YRC Public Data Repository - Protein Structure Prediction

Protein:	IXR1
Organism:	Saccharomyces cerevisiae
Length:	597 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 IXR1.

Description	E-value	Query Range	Subject Range
IXR1 - Protein that binds DNA containing intrastrand cross-links formed by cisplatin, contains two HMG (hig... IXR1_YEAST - Intrastrand cross-link recognition protein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ...	3.0E-86	[1..597]	[1..597]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	7.0E-85	[1..597]	[1..592]
gi\|6755602, gi\|2... - gi\|6755602\|ref\|NP_035569.1\| SRY-box 13 [Mus musculus], gi\|2764544\|emb\|CAA04278.1\| HMG-box transcript...	6.0E-79	[17..472]	[128..517]
gi\|18676887 - gi\|18676887\|dbj\|BAB85048.1\| unnamed protein product [Homo sapiens]	2.0E-74	[19..454]	[205..658]

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Predicted Domain #1

Region A:
Residues: [1-121]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNTGISPKQD DASNSNLLNI GQDHSLQYQG LEHNDSQYRD ASHQTPHQYL NQFQAQPQQQ  60
   61 QQQQQQQQQQ QQQAPYQGHF QQSPQQQQQN VYYPLPPQSL TQPTSQSQQQ QQQQQQQQYA 120
  121 N

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.349	0.136	nuclear chromosome	a.1.1	Globin-like
View	Download	0.244	0.134	nuclear chromosome	a.39.1	EF-hand
View	Download	0.261	0.089	DNA repair	a.29.2	Bromodomain
View	Download	0.274	0.061	DNA binding	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.258	0.004	nuclear chromosome	a.24.12	Outer surface protein C (OspC)
View	Download	0.349	N/A	N/A	a.1.1	Globin-like
View	Download	0.274	N/A	N/A	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.261	N/A	N/A	a.29.2	Bromodomain
View	Download	0.258	N/A	N/A	a.24.12	Outer surface protein C (OspC)
View	Download	0.244	N/A	N/A	a.39.1	EF-hand
View	Download	0.243	N/A	N/A	c.46.1	Rhodanese/Cell cycle control phosphatase

Predicted Domain #2

Region A:
Residues: [122-173]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SNSNSNNNVN VNALPQDFGY MQQTGSGQNY PTINQQQFSE FYNSFLSHLT QK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.285	a.4.1	Homeodomain-like
View	Download	0.369	a.60.4	DNA repair protein Rad51, N-terminal domain
View	Download	0.504	d.42.1	POZ domain
View	Download	0.531	d.68.3	SirA-like
View	Download	0.283	d.58.23	Probable ACP-binding domain of malonyl-CoA ACP transacylase
View	Download	0.263	a.4.1	Homeodomain-like
View	Download	0.254	a.6.1	Putative DNA-binding domain
View	Download	0.234	g.34.1	HIV-1 VPU cytoplasmic domain

Predicted functions:

Term	Confidence	Notes
binding	3.04393542109417	bayes_pls_golite062009
DNA binding	1.88326659692279	bayes_pls_golite062009
nucleic acid binding	1.85157640081091	bayes_pls_golite062009
chromatin binding	1.82810083714605	bayes_pls_golite062009
transcription regulator activity	1.34639198670075	bayes_pls_golite062009
protein binding	1.33904668423876	bayes_pls_golite062009
sequence-specific DNA binding	1.08208740778246	bayes_pls_golite062009
transcription factor activity	0.585772620695985	bayes_pls_golite062009
structure-specific DNA binding	0.45921402500371	bayes_pls_golite062009
transcription factor binding	0.19768703289845	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.16971196361447	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [174-336]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QTNPSVTGTG ASSNNNSNNN NVSSGNNSTS SNPAQLAASQ LNPATAAAAA ANNAAGPASY  60
   61 LSQLPQVQRY YPNNMNALSS LLDPSSAGNA AGNANTATHP GLLPPNLQPQ LTHHQQQMQQ 120
  121 QLQLQQQQQL QQQQQLQQQH QLQQQQQLQQ QHHHLQQQQQ QQQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.071898
Match:	1k99A_
Description:	Upstream binding factor
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	3.04393542109417	bayes_pls_golite062009
DNA binding	1.88326659692279	bayes_pls_golite062009
nucleic acid binding	1.85157640081091	bayes_pls_golite062009
chromatin binding	1.82810083714605	bayes_pls_golite062009
transcription regulator activity	1.34639198670075	bayes_pls_golite062009
protein binding	1.33904668423876	bayes_pls_golite062009
sequence-specific DNA binding	1.08208740778246	bayes_pls_golite062009
transcription factor activity	0.585772620695985	bayes_pls_golite062009
structure-specific DNA binding	0.45921402500371	bayes_pls_golite062009
transcription factor binding	0.19768703289845	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.16971196361447	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [337-427]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HPVVKKLSST QSRIERRKQL KKQGPKRPSS AYFLFSMSIR NELLQQFPEA KVPELSKLAS  60
   61 ARWKELTDDQ KKPFYEEFRT NWEKYRVVRD A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	58.045757
Match:	1i11A_
Description:	Sox-5
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	3.04393542109417	bayes_pls_golite062009
DNA binding	1.88326659692279	bayes_pls_golite062009
nucleic acid binding	1.85157640081091	bayes_pls_golite062009
chromatin binding	1.82810083714605	bayes_pls_golite062009
transcription regulator activity	1.34639198670075	bayes_pls_golite062009
protein binding	1.33904668423876	bayes_pls_golite062009
sequence-specific DNA binding	1.08208740778246	bayes_pls_golite062009
transcription factor activity	0.585772620695985	bayes_pls_golite062009
structure-specific DNA binding	0.45921402500371	bayes_pls_golite062009
transcription factor binding	0.19768703289845	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.16971196361447	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [428-511]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YEKTLPPKRP SGPFIQFTQE IRPTVVKENP DKGLIEITKI IGERWRELDP AKKAEYTETY  60
   61 KKRLKEWESC YPDENDPNGN PTGH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	41.29073
Match:	1cg7A_
Description:	NHP6a
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [512-597]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SHKAMNMNLN MDTKIMENQD SIEHITANAI DSVTGSNSNS TNPNTPVSPP ISLQQQPLQQ  60
   61 QQQQQQQQQH MLLADPTTNG SIIKNE

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.220	0.396	DNA repair	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.236	0.062	nuclear chromosome	b.71.1	Glycosyl hydrolase domain
View	Download	0.227	0.017	nuclear chromosome	c.95.1	Thiolase-like
View	Download	0.320	0.004	nuclear chromosome	c.52.2	tRNA splicing endonuclease, C-terminal domain
View	Download	0.225	N/A	N/A	d.26.3	Chitinase insertion 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:

Predicted functions:

Predicted functions: