Query         gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs    120 out of 1548
Neff          3.5 
Searched_HMMs 23785
Date          Wed Jun  1 02:33:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781196.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 4.3E-18 1.8E-22  134.5   5.3   66   54-119     1-66  (667)
  2 2owo_A DNA ligase; protein/DNA  99.7 4.4E-17 1.8E-21  128.1   7.5   62   58-119     3-64  (671)
  3 1b04_A Protein (DNA ligase); D  99.7 1.3E-16 5.5E-21  125.1   8.6   66   54-119     1-66  (318)
  4 1ta8_A DNA ligase, NAD-depende  99.7 3.2E-16 1.4E-20  122.6   9.2   68   52-119     4-71  (332)
  5 1zau_A DNA ligase; AMP; HET: D  99.6 6.9E-16 2.9E-20  120.6   7.8   71   49-119     3-73  (328)
  6 3jsl_A DNA ligase; NAD+-depend  99.6 2.5E-15 1.1E-19  117.0   6.9   62   58-119     3-64  (318)
  7 3czp_A Putative polyphosphate   21.7      43  0.0018   14.5   2.7   43   43-85    260-302 (500)
  8 3d4u_A Tafia, carboxypeptidase  20.0      32  0.0013   15.3   1.3   14   85-98    214-227 (309)
  9 2xlg_A SLL1785 protein, CUCA;   18.5      10 0.00042   18.5  -1.6   55   19-75    172-231 (239)
 10 1m4l_A Carboxypeptidase A; met  18.2      36  0.0015   15.0   1.2   28   90-117    15-42  (307)

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=99.71  E-value=4.3e-18  Score=134.48  Aligned_cols=66  Identities=33%  Similarity=0.553  Sum_probs=65.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             899999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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=99.69  E-value=4.4e-17  Score=128.10  Aligned_cols=62  Identities=31%  Similarity=0.463  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   58 EAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        58 EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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=99.67  E-value=1.3e-16  Score=125.11  Aligned_cols=66  Identities=32%  Similarity=0.461  Sum_probs=64.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             899999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   54 LSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        54 Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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=99.66  E-value=3.2e-16  Score=122.63  Aligned_cols=68  Identities=29%  Similarity=0.420  Sum_probs=64.7

Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             87899999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   52 TSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        52 ~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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=99.62  E-value=6.9e-16  Score=120.56  Aligned_cols=71  Identities=32%  Similarity=0.450  Sum_probs=66.8

Q ss_pred             CCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             37887899999999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   49 KKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        49 k~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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=99.58  E-value=2.5e-15  Score=117.01  Aligned_cols=62  Identities=29%  Similarity=0.350  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999999999999999975545898569899999999999999978642689897353889
Q gi|254781196|r   58 EAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY  119 (119)
Q Consensus        58 EA~~eie~L~k~I~~Hn~~YY~~D~P~ISDaEYD~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  
>3czp_A Putative polyphosphate kinase 2; PPK2, MCSG, PSI-2, structural genomics, protein structure initiative; HET: MSE; 2.00A {Pseudomonas aeruginosa PAO1}
Probab=21.70  E-value=43  Score=14.48  Aligned_cols=43  Identities=12%  Similarity=-0.126  Sum_probs=33.4

Q ss_pred             HHHHHCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9997213788789999999999999999999997554589856
Q gi|254781196|r   43 SWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLF   85 (119)
Q Consensus        43 ~~~~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 8  
>3d4u_A Tafia, carboxypeptidase B2; protease-inhibitor complex, glycoprotein, hydrolase, metal-binding, metalloprotease, protease, secreted, zinc; 1.70A {Bos taurus} PDB: 3lms_A
Probab=19.96  E-value=32  Score=15.31  Aligned_cols=14  Identities=7%  Similarity=-0.164  Sum_probs=6.1

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             69899999999999
Q gi|254781196|r   85 FTDGLYDRVSERLD   98 (119)
Q Consensus        85 ISDaEYD~L~~eL~   98 (119)
                      ....++..+.+...
T Consensus       214 ~~~~~~~~~~~~~~  227 (309)
T 3d4u_A          214 KDHEELSLVAREAV  227 (309)
T ss_dssp             TTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             89899999999999


No 9  
>2xlg_A SLL1785 protein, CUCA; metal binding protein, cupin; 1.80A {Synechocystis SP} PDB: 2xl7_A 2xl9_A 2xlf_A* 2xla_A
Probab=18.52  E-value=10  Score=18.47  Aligned_cols=55  Identities=16%  Similarity=0.219  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCHHHHHHHHC-----CCHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             588772466202056556600699999721-----378878999999999999999999999
Q gi|254781196|r   19 ITPAQWKKLLTLEAKFLPNKRALESWLDKA-----KKVTSLSKGEAMIEVEYLVKIALHHQK   75 (119)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ka-----k~v~~Lsk~EA~~eie~L~k~I~~Hn~   75 (119)
                      |||++--+..+-||+|--|+-+.  .|++.     |--+++++.+--.-++.++++|+..|+
T Consensus       172 ~t~~~~~~~~~~ap~ygin~~~~--~~e~~~~~~~kl~~~~~~~~~~~~~~~~~~~~~~~~~  231 (239)
T 2xlg_A          172 LTNAQRAAFASEAPKYGINQSSY--FMEYVNTISDKLPAQIAKLKNDKDLERMVEVIEAFNR  231 (239)
T ss_dssp             CC-----CTTTTGGGGTEEECSS--TTSSEEEEESSCCHHHHTCCCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCCCCCE--EEEEECCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             88789999874364015135734--5556305355586789864166747999999998715


No 10 
>1m4l_A Carboxypeptidase A; metalloproteinase, metalloexoproteinase, hydrolase; 1.25A {Bos taurus} SCOP: c.56.5.1 PDB: 1cpx_A 1arl_A 1f57_A 2rfh_A* 3i1u_A* 1arm_A 1ell_P 1elm_P 1ee3_P 1zlh_A 2abz_A 3hlp_A 3huv_A 1yme_A* 3fvl_A* 3fx6_A* 2ctc_A* 1hdq_A 2ctb_A* 1pyt_B ...
Probab=18.25  E-value=36  Score=14.96  Aligned_cols=28  Identities=18%  Similarity=0.271  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             9999999999999786426898973538
Q gi|254781196|r   90 YDRVSERLDALQEQFPELFDEDHPWNTV  117 (119)
Q Consensus        90 YD~L~~eL~~LE~~~PeL~~~dSPT~~V  117 (119)
                      ||.+...|.+|.++||+++.-.++-..+
T Consensus        15 y~ei~~~l~~l~~~~p~~v~~~~iG~S~   42 (307)
T 1m4l_A           15 LDEIYDFMDLLVAEHPQLVSKLQIGRSY   42 (307)
T ss_dssp             HHHHHHHHHHHHHHCTTTEEEEEEEECT
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEEECC
T ss_conf             9999999999998789936999631768


Done!