Query 033056
Match_columns 128
No_of_seqs 102 out of 193
Neff 3.5
Searched_HMMs 29240
Date Mon Mar 25 15:06:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033056.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/033056hhsearch_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 1.4E-66 4.7E-71 387.2 6.8 113 1-114 1-114 (119)
2 2xzm_5 Ribosomal protein S26E 100.0 4.8E-64 1.7E-68 373.5 6.8 111 1-111 1-113 (119)
3 1m06_J J protein, small core p 46.1 11 0.00037 21.1 1.7 15 1-15 1-15 (26)
4 3na7_A HP0958; flagellar bioge 39.1 11 0.00036 29.3 1.3 15 19-33 221-235 (256)
5 3mhs_C SAGA-associated factor 38.9 19 0.00066 25.6 2.5 16 16-31 66-81 (99)
6 1twf_J DNA-directed RNA polyme 35.0 10 0.00034 25.6 0.5 14 19-32 3-16 (70)
7 1lng_A SRP19, signal recogniti 32.5 7.3 0.00025 26.7 -0.6 21 26-46 16-36 (87)
8 1ef4_A Subunit N, DNA-directed 31.6 11 0.00038 24.3 0.2 12 19-30 2-13 (55)
9 1jjd_A Metallothionein, SMTA; 30.9 17 0.00057 23.3 1.0 17 22-38 9-25 (55)
10 3dlu_A SRP19, signal recogniti 30.5 8.2 0.00028 27.4 -0.6 20 27-46 20-39 (106)
11 4ayb_N DNA-directed RNA polyme 30.5 13 0.00045 24.7 0.5 11 20-30 4-14 (66)
12 1kvn_A SRP19; RNA binding prot 25.5 11 0.00038 26.6 -0.6 22 26-47 19-40 (104)
13 1jid_A Signal recognition part 23.3 13 0.00046 27.2 -0.6 21 26-46 31-51 (128)
14 1a6b_B Momulv, zinc finger pro 23.2 28 0.00097 20.6 1.0 14 15-28 5-18 (40)
15 2m0d_A Zinc finger and BTB dom 23.0 38 0.0013 15.4 1.3 14 19-32 2-15 (30)
16 2ecw_A Tripartite motif-contai 21.2 36 0.0012 20.5 1.2 27 20-46 59-85 (85)
17 2g84_A Cytidine and deoxycytid 20.7 29 0.001 26.2 0.8 22 66-87 106-130 (197)
18 1nc8_A Nucleocapsid protein; H 20.0 30 0.001 18.6 0.6 9 20-28 6-14 (29)
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=1.4e-66 Score=387.24 Aligned_cols=113 Identities=58% Similarity=1.007 Sum_probs=96.9
Q ss_pred CCcccccCCCCCCCCCcccceeecCCcceeecccceeeeeecccchhhHHhhHHhhccccccccceeeeeeEEeeeecee
Q 033056 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYDNYVLPKLYAKMQYCVSCAIH 80 (128)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDi~eAsv~~~y~lPKlyvKl~YCVSCAIH 80 (128)
||+|||||||+|+|+|||++|+|+|||+|||||||||+|+|+||||+|++|||+|||||++|+|||||+|+|||||||||
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 cccccccChhhhcccCCCcccccccCCCC-CCCCC
Q 033056 81 SHVVRVRSRTDRRNREPPKRFMRRRDDLP-KPGQP 114 (128)
Q Consensus 81 skVVRvRS~e~RK~r~pp~r~~~~~~~~~-~p~~~ 114 (128)
++|||+||+|+||+|+||++| ++..+.+ +|.++
T Consensus 81 skVVR~RS~e~Rk~r~pp~r~-~~~~~~~~~p~~~ 114 (119)
T 3u5c_a 81 ARIVRVRSREDRKNRAPPQRP-RFNRENKVSPADA 114 (119)
T ss_dssp TSSCCCCCTTTTSCCCCC-----------------
T ss_pred ccccccCChHHcccCCCCCcc-CcccCCccCHHHH
Confidence 999999999999999999999 7654444 56543
No 2
>2xzm_5 Ribosomal protein S26E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_5
Probab=100.00 E-value=4.8e-64 Score=373.53 Aligned_cols=111 Identities=47% Similarity=0.852 Sum_probs=95.8
Q ss_pred CCcccccCCCCCCCCCcccceeecCCcceeecccceeeeeecccchhhHHhhHHhhcccc--ccccceeeeeeEEeeeec
Q 033056 1 MTFKRRNGGRNKHGRGHVNFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQDACIYD--NYVLPKLYAKMQYCVSCA 78 (128)
Q Consensus 1 M~kKRrNnGr~KkgrGhv~~V~C~NCgr~vPKDKAIKrf~irNiVEaaavrDi~eAsv~~--~y~lPKlyvKl~YCVSCA 78 (128)
||+|||||||+|+|||||++|+|+|||+|||||||||+|+|+||||+|++|||+||+||+ +|+|||||+|+|||||||
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 eecccccccChhhhcccCCCcccccccCCCCCC
Q 033056 79 IHSHVVRVRSRTDRRNREPPKRFMRRRDDLPKP 111 (128)
Q Consensus 79 IHskVVRvRS~e~RK~r~pp~r~~~~~~~~~~p 111 (128)
||++|||+||+|+||+|+||++|.....+++.|
T Consensus 81 IH~kIVRvRs~e~Rk~r~pp~~~~~~~~~~~~~ 113 (119)
T 2xzm_5 81 IHSRVVRVRCAEDRRIRRPPIRNRKPQVVKTDA 113 (119)
T ss_dssp HHTTSSCCCCTGGGGCCCC--------------
T ss_pred eeccccccCCHHHcccCCCCCccccCCCCCCCc
Confidence 999999999999999999999983333344433
No 3
>1m06_J J protein, small core protein; bacteriophage, virion; HET: 3DR; 3.50A {Enterobacteria phage ALPHA3}
Probab=46.13 E-value=11 Score=21.11 Aligned_cols=15 Identities=40% Similarity=0.485 Sum_probs=12.8
Q ss_pred CCcccccCCCCCCCC
Q 033056 1 MTFKRRNGGRNKHGR 15 (128)
Q Consensus 1 M~kKRrNnGr~Kkgr 15 (128)
|-+-||+.||+|+.|
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
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}
Probab=39.08 E-value=11 Score=29.26 Aligned_cols=15 Identities=27% Similarity=0.789 Sum_probs=11.9
Q ss_pred cceeecCCcceeecc
Q 033056 19 NFIRCSNCGKCCPKD 33 (128)
Q Consensus 19 ~~V~C~NCgr~vPKD 33 (128)
..|.|.||||.+=.+
T Consensus 221 ~Iv~Cp~CgRIL~~~ 235 (256)
T 3na7_A 221 DMITCPYCGRILYAE 235 (256)
T ss_dssp SCEECTTTCCEEECS
T ss_pred CEEECCCCCeeEEeC
Confidence 579999999976544
No 5
>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=38.91 E-value=19 Score=25.63 Aligned_cols=16 Identities=31% Similarity=0.872 Sum_probs=13.3
Q ss_pred CcccceeecCCcceee
Q 033056 16 GHVNFIRCSNCGKCCP 31 (128)
Q Consensus 16 Ghv~~V~C~NCgr~vP 31 (128)
.....+.|.||+|-|.
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 5667899999999775
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=34.98 E-value=10 Score=25.55 Aligned_cols=14 Identities=36% Similarity=0.752 Sum_probs=11.3
Q ss_pred cceeecCCcceeec
Q 033056 19 NFIRCSNCGKCCPK 32 (128)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (128)
-||+|..||+.+--
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
>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=32.49 E-value=7.3 Score=26.68 Aligned_cols=21 Identities=24% Similarity=0.434 Sum_probs=14.8
Q ss_pred Ccceeecccceeeeeecccch
Q 033056 26 CGKCCPKDKAIKRFLVRNIVE 46 (128)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVE 46 (128)
-||-||+++|+..-.+.-|.|
T Consensus 16 eGRrv~k~~aV~~P~~~EI~~ 36 (87)
T 1lng_A 16 EGRKVPEELAIEKPSLKDIEK 36 (87)
T ss_dssp TTCCSCTTTCBSSCCHHHHHH
T ss_pred hcCccCHHHhccCCCHHHHHH
Confidence 369999999997555444444
No 8
>1ef4_A Subunit N, DNA-directed RNA polymerase; three helix bundle, zinc binding, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: a.4.11.1
Probab=31.59 E-value=11 Score=24.29 Aligned_cols=12 Identities=42% Similarity=0.825 Sum_probs=10.1
Q ss_pred cceeecCCccee
Q 033056 19 NFIRCSNCGKCC 30 (128)
Q Consensus 19 ~~V~C~NCgr~v 30 (128)
-||||-.||..+
T Consensus 2 iPVRCFTCGkvi 13 (55)
T 1ef4_A 2 IPVRCLSCGKPV 13 (55)
T ss_dssp CSSSCSCTTSCC
T ss_pred CCeecCCCCCCh
Confidence 389999999866
No 9
>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1
Probab=30.93 E-value=17 Score=23.28 Aligned_cols=17 Identities=35% Similarity=0.524 Sum_probs=14.9
Q ss_pred eecCCcceeecccceee
Q 033056 22 RCSNCGKCCPKDKAIKR 38 (128)
Q Consensus 22 ~C~NCgr~vPKDKAIKr 38 (128)
-|..|+-.|+.+.||.+
T Consensus 9 aC~~C~c~Vs~~eai~~ 25 (55)
T 1jjd_A 9 ACEPCLCNVDPSKAIDR 25 (55)
T ss_dssp SSTTCCCCBCTTTSEES
T ss_pred cCCCCeeEechHHhhhc
Confidence 48999999999999963
No 10
>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=30.54 E-value=8.2 Score=27.43 Aligned_cols=20 Identities=30% Similarity=0.499 Sum_probs=14.2
Q ss_pred cceeecccceeeeeecccch
Q 033056 27 GKCCPKDKAIKRFLVRNIVE 46 (128)
Q Consensus 27 gr~vPKDKAIKrf~irNiVE 46 (128)
||.|||++|+..-.+..|+|
T Consensus 20 GRRV~k~~aV~nPt~~EI~~ 39 (106)
T 3dlu_A 20 GRIVPRSIAVESPRVEEIVR 39 (106)
T ss_dssp TCCSCTTTSBSSCCHHHHHH
T ss_pred cCccCHHHhccCCCHHHHHH
Confidence 69999999997544444443
No 11
>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=30.53 E-value=13 Score=24.73 Aligned_cols=11 Identities=45% Similarity=0.899 Sum_probs=9.9
Q ss_pred ceeecCCccee
Q 033056 20 FIRCSNCGKCC 30 (128)
Q Consensus 20 ~V~C~NCgr~v 30 (128)
||+|-.||..+
T Consensus 4 PVRCFTCGkvi 14 (66)
T 4ayb_N 4 PIRCFTCGSLI 14 (66)
T ss_dssp CSBCTTTCCBC
T ss_pred CcccCCCcHhH
Confidence 89999999966
No 12
>1kvn_A SRP19; RNA binding protein; NMR {Archaeoglobus fulgidus} SCOP: d.201.1.1 PDB: 1kvv_A
Probab=25.52 E-value=11 Score=26.56 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=16.1
Q ss_pred Ccceeecccceeeeeecccchh
Q 033056 26 CGKCCPKDKAIKRFLVRNIVEQ 47 (128)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVEa 47 (128)
=||.||++.|+..-.+..|+|+
T Consensus 19 eGRRv~k~~aV~nP~~~EI~~a 40 (104)
T 1kvn_A 19 EGRRIPRRFAVPNVKLHELVEA 40 (104)
T ss_dssp TTCCSCGGGCCSSCCHHHHHHH
T ss_pred hCCccCHHHhccCCCHHHHHHH
Confidence 3699999999986655555553
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=23.32 E-value=13 Score=27.19 Aligned_cols=21 Identities=24% Similarity=0.321 Sum_probs=14.8
Q ss_pred Ccceeecccceeeeeecccch
Q 033056 26 CGKCCPKDKAIKRFLVRNIVE 46 (128)
Q Consensus 26 Cgr~vPKDKAIKrf~irNiVE 46 (128)
=||.||+++||..-.+.-|+|
T Consensus 31 eGRRV~k~~aVenPt~~EI~~ 51 (128)
T 1jid_A 31 EGRRIPISKAVENPTATEIQD 51 (128)
T ss_dssp TTCCSCTTTCBSSCCHHHHHH
T ss_pred hcCccCHHHhccCCCHHHHHH
Confidence 369999999997554444444
No 14
>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=23.19 E-value=28 Score=20.59 Aligned_cols=14 Identities=21% Similarity=0.657 Sum_probs=12.1
Q ss_pred CCcccceeecCCcc
Q 033056 15 RGHVNFIRCSNCGK 28 (128)
Q Consensus 15 rGhv~~V~C~NCgr 28 (128)
+++...+.|-|||.
T Consensus 5 ~~~~~~~~C~~Cgk 18 (40)
T 1a6b_B 5 RSQLDRDQCAYCKE 18 (40)
T ss_dssp CCSCCSSSCSSSCC
T ss_pred cCCCCCCeeeECCC
Confidence 67888899999986
No 15
>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}
Probab=23.02 E-value=38 Score=15.40 Aligned_cols=14 Identities=21% Similarity=0.700 Sum_probs=10.1
Q ss_pred cceeecCCcceeec
Q 033056 19 NFIRCSNCGKCCPK 32 (128)
Q Consensus 19 ~~V~C~NCgr~vPK 32 (128)
++..|+.||+....
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 46789999886543
No 16
>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}
Probab=21.22 E-value=36 Score=20.52 Aligned_cols=27 Identities=30% Similarity=0.331 Sum_probs=21.7
Q ss_pred ceeecCCcceeecccceeeeeecccch
Q 033056 20 FIRCSNCGKCCPKDKAIKRFLVRNIVE 46 (128)
Q Consensus 20 ~V~C~NCgr~vPKDKAIKrf~irNiVE 46 (128)
...|..|..-+..+.-..-+.+.||||
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 577999999998887777777777775
No 17
>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=20.66 E-value=29 Score=26.16 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=18.6
Q ss_pred eeeeeeEEeeeec---eeccccccc
Q 033056 66 KLYAKMQYCVSCA---IHSHVVRVR 87 (128)
Q Consensus 66 KlyvKl~YCVSCA---IHskVVRvR 87 (128)
-||+.+.=|..|+ ||++|-||=
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 18
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=20.05 E-value=30 Score=18.56 Aligned_cols=9 Identities=78% Similarity=1.556 Sum_probs=7.4
Q ss_pred ceeecCCcc
Q 033056 20 FIRCSNCGK 28 (128)
Q Consensus 20 ~V~C~NCgr 28 (128)
.+.|.|||.
T Consensus 6 ~~~C~nCgk 14 (29)
T 1nc8_A 6 VIRCWNCGK 14 (29)
T ss_dssp CCBCTTTSC
T ss_pred CCEEEECCc
Confidence 467999997
Done!