Query 001204
Match_columns 1124
No_of_seqs 120 out of 160
Neff 2.2
Searched_HMMs 29240
Date Mon Mar 25 16:19:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001204.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/001204hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1f2v_A COBH, precorrin-8X meth 8.2 82 0.0028 32.9 0.1 17 250-266 3-19 (219)
2 3bts_E Regulatory protein GAL4 5.3 91 0.0031 23.5 -0.9 13 365-377 8-20 (26)
3 3p06_A VP4 protein; CIS-cleava 4.8 1.6E+02 0.0056 29.2 0.1 26 341-366 157-186 (194)
4 2jtx_A Transcription initiatio 4.2 4E+02 0.014 25.5 2.2 16 146-161 18-33 (106)
5 1c05_A Ribosomal protein S4 de 4.1 3.8E+02 0.013 25.9 2.1 20 369-388 18-37 (159)
6 1b43_A Protein (FEN-1); nuclea 4.1 4.4E+02 0.015 27.7 2.7 45 354-399 288-335 (340)
7 3j21_l 50S ribosomal protein L 3.7 2.5E+02 0.0084 25.1 0.3 14 812-825 37-50 (77)
8 2vqe_D 30S ribosomal protein S 3.5 4E+02 0.014 26.9 1.7 26 363-388 49-85 (209)
9 3r8n_D 30S ribosomal protein S 3.4 3.9E+02 0.013 27.4 1.5 27 364-390 46-83 (205)
10 3m50_P N.plumbaginifolia H+-tr 3.2 2.1E+02 0.0073 22.4 -0.5 18 956-973 1-18 (31)
No 1
>1f2v_A COBH, precorrin-8X methylmutase; alpha-beta WIND, doubly wound sheet, isomerase; 2.10A {Pseudomonas denitrificans} SCOP: c.23.17.1 PDB: 1i1h_A*
Probab=8.25 E-value=82 Score=32.87 Aligned_cols=17 Identities=29% Similarity=0.643 Sum_probs=7.7
Q ss_pred CCcCCCCCCcccccCCC
Q 001204 250 FAYHNPYHSQFKYVRPG 266 (1124)
Q Consensus 250 g~~~hp~HsqfKYVRPg 266 (1124)
|.|||-||..|||+..+
T Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (219)
T 1f2v_A 3 GSHHHHHHPEYDYIRDG 19 (219)
T ss_dssp --------CCCCCCCCH
T ss_pred CccccccCCcccCCCCc
Confidence 56778899999999764
No 2
>3bts_E Regulatory protein GAL4; eukaryotic transcription complex, NAD, rossmann fold, acetylation, carbohydrate metabolism, DNA-binding; HET: NAD; 2.70A {Saccharomyces cerevisiae}
Probab=5.35 E-value=91 Score=23.46 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=10.3
Q ss_pred CcccccCCCCHHH
Q 001204 365 ITDFFNFGLNEES 377 (1124)
Q Consensus 365 ISDYFNYGFnE~T 377 (1124)
+-|-|||=|+++.
T Consensus 8 MDDvyNylFdd~d 20 (26)
T 3bts_E 8 MDDVYNYLFDDED 20 (26)
T ss_pred HHHHHHHhcCccc
Confidence 4588999999864
No 3
>3p06_A VP4 protein; CIS-cleavage, intramolecular acyl-enzyme, ester-linkage, ALP protein, protease, polyprotein processing, acyl-enzyme, HYD; 2.10A {Tellina virus 1}
Probab=4.77 E-value=1.6e+02 Score=29.20 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=16.6
Q ss_pred CCCcceeecCCCc----CCCCCCCCCCCCc
Q 001204 341 SHKTIFEVDIDGF----EEKPWKYPGVDIT 366 (1124)
Q Consensus 341 ~~k~IfdvDiD~~----eeKPWRkPGADIS 366 (1124)
+.+.+--+-|++| -+||||+|-.-+|
T Consensus 157 sdralkvvtleqlrqvvgdkpwrkpmvtfs 186 (194)
T 3p06_A 157 SDRALKVVTLEQLRQVVGDKPWRKPMVTFS 186 (194)
T ss_dssp STTSEECCBHHHHHHHHSSCCCSSSCEECC
T ss_pred CccceeeEEHHHHHHHhcCCcccCceEEee
Confidence 3344444555654 5999999976544
No 4
>2jtx_A Transcription initiation factor IIE subunit alpha; TFIIE, TFIIH, activation domains, transcription regulation; NMR {Homo sapiens} PDB: 2rnq_A 2rnr_A
Probab=4.19 E-value=4e+02 Score=25.49 Aligned_cols=16 Identities=19% Similarity=0.192 Sum_probs=0.0
Q ss_pred cCCCccCceEEeccCC
Q 001204 146 ESDSEDDLQIVLNEDN 161 (1124)
Q Consensus 146 dSDSeDdlqiVlNd~~ 161 (1124)
.|||++|-.=..|...
T Consensus 18 ~SDSesd~~e~~~~~~ 33 (106)
T 2jtx_A 18 GDDSESETSESDDDSP 33 (106)
T ss_dssp ----------------
T ss_pred CCccccchhhhccCCC
Confidence 4556666555555554
No 5
>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=4.12 E-value=3.8e+02 Score=25.88 Aligned_cols=20 Identities=15% Similarity=0.408 Sum_probs=17.2
Q ss_pred ccCCCCHHHHHHHHHHHHHh
Q 001204 369 FNFGLNEESWKDYCKQLEQH 388 (1124)
Q Consensus 369 FNYGFnE~TWk~Yc~kq~ql 388 (1124)
|+||..|..|+.|+.+-.++
T Consensus 18 ~~yg~~e~q~~~~~~~a~~~ 37 (159)
T 1c05_A 18 HMYGVNERQFRKTFEEAGKM 37 (159)
T ss_dssp HTTTCCHHHHHHHHHHHTTS
T ss_pred HHhCCCHHHHHHHHHHHHhc
Confidence 79999999999999875544
No 6
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A
Probab=4.11 E-value=4.4e+02 Score=27.75 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=33.3
Q ss_pred CCCCCCCCC-CCCcccc--cCCCCHHHHHHHHHHHHHhhhhhchhhhhh
Q 001204 354 EEKPWKYPG-VDITDFF--NFGLNEESWKDYCKQLEQHRLETTMQSKIR 399 (1124)
Q Consensus 354 eeKPWRkPG-ADISDYF--NYGFnE~TWk~Yc~kq~qlR~E~tmqsKI~ 399 (1124)
++-.|..|- ..|..|| .|||+++.=..+++++.+.+... .|..|.
T Consensus 288 ~~~~~~~pd~~~l~~~~~~~~~f~~~rv~~~~~~~~~~~~~~-~q~~l~ 335 (340)
T 1b43_A 288 YNLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSG-KQSTLE 335 (340)
T ss_dssp CCCCCCCCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHHHHT-TGGGCC
T ss_pred ccCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHhhhcCC-CCCCHH
Confidence 345788775 3477898 89999999999999988776533 355544
No 7
>3j21_l 50S ribosomal protein LX; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=3.66 E-value=2.5e+02 Score=25.09 Aligned_cols=14 Identities=29% Similarity=0.570 Sum_probs=11.4
Q ss_pred hhhhhhhccccccc
Q 001204 812 HLDEIGARHRGKAR 825 (1124)
Q Consensus 812 ~~de~g~RhR~K~R 825 (1124)
--.|||||||-|-.
T Consensus 37 ~Yse~gsrHr~kr~ 50 (77)
T 3j21_l 37 VYSDIGSKHKVKRN 50 (77)
T ss_dssp HHHHHHHHTTCCTT
T ss_pred HHHHHhhhhCCCcc
Confidence 56799999998844
No 8
>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=3.48 E-value=4e+02 Score=26.93 Aligned_cols=26 Identities=12% Similarity=0.408 Sum_probs=22.1
Q ss_pred CCCccc-----------ccCCCCHHHHHHHHHHHHHh
Q 001204 363 VDITDF-----------FNFGLNEESWKDYCKQLEQH 388 (1124)
Q Consensus 363 ADISDY-----------FNYGFnE~TWk~Yc~kq~ql 388 (1124)
..+||| |.|||.|..|+.|+....+.
T Consensus 49 ~k~s~y~~~L~ekqkl~~~Yg~~e~q~~~y~~~a~~~ 85 (209)
T 2vqe_D 49 RRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKK 85 (209)
T ss_dssp CCCCHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHS
T ss_pred CcccHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence 368999 89999999999999876554
No 9
>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=3.42 E-value=3.9e+02 Score=27.36 Aligned_cols=27 Identities=19% Similarity=0.493 Sum_probs=23.1
Q ss_pred CCccc-----------ccCCCCHHHHHHHHHHHHHhhh
Q 001204 364 DITDF-----------FNFGLNEESWKDYCKQLEQHRL 390 (1124)
Q Consensus 364 DISDY-----------FNYGFnE~TWk~Yc~kq~qlR~ 390 (1124)
-+||| |+||..|.-|+.|..+-.+...
T Consensus 46 K~S~y~~qL~eKQklr~~YG~~EkQf~~~~~~A~~~kG 83 (205)
T 3r8n_D 46 RLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKG 83 (205)
T ss_dssp CCCHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHSSS
T ss_pred cccHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence 58898 8999999999999998766544
No 10
>3m50_P N.plumbaginifolia H+-translocating ATPase mRNA; all helical, protein-protein complex, protein binding; HET: EBT; 2.60A {Nicotiana plumbaginifolia} PDB: 3m51_P* 4dx0_P*
Probab=3.20 E-value=2.1e+02 Score=22.37 Aligned_cols=18 Identities=39% Similarity=0.527 Sum_probs=14.7
Q ss_pred hhhhcccCcchhhhhhHH
Q 001204 956 REDWHRLKPHEEILSKRE 973 (1124)
Q Consensus 956 ree~~rlk~hee~~s~r~ 973 (1124)
|-|+|.||.|-|...|+.
T Consensus 1 ~rElhTLkghvESv~KLK 18 (31)
T 3m50_P 1 RRELHTLKGHVEAVVKLK 18 (31)
T ss_dssp CHHHHCHHHHHHHHHHHT
T ss_pred CchhhHHHHHHHHHHHHh
Confidence 457899999999888764
Done!