Query 032901
Match_columns 130
No_of_seqs 103 out of 200
Neff 3.6
Searched_HMMs 29240
Date Mon Mar 25 11:44:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032901.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032901hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3u5c_a 40S ribosomal protein S 100.0 6.4E-63 2.2E-67 368.2 6.4 106 1-106 1-108 (119)
2 2xzm_5 Ribosomal protein S26E 100.0 3.1E-60 1.1E-64 353.7 6.3 101 1-101 1-105 (119)
3 1m06_J J protein, small core p 53.3 7.1 0.00024 21.9 1.7 15 1-15 1-15 (26)
4 3mhs_C SAGA-associated factor 43.0 13 0.00045 26.6 2.1 18 15-32 65-82 (99)
5 1twf_J DNA-directed RNA polyme 41.7 6.7 0.00023 26.5 0.4 14 19-32 3-16 (70)
6 1ef4_A Subunit N, DNA-directed 39.1 6.9 0.00024 25.3 0.2 14 19-32 2-15 (55)
7 4ayb_N DNA-directed RNA polyme 37.6 8.5 0.00029 25.7 0.4 14 19-32 3-16 (66)
8 3na7_A HP0958; flagellar bioge 35.8 12 0.00041 29.0 1.1 13 18-30 220-232 (256)
9 2g84_A Cytidine and deoxycytid 24.6 26 0.00088 26.5 1.2 22 64-85 106-130 (197)
10 2m0d_A Zinc finger and BTB dom 22.6 37 0.0013 15.5 1.2 14 19-32 2-15 (30)
11 2kvf_A Zinc finger and BTB dom 22.1 40 0.0014 15.5 1.3 13 19-31 2-14 (28)
12 1a6b_B Momulv, zinc finger pro 21.0 32 0.0011 20.4 0.9 14 15-28 5-18 (40)
13 2kvh_A Zinc finger and BTB dom 20.3 46 0.0016 15.2 1.3 13 19-31 2-14 (27)
14 2yu5_A Zinc finger protein 473 20.1 81 0.0028 16.3 2.4 16 17-32 9-24 (44)
No 1
>3u5c_a 40S ribosomal protein S26-A, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_a
Probab=100.00 E-value=6.4e-63 Score=368.19 Aligned_cols=106 Identities=61% Similarity=1.004 Sum_probs=94.9
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhccccccccceeeeeeeeeeeecee
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 78 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 78 (130)
||+|||||||+|||||||++|+|+|||+|||| |||+|+|+||||++++|||+|||||++|+|||||+|+|||||||||
T Consensus 1 M~kKRrN~GR~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irNiVeaaavRDi~easv~~~y~lPKlyvKl~YCVSCAIH 80 (119)
T 3u5c_a 1 MPKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYPEYALPKTYNKLHYCVSCAIH 80 (119)
T ss_dssp -CCCCSSTTSCCCSCSCCCEEECTTTCCEEEGGGSCEEEEEECSSCSSTHHHHHHTCCSSSCCCCCEEEEEECCSHHHHH
T ss_pred CCcccccCCCCCCCCCCCccEeeccccccccccceeeEEeCcCcccHHHHHHHHhccchhhccccceeEEEEEeeeeeee
Confidence 99999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred cceeccccccccccCCCCCCCcCCCCCC
Q 032901 79 SHVVRVRSRTNRRIREPPQRFRRRDDVP 106 (130)
Q Consensus 79 skVVRvRS~e~RK~r~pp~~~~~~~~~~ 106 (130)
++||||||+|+||+|+||++|++..+.+
T Consensus 81 skVVR~RS~e~Rk~r~pp~r~~~~~~~~ 108 (119)
T 3u5c_a 81 ARIVRVRSREDRKNRAPPQRPRFNRENK 108 (119)
T ss_dssp TSSCCCCCTTTTSCCCCC----------
T ss_pred ccccccCChHHcccCCCCCccCcccCCc
Confidence 9999999999999999999999966644
No 2
>2xzm_5 Ribosomal protein S26E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_5
Probab=100.00 E-value=3.1e-60 Score=353.69 Aligned_cols=101 Identities=50% Similarity=0.982 Sum_probs=93.8
Q ss_pred CCcccccCCCCCCCCCccccEeccCccccccc--ceeEeeecccchhHHHHhHHHhcccc--ccccceeeeeeeeeeeec
Q 032901 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPK--AIKRFLVRNIVEQAAVRDVQEACVYD--GYTLPKLYAKMQYCVSCA 76 (130)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPK--AIKrf~irNiVEaaavRDi~eAsv~~--~y~lPKlyvKl~YCVSCA 76 (130)
||+|||||||+|||||||++|+|+|||+|||| |||+|+|+||||++++|||+|||+|+ +|+|||||+|+|||||||
T Consensus 1 M~kKRrN~GR~KkgrGhv~~V~C~nCgr~vPKDKAIKrf~irniVeaaavrDi~ea~v~~~~~y~lPKlyvK~~YCVSCA 80 (119)
T 2xzm_5 1 MPVKRRNAGRSQKNRGHTRTVPCTNCGRQVAKDKAVKRYTVRDMVDPSSKRDIQQKLAFENEKQGIPKLYVKLQYCISCA 80 (119)
T ss_dssp -CCCCSSTTCCCCSSSCCCEEECTTTCCEEETTTSEECCEEECSSCHHHHHHHHHSBCSCCCSCCSCCEEECCEECHHHH
T ss_pred CCcccccCCCCCCCCCCCccEeeCCccccCcccceeEEEEeccCccHHHHHHHHhccccccccccccceeeeEEEeeeee
Confidence 99999999999999999999999999999999 99999999999999999999999999 999999999999999999
Q ss_pred eecceeccccccccccCCCCCCCcC
Q 032901 77 IHSHVVRVRSRTNRRIREPPQRFRR 101 (130)
Q Consensus 77 IHskVVRvRS~e~RK~r~pp~~~~~ 101 (130)
||++||||||+|+||+|+||++|++
T Consensus 81 IH~kIVRvRs~e~Rk~r~pp~~~~~ 105 (119)
T 2xzm_5 81 IHSRVVRVRCAEDRRIRRPPIRNRK 105 (119)
T ss_dssp HHTTSSCCCCTGGGGCCCC------
T ss_pred eeccccccCCHHHcccCCCCCcccc
Confidence 9999999999999999999999876
No 3
>1m06_J J protein, small core protein; bacteriophage, virion; HET: 3DR; 3.50A {Enterobacteria phage ALPHA3}
Probab=53.32 E-value=7.1 Score=21.87 Aligned_cols=15 Identities=40% Similarity=0.485 Sum_probs=12.9
Q ss_pred CCcccccCCCCCCCC
Q 032901 1 MTFKRRNGGRNKHGR 15 (130)
Q Consensus 1 M~kKRrNnGR~Kkgr 15 (130)
|-+-||+.||+|+.|
T Consensus 1 mk~~rrs~~r~kgar 15 (26)
T 1m06_J 1 MKKARRSPSRRKGAR 15 (26)
T ss_dssp CCGGGSCCCCCSSSC
T ss_pred CcccccCCCcCCceE
Confidence 778899999999876
No 4
>3mhs_C SAGA-associated factor 11; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3m99_B 3mhh_C 4fjc_C 4fk5_C 4fip_C 2lo2_A 3kjl_E 3kik_E
Probab=43.00 E-value=13 Score=26.58 Aligned_cols=18 Identities=28% Similarity=0.811 Sum_probs=14.2
Q ss_pred CCccccEeccCccccccc
Q 032901 15 RGHVKFIRCSNCGKCCPK 32 (130)
Q Consensus 15 rGhv~~V~C~NCgr~vPK 32 (130)
......+.|.||+|-|.-
T Consensus 65 ~~~s~~~~C~nC~R~vaa 82 (99)
T 3mhs_C 65 QESSQYIHCENCGRDVSA 82 (99)
T ss_dssp CTTSCEEECTTTCCEEEG
T ss_pred ccCCCeEECCCCCCCchh
Confidence 356778999999997753
No 5
>1twf_J DNA-directed RNA polymerases I, II, and III 8.3 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.11.1 PDB: 1i3q_J 1i6h_J 1k83_J* 1nik_J 1nt9_J 1pqv_J 1r5u_J 1r9s_J* 1r9t_J* 1sfo_J* 1twa_J* 1twc_J* 1i50_J* 1twg_J* 1twh_J* 1wcm_J 1y1v_J 1y1w_J 1y1y_J 1y77_J* ...
Probab=41.70 E-value=6.7 Score=26.48 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=12.2
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||+|..||+.+--
T Consensus 3 iPVRCFTCGkvi~~ 16 (70)
T 1twf_J 3 VPVRCFSCGKVVGD 16 (70)
T ss_dssp CCSBCTTTCCBCTT
T ss_pred CCeecCCCCCChHH
Confidence 48999999998866
No 6
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=39.09 E-value=6.9 Score=25.31 Aligned_cols=14 Identities=36% Similarity=0.724 Sum_probs=12.0
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||||-.||..+--
T Consensus 2 iPVRCFTCGkvi~~ 15 (55)
T 1ef4_A 2 IPVRCLSCGKPVSA 15 (55)
T ss_dssp CSSSCSCTTSCCHH
T ss_pred CCeecCCCCCChhH
Confidence 48999999998865
No 7
>4ayb_N DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_N 2y0s_N 2waq_N 4b1o_N 4b1p_O 2pmz_N 3hkz_N
Probab=37.57 E-value=8.5 Score=25.72 Aligned_cols=14 Identities=36% Similarity=0.676 Sum_probs=11.8
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
-||||..||..+--
T Consensus 3 IPVRCFTCGkvi~~ 16 (66)
T 4ayb_N 3 IPIRCFTCGSLIAD 16 (66)
T ss_dssp CCSBCTTTCCBCHH
T ss_pred CCcccCCCcHhHHH
Confidence 38999999998855
No 8
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}
Probab=35.80 E-value=12 Score=29.01 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=10.7
Q ss_pred cccEeccCccccc
Q 032901 18 VKFIRCSNCGKCC 30 (130)
Q Consensus 18 v~~V~C~NCgr~v 30 (130)
...|.|.||||.+
T Consensus 220 ~~Iv~Cp~CgRIL 232 (256)
T 3na7_A 220 GDMITCPYCGRIL 232 (256)
T ss_dssp SSCEECTTTCCEE
T ss_pred CCEEECCCCCeeE
Confidence 3579999999965
No 9
>2g84_A Cytidine and deoxycytidylate deaminase zinc-bindi; zinc-binding region, structural genomics, PSI, protein structure initiative; 1.40A {Nitrosomonas europaea} SCOP: c.97.1.2
Probab=24.59 E-value=26 Score=26.53 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=18.8
Q ss_pred eeeeeeeeeeeec---eecceeccc
Q 032901 64 KLYAKMQYCVSCA---IHSHVVRVR 85 (130)
Q Consensus 64 KlyvKl~YCVSCA---IHskVVRvR 85 (130)
-||+++.=|..|+ ||++|-||=
T Consensus 106 tlYvTlEPC~mCa~Aii~agI~rVv 130 (197)
T 2g84_A 106 ELVTSAEPCVMCFGAVIWSGVRSLV 130 (197)
T ss_dssp EEEEEECCCHHHHHHHHHHCCSEEE
T ss_pred EEEEeCCCCHHHHHHHHHhCcCEEE
Confidence 6899999999997 888887753
No 10
>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}
Probab=22.59 E-value=37 Score=15.50 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=10.1
Q ss_pred ccEeccCccccccc
Q 032901 19 KFIRCSNCGKCCPK 32 (130)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (130)
++..|+.||+....
T Consensus 2 k~~~C~~C~~~f~~ 15 (30)
T 2m0d_A 2 KPYQCDYCGRSFSD 15 (30)
T ss_dssp CCEECTTTCCEESC
T ss_pred cCccCCCCCcccCC
Confidence 46789999876543
No 11
>2kvf_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}
Probab=22.09 E-value=40 Score=15.48 Aligned_cols=13 Identities=38% Similarity=0.723 Sum_probs=9.3
Q ss_pred ccEeccCcccccc
Q 032901 19 KFIRCSNCGKCCP 31 (130)
Q Consensus 19 ~~V~C~NCgr~vP 31 (130)
++..|+.||+...
T Consensus 2 k~~~C~~C~k~f~ 14 (28)
T 2kvf_A 2 RPYSCSVCGKRFS 14 (28)
T ss_dssp CSEECSSSCCEES
T ss_pred cCccCCCCCcccC
Confidence 4678999987543
No 12
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1
Probab=20.98 E-value=32 Score=20.40 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=11.9
Q ss_pred CCccccEeccCccc
Q 032901 15 RGHVKFIRCSNCGK 28 (130)
Q Consensus 15 rGhv~~V~C~NCgr 28 (130)
+++...+.|-|||.
T Consensus 5 ~~~~~~~~C~~Cgk 18 (40)
T 1a6b_B 5 RSQLDRDQCAYCKE 18 (40)
T ss_dssp CCSCCSSSCSSSCC
T ss_pred cCCCCCCeeeECCC
Confidence 57788899999986
No 13
>2kvh_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}
Probab=20.34 E-value=46 Score=15.24 Aligned_cols=13 Identities=31% Similarity=0.496 Sum_probs=9.5
Q ss_pred ccEeccCcccccc
Q 032901 19 KFIRCSNCGKCCP 31 (130)
Q Consensus 19 ~~V~C~NCgr~vP 31 (130)
++..|+.||+...
T Consensus 2 k~~~C~~C~k~f~ 14 (27)
T 2kvh_A 2 KPFSCSLCPQRSR 14 (27)
T ss_dssp CCEECSSSSCEES
T ss_pred cCccCCCcChhhC
Confidence 4678999987544
No 14
>2yu5_A Zinc finger protein 473; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=20.11 E-value=81 Score=16.25 Aligned_cols=16 Identities=19% Similarity=0.563 Sum_probs=11.5
Q ss_pred ccccEeccCccccccc
Q 032901 17 HVKFIRCSNCGKCCPK 32 (130)
Q Consensus 17 hv~~V~C~NCgr~vPK 32 (130)
-.++..|+.|++....
T Consensus 9 ~~k~~~C~~C~k~f~~ 24 (44)
T 2yu5_A 9 GENPFKCSKCDRVFTQ 24 (44)
T ss_dssp CCCSEECSSSSCEESS
T ss_pred CCCCeECCCCCchhCC
Confidence 3568899999875443
Done!