D-I-TASSER A6NIJ5

D-I-TASSER results for A6NIJ5

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

Summary of the Protein

Uniprot ID: A6NIJ5
Protein Name: Putative protein FAM90A20P
Gene Name: FAM90A20P

Input Sequence in FASTA format

>A6NIJ5 (464 residues)
MMARRDPTSWAKRLVRAQTLQKQRRAPVGPRAPPPDEEDPRLKCKNCGAFGHTARSTRCP
MKCWKAALVPATLGKKEGKENLKPWKPGVEANPGPLNKDKGEKEERPRQQDPQRKALLHM
FSGKPPEKPLPNGKGSTESSDYLRVARGPMPVHTTCKRPRMDPVLSGRSATEMSGRGSVL
ASLSPLRKASLSSSSSLGPKERQTGAAADIPRPAVRHQVHETLLVVEPTHSSPEGSCREV
PQAASKTHGLLQAVRTQAQDKRPAVTSQPCPSAATHSLGLGSNLSFGSGAKRPAQAPIQA
CLNFPKKPRLGPFQIPESTIQGGELGAPENLQPPPAATELGPSRSPQMGRRTPAQVPSVE
RQPPHRRPCLPTAQACTMSHHPAASHDGAQPLRVLFRRLENGRWSSSLLAAPSFHSPEKP
GAFLAQSPHVSEKSEAPCVRVPPSVLYEDLQVSSSSEDSDSDLE

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	A6NIJ5-D1	1-464	464		MMARRDPTSWAKRLVRAQTLQKQRRAPVGPRAPPPDEEDPRLKCKNCGAFGHTARSTRCPMKCWKAALVPATLGKKEGKENLKPWKPGVEANPGPLNKDKGEKEERPRQQDPQRKALLHMFSGKPPEKPLPNGKGSTESSDYLRVARGPMPVHTTCKRPRMDPVLSGRSATEMSGRGSVLASLSPLRKASLSSSSSLGPKERQTGAAADIPRPAVRHQVHETLLVVEPTHSSPEGSCREVPQAASKTHGLLQAVRTQAQDKRPAVTSQPCPSAATHSLGLGSNLSFGSGAKRPAQAPIQACLNFPKKPRLGPFQIPESTIQGGELGAPENLQPPPAATELGPSRSPQMGRRTPAQVPSVERQPPHRRPCLPTAQACTMSHHPAASHDGAQPLRVLFRRLENGRWSSSLLAAPSFHSPEKPGAFLAQSPHVSEKSEAPCVRVPPSVLYEDLQVSSSSEDSDSDLE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5639

(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	5ijoJ	0.38	7.41	0.031	0.640	model1_5ijoJ.pdb.gz
2	5u1sA	0.38	7.20	0.038	0.608	model1_5u1sA.pdb.gz
3	6um1A	0.37	7.03	0.043	0.593	model1_6um1A.pdb.gz
4	2uvcG	0.34	7.56	0.051	0.588	model1_2uvcG.pdb.gz
5	6z2wE	0.34	7.61	0.034	0.575	model1_6z2wE.pdb.gz
6	7lkpA	0.34	7.35	0.022	0.571	model1_7lkpA.pdb.gz
7	3hmjG	0.34	7.54	0.048	0.586	model1_3hmjG.pdb.gz
8	6u5vB	0.34	7.12	0.031	0.545	model1_6u5vB.pdb.gz
9	5xjyA	0.34	7.50	0.033	0.571	model1_5xjyA.pdb.gz
10	1vw1A	0.33	7.18	0.041	0.526	model1_1vw1A.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	0.09	catalytic activity
GO:1901363	0.07	heterocyclic compound binding
GO:0097159	0.07	organic cyclic compound binding
GO:0016787	0.07	hydrolase activity
GO:0016772	0.07	transferase activity, transferring phosphorus-containing groups
GO:0016788	0.06	hydrolase activity, acting on ester bonds
GO:0016773	0.06	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.06	kinase activity
GO:0005198	0.06	structural molecule activity
GO:0047451	0.05	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
GO:0046872	0.05	metal ion binding
GO:0031177	0.05	phosphopantetheine binding
GO:0017056	0.05	structural constituent of nuclear pore
GO:0016409	0.05	palmitoyltransferase activity
GO:0016296	0.05	palmitoyl-[acyl-carrier-protein] hydrolase activity
GO:0016295	0.05	myristoyl-[acyl-carrier-protein] hydrolase activity
GO:0005524	0.05	ATP binding
GO:0004335	0.05	galactokinase activity
GO:0004321	0.05	fatty-acyl-CoA synthase activity
GO:0004320	0.05	oleoyl-[acyl-carrier-protein] hydrolase activity
GO:0004319	0.05	enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity
GO:0004318	0.05	enoyl-[acyl-carrier-protein] reductase (NADH) activity
GO:0004314	0.05	[acyl-carrier-protein] S-malonyltransferase activity
GO:0004313	0.05	[acyl-carrier-protein] S-acetyltransferase activity
GO:0005245	0.02	voltage-gated calcium channel activity
GO:0003723	0.02	RNA binding
GO:0097110	0.01	scaffold protein binding
GO:0044822	0.01	poly(A) RNA binding
GO:0032403	0.01	protein complex binding
GO:0019899	0.01	enzyme binding
GO:0016887	0.01	ATPase activity
GO:0016779	0.01	nucleotidyltransferase activity
GO:0008332	0.01	low voltage-gated calcium channel activity
GO:0008331	0.01	high voltage-gated calcium channel activity
GO:0008233	0.01	peptidase activity
GO:0004674	0.01	protein serine/threonine kinase activity
GO:0004540	0.01	ribonuclease activity
GO:0003779	0.01	actin binding
GO:0003713	0.01	transcription coactivator activity
GO:0003682	0.01	chromatin binding
GO:0003677	0.01	DNA binding
GO:0001104	0.01	RNA polymerase II transcription cofactor 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:0051704	0.94	multi-organism process
GO:0009607	0.94	response to biotic stimulus
GO:0009605	0.94	response to external stimulus
GO:0006952	0.94	defense response
GO:0042742	0.93	defense response to bacterium
GO:0009987	0.59	cellular process
GO:0065007	0.51	biological regulation

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	0.97	cell part
GO:0005576	0.93	extracellular region
GO:0044424	0.90	intracellular part
GO:0032991	0.83	macromolecular complex
GO:0043234	0.81	protein complex
GO:0043226	0.58	organelle
GO:0044444	0.57	cytoplasmic part
GO:0043229	0.56	intracellular organelle
GO:0044422	0.53	organelle part
GO:0044446	0.51	intracellular organelle 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	1ea0A	0.200	6.84	0.020	0.315	1.4.1.13	NA
2	0.060	1iq8A	0.189	7.07	0.037	0.302	2.4.2.29	NA
3	0.060	3hz3A	0.268	7.16	0.031	0.433	2.4.1.5	NA
4	0.060	1h0hA	0.266	7.13	0.015	0.429	1.2.1.2	NA
5	0.060	2vkzG	0.306	7.09	0.034	0.489	2.3.1.38 3.1.2.14	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.