YRC Public Data Repository - Protein Structure Prediction

Protein:	DNL4
Organism:	Saccharomyces cerevisiae
Length:	944 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for DNL4.

Description	E-value	Query Range	Subject Range
DNLI4_YEAST - DNA ligase 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DNL4 PE=1 SV=1 DNL4 - DNA ligase required for nonhomologous end-joining (NHEJ), forms stable heterodimer with required cof...	0.0	[1..944]	[1..944]
gi\|18029886 - gi\|18029886\|gb\|AAL56554.1\|AF393656_1 DNA ligase IV [Xenopus laevis]	0.0	[7..936]	[2..906]
gi\|15778121 - gi\|15778121\|dbj\|BAB68506.1\| DNA ligase IV [Gallus gallus]	0.0	[1..939]	[1..910]
gi\|18653446 - gi\|18653446\|gb\|AAL77435.1\|AF479264_1 ligase IV, DNA, ATP-dependent [Homo sapiens]	0.0	[73..938]	[1..840]
DNLI_CANAL - DNA ligase - Candida albicans (Yeast)	0.0	[9..938]	[11..923]
DNLI4_ARATH - DNA ligase 4 OS=Arabidopsis thaliana GN=LIG4 PE=1 SV=1	0.0	[30..936]	[6..904]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[9..862]	[11..845]
DNLI4_SCHPO - DNA ligase 4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lig4 PE=2 SV=2 lig4 - DNA ligase Lig4	0.0	[10..833]	[11..806]
Lig4-PA - The gene Ligase4 is referred to in FlyBase by the symbol Dmel\Lig4 (CG12176, FBgn0030506). It is a p...	0.0	[13..873]	[4..859]

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Predicted Domain #1

Region A:
Residues: [1-242]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM  60
   61 WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG 120
  121 KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC 180
  181 VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR 240
  241 LK

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
DNA ligase activity	10.0279903057926	bayes_pls_golite062009
ligase activity, forming phosphoric ester bonds	9.92846900587219	bayes_pls_golite062009
DNA ligase (ATP) activity	8.51283882444113	bayes_pls_golite062009
DNA ligase (NAD+) activity	3.17397926295565	bayes_pls_golite062009
ligase activity	2.36807839237461	bayes_pls_golite062009
catalytic activity	2.15370807854636	bayes_pls_golite062009
binding	1.82998145778732	bayes_pls_golite062009
protein binding	1.38006517521813	bayes_pls_golite062009
nucleic acid binding	1.06318697852063	bayes_pls_golite062009
DNA binding	0.920391596538289	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [243-309]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDDLSIKVGF AFAPQLAKKV NLSYEKICRT LHDDFLVEEK MDGERIQVHY MNYGESIKFF  60
   61 SRRGIDY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.04
Match:	1fviA
Description:	ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [310-421]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TYLYGASLSS GTISQHLRFT DSVKECVLDG EMVTFDAKRR VILPFGLVKG SAKEALSFNS  60
   61 INNVDFHPLY MVFDLLYLNG TSLTPLPLHQ RKQYLNSILS PLKNIVEIVR SS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.30103
Match:	1fviA_
Description:	ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [422-468]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RCYGVESIKK SLEVAISLGS EGVVLKYYNS SYNVASRNNN WIKVKPE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.30103
Match:	1fviA_
Description:	ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [469-579]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YLEEFGENLD LIVIGRDSGK KDSFMLGLLV LDEEEYKKHQ GDSSEIVDHS SQEKHIQNSR  60
   61 RRVKKILSFC SIANGISQEE FKEIDRKTRG HWKRTSEVAP PASILEFGSK I

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.30103
Match:	1fviA_
Description:	ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [580-733]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PAEWIDPSES IVLEIKSRSL DNTETNMQKY ATNCTLYGGY CKRIRYDKEW TDCYTLNDLY  60
   61 ESRTVKSNPS YQAERSQLGL IRKKRKRVLI SDSFHQNRKQ LPISNIFAGL LFYVLSDYVT 120
  121 EDTGIRITRA ELEKTIVEHG GKLIYNVILK RHSI

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #7

Region A:
Residues: [734-816]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GDVRLISCKT TTECKALIDR GYDILHPNWV LDCIAYKRLI LIEPNYCFNV SQKMRAVAEK  60
   61 RVDCLGDSFE NDISETKLSS LYK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.39794
Match:	1ik9C_
Description:	CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [817-944]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SQLSLPPMGE LEIDSEVRRF PLFLFSNRIA YVPRRKISTE DDIIEMKIKL FGGKITDQQS  60
   61 LCNLIIIPYT DPILRKDCMN EVHEKIKEQI KASDTIPKIA RVVAPEWVDH SINENCQVPE 120
  121 EDFPVVNY

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: