Query 041147
Match_columns 222
No_of_seqs 111 out of 123
Neff 4.2
Searched_HMMs 29240
Date Mon Mar 25 06:38:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041147.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/041147hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2kj8_A Putative prophage CPS-5 58.0 21 0.00073 25.2 5.5 23 8-30 67-90 (118)
2 1dzf_A DNA-directed RNA polyme 36.1 26 0.00088 30.2 3.3 39 1-42 1-42 (215)
3 1m3w_A H10H24; four-helix bund 35.2 28 0.00096 21.4 2.5 22 186-207 4-25 (32)
4 3kkj_A Amine oxidase, flavin-c 34.5 9.4 0.00032 28.1 0.3 24 39-63 309-334 (336)
5 2joi_A Hypothetical protein TA 32.1 11 0.00038 29.9 0.4 8 78-85 21-28 (118)
6 4hnl_A Mandelate racemase/muco 28.0 12 0.00043 33.7 0.0 7 58-64 1-7 (421)
7 1d0c_A Bovine endothelial nitr 27.2 25 0.00085 33.4 1.9 21 186-206 85-105 (444)
8 2q58_A Fragment, farnesyl pyro 27.2 12 0.00041 33.8 -0.3 12 59-70 4-15 (368)
9 4h1z_A Enolase Q92ZS5; dehydra 27.0 13 0.00046 33.6 0.0 7 58-64 1-7 (412)
10 1d1d_A Protein (capsid protein 26.8 27 0.00091 30.8 1.9 30 175-205 170-199 (262)
11 3e7m_A Nitric oxide synthase, 25.9 18 0.00063 34.2 0.7 21 186-206 66-86 (433)
12 4e0q_A COP9 signalosome comple 23.6 22 0.00076 27.9 0.7 35 169-206 46-82 (141)
13 3n5w_A Nitric oxide synthase; 23.3 33 0.0011 32.4 1.9 21 186-206 56-76 (422)
14 2r0q_C Putative transposon TN5 23.2 37 0.0013 27.3 2.0 24 17-40 163-186 (209)
15 2jyl_A Capsid protein P24 (Ca) 22.3 40 0.0014 25.7 1.9 16 192-207 35-50 (105)
16 1baj_A GAG polyprotein; capsid 20.9 47 0.0016 24.9 2.0 16 192-207 17-32 (101)
No 1
>2kj8_A Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA integration, DNA recombination, structural genomics, protein structure initiative; NMR {Escherichia coli k-12}
Probab=57.96 E-value=21 Score=25.21 Aligned_cols=23 Identities=22% Similarity=0.053 Sum_probs=18.5
Q ss_pred chHHHHHHHHHHHHHHHHH-Hhcc
Q 041147 8 PPVVAKKLWKIVRIVFFMI-KAGI 30 (222)
Q Consensus 8 ~pvvaKRlW~vvR~v~fMl-RKGi 30 (222)
+|..++++..++|.+|=++ +.|+
T Consensus 67 s~~t~~~~~~~l~~~~~~Av~~~~ 90 (118)
T 2kj8_A 67 AMERANKARRRCGEVFRYAIVTGR 90 (118)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHHHHHHHHHHcCC
Confidence 5778999999999999664 5674
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=36.14 E-value=26 Score=30.17 Aligned_cols=39 Identities=26% Similarity=0.458 Sum_probs=25.4
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHHHh-c--cccchhhhhHHHH
Q 041147 1 MEIEPTKPPVVAKKLWKIVRIVFFMIKA-G--ISKSKIMVDFHLM 42 (222)
Q Consensus 1 m~ME~~~~pvvaKRlW~vvR~v~fMlRK-G--isKrKLmmDlhLm 42 (222)
|+||.. .-..|||++-|.++-|+|- | ++..-+-+.+.-.
T Consensus 1 ~~m~~~---~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F 42 (215)
T 1dzf_A 1 MDQENE---RNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDF 42 (215)
T ss_dssp ----CC---HHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHH
T ss_pred CCcchH---HHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHH
Confidence 788875 3456999999999999995 6 5665565655533
No 3
>1m3w_A H10H24; four-helix bundle, heme binding, maquette, heme binding protein, electron transport, de novo protein; 2.80A {Synthetic} SCOP: k.8.1.1
Probab=35.17 E-value=28 Score=21.35 Aligned_cols=22 Identities=41% Similarity=0.613 Sum_probs=17.9
Q ss_pred hhhhHHHHHHHHHHHHHHhhHH
Q 041147 186 GQVDKAAEDFIKKFYKDLMLQK 207 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr~Q~ 207 (222)
+++=+--|||+++|-+-|++..
T Consensus 4 geiwklheeflkkfeellklhe 25 (32)
T 1m3w_A 4 GEIWKLHEEFLKKFEELLKLHE 25 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHH
Confidence 4566778999999999888754
No 4
>3kkj_A Amine oxidase, flavin-containing; oxidoreductase, PSR10, Q888A4, X-RAY, structure, PSI, protein structure initiative; HET: FAD; 2.50A {Pseudomonas syringae PV}
Probab=34.52 E-value=9.4 Score=28.14 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=13.5
Q ss_pred HHHHHhhccchhhhhhhhhhc--ccCC
Q 041147 39 FHLMLKRGNKLAGKAIGNLIF--HNHL 63 (222)
Q Consensus 39 lhLmlKR~gK~agKal~nlm~--Hh~~ 63 (222)
++.=+.= |+.|+++|.+-+. ||||
T Consensus 309 v~~A~~s-G~~aA~~I~~~L~~e~~~~ 334 (336)
T 3kkj_A 309 VEGAWLS-GQEAARRLLEHLQLEHHHH 334 (336)
T ss_dssp HHHHHHH-HHHHHHHHHHHTTC-----
T ss_pred HHHHHHH-HHHHHHHHHHHhhccCCcc
Confidence 3444555 7888888887665 5554
No 5
>2joi_A Hypothetical protein TA0095; structural genomics, COG4004 orthologous group, structural genomics consortium, SGC, unknown function; NMR {Thermoplasma acidophilum}
Probab=32.14 E-value=11 Score=29.87 Aligned_cols=8 Identities=25% Similarity=0.276 Sum_probs=4.5
Q ss_pred CCCceeee
Q 041147 78 ISPKEYEF 85 (222)
Q Consensus 78 ~~prEyEF 85 (222)
+.-+||+|
T Consensus 21 ~~MqeY~~ 28 (118)
T 2joi_A 21 GHMREYPV 28 (118)
T ss_dssp --CEEECC
T ss_pred hhhhcccc
Confidence 36788874
No 6
>4hnl_A Mandelate racemase/muconate lactonizing enzyme; dehydratase, magnesium binding, enzyme function initiative,; 1.48A {Enterococcus gallinarum EG2} PDB: 3s47_A
Probab=27.98 E-value=12 Score=33.71 Aligned_cols=7 Identities=29% Similarity=0.643 Sum_probs=0.0
Q ss_pred hcccCCC
Q 041147 58 IFHNHLS 64 (222)
Q Consensus 58 m~Hh~~s 64 (222)
|.|||||
T Consensus 1 mhhhhhh 7 (421)
T 4hnl_A 1 MHHHHHH 7 (421)
T ss_dssp -------
T ss_pred CCcccCC
Confidence 4554443
No 7
>1d0c_A Bovine endothelial nitric oxide synthase heme DOM; alpha-beta fold, oxidoreductase; HET: HEM INE; 1.65A {Bos taurus} SCOP: d.174.1.1 PDB: 1d0o_A* 1d1v_A* 1d1w_A* 1d1x_A* 1d1y_A* 1dm6_A* 1dm7_A* 1dm8_A* 1dmi_A* 1dmj_A* 1dmk_A* 1ed4_A* 1ed5_A* 1ed6_A* 1foi_A* 1foj_A* 1fol_A* 1foo_A* 1fop_A* 1nse_A* ...
Probab=27.18 E-value=25 Score=33.39 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=18.2
Q ss_pred hhhhHHHHHHHHHHHHHHhhH
Q 041147 186 GQVDKAAEDFIKKFYKDLMLQ 206 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr~Q 206 (222)
++|-.+|++||+.||..++.+
T Consensus 85 ~~l~~eA~~Fi~~~y~e~~~~ 105 (444)
T 1d0c_A 85 EQLLSQARDFINQYYSSIKRS 105 (444)
T ss_dssp HHHHHHHHHHHHHHHHHTTCT
T ss_pred HHHHHHHHHHHHHHHHhcccc
Confidence 468899999999999998664
No 8
>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A*
Probab=27.16 E-value=12 Score=33.80 Aligned_cols=12 Identities=33% Similarity=0.310 Sum_probs=0.0
Q ss_pred cccCCCCcccCC
Q 041147 59 FHNHLSSLSCRS 70 (222)
Q Consensus 59 ~Hh~~s~~s~rs 70 (222)
+||||+++|.++
T Consensus 4 ~~~~~~~~s~~~ 15 (368)
T 2q58_A 4 SHHHHHHSSGRE 15 (368)
T ss_dssp ------------
T ss_pred ccccccccCCcc
Confidence 355554444443
No 9
>4h1z_A Enolase Q92ZS5; dehydratase, magnesium binding site, enzyme function initiat isomerase; 2.01A {Sinorhizobium meliloti} PDB: 2ppg_A
Probab=26.96 E-value=13 Score=33.60 Aligned_cols=7 Identities=29% Similarity=0.643 Sum_probs=0.0
Q ss_pred hcccCCC
Q 041147 58 IFHNHLS 64 (222)
Q Consensus 58 m~Hh~~s 64 (222)
|.|||||
T Consensus 1 mhhhhhh 7 (412)
T 4h1z_A 1 MHHHHHH 7 (412)
T ss_dssp -------
T ss_pred CCcccCc
Confidence 4554443
No 10
>1d1d_A Protein (capsid protein); two independent domains helical bundles, virus/viral protein; NMR {Rous sarcoma virus} SCOP: a.28.3.1 a.73.1.1
Probab=26.83 E-value=27 Score=30.85 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=18.9
Q ss_pred cCCCCCCCCCChhhhHHHHHHHHHHHHHHhh
Q 041147 175 DSPFPLKDEGDGQVDKAAEDFIKKFYKDLML 205 (222)
Q Consensus 175 dSpfp~~d~~~~~VD~~AeeFI~rFy~qlr~ 205 (222)
.||-+..+- -+.-..--++|++||||.||.
T Consensus 170 ~s~~si~~I-kQGPkEpf~dfVdRl~kalra 199 (262)
T 1d1d_A 170 EPAGPWADI-TQGPSESFVDFANRLIKAVEG 199 (262)
T ss_dssp CCCCTTTSC-CCCSSSCHHHHHHHHHHHHHT
T ss_pred CCCCCHhHh-hhcCCCcHHHHHHHHHHHHHh
Confidence 455555440 011222478899999999997
No 11
>3e7m_A Nitric oxide synthase, inducible; NOS, heme, tetrahydrobiopterin, oxido calmodulin-binding, FAD, FMN, iron, metal-binding, NADP, oxidoreductase; HET: HEM H4B AT2; 2.00A {Mus musculus} SCOP: d.174.1.1 PDB: 2y37_A* 1r35_A* 3e67_A* 3e68_A* 3e6l_A* 3e6n_A* 3e6o_A* 3e6t_A* 3e7i_A* 3e65_A* 3e7t_A* 3eai_A* 3ebd_A* 3ebf_A* 3nqs_A* 1m8d_A* 1m8e_A* 1m8h_A* 1m8i_A* 1m9t_A* ...
Probab=25.87 E-value=18 Score=34.19 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=18.1
Q ss_pred hhhhHHHHHHHHHHHHHHhhH
Q 041147 186 GQVDKAAEDFIKKFYKDLMLQ 206 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr~Q 206 (222)
++|-.+|+|||+.||..++.+
T Consensus 66 e~l~~eA~~Fi~q~y~e~~~~ 86 (433)
T 3e7m_A 66 EELLPHAIEFINQYYGSFKEA 86 (433)
T ss_dssp HHHHHHHHHHHHHHHTTCSSC
T ss_pred HHHHHHHHHHHHHHHHhcCCC
Confidence 568999999999999888754
No 12
>4e0q_A COP9 signalosome complex subunit 6; MPN (MPR1P and PAD1P N-terminal) domain, unknown function; 2.50A {Drosophila melanogaster}
Probab=23.62 E-value=22 Score=27.94 Aligned_cols=35 Identities=14% Similarity=0.235 Sum_probs=24.1
Q ss_pred ccceeecC-CCCCCC-CCChhhhHHHHHHHHHHHHHHhhH
Q 041147 169 RQLRITDS-PFPLKD-EGDGQVDKAAEDFIKKFYKDLMLQ 206 (222)
Q Consensus 169 r~lrVtdS-pfp~~d-~~~~~VD~~AeeFI~rFy~qlr~Q 206 (222)
+.+.||+| |+|.++ +++-.+| .||.+..++++|.-
T Consensus 46 ~~veV~nsF~~p~~~~~~~~~~d---~~y~~~m~~~~k~v 82 (141)
T 4e0q_A 46 RNIEIMNSFELKTDVIGDETVIN---KDYYNKKEQQYKQV 82 (141)
T ss_dssp TEEEEEEEEECCEEEETTEEEEC---HHHHHHHHHHHHHH
T ss_pred CEEEEEEEEEecccCCCCceeec---HHHHHHHHHHHHHh
Confidence 57899999 777654 3333445 47888888888754
No 13
>3n5w_A Nitric oxide synthase; heme enzyme, substrate inhibitor, Zn oxidoreductase, oxidoreductase-oxidoreductase inhibitor COM; HET: HEM XFJ; 1.73A {Rattus norvegicus} SCOP: d.174.1.1 PDB: 2hx3_A* 2hx4_A* 3b3m_A* 3b3n_A* 3b3o_A* 3b3p_A* 3hsn_A* 3hso_A* 3hsp_A* 3jt3_A* 3jt4_A* 3jt5_A* 3jt6_A* 3jt7_A* 3jt8_A* 3jt9_A* 3jta_A* 3n2r_A* 3n5v_A* 1om4_A* ...
Probab=23.31 E-value=33 Score=32.41 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=18.5
Q ss_pred hhhhHHHHHHHHHHHHHHhhH
Q 041147 186 GQVDKAAEDFIKKFYKDLMLQ 206 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr~Q 206 (222)
++|-.+|+|||+.||..++.+
T Consensus 56 e~ll~eA~~Fi~q~y~e~~~~ 76 (422)
T 3n5w_A 56 DQLFPLAKEFLDQYYSSIKRF 76 (422)
T ss_dssp HHHHHHHHHHHHHHHHHTTCT
T ss_pred HHHHHHHHHHHHHHHHhcccc
Confidence 468999999999999998764
No 14
>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}
Probab=23.24 E-value=37 Score=27.30 Aligned_cols=24 Identities=29% Similarity=0.307 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHhccccchhhhhHH
Q 041147 17 KIVRIVFFMIKAGISKSKIMVDFH 40 (222)
Q Consensus 17 ~vvR~v~fMlRKGisKrKLmmDlh 40 (222)
.+||-+|-|+.+|.|.++++-.|+
T Consensus 163 ~iv~~i~~~~~~G~s~~~Ia~~l~ 186 (209)
T 2r0q_C 163 VIYHRVVEMLEEGQAISKIAKEVN 186 (209)
T ss_dssp HHHHHHHHHHHTTCCHHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHC
Confidence 468888999999998888887776
No 15
>2jyl_A Capsid protein P24 (Ca); HIV-1, carboxy-terminal, dimerization domain, CTD, 3D- NMR, capsid protein (Ca), double mutant; NMR {Human immunodeficiency virus 1} PDB: 2k1c_A* 2l6e_A*
Probab=22.28 E-value=40 Score=25.74 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHhhHH
Q 041147 192 AEDFIKKFYKDLMLQK 207 (222)
Q Consensus 192 AeeFI~rFy~qlr~Q~ 207 (222)
-++|+.|||+.||.-+
T Consensus 35 f~dyVdR~~k~l~ae~ 50 (105)
T 2jyl_A 35 FRDYVDRFYKTLRAEQ 50 (105)
T ss_dssp HHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHhh
Confidence 6789999999999643
No 16
>1baj_A GAG polyprotein; capsid, HIV-1 assembly protein, viral protein; 2.60A {Human immunodeficiency virus 1} SCOP: a.28.3.1
Probab=20.92 E-value=47 Score=24.89 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHhhHH
Q 041147 192 AEDFIKKFYKDLMLQK 207 (222)
Q Consensus 192 AeeFI~rFy~qlr~Q~ 207 (222)
-++|+.|||+.||.-+
T Consensus 17 f~d~v~R~~k~l~~e~ 32 (101)
T 1baj_A 17 FRDYVDRFYKTLRAEQ 32 (101)
T ss_dssp HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHhh
Confidence 6789999999998643
Done!