254780131

254780131

DNA ligase, NAD-dependent

GeneID in NCBI database:8209106Locus tag:CLIBASIA_00050
Protein GI in NCBI database:254780131Protein Accession:YP_003064544.1
Gene range:+(7442, 7801)Protein Length:119aa
Gene description:DNA ligase, NAD-dependent
COG prediction:[L] NAD-dependent DNA ligase (contains BRCT domain type II)
KEGG prediction:DNA ligase, NAD-dependent
SEED prediction:DNA ligase, NAD-dependent
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
cccHHHHHHHHHccccccccHHHHHHHHHHHHHHcccHHHccHHHHccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccccccccccccccc
cccccEEEEcccccccccccHHHHHHHHHHHHHHcHcHHHHHHHccccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccHccccccccccccc
mynfdrvfrsskfenehnitpaQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQkwyyrlddplftdgLYDRVSERLDALQEQfpelfdedhpwntvgy
mynfdrvfrsskfenehnitpaqwkKLLTLEAKFLPNKRALESWLDKAKkvtslskgeaMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEqfpelfdedhpwntvgy
MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
**NFDRVFRSSKFENE*NITPAQWKKLLTLEAK**************************MIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPW**V**
MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
*YNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFD**********
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MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLxxxxxxxxxxxxxxxxxxxxxDHPWNTVGY
MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
254781196119 DNA ligase, NAD-dependent [Candidatus Liberibacter 1e-67
254781172 731 NAD-dependent DNA ligase LigA [Candidatus Liberiba 1e-05
>gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] Length = 119 Back     alignment
 Score =  245 bits (626), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 118/119 (99%), Positives = 119/119 (100%)

Query: 1   MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM 60
           MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM
Sbjct: 1   MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM 60

Query: 61  IEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119
           IEVEYLVKIALHHQKWYYRLD+PLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
Sbjct: 61  IEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119

>gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA [Candidatus Liberibacter asiaticus str. psy62] Length = 731 Back     alignment
 Score = 40.4 bits (93), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 51  VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELF-- 108
           + +LS  +A  E+  L +   +H   YY+   P+  D  YD +  R DA+   FP+L   
Sbjct: 9   IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARS 68

Query: 109 -DEDHPWNTVG 118
            D + P N +G
Sbjct: 69  EDPNGPLNKIG 79

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
254781196119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia 1 1e-63
315121970127 DNA ligase, NAD-dependent [Candidatus Liberibacter sola 1 2e-16
299131914 706 DNA ligase, NAD-dependent [Afipia sp. 1NLS2] Length = 7 1 6e-07
209550159 718 NAD-dependent DNA ligase LigA [Rhizobium leguminosarum 1 1e-06
90418183 703 DNA ligase [Aurantimonas manganoxydans SI85-9A1] Length 1 3e-06
190892570 718 DNA ligase (NAD+) protein [Rhizobium etli CIAT 652] Len 1 3e-06
218515813 216 NAD-dependent DNA ligase LigA [Rhizobium etli 8C-3] Len 1 3e-06
327194610 718 DNA ligase (NAD+) protein [Rhizobium etli CNPAF512] Len 1 4e-06
316933200 715 NAD-dependent DNA ligase [Rhodopseudomonas palustris DX 1 4e-06
322437173 704 DNA ligase, NAD-dependent [Acidobacterium sp. MP5ACTX9] 1 4e-06
>gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] Length = 119 Back     alignment and organism information
 Score =  245 bits (626), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/119 (99%), Positives = 119/119 (100%)

Query: 1   MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM 60
           MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM
Sbjct: 1   MYNFDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAM 60

Query: 61  IEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119
           IEVEYLVKIALHHQKWYYRLD+PLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY
Sbjct: 61  IEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVGY 119


Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|315121970|ref|YP_004062459.1| DNA ligase, NAD-dependent [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 127 Back     alignment and organism information
>gi|299131914|ref|ZP_07025109.1| DNA ligase, NAD-dependent [Afipia sp. 1NLS2] Length = 706 Back     alignment and organism information
>gi|209550159|ref|YP_002282076.1| NAD-dependent DNA ligase LigA [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 718 Back     alignment and organism information
>gi|90418183|ref|ZP_01226095.1| DNA ligase [Aurantimonas manganoxydans SI85-9A1] Length = 703 Back     alignment and organism information
>gi|190892570|ref|YP_001979112.1| DNA ligase (NAD+) protein [Rhizobium etli CIAT 652] Length = 718 Back     alignment and organism information
>gi|218515813|ref|ZP_03512653.1| NAD-dependent DNA ligase LigA [Rhizobium etli 8C-3] Length = 216 Back     alignment and organism information
>gi|327194610|gb|EGE61460.1| DNA ligase (NAD+) protein [Rhizobium etli CNPAF512] Length = 718 Back     alignment and organism information
>gi|316933200|ref|YP_004108182.1| NAD-dependent DNA ligase [Rhodopseudomonas palustris DX-1] Length = 715 Back     alignment and organism information
>gi|322437173|ref|YP_004219385.1| DNA ligase, NAD-dependent [Acidobacterium sp. MP5ACTX9] Length = 704 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
smart00532 441 smart00532, LIGANc, Ligase N family 2e-09
pfam01653 315 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase ad 1e-08
PRK07956 665 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validate 1e-08
cd00114 307 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation 6e-08
TIGR00575 652 TIGR00575, dnlj, DNA ligase, NAD-dependent 1e-07
PRK14351 689 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisio 4e-06
COG0272 667 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT d 2e-09
>gnl|CDD|128805 smart00532, LIGANc, Ligase N family Back     alignment and domain information
>gnl|CDD|145016 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation domain Back     alignment and domain information
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain Back     alignment and domain information
>gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent Back     alignment and domain information
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
TIGR00575 706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 99.84
PRK08097 563 ligB NAD-dependent DNA ligase LigB; Reviewed 99.82
COG0272 667 Lig NAD-dependent DNA ligase (contains BRCT domain type 99.8
PRK07956 668 ligA NAD-dependent DNA ligase LigA; Validated 99.77
smart00532 441 LIGANc Ligase N family. 99.74
pfam01653 315 DNA_ligase_aden NAD-dependent DNA ligase adenylation do 99.74
cd00114 307 LIGANc NAD+ dependent DNA ligase adenylation domain. DN 99.65
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>smart00532 LIGANc Ligase N family Back     alignment and domain information
>pfam01653 DNA_ligase_aden NAD-dependent DNA ligase adenylation domain Back     alignment and domain information
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
2owo_A 671 Last Stop On The Road To Repair: Structure Of E.Col 4e-22
1b04_A 318 Structure Of The Adenylation Domain Of An Nad+ Depe 2e-20
1zau_A 328 Adenylation Domain Of Nad+ Dependent Dna Ligase Fro 6e-20
1ta8_A 332 Structural Rearrangement Accompanying Nad+ Synthesi 1e-18
1tae_A 332 Structural Rearrangement Accompanying Nad+ Synthesi 2e-18
1dgs_A 667 Crystal Structure Of Nad+-Dependent Dna Ligase From 3e-17
1v9p_A 584 Crystal Structure Of Nad+-Dependent Dna Ligase Leng 6e-17
3pn1_A 318 Novel Bacterial Nad+-Dependent Dna Ligase Inhibitor 6e-17
3jsl_A 318 Crystal Structure Of The Adenylation Domain Of Nad+ 2e-14
gi|149242732|pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna Ligase Bound To Nicked Dna-Adenylate Length = 671 Back     alignment and structure
 Score =  107 bits (269), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 27/62 (43%)

Query: 57  GEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNT 116
                ++  L     HH+  Y+ +D P   D  YDR+   L  L+ + PEL   D P   
Sbjct: 2   ESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQR 61

Query: 117 VG 118
           VG
Sbjct: 62  VG 63


>gi|6573451|pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent Ligase Length = 318 Back     alignment and structure
>gi|71042246|pdb|1ZAU|A Chain A, Adenylation Domain Of Nad+ Dependent Dna Ligase From M.Tuberculosis Length = 328 Back     alignment and structure
>gi|56966057|pdb|1TA8|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332 Back     alignment and structure
>gi|56966058|pdb|1TAE|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332 Back     alignment and structure
>gi|11513386|pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T. Filiformis Length = 667 Back     alignment and structure
>gi|47169437|pdb|1V9P|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase Length = 584 Back     alignment and structure
>gi|317455470|pdb|3PN1|A Chain A, Novel Bacterial Nad+-Dependent Dna Ligase Inhibitors With Broad Spectrum Potency And Antibacterial Efficacy In Vivo Length = 318 Back     alignment and structure
>gi|281307118|pdb|3JSL|A Chain A, Crystal Structure Of The Adenylation Domain Of Nad+- Dependent Dna Ligase From Staphylococcus Aureus Length = 318 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 1e-11
2owo_A 671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 1e-09
1ta8_A 332 DNA ligase, NAD-dependent; nucleotidyl transferase fold 2e-09
3jsl_A 318 DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA 2e-08
1b04_A 318 Protein (DNA ligase); DNA replication; 2.80A {Bacillus 6e-08
1zau_A 328 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tub 7e-08
>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* Length = 667 Back     alignment and structure
 Score = 63.3 bits (154), Expect = 1e-11
 Identities = 23/66 (34%), Positives = 33/66 (50%)

Query: 54  LSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
           +++ EA   +  L  +  +H   YY L DP  +D  YDR+   L  L+E+FPE    D P
Sbjct: 1   MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSP 60

Query: 114 WNTVGY 119
              VG 
Sbjct: 61  TEQVGA 66


>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Length = 671 Back     alignment and structure
>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* Length = 332 Back     alignment and structure
>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* Length = 318 Back     alignment and structure
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus stearothermophilus} SCOP: d.142.2.2 Length = 318 Back     alignment and structure
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Length = 328 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 99.75
2owo_A 671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 99.72
1b04_A 318 Protein (DNA ligase); DNA replication; 2.80A {Geobacill 99.7
1ta8_A 332 DNA ligase, NAD-dependent; nucleotidyl transferase fold 99.69
1zau_A 328 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tub 99.66
3jsl_A 318 DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA 99.61
>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* Back     alignment and structure
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



>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2 Back     alignment and structure
>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* Back     alignment and structure
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Back     alignment and structure
>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* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
d1ta8a_ 313 d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA 2e-08
d1dgsa3 314 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependen 3e-08
d1b04a_ 312 d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA 8e-08
>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} Length = 313 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]
 Score = 51.1 bits (121), Expect = 2e-08
 Identities = 19/64 (29%), Positives = 29/64 (45%)

Query: 54  LSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
           L+   A    + L K    +   YY  D P   D +YDR+ + L  ++ +FP+L   D P
Sbjct: 2   LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSP 61

Query: 114 WNTV 117
              V
Sbjct: 62  TQRV 65


>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Length = 314 Back     information, alignment and structure
>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Length = 312 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
d1dgsa3 314 Adenylation domain of NAD+-dependent DNA ligase {Thermu 99.71
d1ta8a_ 313 Adenylation domain of NAD+-dependent DNA ligase {Entero 99.69
d1b04a_ 312 Adenylation domain of NAD+-dependent DNA ligase {Bacill 99.65
>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]
Probab=99.71  E-value=3.7e-18  Score=129.54  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~~YD~L~~eL~~le~~~p~l~~~~s~~~~vg~   66 (314)
T d1dgsa3           1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGA   66 (314)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHHHHTTSSGGGCCTTSGGGGCSS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             988999999999999999999997648999789999999999999999869000267896400112



>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} Back     information, alignment and structure
>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 119 DNA ligase, NAD-dependent [Candidatus Liberibacter
2owo_A_1-60_117-236 180 (A:1-60,A:117-236) DNA ligase; protein/DNA complex 2e-12
1zau_A_1-6969 (A:1-69) DNA ligase; AMP; HET: DNA AMP; 3.15A {Myc 1e-10
>2owo_A (A:1-60,A:117-236) DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12}Length = 180 Back     alignment and structure
 Score = 65.7 bits (160), Expect = 2e-12
 Identities = 17/56 (30%), Positives = 25/56 (44%)

Query: 58  EAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113
               ++  L     HH+  Y+ +D P   D  YDR+   L  L+ + PEL   D P
Sbjct: 3   SIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSP 58


>1zau_A (A:1-69) DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}Length = 69 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target119 DNA ligase, NAD-dependent [Candidatus Liberibacter asia
1zau_A_1-6969 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu 99.76
2owo_A_1-60_117-236 180 DNA ligase; protein/DNA complex, ligase/DNA comple 99.71
>1zau_A (A:1-69) DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Back     alignment and structure
Probab=99.76  E-value=1.4e-18  Score=134.41  Aligned_cols=68  Identities=31%  Similarity=0.452  Sum_probs=66.6

Q ss_pred             CCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             47777789999999999999999999997544589856989999999999999997874268989735
Q gi|254780131|r   48 AKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWN  115 (119)
Q Consensus        48 ak~v~~Lsk~EA~~eie~L~k~I~~Hn~~YY~~D~P~ISD~EYD~L~~eL~~LE~~~PeL~~~dSPT~  115 (119)
                      ++++.+|++.+++.++..|+++|.+|+++||++|+|+|||++||+|+++|..||.+||+|+.+|||||
T Consensus         2 ~~~~~~~~~~~~~~~~~~L~~~i~~~~~~YY~~~~p~isD~~YD~l~~eL~~lE~~~P~l~~~dSPTq   69 (69)
T 1zau_A            2 SSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQ   69 (69)
T ss_dssp             ------CCHHHHHTTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHHHHHHTSSTTCCTTCTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             98864527299999999999999999999864899979889999999999999986901026898530



>2owo_A (A:1-60,A:117-236) DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure