Query 042443
Match_columns 95
No_of_seqs 103 out of 125
Neff 2.6
Searched_HMMs 29240
Date Mon Mar 25 10:29:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042443.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042443hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1v9f_A Ribosomal large subunit 94.6 0.0062 2.1E-07 46.0 0.0 27 69-95 15-41 (325)
2 1dm9_A Hypothetical 15.5 KD pr 93.8 0.04 1.4E-06 37.7 2.9 27 69-95 7-33 (133)
3 3r8n_D 30S ribosomal protein S 93.3 0.033 1.1E-06 41.6 1.8 26 70-95 94-119 (205)
4 1c05_A Ribosomal protein S4 de 92.9 0.046 1.6E-06 38.4 2.1 26 70-95 50-75 (159)
5 1p9k_A ORF, hypothetical prote 92.9 0.015 5E-07 36.0 -0.5 27 69-95 19-45 (79)
6 2vqe_D 30S ribosomal protein S 91.4 0.11 3.7E-06 38.2 2.5 26 70-95 98-123 (209)
7 2cqj_A BRMS2, U3 small nucleol 86.2 0.44 1.5E-05 29.6 2.3 26 70-95 7-32 (71)
8 3bbn_D Ribosomal protein S4; s 76.8 0.38 1.3E-05 35.6 -0.7 26 70-95 88-113 (201)
9 2xzm_D Ribosomal protein S4 co 50.7 5.9 0.0002 28.7 1.4 26 70-95 106-131 (181)
10 3j20_D 30S ribosomal protein S 50.2 8.5 0.00029 28.0 2.2 25 70-94 102-126 (180)
11 1tc3_C Protein (TC3 transposas 38.8 28 0.00094 17.2 2.5 18 76-94 26-43 (51)
12 1wgl_A TOLL-interacting protei 36.7 25 0.00086 21.2 2.5 19 76-94 15-33 (59)
13 1j9i_A GPNU1 DBD;, terminase s 35.9 20 0.0007 20.7 1.9 18 77-95 8-25 (68)
14 1otr_A Protein CUE2; protein-p 33.1 31 0.001 20.4 2.4 19 75-93 9-27 (49)
15 2glo_A Brinker CG9653-PA; prot 32.2 37 0.0013 18.9 2.6 19 76-95 30-48 (59)
16 3u5c_J 40S ribosomal protein S 31.4 32 0.0011 25.5 2.8 26 70-95 106-131 (197)
17 2og0_A Excisionase; protein-DN 30.3 33 0.0011 20.3 2.2 23 73-95 5-27 (52)
18 2dhy_A CUE domain-containing p 22.6 57 0.002 20.2 2.4 19 76-94 24-42 (67)
19 1jko_C HIN recombinase, DNA-in 21.3 55 0.0019 16.4 1.8 17 77-94 27-43 (52)
20 1z4h_A TORI, TOR inhibition pr 21.3 56 0.0019 18.8 2.0 23 70-94 10-32 (66)
No 1
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A
Probab=94.56 E-value=0.0062 Score=46.01 Aligned_cols=27 Identities=44% Similarity=0.774 Sum_probs=0.0
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|.|||++|++.++.+||+.+|+||++
T Consensus 15 ~g~RLd~~L~~~~~~~SR~~~~~lI~~ 41 (325)
T 1v9f_A 15 LGQRLDQALAEMFPDYSRSRIKEWILD 41 (325)
T ss_dssp ---------------------------
T ss_pred CCchHHHHHHhhccccCHHHHHHHHHC
Confidence 478999999999999999999999974
No 2
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A
Probab=93.84 E-value=0.04 Score=37.75 Aligned_cols=27 Identities=19% Similarity=0.062 Sum_probs=23.3
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.+.|||++|+......||+.++.||.+
T Consensus 7 ~~~RLDk~L~~~~~~~SRs~a~~li~~ 33 (133)
T 1dm9_A 7 VEVRLDKWLWAARFYKTRALAREMIEG 33 (133)
T ss_dssp TCCBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred cchhHHHHHHHCCCCCCHHHHHHHHHC
Confidence 378999999997666799999999964
No 3
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ...
Probab=93.26 E-value=0.033 Score=41.61 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=23.9
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
+.|||.+|+++....||+.+++||.+
T Consensus 94 e~RLD~~L~r~g~~~SR~~ArqLI~~ 119 (205)
T 3r8n_D 94 EGRLDNVVYRMGFGATRAEARQLVSH 119 (205)
T ss_dssp HTBTTHHHHTTSSCSSHHHHHHHHHT
T ss_pred HhhHHHHHHHhcchhHHHHHHHHHHC
Confidence 68999999999889999999999974
No 4
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C
Probab=92.94 E-value=0.046 Score=38.44 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=23.9
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
+.|||.+|++.....||+.+++||.+
T Consensus 50 e~RLD~~L~~~g~~~SR~~ar~lI~~ 75 (159)
T 1c05_A 50 ESRLDNLVYRLGLARTRRQARQLVTH 75 (159)
T ss_dssp HHBHHHHHHHTTSCSSHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHHC
Confidence 57999999999889999999999974
No 5
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6
Probab=92.85 E-value=0.015 Score=36.00 Aligned_cols=27 Identities=11% Similarity=-0.143 Sum_probs=21.7
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.+.|||++|++.--..||+.+++||++
T Consensus 19 ~~~RLdk~L~~~g~~~SR~~a~~lI~~ 45 (79)
T 1p9k_A 19 PHVELCDLLKLEGWSESGAQAKIAIAE 45 (79)
T ss_dssp SCCCHHHHHHHHTSCSSSSTTSHHHHH
T ss_pred CCchHHHHHHHCCCCCCHHHHHHHHHC
Confidence 357999999998323499999999963
No 6
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Probab=91.38 E-value=0.11 Score=38.23 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=23.8
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
+.|||.+|++.....||+.+++||.+
T Consensus 98 e~RLD~~L~~~g~~~SR~~arqLI~~ 123 (209)
T 2vqe_D 98 ESRLDNVVYRLGFAVSRRQARQLVRH 123 (209)
T ss_dssp HTBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCcCCHHHHHHHHHC
Confidence 68999999999888999999999964
No 7
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=86.21 E-value=0.44 Score=29.55 Aligned_cols=26 Identities=19% Similarity=0.140 Sum_probs=23.4
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|.++----||+..+++|.+
T Consensus 7 ~~RLD~~l~~~gla~SR~~A~~lI~~ 32 (71)
T 2cqj_A 7 GRRLPTVLLKLRMAQHLQAAVAFVEQ 32 (71)
T ss_dssp EEEHHHHHHHTTCSSSHHHHHHHHHT
T ss_pred HHHHHHHHHHhCCcCCHHHHHHHHHC
Confidence 36999999999988899999999974
No 8
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=76.81 E-value=0.38 Score=35.63 Aligned_cols=26 Identities=15% Similarity=0.050 Sum_probs=23.4
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|+++....||+.+++||.+
T Consensus 88 e~RLD~~L~r~g~a~SR~~ArqLI~~ 113 (201)
T 3bbn_D 88 EMRLDNILFRLGMAPTIPGARQLVNH 113 (201)
T ss_dssp HSBTTTTTTTTTSSSSSHHHHHHHHT
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHhC
Confidence 46999999999888899999999974
No 9
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Probab=50.73 E-value=5.9 Score=28.68 Aligned_cols=26 Identities=23% Similarity=0.098 Sum_probs=22.8
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|+.+----||+..+++|.+
T Consensus 106 e~RLD~vL~~~G~a~SR~~Ar~LI~~ 131 (181)
T 2xzm_D 106 ERRLQTRVFKLNLANSIHHSRVLIRQ 131 (181)
T ss_dssp TTBHHHHHHHTTCSSSTTHHHHHTTT
T ss_pred ccchhHHHHhccccCCHHHHHHHHHC
Confidence 46999999998877899999999974
No 10
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=50.22 E-value=8.5 Score=28.04 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=22.3
Q ss_pred cChhHHHHHHhchhchHHHHHHHHh
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~ 94 (95)
..|||.+|+++----||+..+++|.
