Query 029658
Match_columns 190
No_of_seqs 108 out of 238
Neff 4.1
Searched_HMMs 29240
Date Tue Mar 26 18:30:56 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/029658.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_2276-2280//hhsearch_pdb/029658hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3r84_A Mediator of RNA polymer 1.0 1 1 15.4 2.3 24 151-174 60-86 (86)
2 3owt_C Regulatory protein SIR3 1.0 1 1 13.8 0.8 16 14-29 12-27 (27)
3 2hnh_A DNA polymerase III alph 1.0 1 1 13.4 -3.2 13 117-129 257-269 (910)
4 3din_C Preprotein translocase 1.0 1 1 13.0 6.2 108 57-170 304-422 (431)
5 3dl8_G Preprotein translocase 1.0 1 1 13.0 4.4 106 57-169 309-426 (429)
6 1v74_A Colicin D; colicin D - 1.0 1 1 12.9 1.6 16 155-171 12-27 (107)
7 3j01_A Preprotein translocase 1.0 1 1 12.8 7.1 109 56-170 307-426 (435)
8 3rj1_A Mediator of RNA polymer 1.0 1 1 12.7 -3.2 25 153-177 81-108 (131)
9 2hpi_A DNA polymerase III alph 1.0 1 1 12.7 -3.0 14 116-129 270-283 (1220)
10 3fjv_A Uncharacterized novel p 1.0 1 1 12.6 1.9 12 152-163 49-60 (194)
No 1
>3r84_A Mediator of RNA polymerase II transcription subun; four-helix bundle, nucleus; HET: MSE; 2.05A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=15.43 Aligned_cols=24 Identities=17% Similarity=0.487 Sum_probs=18.5
Q ss_pred HHHHHHHHHHH---HHHCCCCCCCCCC
Q ss_conf 99999999998---6407336888865
Q 029658 151 VLTMKRQILHM---IKYKYVPFNIGKP 174 (190)
Q Consensus 151 ~ltm~rqI~HM---iKyrYvPf~~gK~ 174 (190)
...|||||++| |--+-+|-+.+|+
T Consensus 60 ~v~LrkEIk~LdEnig~~~LPinv~~k 86 (86)
T 3r84_A 60 TTQLRKEIQLLDENVGTRLLPINVNKK 86 (86)
T ss_dssp HHHHHHHHHHHHHTBTTTBCCC-----
T ss_pred HHHHHHHHHHHHHCCCCEEECCCCCCC
T ss_conf 999999999998733771325427989
No 2
>3owt_C Regulatory protein SIR3; RCT domain, protein binding; 2.00A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=13.82 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHC
Q ss_conf 9999999898876521
Q 029658 14 KWKSDFSRKFQYYLDK 29 (190)
Q Consensus 14 ~~~~~~~~~yq~~LDk 29 (190)
...++++.+||..||+
T Consensus 12 atlsklkkkyqiildr 27 (27)
T 3owt_C 12 ATLSKLKKKYQIILDR 27 (27)
T ss_pred HHHHHHHHHHEEEECC
T ss_conf 8899887654133149
No 3
>2hnh_A DNA polymerase III alpha subunit; DNA replication, nucleotidyltransferase, beta, PHP, transferase; HET: DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Probab=1.00 E-value=1 Score=13.37 Aligned_cols=13 Identities=15% Similarity=0.061 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 7999999999873
Q 029658 117 LTKAFVVAFFLTF 129 (190)
Q Consensus 117 ~tra~~ia~~~Tf 129 (190)
...+.-|+--|.+
T Consensus 257 l~nt~~Ia~~c~~ 269 (910)
T 2hnh_A 257 LANTVEIAKRCNV 269 (910)
T ss_dssp HHHHHHHHHHCCC
T ss_pred HHHHHHHHHHCEE
T ss_conf 9989999985267
No 4
>3din_C Preprotein translocase subunit SECY; protein translocation, membrane protein, ATPase, ATP-binding membrane, nucleotide-binding, protein transport; HET: ADP; 4.50A {Thermotoga maritima MSB8}
Probab=1.00 E-value=1 Score=12.99 Aligned_cols=108 Identities=15% Similarity=0.230 Sum_probs=54.5
Q ss_pred CEEEEHHHHHHHHHHHHHHHCCCCCCCHHHH----CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH---HH
Q ss_conf 3787334789999998885239998900110----0489999999987798644785368999979999999998---73
Q 029658 57 GFYIVTYGLGIYILNLLIGFLSPSVDPELEA----LNTASLPTKGSDEFKPFVRRLPEFKFWYALTKAFVVAFFL---TF 129 (190)
Q Consensus 57 g~yiVtY~LgIylLnlfi~FLtP~~Dp~l~~----edg~~Lp~~~~~EFrPFiRRLPEFkFW~~~tra~~ia~~~---Tf 129 (190)
.+|.+.|.+-|....-|-.+++ ++|+... +.|...|.-... +|-.+-|..--.=.....|..+++++ .+
T Consensus 304 ~~y~~~y~~lii~Fs~fy~~i~--~np~diA~~lkk~G~~IpGiRpG--~~T~~yL~~vi~rit~~Ga~~L~~iavlp~~ 379 (431)
T 3din_C 304 FLYLLIYGLLVFFFTYFYSVVI--FDPREISENIRKYGGYIPGLRPG--RSTEQYLHRVLNRVTFIGAVFLVVIALLPYL 379 (431)
T ss_dssp HHHHHHHHHHHHHHHHHHHTCT--THHHHHTTSCCCCBCSSCCCCCT--THHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHHCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7999999999999999999980--59999999999879917797998--3689999999999999839999999997899
Q ss_pred HCC-CCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 114-5555145---9999999999999999999998640733688
Q 029658 130 FSV-LDVPVFW---PILLCYWIFLFVLTMKRQILHMIKYKYVPFN 170 (190)
Q Consensus 130 f~~-fDiPVfW---PiLl~Yfi~Lf~ltm~rqI~HMiKyrYvPf~ 170 (190)
... +++|.+- .+|.+ +..-.=|+++--.|++..+|-.|-
T Consensus 380 ~~~~~g~~~~~gGTslLI~--Vgv~l~~~~qi~s~~~~~~Y~g~~ 422 (431)
T 3din_C 380 VQGAIKVNVWIGGTSALIA--VGVALDIIQQMETHMVMRHYEGFI 422 (431)
T ss_dssp HTTTSCCSCCTTHHHHHHH--HHHHHHHHHHHHHHCCCCCSSTTC
T ss_pred HHHHHCCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9997377733664221433--998999999999999898748998
No 5
>3dl8_G Preprotein translocase subunit SECY; RECA-type ATPase membrane protein translocation protein- protein complex, ATP-binding, cell membrane; 7.50A {Aquifex aeolicus}
Probab=1.00 E-value=1 Score=12.98 Aligned_cols=106 Identities=21% Similarity=0.279 Sum_probs=50.8
Q ss_pred CEEEEHHHHHHHHHHHHHHHCCCCCCCHHHH----CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH---HH
Q ss_conf 3787334789999998885239998900110----0489999999987798644785368999979999999998---73
Q 029658 57 GFYIVTYGLGIYILNLLIGFLSPSVDPELEA----LNTASLPTKGSDEFKPFVRRLPEFKFWYALTKAFVVAFFL---TF 129 (190)
Q Consensus 57 g~yiVtY~LgIylLnlfi~FLtP~~Dp~l~~----edg~~Lp~~~~~EFrPFiRRLPEFkFW~~~tra~~ia~~~---Tf 129 (190)
.+|.+.|.+-|....-|-.+++ ++|+... +.|...|.-... +|-.+-|..--.=.....|..+++++ .+
T Consensus 309 ~~y~~~y~~lii~Fs~fy~~i~--~np~diA~~lkk~G~~IpGiRpG--~~T~~yL~~vi~rit~~Ga~~L~~iavlp~~ 384 (429)
T 3dl8_G 309 IFYNFLYVTFIVFFTYFYTAVL--INPVELAENLHKAGAFIPGVRPG--QDTVKYLERIINRLIFFGALFLSVIALIPIL 384 (429)
T ss_dssp HHHHHHHHHHHHHHHHHHHTCT--THHHHHHHTCCCCBSSSBCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHC--CCHHHHHHHHHHCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6999999999999999999971--59999999999879917897998--4689999999998889709999999998999
Q ss_pred HCC-CCCCCHH---HHHHHHHHHHHHHHHHHHH-HHHHHHCCCCC
Q ss_conf 114-5555145---9999999999999999999-99864073368
Q 029658 130 FSV-LDVPVFW---PILLCYWIFLFVLTMKRQI-LHMIKYKYVPF 169 (190)
Q Consensus 130 f~~-fDiPVfW---PiLl~Yfi~Lf~ltm~rqI-~HMiKyrYvPf 169 (190)
... +++|.+- .+|.+ +-..+...+|| .|++..+|-.|
T Consensus 385 ~~~~~g~~~~~gGTslLI~---Vgv~l~~~~qi~s~l~~~~Y~g~ 426 (429)
T 3dl8_G 385 ISVWFNIPFYFGGTTALIV---VGVALDTFRQIETYLIQKKYKSY 426 (429)
T ss_dssp HTTSSCCSCCCSTHHHHHH---HHHHHHHHHHHHHHCCCCCTTCS
T ss_pred HHHHHCCCCCCCCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9987287720664221333---99899999999999999987776
No 6
>1v74_A Colicin D; colicin D - IMMD complex, cytotoxicity, transfer RNAse, protein-protein inhibition; HET: 1PE; 2.00A {Escherichia coli} SCOP: d.243.1.1 PDB: 1tfo_A 1tfk_A*
Probab=1.00 E-value=1 Score=12.86 Aligned_cols=16 Identities=25% Similarity=0.266 Sum_probs=11.4
Q ss_pred HHHHHHHHHHCCCCCCC
Q ss_conf 99999986407336888
Q 029658 155 KRQILHMIKYKYVPFNI 171 (190)
Q Consensus 155 ~rqI~HMiKyrYvPf~~ 171 (190)
++|.+||-||.+ -|.+
T Consensus 12 ~~qLqkkfkHa~-DFGi 27 (107)
T 1v74_A 12 RKQLDKKYKHAG-DFGI 27 (107)
T ss_dssp HHHHHHHGGGGG-GGTC
T ss_pred HHHHHHHHCCCC-CCCC
T ss_conf 789876741143-1154
No 7
>3j01_A Preprotein translocase SECY subunit; ribonucleoprotein, nucleotide-binding, PR biosynthesis, translation, zinc-finger, 70S ribosome, ribos translocon; 7.10A {Escherichia coli 536} PDB: 2akh_Y 2aki_Y
Probab=1.00 E-value=1 Score=12.77 Aligned_cols=109 Identities=17% Similarity=0.324 Sum_probs=56.3
Q ss_pred CCEEEEHHHHHHHHHHHHHHHCCCCCCCHHHH----CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH---H
Q ss_conf 43787334789999998885239998900110----0489999999987798644785368999979999999998---7
Q 029658 56 QGFYIVTYGLGIYILNLLIGFLSPSVDPELEA----LNTASLPTKGSDEFKPFVRRLPEFKFWYALTKAFVVAFFL---T 128 (190)
Q Consensus 56 ~g~yiVtY~LgIylLnlfi~FLtP~~Dp~l~~----edg~~Lp~~~~~EFrPFiRRLPEFkFW~~~tra~~ia~~~---T 128 (190)
+-.|.+.|++-|....-|-.++ .++|+... +.|...|.-... +|=.+-|..--.=.....|..+++++ .
T Consensus 307 ~~~~~~~y~~lii~F~~fyt~i--~~np~diA~~lkk~G~~IpGiRpG--~~T~~yL~~vi~rit~~Ga~~L~~iavlP~ 382 (435)
T 3j01_A 307 QPLYVLLYASAIIFFCFFYTAL--VFNPRETADNLKKSGAFVPGIRPG--EQTAKYIDKVMTRLTLVGALYITFICLIPE 382 (435)
T ss_dssp GGGGTHHHHHHHHHHHHHHHHH--SSCTTHHHHHTTSTTCSSSCCSSS--SSSCSHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7199999999999999999998--269999999999869807785898--468999999999999998999999999999
Q ss_pred HHC-CCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 311-45555145---9999999999999999999998640733688
Q 029658 129 FFS-VLDVPVFW---PILLCYWIFLFVLTMKRQILHMIKYKYVPFN 170 (190)
Q Consensus 129 ff~-~fDiPVfW---PiLl~Yfi~Lf~ltm~rqI~HMiKyrYvPf~ 170 (190)
+.. .+++|.+- .+|.+ +..-.=|+++--.||+..+|-.|-
T Consensus 383 ~l~~~~~~~~~~gGTslLI~--VgV~ldt~~qi~s~l~~~~Y~g~~ 426 (435)
T 3j01_A 383 FMRDAMKVPFYFGGTSLLIV--VVVIMDFMAQVQTLMMSSQYESAL 426 (435)
T ss_dssp HTTSCCSSSSSSCCHHHHHT--HHHHHHHHHHHHHHTSCCCCCCSC
T ss_pred HHHHHHCCCEECCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99986145700343758989--999999999999999999889997
No 8
>3rj1_A Mediator of RNA polymerase II transcription subun; RNA polymeras II, POL II, head module, head, regulator, helical bundle; 4.30A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=12.74 Aligned_cols=25 Identities=20% Similarity=0.565 Sum_probs=18.1
Q ss_pred HHHHHHHHH---HHHCCCCCCCCCCCCC
Q ss_conf 999999998---6407336888865447
Q 029658 153 TMKRQILHM---IKYKYVPFNIGKPRYG 177 (190)
Q Consensus 153 tm~rqI~HM---iKyrYvPf~~gK~~y~ 177 (190)
.+||||++| |--+-+|.+.+|+.-+
T Consensus 81 ~LRkEIk~LDEniG~~lLPInV~kKa~~ 108 (131)
T 3rj1_A 81 QLRKEIQLLDENVGTRLLPINVNKKALG 108 (131)
T ss_dssp TTTTTTSSTTTCC---------------
T ss_pred HHHHHHHHHHHCCCCEEECEECCCCCCC
T ss_conf 9999999998712772432024620000
No 9
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like nucleotidyltransferase fold, transferase; HET: DNA; 3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*
Probab=1.00 E-value=1 Score=12.68 Aligned_cols=14 Identities=7% Similarity=0.107 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 97999999999873
Q 029658 116 ALTKAFVVAFFLTF 129 (190)
Q Consensus 116 ~~tra~~ia~~~Tf 129 (190)
.+..+.-||=-|.+
T Consensus 270 al~NT~~IA~~c~~ 283 (1220)
T 2hpi_A 270 PFDNTVEIARMCDV 283 (1220)
T ss_dssp HHHHHHHHHHTCCC
T ss_pred HHHHHHHHHHHCEE
T ss_conf 99999999972888
No 10
>3fjv_A Uncharacterized novel protein; YP_111841.1, novel protein of unknown function; HET: MSE; 1.90A {Burkholderia pseudomallei K96243}
Probab=1.00 E-value=1 Score=12.64 Aligned_cols=12 Identities=33% Similarity=0.487 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999864
Q 029658 152 LTMKRQILHMIK 163 (190)
Q Consensus 152 ltm~rqI~HMiK 163 (190)
.||+.|||-|+.
T Consensus 49 ~Tv~~QIQEMlr 60 (194)
T 3fjv_A 49 TTIRYQIHEMLH 60 (194)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
T ss_conf 799999999999
Done!