YRC Public Data Repository - Protein Structure Prediction

Protein:	lig4
Organism:	Schizosaccharomyces pombe
Length:	923 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 lig4.

Description	E-value	Query Range	Subject Range
DNL4_PONPY - DNA ligase 4 - Pongo pygmaeus (Orangutan) DNLI4_PONAB - DNA ligase 4 OS=Pongo abelii GN=DNL4 PE=2 SV=1	694.0	[0..13]	[907..8]
LIG4 - ligase IV, DNA, ATP-dependent gi\|123998021, gi... - gi\|123998021\|gb\|ABM86612.1\| ligase IV, DNA, ATP-dependent [synthetic construct], gi\|123983318\|gb\|ABM...	693.0	[0..13]	[907..8]
gi\|114650629, gi... - gi\|114650629\|ref\|XP_001135359.1\| PREDICTED: DNA ligase IV isoform 1 [Pan troglodytes], gi\|114650627\|...	692.0	[0..13]	[907..8]
gi\|73989476 - gi\|73989476\|ref\|XP_542663.2\| PREDICTED: similar to DNA ligase IV [Canis familiaris]	687.0	[0..13]	[907..8]
gi\|149057556, gi... - gi\|27703746\|ref\|XP_225045.1\| PREDICTED: similar to DNA ligase IV [Rattus norvegicus], gi\|157824095\|r...	677.0	[0..13]	[907..8]
DNLI4_MOUSE - DNA ligase 4 OS=Mus musculus GN=Lig4 PE=2 SV=2 gi\|146327388 - gi\|146327388\|gb\|AAI41418.1\| Ligase IV, DNA, ATP-dependent [synthetic construct]	674.0	[0..13]	[912..8]
gi\|49256305, gi\|... - gi\|49256305\|gb\|AAH74385.1\| Lig4-A protein [Xenopus laevis], gi\|148235991\|ref\|NP_001081114.1\| DNA lig...	674.0	[0..13]	[907..13]

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Predicted Domain #1

Region A:
Residues: [1-648]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDEAKETVFT KPQNHSSTLE FYDFVTTLLE PLSRIGKTRK SKTSNLDPYE LKRKILLDYF  60
   61 NKWRQHVGPD LYPLLRLSNL IFLDRERGSY GFKEFGLGKL FIRAMHLSPT SEDAKSLKNW 120
  121 RGSESKHTGD FSTMLQDILQ RRAYRTFPGA FTVGDVNALL DQLADASSEY VLNFLPYLTL 180
  181 IRDTRVNILE QFYRSLSPLE LRWLIPILLK VRKYGTSEKF ILSVFHPDAA RLYRLCSSLK 240
  241 RICWELYDPS RSLDETETDV EVFSCFQPQL ANFKKKDLHQ TLEAMGNKPF WIEEKLDGER 300
  301 IQLHMSSGKF QFYSRNARSY TYAYGSSYFD EQSRLTQYII GAFDKRISQI ILDGEMVTWD 360
  361 PVLETVIPYG SLRSIFEDSS SHSSYSPYYV VFDILYLNGK SLVKYSLESR RRILEKVIVR 420
  421 ESHRMSILPY KVGSTIEDIE AELRNVIQEG SEGLVIKKPS GSYHLGERMD DWIKVKPYYL 480
  481 QGFGEDLDCL ILGGYFGRGK QSGKINSFLC GLRMDYTPKD HSEKFQSFVR VGGGFTYFDR 540
  541 DIIRKETEGK WLPWSSDALE YMELAGTKQD FEKPDMWIHP KDSLVLQIKA AEVVVSNRFK 600
  601 TNYTLRFPRL EKVRLDRSWK DALTINEFFT LKNAVEKQDN VSFHVNKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	136.0
Match:	1x9nA
Description:	Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA
Matching Structure (courtesy of the PDB):

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	3.1488483282989	bayes_pls_golite062009
ligase activity	2.44151794329612	bayes_pls_golite062009
catalytic activity	2.15370807854636	bayes_pls_golite062009
nucleic acid binding	1.4725380374617	bayes_pls_golite062009
binding	1.23714137231717	bayes_pls_golite062009
DNA binding	1.1855473374207	bayes_pls_golite062009
protein binding	0.352542259246499	bayes_pls_golite062009
nucleotidyltransferase activity	0.316166307022498	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [649-826]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RKVSQKREKQ KKFLYDEPTF KKEASPHSDV LKNLHFVVLP PTELHETKAG LQQIIIENGG  60
   61 LIHQGVGNFG KERLFLVADR VSTRVSIERS KNMCTIIRSQ WVMDSVNNQR LMPQWSYLLF 120
  121 SKDEKYSWKT ALESLSAKSL SNLLVELKQL DLSKEYSKIS DDTSILNLTI SKEEASFV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.522879
Match:	1z56C
Description:	Co-Crystal Structure of Lif1p-Lig4p
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [827-923]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GAFPFLKFTV FLDLKGIENS ELYDVRMGQY RLTKCILLWN GATIEKDISS KKLTHVVMFV  60
   61 EDSTRLEQLT KACELTQHRK FTQPSYFQRY GGSFCIP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.154902
Match:	1wf6A
Description:	The third BRCA1 C-terminus (BRCT) domain of Similar to S.pombe rad4+/cut5+ product
Matching Structure (courtesy of the PDB):

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: