_conf 09998877652269
Q 029683 176 YKIEGKQVTILVKQ 189 (189)
Q Consensus 176 y~~~~~qLP~i~~~ 189 (189)
|+++++|||||+.+
T Consensus 163 y~i~~~qLP~I~~~ 176 (210)
T 3h0g_E 163 YKLRETQLPRIQLA 176 (210)
T ss_dssp TCCCTTTSCCCCTT
T ss_pred CCCCHHHCCCCCCC
T ss_conf 29997888964566
No 2
>1dzf_A DNA-directed RNA polymerases I, II, and III 27 KD polypeptide; RNA polymerase subunit; 1.9A {Saccharomyces cerevisiae} SCOP: c.52.3.1 d.78.1.1 PDB: 1i3q_E 1i50_E 1i6h_E 1k83_E* 1nik_E 1nt9_E 1pqv_E 1r5u_E 1r9s_E* 1r9t_E* 1sfo_E* 1twa_E* 1twc_E* 1twf_E* 1twg_E* 1twh_E* 1wcm_E 1y1v_E 1y1w_E 1y1y_E ...
Probab=1.00 E-value=1 Score=383.76 Aligned_cols=167 Identities=25% Similarity=0.403 Sum_probs=162.5
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCC---CCCCCCCEEEECCCCCCCCCE------EEEECC
Q ss_conf 96679999999998999844999867910003797789988299---999875079802889999818------999449
Q 029683 22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD---KCDLESLRLCLPLRSNPSKKM------LVVYLG 92 (189)
Q Consensus 22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~eF~~~f~~---~~~r~~L~~~~~~~~dp~~~i------~VfF~~ 92 (189)
.+.++.||||||||++|||+||||.|+++|+++|+++|+++||+ .|+|++|+|++++.+||++++ ||||++
T Consensus 5 ~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~VfF~~ 84 (215)
T 1dzf_A 5 NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCD 84 (215)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECS
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHCCCCCCCCHHHEEEEECCCCCHHHHHCCCCCEEEEECC
T ss_conf 57899999999999999975489846876752899999999704569976466599805887724442357736999369
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHCCCC-CEEEEEEECCCEECCCCCEECCCCCCCCHHHHHH
Q ss_conf 986436589999999842168666999975899998898601148-1178434031001045420117511059789999
Q 029683 93 TEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDK 171 (189)
Q Consensus 93 ~~kvgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ak~~i~~~~-~~iE~F~e~ELl~nit~H~lVP~H~~l~~eE~~~ 171 (189)
+++||+|+||.|+++| .++|++++|||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+|||++
T Consensus 85 ~~~vgvk~ir~~~~~~-~~e~~~~~IlV~q~~itp~Ak~~l~~~~~~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE~~~ 163 (215)
T 1dzf_A 85 EPSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRE 163 (215)
T ss_dssp SSEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSCGGGSTTSCEEEECCHHHHHH
T ss_pred CCCCCHHHHHHHHHHH-HHCCCCEEEEEECCCCCHHHHHHHHHHCCCEEEEEEHHHHEECCCCCEECCCEEECCHHHHHH
T ss_conf 8864657899999999-756776699998898996999999872673499963588163554313446667706789999
Q ss_pred HHHHCCCCCCCCCCCCCC
Q ss_conf 998709998877652269
Q 029683 172 LMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 172 lL~~y~~~~~qLP~i~~~ 189 (189)
||++|+++++|||||+.+
T Consensus 164 lL~~y~i~~~qLP~I~~~ 181 (215)
T 1dzf_A 164 LLKRYRLKESQLPRIQRA 181 (215)
T ss_dssp HHHHTTCCGGGSCEECTT
T ss_pred HHHHCCCCHHHCCCEECC
T ss_conf 998749997889932163
No 3
>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure initiative, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.78.1.1
Probab=1.00 E-value=1 Score=113.29 Aligned_cols=42 Identities=21% Similarity=0.407 Sum_probs=40.5
Q ss_pred CEECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 001045420117511059789999998709998877652269
Q 029683 148 LLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 148 Ll~nit~H~lVP~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~ 189 (189)
|+||||+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus 1 l~vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~~~ 42 (77)
T 1eik_A 1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTT 42 (77)
T ss_dssp CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTT
T ss_pred CCCCCCCCEECCCEEECCHHHHHHHHHHCCCCHHHCCEEECC
T ss_conf 921376623647979839999999999839998899904573
No 4
>1hmj_A RPB5, protein (subunit H); RNA polymerase, archaea; NMR {Methanocaldococcus jannaschii} SCOP: d.78.1.1
Probab=1.00 E-value=1 Score=108.35 Aligned_cols=40 Identities=35% Similarity=0.666 Sum_probs=38.6
Q ss_pred ECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 1045420117511059789999998709998877652269
Q 029683 150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 150 ~nit~H~lVP~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~ 189 (189)
||||+|+|||+|++||+|||++||++|+++++|||||+.+
T Consensus 1 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~~~ 40 (78)
T 1hmj_A 1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYED 40 (78)
T ss_pred CCCCCEEECCCEEECCHHHHHHHHHHCCCCHHHCCEEECC
T ss_conf 9865603578968879999999999839998899905472
No 5
>4ayb_H DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_H 2y0s_H 2waq_H 4b1o_H 4b1p_Z 2pmz_H 3hkz_H
Probab=1.00 E-value=1 Score=107.23 Aligned_cols=45 Identities=31% Similarity=0.413 Sum_probs=42.5
Q ss_pred ECCCEECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 031001045420117511059789999998709998877652269
Q 029683 145 ITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 145 e~ELl~nit~H~lVP~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~ 189 (189)
.++++||||+|+|||+|++|++||++++|++|+++++|||+|+.+
T Consensus 4 ~~~~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~~~ 48 (84)
T 4ayb_H 4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRAS 48 (84)
T ss_dssp ----CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEESS
T ss_pred CCCCEECCCCCCCCCCEEECCHHHHHHHHHHHCCCHHHCCEECCC
T ss_conf 303205552065479838879999999999855898689961462
No 6
>4f0q_A Restriction endonuclease; cytosine methylation-dependent endonuclease, hydrolase; 2.05A {Mycobacterium SP} PDB: 4f0p_A
Probab=1.00 E-value=1 Score=19.33 Aligned_cols=55 Identities=9% Similarity=0.101 Sum_probs=41.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHCCCCCEEEEEEECCC
Q ss_conf 4998643658999999984216866699997589999889860114811784340310
Q 029683 91 LGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDL 148 (189)
Q Consensus 91 ~~~~kvgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ak~~i~~~~~~iE~F~e~EL 148 (189)
..+..||.+.|+.++..+ .+...+|+|+-+.-|..|.+.+..-...|.++.=.+|
T Consensus 360 ~~~~~Vg~~~I~~f~g~l---~~~~~GifITTS~Ft~~A~~ea~~d~~pI~LIdG~~L 414 (456)
T 4f0q_A 360 QPTSSVSPEQVARVVARL---RRGWIGVYVTTGSFSRQAQVEIIDDQYPVVLIAGGTL 414 (456)
T ss_dssp CTTSEECHHHHHHHHTTC---CTTEEEEEEESSEECHHHHHHHHHTTCCEEEECHHHH
T ss_pred CCCCCCCHHHHHHHHHHH---CCCCEEEEEECCCCCHHHHHHHHCCCCCEEEECHHHH
T ss_conf 588987889999998765---2798699998884788999998738984899738999
No 7
>1y88_A Hypothetical protein AF1548; APC5567, structural genomics, protein structure INIT PSI, midwest center for structural genomics center, MCSG; 1.85A {Archaeoglobus fulgidus} SCOP: a.60.4.3 c.52.1.30
Probab=1.00 E-value=1 Score=17.13 Aligned_cols=127 Identities=10% Similarity=0.109 Sum_probs=68.6
Q ss_pred HHHHHHHCCCCCCCCCC-CCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCEEEEECCC-CCCCHHHH------HHHH
Q ss_conf 98999844999867910-0037977899882999998750798028899998189994499-86436589------9999
Q 029683 34 RTVLQMLNDRGYAVPNS-ELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGT-EEIRTQAI------RGLY 105 (189)
Q Consensus 34 rTv~eMl~DRGY~V~~~-el~~sl~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~-~kvgvk~I------r~~~ 105 (189)
.-+.+.++.+||.+... .++ +..+ ....-+.+.+. ...++|. +-. ..++...+ ...+
