Psyllid ID: psy14581

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARCISY
ccccHHHHHHHHHHccccEEccccccccccccccccccccccccEEEEEccccccccccccccEEEEccccEEEcccccccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccc
cccccHHHHHEcccccEEEEEcccccEEEccccccccccccccEEEEEEEccccccccccccEEEEEccEEEEEcccccHHHcccHHHHHHHHHHHcccccccccccHHHHHHHHHHccEEEcc
maknercyseikydgervqvhKKGNEFKYFSrslkpvlehkaqpvweisgaefsqaeihtadgisirfprvtkirddkdwktatnlpELKVLFKKsketsdftlkpkydRIKNLKLQKARCISY
maknercyseikydgervqvhKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEihtadgisirfprvtkirddkdwktatnlpelkvlfkksketsdftlkpkydriknlklqkarcisy
MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARCISY
*********EIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFK*************YDRI*************
*****RCYSEIKYDGE*****KKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVL********************************
MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARCISY
****ERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARCIS*
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MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARCISY
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query124 2.2.26 [Sep-21-2011]
P49916 1009 DNA ligase 3 OS=Homo sapi yes N/A 0.548 0.067 0.691 5e-22
P97386 1015 DNA ligase 3 OS=Mus muscu yes N/A 0.548 0.066 0.661 4e-21
P33798552 DNA ligase OS=Variola vir no N/A 0.379 0.085 0.592 3e-12
P20492552 DNA ligase OS=Vaccinia vi no N/A 0.435 0.097 0.592 3e-12
O57250552 DNA ligase OS=Vaccinia vi no N/A 0.435 0.097 0.592 3e-12
P16272552 DNA ligase OS=Vaccinia vi no N/A 0.435 0.097 0.592 3e-12
Q67480564 DNA ligase OS=Fowlpox vir N/A N/A 0.427 0.093 0.547 2e-11
Q9YMV2 548 DNA ligase OS=Lymantria d N/A N/A 0.266 0.060 0.702 5e-09
Q54QM4 1175 DNA ligase 3 OS=Dictyoste yes N/A 0.362 0.038 0.521 1e-07
Q869E11192 DNA ligase 1 OS=Dictyoste no N/A 0.645 0.067 0.325 8e-06
>sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2 Back     alignment and function desciption
 Score =  102 bits (255), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 58/68 (85%)

Query: 37  VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
           V + K   VWEI+GAEFS++E HTADGISIRFPR T+IRDDKDWK+ATNLP+LK L++ S
Sbjct: 773 VPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLS 832

Query: 97  KETSDFTL 104
           KE +DFT+
Sbjct: 833 KEKADFTV 840
Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 5EC: .EC: 1EC: .EC: 1
>sp|P97386|DNLI3_MOUSE DNA ligase 3 OS=Mus musculus GN=Lig3 PE=1 SV=2 Back     alignment and function description
>sp|P33798|DNLI_VAR67 DNA ligase OS=Variola virus (isolate Human/India/Ind3/1967) GN=LIG PE=3 SV=1 Back     alignment and function description
>sp|P20492|DNLI_VACCC DNA ligase OS=Vaccinia virus (strain Copenhagen) GN=LIG PE=1 SV=1 Back     alignment and function description
>sp|O57250|DNLI_VACCA DNA ligase OS=Vaccinia virus (strain Ankara) GN=LIG PE=3 SV=1 Back     alignment and function description
>sp|P16272|DNLI_VACCW DNA ligase OS=Vaccinia virus (strain Western Reserve) GN=LIG PE=1 SV=1 Back     alignment and function description
>sp|Q67480|DNLI_FOWPN DNA ligase OS=Fowlpox virus (strain NVSL) GN=LIG PE=3 SV=2 Back     alignment and function description
>sp|Q9YMV2|DNLI_NPVLD DNA ligase OS=Lymantria dispar multicapsid nuclear polyhedrosis virus GN=LIG PE=1 SV=1 Back     alignment and function description
>sp|Q54QM4|DNLI3_DICDI DNA ligase 3 OS=Dictyostelium discoideum GN=lig3 PE=3 SV=1 Back     alignment and function description
>sp|Q869E1|DNLI1_DICDI DNA ligase 1 OS=Dictyostelium discoideum GN=lig1 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query124
395536076 1003 PREDICTED: DNA ligase 3 [Sarcophilus har 0.548 0.067 0.720 8e-22
260841228 928 hypothetical protein BRAFLDRAFT_119901 [ 0.5 0.066 0.806 2e-21
405958255 878 DNA ligase 3 [Crassostrea gigas] 0.5 0.070 0.758 3e-21
57525295 902 DNA ligase 3 [Gallus gallus] gi|53128173 0.548 0.075 0.705 3e-21
344285688 1014 PREDICTED: LOW QUALITY PROTEIN: DNA liga 0.588 0.071 0.657 5e-21
334324598 1217 PREDICTED: DNA ligase 3 [Monodelphis dom 0.548 0.055 0.705 5e-21
193700124 875 PREDICTED: DNA ligase 3-like [Acyrthosip 0.516 0.073 0.734 6e-21
239791831 311 ACYPI004007 [Acyrthosiphon pisum] 0.516 0.205 0.734 8e-21
196007104 823 hypothetical protein TRIADDRAFT_57566 [T 0.580 0.087 0.653 1e-20
91076374 853 PREDICTED: similar to rCG33581 [Triboliu 0.516 0.075 0.75 1e-20
>gi|395536076|ref|XP_003770046.1| PREDICTED: DNA ligase 3 [Sarcophilus harrisii] Back     alignment and taxonomy information
 Score =  107 bits (268), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 59/68 (86%)

Query: 37  VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
           V + K  PVWEI+GAEFS+AE HTADGISIRFPR T+IRDDKDWK+ATNLP+LK L++ S
Sbjct: 771 VPDPKKAPVWEITGAEFSKAEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKKLYQLS 830

Query: 97  KETSDFTL 104
           KE +DFT+
Sbjct: 831 KEKADFTV 838

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota
>gi|260841228|ref|XP_002613830.1| hypothetical protein BRAFLDRAFT_119901 [Branchiostoma floridae] gi|229299220|gb|EEN69839.1| hypothetical protein BRAFLDRAFT_119901 [Branchiostoma floridae] Back     alignment and taxonomy information
>gi|405958255|gb|EKC24400.1| DNA ligase 3 [Crassostrea gigas] Back     alignment and taxonomy information
>gi|57525295|ref|NP_001006215.1| DNA ligase 3 [Gallus gallus] gi|53128173|emb|CAG31277.1| hypothetical protein RCJMB04_4j11 [Gallus gallus] Back     alignment and taxonomy information
>gi|344285688|ref|XP_003414592.1| PREDICTED: LOW QUALITY PROTEIN: DNA ligase 3-like [Loxodonta africana] Back     alignment and taxonomy information
>gi|334324598|ref|XP_001373823.2| PREDICTED: DNA ligase 3 [Monodelphis domestica] Back     alignment and taxonomy information
>gi|193700124|ref|XP_001943689.1| PREDICTED: DNA ligase 3-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|239791831|dbj|BAH72329.1| ACYPI004007 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|196007104|ref|XP_002113418.1| hypothetical protein TRIADDRAFT_57566 [Trichoplax adhaerens] gi|190583822|gb|EDV23892.1| hypothetical protein TRIADDRAFT_57566 [Trichoplax adhaerens] Back     alignment and taxonomy information
>gi|91076374|ref|XP_967954.1| PREDICTED: similar to rCG33581 [Tribolium castaneum] gi|270002897|gb|EEZ99344.1| ligase III [Tribolium castaneum] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query124
UNIPROTKB|F1P394 900 LIG3 "DNA ligase" [Gallus gall 0.741 0.102 0.557 2.1e-21
UNIPROTKB|P49916 1009 LIG3 "DNA ligase 3" [Homo sapi 0.798 0.098 0.529 4.1e-21
UNIPROTKB|I3L9T2 390 I3L9T2 "Uncharacterized protei 0.741 0.235 0.536 1.8e-20
UNIPROTKB|E2RNT6 938 LIG3 "DNA ligase" [Canis lupus 0.741 0.098 0.536 5.5e-20
UNIPROTKB|J9P597 957 LIG3 "DNA ligase" [Canis lupus 0.741 0.096 0.536 5.6e-20
RGD|1309875943 Lig3 "ligase III, DNA, ATP-dep 0.741 0.097 0.526 9e-20
UNIPROTKB|D4A2K2955 Lig3 "DNA ligase" [Rattus norv 0.741 0.096 0.526 9.2e-20
UNIPROTKB|D4A837 1014 Lig3 "DNA ligase" [Rattus norv 0.741 0.090 0.526 1e-19
MGI|MGI:109152 1015 Lig3 "ligase III, DNA, ATP-dep 0.741 0.090 0.526 1e-19
DICTYBASE|DDB_G0283857 1175 lig3 "DNA ligase III" [Dictyos 0.362 0.038 0.521 2.9e-19
UNIPROTKB|F1P394 LIG3 "DNA ligase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
 Score = 262 (97.3 bits), Expect = 2.1e-21, P = 2.1e-21
 Identities = 53/95 (55%), Positives = 70/95 (73%)

Query:    10 EIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69
             +I  D  ++    K N+  Y+   + P  + K  PVWEI+GAEFS+AE HTADGISIRFP
Sbjct:   658 KISKDPSKIPSWLKINKI-YYPDFIVP--DPKKAPVWEITGAEFSKAEAHTADGISIRFP 714

Query:    70 RVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTL 104
             R T+IRDDKDWKTATNLP+LK L++ SKE ++F++
Sbjct:   715 RCTRIRDDKDWKTATNLPQLKELYQLSKEKAEFSV 749
GO:0003677 "DNA binding" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA
GO:0005524 "ATP binding" evidence=IEA
GO:0006260 "DNA replication" evidence=IEA
GO:0006310 "DNA recombination" evidence=IEA
GO:0003910 "DNA ligase (ATP) activity" evidence=IEA
GO:0000795 "synaptonemal complex" evidence=IEA
GO:0005739 "mitochondrion" evidence=IEA
GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA
GO:0043504 "mitochondrial DNA repair" evidence=IEA
GO:0045910 "negative regulation of DNA recombination" evidence=IEA
UNIPROTKB|P49916 LIG3 "DNA ligase 3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3L9T2 I3L9T2 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNT6 LIG3 "DNA ligase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|J9P597 LIG3 "DNA ligase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1309875 Lig3 "ligase III, DNA, ATP-dependent" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|D4A2K2 Lig3 "DNA ligase" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|D4A837 Lig3 "DNA ligase" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:109152 Lig3 "ligase III, DNA, ATP-dependent" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0283857 lig3 "DNA ligase III" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P97386DNLI3_MOUSE6, ., 5, ., 1, ., 10.66170.54830.0669yesN/A
P49916DNLI3_HUMAN6, ., 5, ., 1, ., 10.69110.54830.0673yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query124
cd07967139 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/o 1e-30
cd07902213 cd07902, Adenylation_DNA_ligase_III, Adenylation d 2e-19
TIGR00574514 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1 4e-16
TIGR00574 514 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1 3e-13
cd07893129 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligo 3e-12
cd07969144 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oli 6e-12
pfam01068195 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligas 3e-11
cd07898201 cd07898, Adenylation_DNA_ligase, Adenylation domai 1e-10
cd07903225 cd07903, Adenylation_DNA_ligase_IV, Adenylation do 9e-10
cd07901207 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenyla 4e-09
PRK01109 590 PRK01109, PRK01109, ATP-dependent DNA ligase; Prov 6e-08
cd07968140 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/ol 5e-07
PLN03113744 PLN03113, PLN03113, DNA ligase 1; Provisional 7e-07
PRK01109590 PRK01109, PRK01109, ATP-dependent DNA ligase; Prov 4e-06
pfam0467995 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligas 6e-06
COG1793 444 COG1793, CDC9, ATP-dependent DNA ligase [DNA repli 1e-05
PRK03180 508 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed 2e-05
cd07900219 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation 1e-04
COG1793444 COG1793, CDC9, ATP-dependent DNA ligase [DNA repli 4e-04
cd07972122 cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleo 0.003
>gnl|CDD|153436 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information 
 Score =  105 bits (265), Expect = 1e-30
 Identities = 44/61 (72%), Positives = 52/61 (85%), Gaps = 3/61 (4%)

Query: 31  SRSLKP---VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLP 87
           ++SL P   V + K  PVWEI+GAEFS++E HTADGISIRFPRVT+IRDDKDWKTAT+LP
Sbjct: 79  NKSLVPDFIVKDPKKAPVWEITGAEFSKSEAHTADGISIRFPRVTRIRDDKDWKTATSLP 138

Query: 88  E 88
           E
Sbjct: 139 E 139

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Length = 139
>gnl|CDD|185712 cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA Ligase III Back     alignment and domain information
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>gnl|CDD|153435 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>gnl|CDD|153438 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|216280 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain Back     alignment and domain information
>gnl|CDD|185709 cd07898, Adenylation_DNA_ligase, Adenylation domain of ATP-dependent DNA Ligases Back     alignment and domain information
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA Ligase IV Back     alignment and domain information
>gnl|CDD|185711 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of archaeal and bacterial LigB-like DNA ligases Back     alignment and domain information
>gnl|CDD|234900 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|215584 PLN03113, PLN03113, DNA ligase 1; Provisional Back     alignment and domain information
>gnl|CDD|234900 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|218210 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligase C terminal region Back     alignment and domain information
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of eukaryotic DNA Ligase I Back     alignment and domain information
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|153441 cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 124
KOG0967|consensus714 99.88
KOG0966|consensus 881 99.74
cd07967139 OBF_DNA_ligase_III The Oligonucleotide/oligosaccha 99.67
PLN03113744 DNA ligase 1; Provisional 99.64
PRK01109590 ATP-dependent DNA ligase; Provisional 99.63
cd07969144 OBF_DNA_ligase_I The Oligonucleotide/oligosacchari 99.6
PRK09247539 ATP-dependent DNA ligase; Validated 99.53
PRK03180508 ligB ATP-dependent DNA ligase; Reviewed 99.49
TIGR00574514 dnl1 DNA ligase I, ATP-dependent (dnl1). All prote 99.47
cd07972122 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligo 99.46
cd07893129 OBF_DNA_ligase The Oligonucleotide/oligosaccharide 99.33
cd07968140 OBF_DNA_ligase_IV The Oligonucleotide/oligosacchar 99.31
cd08039235 Adenylation_DNA_ligase_Fungal Adenylation domain o 99.15
PLN03113 744 DNA ligase 1; Provisional 99.04
cd07900219 Adenylation_DNA_ligase_I_Euk Adenylation domain of 98.92
PHA02587488 30 DNA ligase; Provisional 98.87
PF0467997 DNA_ligase_A_C: ATP dependent DNA ligase C termina 98.84
PRK03180 508 ligB ATP-dependent DNA ligase; Reviewed 98.83
cd07898201 Adenylation_DNA_ligase Adenylation domain of ATP-d 98.79
cd07905194 Adenylation_DNA_ligase_LigC Adenylation domain of 98.77
cd07903225 Adenylation_DNA_ligase_IV Adenylation domain of DN 98.77
PRK01109 590 ATP-dependent DNA ligase; Provisional 98.76
cd07901207 Adenylation_DNA_ligase_Arch_LigB Adenylation domai 98.75
cd07902213 Adenylation_DNA_ligase_III Adenylation domain of D 98.72
cd07897207 Adenylation_DNA_ligase_Bac1 Adenylation domain of 98.72
TIGR00574 514 dnl1 DNA ligase I, ATP-dependent (dnl1). All prote 98.72
PRK09247 539 ATP-dependent DNA ligase; Validated 98.69
cd07906190 Adenylation_DNA_ligase_LigD_LigC Adenylation domai 98.67
TIGR02779 298 NHEJ_ligase_lig DNA polymerase LigD, ligase domain 98.67
PF01068202 DNA_ligase_A_M: ATP dependent DNA ligase domain; I 98.63
COG1793 444 CDC9 ATP-dependent DNA ligase [DNA replication, re 98.61
PRK09633 610 ligD ATP-dependent DNA ligase; Reviewed 98.57
cd07971115 OBF_DNA_ligase_LigD The Oligonucleotide/oligosacch 98.49
PRK07636 275 ligB ATP-dependent DNA ligase; Reviewed 98.47
PHA02587 488 30 DNA ligase; Provisional 98.43
cd06846182 Adenylation_DNA_ligase_like Adenylation domain of 98.42
PRK08224 350 ligC ATP-dependent DNA ligase; Reviewed 98.42
PRK05972 860 ligD ATP-dependent DNA ligase; Reviewed 98.4
PRK09632 764 ATP-dependent DNA ligase; Reviewed 98.4
TIGR02779298 NHEJ_ligase_lig DNA polymerase LigD, ligase domain 98.35
COG1793444 CDC9 ATP-dependent DNA ligase [DNA replication, re 98.31
cd07895215 Adenylation_mRNA_capping Adenylation domain of GTP 98.09
TIGR02776 552 NHEJ_ligase_prk DNA ligase D. Members of this prot 98.08
cd07970122 OBF_DNA_ligase_LigC The Oligonucleotide/oligosacch 98.04
PRK09633 610 ligD ATP-dependent DNA ligase; Reviewed 97.91
cd08040108 OBF_DNA_ligase_family The Oligonucleotide/oligosac 97.5
PHA00454 315 ATP-dependent DNA ligase 97.45
PRK09632764 ATP-dependent DNA ligase; Reviewed 97.44
cd07896174 Adenylation_kDNA_ligase_like Adenylation domain of 97.43
PRK05972 860 ligD ATP-dependent DNA ligase; Reviewed 97.28
cd07894 342 Adenylation_RNA_ligase Adenylation domain of RNA c 96.93
PRK09125 282 DNA ligase; Provisional 96.25
PRK07636275 ligB ATP-dependent DNA ligase; Reviewed 93.46
PRK08224350 ligC ATP-dependent DNA ligase; Reviewed 93.08
KOG4437|consensus482 84.81
>KOG0967|consensus Back     alignment and domain information 
Probab=99.88  E-value=3.2e-23  Score=179.90  Aligned_cols=70  Identities=36%  Similarity=0.641  Sum_probs=63.4

Q ss_pred             eEEeecCccceeeccccccceeccceeccccceecc--------ceEeecccceeeecCCCccccCCHHHHHHHHHHc
Q psy14581         27 FKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTAD--------GISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS   96 (124)
Q Consensus        27 ~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~--------G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~   96 (124)
                      +.-|...++|++|+.|..||||++|+++.||.|.+.        |++||||||+|||+||.++||||.+++.+||++|
T Consensus       627 ~y~~d~s~kPd~wf~p~~VwEvk~Adlt~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~peeAtts~qiaemY~~Q  704 (714)
T KOG0967|consen  627 YYRFDESLKPDVWFEPTEVWEVKAADLTLSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNPEEATTSSQIAEMYQAQ  704 (714)
T ss_pred             hcccCccCCCccccCHHHHHHHhhccccccchhHhhhcCcCCCCceeEecceeeEeeccCChhhcccHHHHHHHHHHH
Confidence            333444448999999999999999999999999863        8999999999999999999999999999999998

>KOG0966|consensus Back     alignment and domain information
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PLN03113 DNA ligase 1; Provisional Back     alignment and domain information
>PRK01109 ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins Back     alignment and domain information
>PLN03113 DNA ligase 1; Provisional Back     alignment and domain information
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I Back     alignment and domain information
>PHA02587 30 DNA ligase; Provisional Back     alignment and domain information
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases Back     alignment and domain information
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV Back     alignment and domain information
>PRK01109 ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases Back     alignment and domain information
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III Back     alignment and domain information
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases Back     alignment and domain information
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain Back     alignment and domain information
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PHA02587 30 DNA ligase; Provisional Back     alignment and domain information
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases Back     alignment and domain information
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK09632 ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain Back     alignment and domain information
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes Back     alignment and domain information
>TIGR02776 NHEJ_ligase_prk DNA ligase D Back     alignment and domain information
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>PHA00454 ATP-dependent DNA ligase Back     alignment and domain information
>PRK09632 ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins Back     alignment and domain information
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins Back     alignment and domain information
>PRK09125 DNA ligase; Provisional Back     alignment and domain information
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>KOG4437|consensus Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query124
3l2p_A579 Human Dna Ligase Iii Recognizes Dna Ends By Dynamic 2e-20
1x9n_A688 Crystal Structure Of Human Dna Ligase I Bound To 5' 9e-05
4eq5_A 571 Dna Ligase From The Archaeon Thermococcus Sibiricus 5e-04
3vnn_A139 Crystal Structure Of A Sub-Domain Of The Nucleotidy 8e-04
2hiv_A621 Atp-Dependent Dna Ligase From S. Solfataricus Lengt 9e-04
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic Switching Between Two Dna Bound States Length = 579 Back     alignment and structure 
Iteration: 1

 Score = 94.0 bits (232), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 52/61 (85%)
Query: 37  VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
           V + K   VWEI+GAEFS++E HTADGISIRFPR T+IRDDKDWK+ATNLP+LK L++ S
Sbjct: 519 VPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLS 578
Query: 97  K 97
           K
Sbjct: 579 K 579
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To 5'-Adenylated, Nicked Dna Length = 688 Back     alignment and structure
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus Length = 571 Back     alignment and structure
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The Nucleotidyltransferase (Adenylation) Domain Of Human Dna Ligase Iv Length = 139 Back     alignment and structure
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus Length = 621 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query124
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 2e-20
3l2p_A 579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 2e-11
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 4e-18
2hiv_A 621 Thermostable DNA ligase; ATP-dependent, open confo 1e-10
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 5e-18
2cfm_A 561 Thermostable DNA ligase; protein-nucleotide comple 4e-11
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 8e-18
3gde_A 558 DNA ligase; DNA-binding domain, adenylation domain 1e-11
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 2e-16
1x9n_A 688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 2e-08
3vnn_A139 DNA ligase 4; non-homologous END joining, DNA repa 1e-12
1a0i_A 348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 3e-07
1vs0_A 310 Putative DNA ligase-like protein RV0938/MT0965; OB 8e-06
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Length = 579 Back     alignment and structure
 Score = 84.0 bits (208), Expect = 2e-20
 Identities = 45/80 (56%), Positives = 57/80 (71%), Gaps = 3/80 (3%)

Query: 21  HKKGNEFKYFSRSLKP---VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDD 77
             K   +   ++   P   V + K   VWEI+GAEFS++E HTADGISIRFPR T+IRDD
Sbjct: 500 PSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDD 559

Query: 78  KDWKTATNLPELKVLFKKSK 97
           KDWK+ATNLP+LK L++ SK
Sbjct: 560 KDWKSATNLPQLKELYQLSK 579
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Length = 579 Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Length = 621 Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Length = 621 Back     alignment and structure
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Length = 561 Back     alignment and structure
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Length = 561 Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Length = 558 Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Length = 558 Back     alignment and structure
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Length = 688 Back     alignment and structure
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Length = 688 Back     alignment and structure
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens} Length = 139 Back     alignment and structure
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1 Length = 348 Back     alignment and structure
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis} Length = 310 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query124
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 99.61
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 99.5
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 99.5
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 99.49
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 99.42
3vnn_A139 DNA ligase 4; non-homologous END joining, DNA repa 99.14
1vs0_A 310 Putative DNA ligase-like protein RV0938/MT0965; OB 98.56
3gde_A 558 DNA ligase; DNA-binding domain, adenylation domain 98.55
1vs0_A310 Putative DNA ligase-like protein RV0938/MT0965; OB 98.5
1x9n_A 688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 98.49
3l2p_A 579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 98.48
2hiv_A 621 Thermostable DNA ligase; ATP-dependent, open confo 98.47
2cfm_A 561 Thermostable DNA ligase; protein-nucleotide comple 98.42
1a0i_A 348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 98.27
1ckm_A 330 MRNA capping enzyme; nucleotidyltransferase; HET: 97.53
1p16_A 395 GTP--RNA, mRNA capping enzyme alpha subunit; guany 97.36
3rtx_A 343 MRNA-capping enzyme; guanylyltransferase, RNA poly 96.84
1fvi_A 297 Chlorella virus DNA ligase-adenylate; adenylated D 96.81
1a0i_A348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 96.78
1fvi_A297 Chlorella virus DNA ligase-adenylate; adenylated D 95.4
3kyh_C 461 MRNA-capping enzyme subunit alpha; 5' modification 93.96
2vug_A 389 PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transfe 93.94
1p16_A395 GTP--RNA, mRNA capping enzyme alpha subunit; guany 93.06
1ckm_A330 MRNA capping enzyme; nucleotidyltransferase; HET: 87.5
1s68_A 249 RNA ligase 2; ribonucleic acid ligase, RNA repair; 84.95
2hvq_A 335 ORF1, hypothetical 37.6 kDa protein in GP24-HOC in 80.13
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Back     alignment and structure
Probab=99.61  E-value=1.5e-16  Score=137.03  Aligned_cols=66  Identities=64%  Similarity=1.026  Sum_probs=52.8

Q ss_pred             cCccceeec-cc--cccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHHHHcc
Q psy14581         32 RSLKPVLEH-KA--QPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSK   97 (124)
Q Consensus        32 Rn~ep~t~~-~P--s~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~~   97 (124)
                      .+..|++|. .|  +.||||++++++.|+.|+++|++||||||.++|+||+|+||+|+++|.+||+.++
T Consensus       511 ~~~~pd~~~~~P~~~~V~Ei~~~~i~~S~~~~~~G~sLRFPR~~riR~DK~~~ea~t~~~l~~l~~~~~  579 (579)
T 3l2p_A          511 KIYYPDFIVPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSK  579 (579)
T ss_dssp             --------------CEEEEEEESCEEECTTSSSTTEEESSCEECCCCSSCCSSSSCBHHHHHHHHHTCC
T ss_pred             CCCCCcEEEecCCCCeEEEEEeeEEeecCCcccCCEEEECCeEEEEeCCCChHHCCCHHHHHHHHhhcC
Confidence            455688774 44  8999999999999999988999999999999999999999999999999998874
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Back     alignment and structure
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Back     alignment and structure
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens} Back     alignment and structure
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis} Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Back     alignment and structure
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis} Back     alignment and structure
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Back     alignment and structure
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Back     alignment and structure
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Back     alignment and structure
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1 Back     alignment and structure
>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} SCOP: b.40.4.6 d.142.2.3 PDB: 1ckn_A* 1cko_A* 1ckn_B* Back     alignment and structure
>1p16_A GTP--RNA, mRNA capping enzyme alpha subunit; guanylyltransferase, transcription, capping, CTD, mRNA; HET: SEP G GTP; 2.70A {Candida albicans} SCOP: b.40.4.6 d.142.2.3 Back     alignment and structure
>3rtx_A MRNA-capping enzyme; guanylyltransferase, RNA polymerase II CTD, lysyl-N-GMP, NUC mRNA capping, transferase; HET: SEP GUN; 2.81A {Mus musculus} PDB: 3s24_A Back     alignment and structure
>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A* Back     alignment and structure
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1 Back     alignment and structure
>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A* Back     alignment and structure
>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP; 2.9A {Pyrococcus abyssi GE5} Back     alignment and structure
>1p16_A GTP--RNA, mRNA capping enzyme alpha subunit; guanylyltransferase, transcription, capping, CTD, mRNA; HET: SEP G GTP; 2.70A {Candida albicans} SCOP: b.40.4.6 d.142.2.3 Back     alignment and structure
>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} SCOP: b.40.4.6 d.142.2.3 PDB: 1ckn_A* 1cko_A* 1ckn_B* Back     alignment and structure
>1s68_A RNA ligase 2; ribonucleic acid ligase, RNA repair; HET: AMP; 1.90A {Enterobacteria phage T4} SCOP: d.142.2.4 Back     alignment and structure
>2hvq_A ORF1, hypothetical 37.6 kDa protein in GP24-HOC intergenic region; RNA, ligase, lysine adenylate; HET: APK; 2.40A {Enterobacteria phage T4} PDB: 2hvr_A* 2hvs_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 124
d1x9na2148 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (H 2e-13
d1a0ia2239 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-te 1e-04
d1x9na3220 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human ( 2e-04
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 148 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-13
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 20  VHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRV 71
           V      +     ++ P        VWE+  A+ S + I+ A         GIS+RFPR 
Sbjct: 63  VLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRF 122

Query: 72  TKIRDDKDWKTATNLPELKVLFKK 95
            ++R+DK  + AT   ++  L++K
Sbjct: 123 IRVREDKQPEQATTSAQVACLYRK 146
>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]} Length = 239 Back     information, alignment and structure
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 220 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query124
d1x9na2148 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 99.74
d1x9na3220 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 98.75
d1a0ia2239 ATP-dependent DNA ligase, N-terminal domain {Bacte 98.24
d1s68a_233 RNA ligase 2, N-terminal domain {Bacteriophage T4 97.77
d1fvia2188 ATP-dependent DNA ligase, N-terminal domain {Chlor 97.41
d1p16a2245 mRNA capping enzyme alpha subunit {Yeast (Candida 95.62
d1ckma2228 RNA guanylyltransferase (mRNA capping enzyme), N-t 94.44
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1e-18  Score=125.10  Aligned_cols=68  Identities=32%  Similarity=0.560  Sum_probs=61.3

Q ss_pred             eecCccceeeccccccceeccceeccccceec--------cceEeecccceeeecCCCccccCCHHHHHHHHHHcc
Q psy14581         30 FSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSK   97 (124)
Q Consensus        30 fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~--------~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~~   97 (124)
                      ......|++|.+|+.|+||++++++.|+.|.+        .|++||||||.++|+||+|+||+|+++|.+||++|+
T Consensus        73 ~~~~~~~~~wv~P~~V~Ev~~~~it~s~~~~~~~~~~~~~~g~sLRfPr~~riR~DK~~~e~~t~~~l~~l~~~Q~  148 (148)
T d1x9na2          73 IDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQS  148 (148)
T ss_dssp             CSSSCCCSEEECSCCEEEEEESEEEEESSCCTTTTTSCSSCEEEEESCEEEEECTTCCGGGSCBHHHHHHHHHHHC
T ss_pred             ccCccCCcEEeccceEEEEEeeeeeeccceeeccccccCCCceEEEcCEEEEEeCCCChHHCcCHHHHHHHHHhcC
Confidence            34455799999999999999999999988864        489999999999999999999999999999998875
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1s68a_ d.142.2.4 (A:) RNA ligase 2, N-terminal domain {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d1fvia2 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Back     information, alignment and structure
>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]} Back     information, alignment and structure
>d1ckma2 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Back     information, alignment and structure