D-I-TASSER Q8IX06

D-I-TASSER results for Q8IX06

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q8IX06
Protein Name: Putative exonuclease GOR
Gene Name: REXO1L1P

Input Sequence in FASTA format

>Q8IX06 (675 residues)
MLRATAPCWFPPGYPEAKKVAEEAALEASRHLGGEQSQAGAPEGSKMLRATAPCWFRPGY
PEAKKVAKEAAPEASRHLGAEQSPAGAPEGSKMLRATAPCWFPPGYPEAKKVAEEAALEA
PEFPLPSHQPAQSFGLWVPQMHKQASAFVDIQAEPQNRGPAVPPAWPKMVTESCYFPAQR
GSACRLPAAPRLTERPSGVRISAPRKRKTIAHSSSPCLVTGYTDAKRTRVASSSQRSRGS
KVGRQPGKTRNRSGMACKTTATTSSKRIVRRASLPSLSLKKPIILRSSGCQVPTVLRRGY
LQLFTEECLKFCASKQEAEEKALNEEKVAYDCSPNKNRYLNVVLNTLKRLKGLTPSSMPG
LSRAALYSRLQEFLLTQDQLKENGYPFPHPERPGGAVLFTGQGKGPGDSSCRVCCRCGTE
YLVSSSGRCVRDQLCYYHWGRVRSSQVAGGRVSQYTCCAAAPGSVGCQVAKQHVRDGRKE
SLDGFVETFKKELSRDAYPGIYALDCEMCYTTHGLELTRVTVVDADMRVVYDTFVKPDNE
IVDYNTRFSGVTEADVAKTSITLPQVQAILLSFFSAQTILIGHSLESDLLALKLIHSTVV
DTAVLFPHYLGFPYKRSLRNLAADYLAQIIQDSQDGHNSSEDASACLQLVMWKVRQRAQI
QPRHRSASPAALACP

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q8IX06-D1	1-355	355		MLRATAPCWFPPGYPEAKKVAEEAALEASRHLGGEQSQAGAPEGSKMLRATAPCWFRPGYPEAKKVAKEAAPEASRHLGAEQSPAGAPEGSKMLRATAPCWFPPGYPEAKKVAEEAALEAPEFPLPSHQPAQSFGLWVPQMHKQASAFVDIQAEPQNRGPAVPPAWPKMVTESCYFPAQRGSACRLPAAPRLTERPSGVRISAPRKRKTIAHSSSPCLVTGYTDAKRTRVASSSQRSRGSKVGRQPGKTRNRSGMACKTTATTSSKRIVRRASLPSLSLKKPIILRSSGCQVPTVLRRGYLQLFTEECLKFCASKQEAEEKALNEEKVAYDCSPNKNRYLNVVLNTLKRLKGLTP
2	Q8IX06-D2	356-675	320		SSMPGLSRAALYSRLQEFLLTQDQLKENGYPFPHPERPGGAVLFTGQGKGPGDSSCRVCCRCGTEYLVSSSGRCVRDQLCYYHWGRVRSSQVAGGRVSQYTCCAAAPGSVGCQVAKQHVRDGRKESLDGFVETFKKELSRDAYPGIYALDCEMCYTTHGLELTRVTVVDADMRVVYDTFVKPDNEIVDYNTRFSGVTEADVAKTSITLPQVQAILLSFFSAQTILIGHSLESDLLALKLIHSTVVDTAVLFPHYLGFPYKRSLRNLAADYLAQIIQDSQDGHNSSEDASACLQLVMWKVRQRAQIQPRHRSASPAALACP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.631

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

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	7eeiA	0.28	7.93	0.031	0.443	model1_7eeiA.pdb.gz
2	6l42A1	0.28	8.27	0.034	0.449	model1_6l42A1.pdb.gz
3	7cu3A	0.28	7.55	0.031	0.415	model1_7cu3A.pdb.gz
4	6r9tA	0.28	7.29	0.030	0.415	model1_6r9tA.pdb.gz
5	7cklA	0.28	7.83	0.041	0.430	model1_7cklA.pdb.gz
6	6y6kA	0.27	8.19	0.035	0.443	model1_6y6kA.pdb.gz
7	4f1nA	0.27	7.47	0.041	0.416	model1_4f1nA.pdb.gz
8	7naqc	0.27	7.18	0.044	0.397	model1_7naqc.pdb.gz
9	5z9xA	0.27	3.09	0.223	0.295	model1_5z9xA.pdb.gz
10	6eojA	0.27	7.92	0.036	0.430	model1_6eojA.pdb.gz

(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	0.85	catalytic activity
GO:0016787	0.84	hydrolase activity
GO:0016788	0.83	hydrolase activity, acting on ester bonds
GO:1901363	0.78	heterocyclic compound binding
GO:0097159	0.78	organic cyclic compound binding
GO:0004518	0.75	nuclease activity
GO:0004527	0.74	exonuclease activity
GO:0008408	0.64	3'-5' exonuclease activity
GO:0004540	0.59	ribonuclease activity
GO:0000175	0.58	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:0009987	0.92	cellular process
GO:0008152	0.74	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0043170	0.67	macromolecule metabolic process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0006807	0.62	nitrogen compound metabolic process
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:0065007	0.58	biological regulation
GO:0044699	0.58	single-organism process
GO:0090304	0.56	nucleic acid metabolic process
GO:0050789	0.55	regulation of biological process
GO:0050794	0.52	regulation of cellular process
GO:0016070	0.51	RNA metabolic 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043226	0.90	organelle
GO:0043229	0.89	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0044422	0.75	organelle part
GO:0044446	0.74	intracellular organelle part
GO:0043227	0.74	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0032991	0.72	macromolecular complex
GO:0043234	0.64	protein complex
GO:0043232	0.63	intracellular non-membrane-bounded organelle
GO:0005634	0.61	nucleus
GO:0005737	0.58	cytoplasm
GO:0044428	0.56	nuclear 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	1itwB	0.241	7.66	0.052	0.364	1.1.1.42	NA
2	0.060	2wyhA	0.231	7.91	0.044	0.366	3.2.1.24	NA
3	0.060	3ikmD	0.233	8.47	0.024	0.390	2.7.7.7	NA
4	0.060	1bglA	0.229	8.35	0.038	0.381	3.2.1.23	NA
5	0.060	1ahpA	0.250	8.15	0.042	0.402	2.4.1.1	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.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	1pygC	0.253	8.06	0.039	0.404	0.22	PDP	complex1.pdb.gz	514,515,516,548,549,552
2	0.01	7gpbD	0.220	8.55	0.043	0.370	0.16	PLP	complex2.pdb.gz	585,586,587,588,590
3	0.01	1abbA	0.215	8.41	0.036	0.358	0.10	PDP	complex3.pdb.gz	519,583,587
4	0.01	1xoiA	0.252	8.00	0.046	0.400	0.12	NBG	complex4.pdb.gz	439,469,547
5	0.01	2iegA	0.252	8.00	0.039	0.399	0.22	FRY	complex5.pdb.gz	416,516,545
6	0.01	1c8lA	0.223	7.84	0.042	0.348	0.17	BIN	complex6.pdb.gz	468,546,547
7	0.01	2offA	0.228	7.78	0.031	0.354	0.19	OFF	complex7.pdb.gz	545,546,548
8	0.01	1l5sB	0.253	8.03	0.038	0.400	0.12	700	complex8.pdb.gz	475,515,516
9	0.01	2ieiA	0.252	7.97	0.042	0.399	0.20	FRX	complex9.pdb.gz	475,516,518
10	0.01	3mtaA	0.221	8.09	0.045	0.353	0.10	22O	complex10.pdb.gz	514,515,516

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.