Query 032114
Match_columns 147
No_of_seqs 113 out of 586
Neff 6.3
Searched_HMMs 29240
Date Mon Mar 25 15:45:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032114.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032114hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3jsl_A DNA ligase; NAD+-depend 38.4 19 0.00064 29.5 2.7 29 118-146 84-117 (318)
2 1ta8_A DNA ligase, NAD-depende 33.0 23 0.00077 29.1 2.4 29 118-146 91-125 (332)
3 2elu_A Zinc finger protein 406 31.8 16 0.00055 20.2 0.9 21 112-135 12-32 (37)
4 1b04_A Protein (DNA ligase); D 28.0 20 0.00069 29.2 1.3 29 118-146 86-119 (318)
5 3uq8_A DNA ligase; adenylated 27.2 34 0.0011 28.0 2.4 29 118-146 82-119 (322)
6 3j21_R 50S ribosomal protein L 25.4 40 0.0014 22.9 2.2 27 42-70 33-59 (97)
7 1zau_A DNA ligase; AMP; HET: D 25.0 42 0.0014 27.4 2.6 29 118-146 94-128 (328)
8 1wi5_A RRP5 protein homolog; S 22.9 1.3E+02 0.0043 20.1 4.5 24 42-65 66-89 (119)
9 2vqe_M 30S ribosomal protein S 22.8 39 0.0013 23.9 1.8 22 118-139 46-67 (126)
10 1vq8_Q 50S ribosomal protein L 22.5 49 0.0017 22.4 2.2 27 42-70 32-58 (96)
11 1pmi_A PMI, phosphomannose iso 21.8 16 0.00054 31.0 -0.5 29 28-57 271-299 (440)
12 3jyw_Q 60S ribosomal protein L 21.0 47 0.0016 23.3 1.9 28 41-70 30-57 (116)
No 1
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A*
Probab=38.37 E-value=19 Score=29.46 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=25.8
Q ss_pred cCCCHHHHHHHHHHHhh-----cceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDE-----MYQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~-----~Y~~~~~iD~l~ 146 (147)
+.++.+++..|.++|++ .|.+++-||||+
T Consensus 84 n~f~~eel~~f~~r~~~~l~~~~~~~EpKiDGla 117 (318)
T 3jsl_A 84 NAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLA 117 (318)
T ss_dssp EECSHHHHHHHHHHHHHHTCSCCEEEEEEECSEE
T ss_pred ccCCHHHHHHHHHHHHhhcCCceEEEEEeecceE
Confidence 36899999999999976 899999999985
No 2
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Probab=33.02 E-value=23 Score=29.13 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=25.2
Q ss_pred cCCCHHHHHHHHHHHhhc------ceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDEM------YQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~~------Y~~~~~iD~l~ 146 (147)
+.++.+++..|.++|++. |.+++-||||+
T Consensus 91 n~f~~eel~~w~~rv~~~l~~~~~~~~EpKiDGla 125 (332)
T 1ta8_A 91 DGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLA 125 (332)
T ss_dssp EECSHHHHHHHHHHHHHHHSSCCCEEEEEEECSEE
T ss_pred ccCCHHHHHHHHHHHHHhcCCCceEEEeeeecceE
Confidence 368899999999998764 99999999985
No 3
>2elu_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2elw_A
Probab=31.82 E-value=16 Score=20.22 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=15.2
Q ss_pred eeeccccCCCHHHHHHHHHHHhhc
Q 032114 112 IFFCKTDPLSKDNFELLKRRIDEM 135 (147)
Q Consensus 112 c~lC~~~~l~~~~~~~l~~~I~~~ 135 (147)
|.+|+ ++++ +++.|.+.|++.
T Consensus 12 crfck-kkys--dvknlikhire~ 32 (37)
T 2elu_A 12 CRFCK-KKYS--DVKNLIKHIRDA 32 (37)
T ss_dssp ETTTT-EECS--SHHHHHHHHHHT
T ss_pred HHHHH-HHHH--HHHHHHHHHHHh
Confidence 78897 5775 567777887764
No 4
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2
Probab=27.96 E-value=20 Score=29.21 Aligned_cols=29 Identities=10% Similarity=0.227 Sum_probs=24.9
Q ss_pred cCCCHHHHHHHHHHHhhc-----ceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDEM-----YQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~~-----Y~~~~~iD~l~ 146 (147)
+.++.+++..|.++|++. |.+++-||||+
T Consensus 86 n~f~~eel~~f~~rv~~~l~~~~~~~EpKiDGla 119 (318)
T 1b04_A 86 NAFGEGDLRDFDRRVRQEVGEAAYVCELAIDGLA 119 (318)
T ss_dssp EECSTTHHHHHHHHHHHHHSSCCEEEEEEESSEE
T ss_pred ccCCHHHHHHHHHHHHHhccCceEEEEEecccEE
Confidence 357889999999998765 99999999985
No 5
>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A*
Probab=27.20 E-value=34 Score=27.97 Aligned_cols=29 Identities=14% Similarity=0.194 Sum_probs=25.0
Q ss_pred cCCCHHHHHHHHHHHhh---------cceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDE---------MYQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~---------~Y~~~~~iD~l~ 146 (147)
+.++.+++..|.++|++ .|.+++-||||+
T Consensus 82 n~~~~eel~~f~~rv~~~l~~~~~~~~~~~EpKiDGla 119 (322)
T 3uq8_A 82 NAFSDAEFNAFVARIEDRLILLPAPLTFCCEPKLDGLA 119 (322)
T ss_dssp EECSHHHHHHHHHHHHHHCSSCCSSCEEEEEEEESSEE
T ss_pred ccCCHHHHHHHHHHHHHhccCCCcCceEEEEEeeceEE
Confidence 36889999999999875 499999999985
No 6
>3j21_R 50S ribosomal protein L21E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=25.41 E-value=40 Score=22.87 Aligned_cols=27 Identities=15% Similarity=0.287 Sum_probs=21.4
Q ss_pred CCCCCCCceEEEEeecccCCCCccccccc
Q 032114 42 HKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
..|+.||.|.|.+| .+...-+|+.+|.
T Consensus 33 ~~yk~Gd~VdIk~~--gsvqKGmPhk~yH 59 (97)
T 3j21_R 33 QEFEVGQRVHIVIE--PSYHKGMPDPRFH 59 (97)
T ss_dssp CCCCTTCEEEECCC--TTCCSSCCCGGGT
T ss_pred HHhcCCCEEEEEec--CceEcCCCCcccC
Confidence 78999999999765 3446678888875
No 7
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Probab=24.97 E-value=42 Score=27.44 Aligned_cols=29 Identities=14% Similarity=0.177 Sum_probs=25.0
Q ss_pred cCCCHHHHHHHHHHHhh------cceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDE------MYQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~------~Y~~~~~iD~l~ 146 (147)
+.++.+++..|.++|++ .|.+++-||||+
T Consensus 94 n~f~~eel~~f~~rv~~~l~~~~~~~~EpKiDGla 128 (328)
T 1zau_A 94 NAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVA 128 (328)
T ss_dssp CBSSHHHHHHHHHGGGTTTCSCSCEEEEEEECSEE
T ss_pred ccCCHHHHHHHHHHHHHhcCCCcceEEeeecceEE
Confidence 46889999999999875 499999999985
No 8
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5
Probab=22.88 E-value=1.3e+02 Score=20.14 Aligned_cols=24 Identities=17% Similarity=0.109 Sum_probs=18.7
Q ss_pred CCCCCCCceEEEEeecccCCCCcc
Q 032114 42 HKHVVSDPLSVKVNSITSIDTKMP 65 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~~t~~~ 65 (147)
..|+.||.|.+.|-++...+....
T Consensus 66 ~~~~~Gd~V~vkV~~vd~~~~~i~ 89 (119)
T 1wi5_A 66 AKLKVGQYLNCIVEKVKGNGGVVS 89 (119)
T ss_dssp CCCCTTCEEEEEEEECCTTSCEEE
T ss_pred CEeCCCCEEEEEEEEEeCCCCEEE
Confidence 469999999999999886644333
No 9
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...
Probab=22.84 E-value=39 Score=23.95 Aligned_cols=22 Identities=9% Similarity=0.274 Sum_probs=19.2
Q ss_pred cCCCHHHHHHHHHHHhhcceEE
Q 032114 118 DPLSKDNFELLKRRIDEMYQVF 139 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~~Y~~~ 139 (147)
..++++|++.+++.|+++|.++
T Consensus 46 ~~Lt~~ei~~l~~~i~~~~~ve 67 (126)
T 2vqe_M 46 KDLTEAEVVRLREYVENTWKLE 67 (126)
T ss_dssp GGCCHHHHHHHHHHHHTTSCCH
T ss_pred CcCCHHHHHHHHHHHHHhCcch
Confidence 4689999999999999988664
No 10
>1vq8_Q 50S ribosomal protein L21E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_Q* 1vq5_Q* 1vq6_Q* 1vq7_Q* 1s72_Q* 1vq9_Q* 1vqk_Q* 1vql_Q* 1vqm_Q* 1vqn_Q* 1vqo_Q* 1vqp_Q* 1yhq_Q* 1yi2_Q* 1yij_Q* 1yit_Q* 1yj9_Q* 1yjn_Q* 1yjw_Q* 2otj_Q* ...
Probab=22.54 E-value=49 Score=22.39 Aligned_cols=27 Identities=7% Similarity=0.164 Sum_probs=21.0
Q ss_pred CCCCCCCceEEEEeecccCCCCccccccc
Q 032114 42 HKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
..|+.||.|.|.+|- |...-+|+.+|.
T Consensus 32 ~~yk~Gd~VdIk~~~--svqKGmPhk~yH 58 (96)
T 1vq8_Q 32 EEFDDGEKVHLKIDP--SVPNGRFHPRFD 58 (96)
T ss_dssp CCCCTTCEEEECCCT--TCCSSCCCGGGT
T ss_pred HHcCCCCEEEEEecC--CccCCCCcccCC
Confidence 789999999998653 335578888876
No 11
>1pmi_A PMI, phosphomannose isomerase; aldose-ketose isomerase; 1.70A {Candida albicans} SCOP: b.82.1.3
Probab=21.83 E-value=16 Score=31.04 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=25.3
Q ss_pred hcccceeeccCCCCCCCCCCCceEEEEeec
Q 032114 28 QSSCLGFYLRDNYPHKHVVSDPLSVKVNSI 57 (147)
Q Consensus 28 ~~~~~af~lpg~~p~~Y~~Gd~V~v~vNkl 57 (147)
... +++|+|.-.||.|-.|+-|++..|+=
T Consensus 271 ~pG-ea~flpAg~~HAYl~G~~vE~Ma~SD 299 (440)
T 1pmi_A 271 NKG-EAMFLQAKDPHAYISGDIIECMAASD 299 (440)
T ss_dssp CTT-CEEEECTTCCEEEEEEEEEEEEESCC
T ss_pred CCC-CEEecCCCCccccCCCcEEEEeccCC
Confidence 446 78999999999999999999998753
No 12
>3jyw_Q 60S ribosomal protein L21(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_Q
Probab=20.96 E-value=47 Score=23.32 Aligned_cols=28 Identities=32% Similarity=0.490 Sum_probs=22.1
Q ss_pred CCCCCCCCceEEEEeecccCCCCccccccc
Q 032114 41 PHKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 41 p~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
-..|+.||.|.|.+| .+...-+|+.+|.
T Consensus 30 m~~yk~GD~VdIk~~--gsVqKGmPHk~YH 57 (116)
T 3jyw_Q 30 LKVYKVGDIVDIKAN--GSIQKGMPHKFYQ 57 (116)
T ss_dssp TCCCCTTCBCCBCCC--SSSCTTCCCSTTS
T ss_pred HHHhCCCCEEEEecc--CccCCCCCCcccC
Confidence 478999999999765 3446678988886
Done!