YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|123998021, gi...
Organism:	synthetic construct
Length:	911 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 gi|123998021, gi....

Description	E-value	Query Range	Subject Range
gi\|114650629, gi... - gi\|114650629\|ref\|XP_001135359.1\| PREDICTED: DNA ligase IV isoform 1 [Pan troglodytes], gi\|114650627\|...	0.0	[1..911]	[1..911]
DNL4_PONPY - DNA ligase 4 - Pongo pygmaeus (Orangutan) DNLI4_PONAB - DNA ligase 4 OS=Pongo abelii GN=DNL4 PE=2 SV=1	0.0	[1..911]	[1..911]
gi\|73989476 - gi\|73989476\|ref\|XP_542663.2\| PREDICTED: similar to DNA ligase IV [Canis familiaris]	0.0	[1..910]	[1..910]
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]	0.0	[1..911]	[1..911]
gi\|149057556, gi... - gi\|27703746\|ref\|XP_225045.1\| PREDICTED: similar to DNA ligase IV [Rattus norvegicus], gi\|157824095\|r...	0.0	[1..911]	[1..911]
DNLI4_CHICK - DNA ligase 4 OS=Gallus gallus GN=LIG4 PE=2 SV=2	0.0	[6..911]	[11..912]
gi\|18029886 - gi\|18029886\|gb\|AAL56554.1\|AF393656_1 DNA ligase IV [Xenopus laevis]	0.0	[2..911]	[7..911]

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Predicted Domain #1

Region A:
Residues: [1-650]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV  60
   61 TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP RDGKDALKLL NYRTPTGTHG 120
  121 DAGDFAMIAY FVLKPRCLQK GSLTIQQVND LLDSIASNNS AKRKDLIKKS LLQLITQSSA 180
  181 LEQKWLIRMI IKDLKLGVSQ QTIFSVFHND AAELHNVTTD LEKVCRQLHD PSVGLSDISI 240
  241 TLFSAFKPML AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD 300
  301 QFGASPTEGS LTPFIHNAFK ADIQICILDG EMMAYNPNTQ TFMQKGTKFD IKRMVEDSDL 360
  361 QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI EIVQKTQAHT KNEVIDALNE 420
  421 AIDKREEGIM VKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM 480
  481 SHFLCAVAEK PPPGEKPSVF HTLSRVGSGC TMKELYDLGL KLAKYWKPFH RKAPPSSILC 540
  541 GTEKPEVYIE PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE 600
  601 QLRGKASGKL ASKHLYIGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	145.0
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	2.36807839237461	bayes_pls_golite062009
catalytic activity	2.15370807854636	bayes_pls_golite062009
binding	1.82998145778732	bayes_pls_golite062009
nucleic acid binding	1.4725380374617	bayes_pls_golite062009
protein binding	1.38006517521813	bayes_pls_golite062009
DNA binding	1.1855473374207	bayes_pls_golite062009
nucleotidyltransferase activity	0.316166307022498	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [651-809]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NVNKISNIFE DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV IAGSENIRVK  60
   61 NIILSNKHDV VKPAWLLECF KTKSFVPWQP RFMIHMCPST KEHFAREYDC YGDSYFIDTD 120
  121 LNQLKEVFSG IKNSNEQTPE EMASLIADLE YRYSWDCSP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.69897
Match:	2e2wA
Description:	No description for 2e2wA was found.

Predicted Domain #3

Region A:
Residues: [810-911]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSMFRRHTVY LDSYAVINDL STKNEGTRLA IKALELRFHG AKVVSCLAEG VSHVIIGEDH  60
   61 SRVADFKAFR RTFKRKFKIL KESWVTDSID KCELQEENQY LI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.522879
Match:	1jnxX
Description:	Breast cancer associated protein, BRCA1
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: