Query 032843
Match_columns 132
No_of_seqs 109 out of 193
Neff 3.4
Searched_HMMs 29240
Date Mon Mar 25 10:28:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032843.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032843hhsearch_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 7.1E-67 2.4E-71 390.6 6.8 108 1-108 1-108 (119)
2 2xzm_5 Ribosomal protein S26E 100.0 4.9E-64 1.7E-68 375.3 6.8 103 1-103 1-105 (119)
3 1m06_J J protein, small core p 48.1 9.7 0.00033 21.4 1.7 15 1-15 1-15 (26)
4 3mhs_C SAGA-associated factor 42.1 17 0.00057 26.1 2.6 16 16-31 66-81 (99)
5 1lng_A SRP19, signal recogniti 37.3 5.5 0.00019 27.4 -0.6 23 26-48 16-38 (87)
6 1twf_J DNA-directed RNA polyme 36.4 8.8 0.0003 26.0 0.4 14 19-32 3-16 (70)
7 3na7_A HP0958; flagellar bioge 36.1 13 0.00043 29.0 1.3 15 19-33 221-235 (256)
8 3dlu_A SRP19, signal recogniti 34.8 6.4 0.00022 28.2 -0.6 22 27-48 20-41 (106)
9 1ef4_A Subunit N, DNA-directed 31.9 10 0.00034 24.6 0.1 12 19-30 2-13 (55)
10 4ayb_N DNA-directed RNA polyme 30.9 12 0.00042 25.0 0.4 11 20-30 4-14 (66)
11 1kvn_A SRP19; RNA binding prot 29.1 8.9 0.0003 27.2 -0.6 23 26-48 19-41 (104)
12 1jjd_A Metallothionein, SMTA; 28.5 19 0.00067 23.1 1.0 16 22-37 9-24 (55)
13 1jid_A Signal recognition part 27.4 10 0.00035 28.0 -0.6 23 26-48 31-53 (128)
14 2ecw_A Tripartite motif-contai 25.1 26 0.00089 21.3 1.1 27 20-46 59-85 (85)
15 2ys4_A Hydrocephalus-inducing 22.7 48 0.0016 22.4 2.2 24 23-46 31-54 (122)
16 2g84_A Cytidine and deoxycytid 22.7 23 0.00078 26.9 0.6 22 66-87 106-130 (197)
17 2m0d_A Zinc finger and BTB dom 22.1 41 0.0014 15.4 1.3 13 19-31 2-14 (30)
18 1a6b_B Momulv, zinc finger pro 21.9 28 0.00096 20.7 0.8 14 15-28 5-18 (40)
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=7.1e-67 Score=390.61 Aligned_cols=108 Identities=62% Similarity=1.010 Sum_probs=96.9
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccccceeeeEEeeeecee
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYDGYTLPKLYAKMQYCVSCAIH 80 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~~y~lPKlyvKl~YCVSCAIH 80 (132)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||++++|||+|||||++|+|||||+|+|||||||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCchhhccCCCCCCCcCCCCCC
Q 032843 81 SHVVRVRSRTNRRIREPPQRFRRRDDVP 108 (132)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~~~~~ 108 (132)
++||||||+|+||+|+||++|++..+.+
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 9999999999999999999999976654
No 2
>2xzm_5 Ribosomal protein S26E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_5
Probab=100.00 E-value=4.9e-64 Score=375.27 Aligned_cols=103 Identities=51% Similarity=0.988 Sum_probs=95.8
Q ss_pred CCcccccCCCCCCCCCccceEeecCCcceeecccceeeeeecccchhhHHhhHHhhcccc--ccccccceeeeEEeeeec
Q 032843 1 MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVYD--GYTLPKLYAKMQYCVSCA 78 (132)
Q Consensus 1 M~kKRrNnGR~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDiseAsv~~--~y~lPKlyvKl~YCVSCA 78 (132)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||++++|||+||+||+ +|+|||||+|+|||||||
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 999999999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred eecccccccCchhhccCCCCCCCcC
Q 032843 79 IHSHVVRVRSRTNRRIREPPQRFRR 103 (132)
Q Consensus 79 IHskVVRvRS~e~RK~r~pp~r~~~ 103 (132)
||++||||||+|+||+|+||++|++
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=48.06 E-value=9.7 Score=21.44 Aligned_cols=15 Identities=40% Similarity=0.485 Sum_probs=12.8
Q ss_pred CCcccccCCCCCCCC
Q 032843 1 MTFKRRNGGRNKHGR 15 (132)
Q Consensus 1 M~kKRrNnGR~Kkgr 15 (132)
|-+-||+.||+|+.|
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 778899999999875
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=42.07 E-value=17 Score=26.11 Aligned_cols=16 Identities=31% Similarity=0.889 Sum_probs=13.4
Q ss_pred CccceEeecCCcceee
Q 032843 16 GHVKFIRCSNCGKCCP 31 (132)
Q Consensus 16 Ghv~~V~C~NCgr~vP 31 (132)
.....+.|.||+|-|.
T Consensus 66 ~~s~~~~C~nC~R~va 81 (99)
T 3mhs_C 66 ESSQYIHCENCGRDVS 81 (99)
T ss_dssp TTSCEEECTTTCCEEE
T ss_pred cCCCeEECCCCCCCch
Confidence 5677899999999775
No 5
>1lng_A SRP19, signal recognition particle 19 kDa protein; protein-RNA complex, signaling protein/RNA complex; 2.30A {Methanocaldococcus jannaschii} SCOP: d.201.1.1 PDB: 2v3c_A 3ndb_A 1l9a_A*
Probab=37.31 E-value=5.5 Score=27.44 Aligned_cols=23 Identities=22% Similarity=0.377 Sum_probs=16.9
Q ss_pred Ccceeecccceeeeeecccchhh
Q 032843 26 CGKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVEaa 48 (132)
-||.|||++|+..-++..|.|+.
T Consensus 16 eGRrv~k~~aV~~P~~~EI~~a~ 38 (87)
T 1lng_A 16 EGRKVPEELAIEKPSLKDIEKAL 38 (87)
T ss_dssp TTCCSCTTTCBSSCCHHHHHHHH
T ss_pred hcCccCHHHhccCCCHHHHHHHH
Confidence 36999999999766666655543
No 6
>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=36.44 E-value=8.8 Score=25.97 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=11.3
Q ss_pred ceEeecCCcceeec
Q 032843 19 KFIRCSNCGKCCPK 32 (132)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (132)
-||+|..||+.+--
T Consensus 3 iPVRCFTCGkvi~~ 16 (70)
T 1twf_J 3 VPVRCFSCGKVVGD 16 (70)
T ss_dssp CCSBCTTTCCBCTT
T ss_pred CCeecCCCCCChHH
Confidence 48999999987643
No 7
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}
Probab=36.13 E-value=13 Score=28.98 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=11.8
Q ss_pred ceEeecCCcceeecc
Q 032843 19 KFIRCSNCGKCCPKD 33 (132)
Q Consensus 19 ~~V~C~NCgr~vPKD 33 (132)
..|.|.||||.+=.+
T Consensus 221 ~Iv~Cp~CgRIL~~~ 235 (256)
T 3na7_A 221 DMITCPYCGRILYAE 235 (256)
T ss_dssp SCEECTTTCCEEECS
T ss_pred CEEECCCCCeeEEeC
Confidence 579999999976443
No 8
>3dlu_A SRP19, signal recognition particle 19 kDa protein; protein-RNA, cytoplasm, ribonucleoprotein, RNA-binding, RNA binding protein; 1.80A {Pyrococcus furiosus} PDB: 3dlv_B
Probab=34.81 E-value=6.4 Score=28.15 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=16.3
Q ss_pred cceeecccceeeeeecccchhh
Q 032843 27 GKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 27 gr~vPKDKAIKrf~irNiVEaa 48 (132)
||.|||++|+..-.+..|+|+.
T Consensus 20 GRRV~k~~aV~nPt~~EI~~a~ 41 (106)
T 3dlu_A 20 GRIVPRSIAVESPRVEEIVRAA 41 (106)
T ss_dssp TCCSCTTTSBSSCCHHHHHHHH
T ss_pred cCccCHHHhccCCCHHHHHHHH
Confidence 6999999999766665555543
No 9
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=31.93 E-value=10 Score=24.63 Aligned_cols=12 Identities=42% Similarity=0.844 Sum_probs=10.1
Q ss_pred ceEeecCCccee
Q 032843 19 KFIRCSNCGKCC 30 (132)
Q Consensus 19 ~~V~C~NCgr~v 30 (132)
-||||-.||..+
T Consensus 2 iPVRCFTCGkvi 13 (55)
T 1ef4_A 2 IPVRCLSCGKPV 13 (55)
T ss_dssp CSSSCSCTTSCC
T ss_pred CCeecCCCCCCh
Confidence 389999999865
No 10
>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=30.88 E-value=12 Score=25.01 Aligned_cols=11 Identities=45% Similarity=0.899 Sum_probs=9.9
Q ss_pred eEeecCCccee
Q 032843 20 FIRCSNCGKCC 30 (132)
Q Consensus 20 ~V~C~NCgr~v 30 (132)
||||-.||..+
T Consensus 4 PVRCFTCGkvi 14 (66)
T 4ayb_N 4 PIRCFTCGSLI 14 (66)
T ss_dssp CSBCTTTCCBC
T ss_pred CcccCCCcHhH
Confidence 89999999866
No 11
>1kvn_A SRP19; RNA binding protein; NMR {Archaeoglobus fulgidus} SCOP: d.201.1.1 PDB: 1kvv_A
Probab=29.14 E-value=8.9 Score=27.22 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=17.8
Q ss_pred Ccceeecccceeeeeecccchhh
Q 032843 26 CGKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVEaa 48 (132)
=||.||++.||..-.+..|+|+.
T Consensus 19 eGRRv~k~~aV~nP~~~EI~~a~ 41 (104)
T 1kvn_A 19 EGRRIPRRFAVPNVKLHELVEAS 41 (104)
T ss_dssp TTCCSCGGGCCSSCCHHHHHHHH
T ss_pred hCCccCHHHhccCCCHHHHHHHH
Confidence 36999999999877766666654
No 12
>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1
Probab=28.47 E-value=19 Score=23.10 Aligned_cols=16 Identities=31% Similarity=0.459 Sum_probs=14.4
Q ss_pred eecCCcceeeccccee
Q 032843 22 RCSNCGKCCPKDKAIK 37 (132)
Q Consensus 22 ~C~NCgr~vPKDKAIK 37 (132)
-|..|+-.|+.+.||.
T Consensus 9 aC~~C~c~Vs~~eai~ 24 (55)
T 1jjd_A 9 ACEPCLCNVDPSKAID 24 (55)
T ss_dssp SSTTCCCCBCTTTSEE
T ss_pred cCCCCeeEechHHhhh
Confidence 4899999999999996
No 13
>1jid_A Signal recognition particle 19 kDa protein; signal recognition particle (SRP), protein-RNA complex, GGAG tetraloop, signaling protein/RNA complex; HET: 5BU A23; 1.80A {Homo sapiens} SCOP: d.201.1.1 PDB: 3ktv_B* 1mfq_B* 1ry1_B* 2go5_B 2j37_B
Probab=27.44 E-value=10 Score=27.99 Aligned_cols=23 Identities=22% Similarity=0.278 Sum_probs=16.8
Q ss_pred Ccceeecccceeeeeecccchhh
Q 032843 26 CGKCCPKDKAIKRFLVRNIVEQA 48 (132)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVEaa 48 (132)
=||.||+++||..-++..|+|+.
T Consensus 31 eGRRV~k~~aVenPt~~EI~~a~ 53 (128)
T 1jid_A 31 EGRRIPISKAVENPTATEIQDVC 53 (128)
T ss_dssp TTCCSCTTTCBSSCCHHHHHHHH
T ss_pred hcCccCHHHhccCCCHHHHHHHH
Confidence 36999999999766665555543
No 14
>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}
Probab=25.06 E-value=26 Score=21.32 Aligned_cols=27 Identities=30% Similarity=0.331 Sum_probs=22.2
Q ss_pred eEeecCCcceeecccceeeeeecccch
Q 032843 20 FIRCSNCGKCCPKDKAIKRFLVRNIVE 46 (132)
Q Consensus 20 ~V~C~NCgr~vPKDKAIKrf~irNiVE 46 (132)
...|..|..-+..+.-..-+.+.||||
T Consensus 59 ~~~CP~Cr~~~~~~~~~~n~~l~~~ve 85 (85)
T 2ecw_A 59 KGNCPVCRVPYPFGNLKPNLHVANIVE 85 (85)
T ss_dssp CBCCTTTCCCCCTTCCEECSCCCSSCC
T ss_pred CCCCCCCCCcCCHHhCCcCHHHHHhhC
Confidence 578999999998887777777888875
No 15
>2ys4_A Hydrocephalus-inducing protein homolog; hydin, PAPD-like, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=22.73 E-value=48 Score=22.40 Aligned_cols=24 Identities=38% Similarity=0.344 Sum_probs=21.3
Q ss_pred ecCCcceeecccceeeeeecccch
Q 032843 23 CSNCGKCCPKDKAIKRFLVRNIVE 46 (132)
Q Consensus 23 C~NCgr~vPKDKAIKrf~irNiVE 46 (132)
=-++|.|.-++++.+.|.|+|+=+
T Consensus 31 ~l~fg~~~v~~~~~~~~~l~N~g~ 54 (122)
T 2ys4_A 31 KLNFSTCPVKYSTQKILLVRNIGN 54 (122)
T ss_dssp EECCCSEESSSCEEEEEEEECCSS
T ss_pred eeecCCeecCCeEEEEEEEEECCC
Confidence 468899999999999999999844
No 16
>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=22.68 E-value=23 Score=26.89 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=18.7
Q ss_pred cceeeeEEeeeec---eeccccccc
Q 032843 66 KLYAKMQYCVSCA---IHSHVVRVR 87 (132)
Q Consensus 66 KlyvKl~YCVSCA---IHskVVRvR 87 (132)
-||+++.=|..|+ ||++|-||=
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 5799999999997 888887763
No 17
>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}
Probab=22.11 E-value=41 Score=15.38 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=9.7
Q ss_pred ceEeecCCcceee
Q 032843 19 KFIRCSNCGKCCP 31 (132)
Q Consensus 19 ~~V~C~NCgr~vP 31 (132)
++..|+.||+...
T Consensus 2 k~~~C~~C~~~f~ 14 (30)
T 2m0d_A 2 KPYQCDYCGRSFS 14 (30)
T ss_dssp CCEECTTTCCEES
T ss_pred cCccCCCCCcccC
Confidence 4678999988654
No 18
>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=21.94 E-value=28 Score=20.73 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=12.0
Q ss_pred CCccceEeecCCcc
Q 032843 15 RGHVKFIRCSNCGK 28 (132)
Q Consensus 15 rGhv~~V~C~NCgr 28 (132)
+++...+.|-|||.
T Consensus 5 ~~~~~~~~C~~Cgk 18 (40)
T 1a6b_B 5 RSQLDRDQCAYCKE 18 (40)
T ss_dssp CCSCCSSSCSSSCC
T ss_pred cCCCCCCeeeECCC
Confidence 57888899999986
Done!