T Consensus 102 e~RLD~~L~~~G~a~SR~~Ar~LI~ 126 (180)
T 3j20_D 102 ERRLQTIVYKKGLARTMRQARQLIV 126 (180)
T ss_dssp HTSHHHHHHHHTSSSSHHHHHHHHH
T ss_pred hhhhhheeecCcccCcHHHHHHHHH
Confidence 4699999999887779999999996
No 11
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2
Probab=38.80 E-value=28 Score=17.18 Aligned_cols=18 Identities=17% Similarity=0.228 Sum_probs=13.7
Q ss_pred HHHHhchhchHHHHHHHHh
Q 042443 76 ICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~ 94 (95)
-+|+.+ ..|++.|..||.
T Consensus 26 ~IA~~l-gis~~Tv~~~~~ 43 (51)
T 1tc3_C 26 EMSRKI-SRSRHCIRVYLK 43 (51)
T ss_dssp HHHHHH-TCCHHHHHHHHH
T ss_pred HHHHHH-CcCHHHHHHHHh
Confidence 345555 689999999986
No 12
>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, immune system; NMR {Homo sapiens} SCOP: a.5.2.4
Probab=36.72 E-value=25 Score=21.23 Aligned_cols=19 Identities=16% Similarity=0.190 Sum_probs=16.2
Q ss_pred HHHHhchhchHHHHHHHHh
Q 042443 76 ICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~ 94 (95)
.|.++||++++..|+.-++
T Consensus 15 ~L~emFP~ld~~~I~~vL~ 33 (59)
T 1wgl_A 15 AIQDMFPNMDQEVIRSVLE 33 (59)
T ss_dssp HHHHHCSSSCHHHHHHHHT
T ss_pred HHHHHCCCCCHHHHHHHHH
Confidence 5788999999999998664
No 13
>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5
Probab=35.89 E-value=20 Score=20.70 Aligned_cols=18 Identities=33% Similarity=0.351 Sum_probs=13.2
Q ss_pred HHHhchhchHHHHHHHHhC
Q 042443 77 CLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 77 LAeLfPeySRSrIQ~WI~~ 95 (95)
+|+++ ..|++.|+.|+.+
T Consensus 8 ~a~~L-gvS~~Tl~rw~~~ 25 (68)
T 1j9i_A 8 LADIF-GASIRTIQNWQEQ 25 (68)
T ss_dssp HHHHT-TCCHHHHHHHTTT
T ss_pred HHHHH-CcCHHHHHHHHHC
Confidence 34444 7899999999863
No 14
>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4
Probab=33.08 E-value=31 Score=20.42 Aligned_cols=19 Identities=21% Similarity=0.408 Sum_probs=16.1
Q ss_pred HHHHHhchhchHHHHHHHH
Q 042443 75 EICLERFQQYSRTYIQSWI 93 (95)
Q Consensus 75 qvLAeLfPeySRSrIQ~WI 93 (95)
+.|.++||..+...|+.-+
T Consensus 9 ~~L~EMFP~~~~~~ik~~L 27 (49)
T 1otr_A 9 SILMDMFPAISKSKLQVHL 27 (49)
T ss_dssp HHHHHHCSSSCHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 4688999999999998754
No 15
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}
Probab=32.19 E-value=37 Score=18.94 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=14.1
Q ss_pred HHHHhchhchHHHHHHHHhC
Q 042443 76 ICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~~ 95 (95)
.+|..| +.|++.|..|+++
T Consensus 30 ~vA~~~-gIs~~tl~~W~~~ 48 (59)
T 2glo_A 30 ATARKY-NIHRRQIQKWLQC 48 (59)
T ss_dssp HHHHHT-TSCHHHHHHHHTT
T ss_pred HHHHHH-CcCHHHHHHHHHH
Confidence 455555 5699999999864
No 16
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Probab=31.40 E-value=32 Score=25.46 Aligned_cols=26 Identities=23% Similarity=0.073 Sum_probs=22.7
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|..+-=--||+..+++|.+
T Consensus 106 e~RLD~~L~r~G~a~Sr~~ArqLI~~ 131 (197)
T 3u5c_J 106 ERRLQTQVYKLGLAKSVHHARVLITQ 131 (197)
T ss_dssp TTSHHHHHHHSSTTSSHHHHHHHHHT
T ss_pred HHHHHHHHHHccccCCHHHHHHHHHc
Confidence 46999999998877799999999974
No 17
>2og0_A Excisionase; protein-DNA complex, DNA architectural protein, 'winged'HELI protein, phage excision; 1.90A {Enterobacteria phage lambda} SCOP: a.6.1.7 PDB: 1lx8_A 1rh6_A 2ief_A
Probab=30.28 E-value=33 Score=20.31 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=18.9
Q ss_pred hHHHHHHhchhchHHHHHHHHhC
Q 042443 73 LDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 73 LDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
|+++...+|..-|.+.|.+||++
T Consensus 5 l~EwA~~~~~~~s~~Tl~r~ar~ 27 (52)
T 2og0_A 5 LQEWNARQRRPRSLETVRRWVRE 27 (52)
T ss_dssp HHHHHHTSSSCCCHHHHHHHHHT
T ss_pred HHHHHHHhcCCCCHHHHHHHHHC
Confidence 67777777767899999999975
No 18
>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=22.64 E-value=57 Score=20.25 Aligned_cols=19 Identities=11% Similarity=0.013 Sum_probs=15.8
Q ss_pred HHHHhchhchHHHHHHHHh
Q 042443 76 ICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~ 94 (95)
.|.++||++.+..|+.-++
T Consensus 24 ~L~~MFP~lD~~vI~~vL~ 42 (67)
T 2dhy_A 24 DFKTMFPNMDYDIIECVLR 42 (67)
T ss_dssp HHHHHCSSSCHHHHHHHHH
T ss_pred HHHHHCCCCCHHHHHHHHH
Confidence 4788999999999987653
No 19
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C
Probab=21.32 E-value=55 Score=16.44 Aligned_cols=17 Identities=6% Similarity=-0.013 Sum_probs=12.8
Q ss_pred HHHhchhchHHHHHHHHh
Q 042443 77 CLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 77 LAeLfPeySRSrIQ~WI~ 94 (95)
+|+.+ ..|++.|..|+.
T Consensus 27 ia~~l-gvs~~Tv~r~l~ 43 (52)
T 1jko_C 27 LAIIF-GIGVSTLYRYFP 43 (52)
T ss_dssp HHHTT-SCCHHHHHHHSC
T ss_pred HHHHH-CCCHHHHHHHHH
Confidence 44555 689999999975
No 20
>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}
Probab=21.30 E-value=56 Score=18.83 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=17.7
Q ss_pred cChhHHHHHHhchhchHHHHHHHHh
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~ 94 (95)
-.|++++++.+ ..||+.|-+||+
T Consensus 10 ~l~~~eva~~l--gvsrstiy~~~~ 32 (66)
T 1z4h_A 10 LVDLKFIMADT--GFGKTFIYDRIK 32 (66)
T ss_dssp EECHHHHHHHH--SSCHHHHHHHHH
T ss_pred ccCHHHHHHHH--CcCHHHHHHHHH
Confidence 56777766544 689999999986
Done!