T Consensus 22 ~~va~~L~~~Gy~i~~~v~v~----------~r~~-dggIDIIA~k~---~~~v~VE-vK~r~~v~~~~V~~~~~~~~~~ 86 (199)
T 1y88_A 22 HMVARLLEEHGFETKTNVIVQ----------GNCV-EQEIDVVAERD---GERYMIE-CKFHNIPVYTGLKEAMYTYARF 86 (199)
T ss_dssp HHHHHHHHTTTCEEEEEEEEE----------CSSS-EEEEEEEEEET---TEEEEEE-ECCCSSSCEECHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCEEEEEECCC----------CCCC-CCCEEEEEEEC---CEEEEEE-ECCCCCCCCCCHHHHHHHHHHH
T ss_conf 999999997899899710236----------7778-99679999989---9999999-3203689985511888755565
Q ss_pred HHHHHCCCCCEEEEEECCCCCHHHHHHHCCCCCEEEEE---EECCCEECCCCCEECCC-CCCCCHHHHHHHHHHC
Q ss_conf 99842168666999975899998898601148117843---40310010454201175-1105978999999870
Q 029683 106 GQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIF---YITDLLVNVTKHILQPK-HEVLSAGERDKLMKKY 176 (189)
Q Consensus 106 ~~~~~~eni~~~IiV~q~~lt~~Ak~~i~~~~~~iE~F---~e~ELl~nit~H~lVP~-H~~l~~eE~~~lL~~y 176 (189)
..+ ...+..++++|+-+.-|+.|++.....+..+-.. ...+|.--|-+..|-|- ---||++|+..||.+=
T Consensus 87 ~d~-~~~~a~~g~VVTn~~FT~~A~~~A~~~~I~Li~wd~p~g~~L~~~i~~~~l~pi~~l~~~~~e~~~l~~~~ 160 (199)
T 1y88_A 87 LDV-EKHGFTQPWIFTNTKFSEEAKKYAGCVGIKLTGWSYPEKEGIEVLLESKGLYPITILRIDKEVLDELVRAG 160 (199)
T ss_dssp HHH-GGGTCSEEEEECSSEECHHHHHHHHHHTCEEECSSCSTTTSHHHHHHTTTCCBGGGSSCCHHHHHHHHHTT
T ss_pred HHH-HCCCCCEEEEEECCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHCCCCCEEEEEECHHHHHHHHCCC
T ss_conf 310-00479879999999779899999987896899778876478999999728997488860899986441079
No 8
>2i7u_A Four-alpha-helix bundle; HOMO dimer, anesthetic binding, de novo protein/ligand binding protein complex; NMR {Synthetic} PDB: 2jst_A
Probab=1.00 E-value=1 Score=16.49 Aligned_cols=10 Identities=70% Similarity=1.484 Sum_probs=6.7
Q ss_pred CCCCCCCCCC
Q ss_conf 9999988852
Q 029683 2 GGSGGGGECI 11 (189)
Q Consensus 2 ~~~~~~~~~~ 11 (189)
||.||||+-|
T Consensus 29 gggggggelm 38 (62)
T 2i7u_A 29 GGGGGGGELM 38 (62)
T ss_dssp SSCSSSCHHH
T ss_pred CCCCCHHHHH
T ss_conf 8998458899
No 9
>2lz1_A Nuclear factor erythroid 2-related factor 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=15.69 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=14.8
Q ss_pred CCCHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 059789999998709998877652
Q 029683 163 VLSAGERDKLMKKYKIEGKQVTIL 186 (189)
Q Consensus 163 ~l~~eE~~~lL~~y~~~~~qLP~i 186 (189)
-|+-+|-.++|++|++.+.||-.|
T Consensus 42 nLpv~eFn~lL~~~~Lt~~Ql~lI 65 (90)
T 2lz1_A 42 NLPVVDFNEMMSKEQFNEAQLALI 65 (90)
T ss_dssp HSCHHHHHHHHHHSCCCHHHHHHH
T ss_pred HCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 787999999999769999999999
No 10
>2jmk_A Hypothetical protein TA0956; protein binding; NMR {Thermoplasma acidophilum} PDB: 2k24_A
Probab=1.00 E-value=1 Score=15.66 Aligned_cols=57 Identities=12% Similarity=0.229 Sum_probs=41.0
Q ss_pred HHHHHHHHCC--C--CCCCCCEEEECCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf 7789988299--9--9987507980288999981899944998643658999999984216866
Q 029683 56 LTEFRFTFGD--K--CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALH 115 (189)
Q Consensus 56 l~eF~~~f~~--~--~~r~~L~~~~~~~~dp~~~i~VfF~~~~kvgvk~Ir~~~~~~~~~eni~ 115 (189)
+.+|.++|.- . |.-...-|.+ .+...+-+-|-|++......+.|++.++.. .+.+..
T Consensus 46 l~dFIsryARTDEImPEDKTvGFvv--iN~dKK~mSvsFsd~~~~~K~~i~ei~kky-kd~Gyk 106 (111)
T 2jmk_A 46 MMDFISRFARTDEIMPEDKTVGFVV--VNADKKLMSVSFSDIDENMKKVIKATAEKF-KNKGFK 106 (111)
T ss_dssp HHHHHHHHCCCSCCCSSCEEEEEEE--EETTTTEEEEEECSCCTTHHHHHHHHHHHG-GGGCCE
T ss_pred HHHHHHHHHCCCCCCCCCCEEEEEE--EECCCEEEEEEEEHHHHHHHHHHHHHHHHH-HCCCCE
T ss_conf 9999998632143577776267999--906870899881322456899999999986-437852
Done!