Query gi|254780131|ref|YP_003064544.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs 121 out of 1551
Neff 3.6
Searched_HMMs 23785
Date Sun May 22 14:16:35 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780131.hhm -d /home/congqian_1/database/pdb/pdb70.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1dgs_A DNA ligase; AMP complex 99.7 7.9E-19 3.3E-23 135.0 5.2 66 54-119 1-66 (667)
2 2owo_A DNA ligase; protein/DNA 99.7 7.7E-18 3.2E-22 129.0 7.5 62 58-119 3-64 (671)
3 1b04_A Protein (DNA ligase); D 99.7 3.8E-17 1.6E-21 124.8 8.5 66 54-119 1-66 (318)
4 1ta8_A DNA ligase, NAD-depende 99.7 7.7E-17 3.3E-21 122.9 9.1 68 52-119 4-71 (332)
5 1zau_A DNA ligase; AMP; HET: D 99.7 1.4E-16 5.7E-21 121.4 7.8 71 49-119 3-73 (328)
6 3jsl_A DNA ligase; NAD+-depend 99.6 8E-16 3.4E-20 116.7 6.8 62 58-119 3-64 (318)
7 2xlg_A SLL1785 protein, CUCA; 32.8 5.4 0.00023 20.0 -0.7 61 13-75 166-231 (239)
8 3czp_A Putative polyphosphate 20.4 46 0.0019 14.3 3.6 43 43-85 260-302 (500)
9 3d4u_A Tafia, carboxypeptidase 19.4 33 0.0014 15.2 1.3 22 83-104 212-234 (309)
10 3mn8_A LP15968P; catalytic dom 18.1 37 0.0016 14.9 1.3 28 90-117 43-70 (435)
No 1
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*
Probab=99.75 E-value=7.9e-19 Score=135.05 Aligned_cols=66 Identities=35% Similarity=0.565 Sum_probs=64.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 899999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
|++.+++.+++.|+++|.+||++||++++|+|||++||+|+++|..||++||+++.+||||++||+
T Consensus 1 m~~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~Le~~~p~~~~~~spt~~vG~ 66 (667)
T 1dgs_A 1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGA 66 (667)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHHHTTSSGGGCCTTSGGGGCSS
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 987999999999999999999998648999789899999999999999868055699998532477
No 2
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12}
Probab=99.72 E-value=7.7e-18 Score=129.02 Aligned_cols=62 Identities=31% Similarity=0.463 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 58 EAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 58 EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
+++.|++.|+++|.+||++||++++|+|||++||+|+++|.+||.+||+++.++|||++||.
T Consensus 3 ~~~~~i~~L~~~i~~~~~~YY~~~~p~isD~eYD~L~~eL~~le~~~p~~~~~~spt~~VG~ 64 (671)
T 2owo_A 3 SIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRVGA 64 (671)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHHHHHHHCTTSCCTTSGGGCCSC
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 79999999999999999987449999789899999999999999868155699998654466
No 3
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2
Probab=99.70 E-value=3.8e-17 Score=124.76 Aligned_cols=66 Identities=32% Similarity=0.458 Sum_probs=64.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 899999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 54 LSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
|++.+++.+++.|+++|.+||++||+.++|+|||++||.|+++|.+||.+||+|+..+||+++||.
T Consensus 1 m~~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~l~~~~sp~~~v~~ 66 (318)
T 1b04_A 1 MDRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRIGG 66 (318)
T ss_dssp -CHHHHHHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHHHHHHHCGGGCCTTCGGGGTCC
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 987999999999999999999998638999798899999999999999868133689998655587
No 4
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis V583} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Probab=99.69 E-value=7.7e-17 Score=122.90 Aligned_cols=68 Identities=29% Similarity=0.421 Sum_probs=64.9
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 77899999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 52 TSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 52 ~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
..|+..+++.+++.|+++|.+||++||+.++|+|||++||+|+++|..||.+||+|+.++|||++||.
T Consensus 4 ~~~~~~~~~~r~~~L~~~i~~~~~~YY~~g~p~ISD~eYD~L~~~L~~le~~~p~l~~~~spt~~VG~ 71 (332)
T 1ta8_A 4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGG 71 (332)
T ss_dssp -CCCHHHHHHHHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCC
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 87888899999999999999999998639999798899999999999999868145689997444577
No 5
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Probab=99.66 E-value=1.4e-16 Score=121.39 Aligned_cols=71 Identities=32% Similarity=0.450 Sum_probs=67.0
Q ss_pred CCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 77777899999999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 49 KKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 49 k~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
.+..+.+..++..|++.|+++|.+||++||+.++|+|||++||+|+++|.+||.+||+|+.++|||++||.
T Consensus 3 ~~~~~~~~~~~~~~~~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~l~~~~spt~~v~~ 73 (328)
T 1zau_A 3 SPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGG 73 (328)
T ss_dssp -----CCHHHHHTTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHHHHHHTSSTTCCTTCTTTTCSS
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 88656360999999999999999999998659999898899999999999999869033589997424477
No 6
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB: 3jsn_A*
Probab=99.61 E-value=8e-16 Score=116.71 Aligned_cols=62 Identities=27% Similarity=0.342 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99999999999999999975445898569899999999999999978742689897353889
Q gi|254780131|r 58 EAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119 (119)
Q Consensus 58 EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~~VGy 119 (119)
++..|++.|+++|.+||++||+.++|+|||++||+|+++|..||.+||+|+..+|||++||.
T Consensus 3 ~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~l~~~~spt~~vg~ 64 (318)
T 3jsl_A 3 DLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGG 64 (318)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHHHHHHHHCGGGCCTTCGGGGGCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 19999999999999999998728999798899999999999999868011478998755475
No 7
>2xlg_A SLL1785 protein, CUCA; metal binding protein, cupin; 1.80A {Synechocystis SP} PDB: 2xl7_A 2xl9_A 2xlf_A* 2xla_A
Probab=32.75 E-value=5.4 Score=20.04 Aligned_cols=61 Identities=16% Similarity=0.218 Sum_probs=49.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCC-----CCHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 132007589998998644165245522168986214-----777778999999999999999999999
Q gi|254780131|r 13 FENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKA-----KKVTSLSKGEAMIEVEYLVKIALHHQK 75 (119)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~ka-----k~v~~Lsk~EA~~eie~L~k~I~~Hn~ 75 (119)
+.+--.|||++--|..+.+|+|--|.-++ -|++. |=-+++++.+--.-++.+++.|...|+
T Consensus 166 ~~~~P~~t~~~~~~~~~~ap~ygin~~~~--~~e~~~~~~~kl~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (239)
T 2xlg_A 166 LNNLPELTNAQRAAFASEAPKYGINQSSY--FMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNR 231 (239)
T ss_dssp TTSCCCCC-----CTTTTGGGGTEEECSS--TTSSEEEEESSCCHHHHTCCCHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHCCCCCCCCCCE--EEEEECCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 57899888789999874364015135734--5556305355586789864166747999999998715
No 8
>3czp_A Putative polyphosphate kinase 2; PPK2, MCSG, PSI-2, structural genomics, protein structure initiative; HET: MSE; 2.00A {Pseudomonas aeruginosa PAO1}
Probab=20.36 E-value=46 Score=14.33 Aligned_cols=43 Identities=12% Similarity=-0.132 Sum_probs=33.5
Q ss_pred HHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9862147777789999999999999999999997544589856
Q gi|254780131|r 43 SWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLF 85 (119)
Q Consensus 43 ~~m~kak~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~I 85 (119)
+-|...-.-.+|+|.+.+.+++.|.+.|..-....|....|+|
T Consensus 260 ~~l~~~d~~~~~~k~~y~~~l~~lq~~L~~lq~~~~~~~~~vl 302 (500)
T 3czp_A 260 GLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIRDKRFRQHSLV 302 (500)
T ss_dssp HHHHTCCTTCCCCHHHHHHHHHHHHHHHHHHHHSGGGGGCEEE
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf 7401289555779999999999999999999999997499189
No 9
>3d4u_A Tafia, carboxypeptidase B2; protease-inhibitor complex, glycoprotein, hydrolase, metal-binding, metalloprotease, protease, secreted, zinc; 1.70A {Bos taurus} PDB: 3lms_A
Probab=19.45 E-value=33 Score=15.19 Aligned_cols=22 Identities=9% Similarity=-0.061 Sum_probs=9.9
Q ss_pred CCCCHHHHHHHHHHHH-HHHHHC
Q ss_conf 8569899999999999-999978
Q gi|254780131|r 83 PLFTDGLYDRVSERLD-ALQEQF 104 (119)
Q Consensus 83 P~ISD~EYD~L~~eL~-~LE~~~ 104 (119)
+.....++..+.+... ++...+
T Consensus 212 ~~~~~~~~~~~~~~~~~a~~~~~ 234 (309)
T 3d4u_A 212 RSKDHEELSLVAREAVFAMENIH 234 (309)
T ss_dssp CCTTHHHHHHHHHHHHHHHHHHS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 99898999999999999998623
No 10
>3mn8_A LP15968P; catalytic domain of alpha/beta-hydrolase fold, C-terminal, A transthyretin-like domain, hydrolase; HET: NAG GEM; 2.70A {Drosophila melanogaster}
Probab=18.07 E-value=37 Score=14.89 Aligned_cols=28 Identities=7% Similarity=0.237 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 9999999999999787426898973538
Q gi|254780131|r 90 YDRVSERLDALQEQFPELFDEDHPWNTV 117 (119)
Q Consensus 90 YD~L~~eL~~LE~~~PeL~~~dSPT~~V 117 (119)
|+.+...|..|+++||++..-.|+-+.+
T Consensus 43 y~e~~~~l~~l~~~yP~~~~l~~IG~S~ 70 (435)
T 3mn8_A 43 QEQLEDLFAGLEKAYPNQAKVHFLGRSL 70 (435)
T ss_dssp HHHHHHHHHHHHHHSTTTEEEEEEEECT
T ss_pred HHHHHHHHHHHHHHCCCCEEEEEEEECC
T ss_conf 9999999999998789927999615888
Done!