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COFACTOR result for job id QHD43415_3

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>QHD43415_3 (1945 residues)
APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADA
VIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEE
EEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQ
TTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVV
GPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF
DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEE
VTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPS
IISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY
GARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVS
SPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTY
LDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKY
PQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYC
NKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKH
ITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDN
YYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVT
FFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILK
PANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTI
ANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTI
AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDL
TAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPIS
AMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYA
NGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSAS
VYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEA
ELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYN
KVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
PFKLTCATTRQVVNVVTTKIALKGG

Download query sequence and structure

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6sytA	0.30	10.94	0.044	0.451	Download
2	5a22A	0.29	10.36	0.036	0.431	Download
3	5yz0A	0.28	10.84	0.046	0.417	Download
4	6bcuA	0.27	11.02	0.042	0.418	Download
5	6ez8A	0.27	10.92	0.041	0.410	Download
6	6emkA	0.27	10.57	0.040	0.400	Download
7	6jxaA	0.27	12.07	0.043	0.436	Download
8	5h64A	0.26	11.02	0.038	0.400	Download
9	6eqoA	0.26	10.74	0.032	0.390	Download
10	6r9tA	0.26	11.05	0.033	0.395	Download

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	0.94	catalytic activity
GO:0016787	0.81	hydrolase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0140096	0.76	catalytic activity, acting on a protein
GO:0016740	0.74	transferase activity
GO:0003676	0.68	nucleic acid binding
GO:1990380	0.61	Lys48-specific deubiquitinase activity
GO:0042802	0.61	identical protein binding
GO:0004483	0.61	mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0004482	0.61	mRNA (guanine-N7-)-methyltransferase activity
GO:0004386	0.61	helicase activity
GO:0003968	0.61	RNA-directed 5'-3' RNA polymerase activity
GO:0003727	0.61	single-stranded RNA binding
GO:0003725	0.61	double-stranded RNA binding
GO:0000175	0.61	3'-5'-exoribonuclease activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044238	0.86	primary metabolic process
GO:0043170	0.86	macromolecule metabolic process
GO:0006807	0.86	nitrogen compound metabolic process
GO:0065007	0.78	biological regulation
GO:0080090	0.76	regulation of primary metabolic process
GO:0051171	0.76	regulation of nitrogen compound metabolic process
GO:0031323	0.76	regulation of cellular metabolic process
GO:0010605	0.76	negative regulation of macromolecule metabolic process
GO:0010629	0.75	negative regulation of gene expression
GO:0051252	0.73	regulation of RNA metabolic process
GO:0009987	0.73	cellular process
GO:2001141	0.71	regulation of RNA biosynthetic process
GO:0080134	0.71	regulation of response to stress
GO:0045088	0.70	regulation of innate immune response
GO:0050896	0.68	response to stimulus
GO:0044237	0.68	cellular metabolic process
GO:0044092	0.68	negative regulation of molecular function
GO:0048585	0.67	negative regulation of response to stimulus
GO:0045824	0.66	negative regulation of innate immune response
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0043412	0.64	macromolecule modification
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:2000112	0.63	regulation of cellular macromolecule biosynthetic process
GO:0039653	0.62	suppression by virus of host transcription
GO:0039507	0.62	suppression by virus of host molecular function
GO:0039503	0.62	suppression by virus of host innate immune response
GO:0010608	0.58	posttranscriptional regulation of gene expression
GO:0048523	0.55	negative regulation of cellular process
GO:0039604	0.54	suppression by virus of host translation
GO:0039579	0.54	suppression by virus of host ISG15 activity
GO:0006139	0.51	nucleobase-containing compound metabolic process
GO:0090304	0.50	nucleic acid metabolic process
GO:0048522	0.50	positive regulation of cellular process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0033646	0.87	host intracellular part
GO:0039714	0.81	cytoplasmic viral factory
GO:0044424	0.51	intracellular part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2vuaA	0.097	7.61	0.033	0.123	3.4.24.69	NA
2	0.060	3h09B	0.185	9.33	0.031	0.258	3.4.21.72	348,362
3	0.060	2pffD	0.196	10.63	0.028	0.295	2.3.1.86	NA
4	0.060	3btaA	0.227	9.31	0.043	0.313	3.4.24.69	NA
5	0.060	1llwA	0.221	10.04	0.031	0.319	1.4.7.1	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Download result.tar.bz2 for all prediction results]

Reference:

Chengxin Zhang, Peter L Freddolino, and Yang Zhang. COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017)
Ambrish Roy, Jianyi Yang, and Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, 40:W471-W477 (2012).

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