D-I-TASSER Q6ZW49

D-I-TASSER results for Q6ZW49

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

Summary of the Protein

Uniprot ID: Q6ZW49
Protein Name: PAX-interacting protein 1
Gene Name: PAXIP1

Input Sequence in FASTA format

>Q6ZW49 (1069 residues)
MSDQAPKVPEEMFREVKYYAVGDIDPQVIQLLKAGKAKEVSYNALASHIISEDGDNPEVG
EAREVFDLPVVKPSWVILSVQCGTLLPVNGFSPESCQIFFGITACLSQVSSEDRSALWAL
VTFYGGDCQLTLNKKCTHLIVPEPKGEKYECALKRASIKIVTPDWVLDCVSEKTKKDEAF
YHPRLIIYEEEEEEEEEEEEVENEEQDSQNEGSTDEKSSPASSQEGSPSGDQQFSPKSNT
EKSKGELMFDDSSDSSPEKQERNLNWTPAEVPQLAAAKRRLPQGKEPGLINLCANVPPVP
GNILPPEVRGNLMAAGQNLQSSERSEMIATWSPAVRTLRNITNNADIQQMNRPSNVAHIL
QTLSAPTKNLEQQVNHSQQGHTNANAVLFSQVKVTPETHMLQQQQQAQQQQQQHPVLHLQ
PQQIMQLQQQQQQQISQQPYPQQPPHPFSQQQQQQQQAHPHQFSQQQLQFPQQQLHPPQQ
LHRPQQQLQPFQQQHALQQQFHQLQQHQLQQQQLAQLQQQHSLLQQQQQQQIQQQQLQRM
HQQQQQQQMQSQTAPHLSQTSQALQHQVPPQQPPQQQQQQQPPPSPQQHQLFGHDPAVEI
PEEGFLLGCVFAIADYPEQMSDKQLLATWKRIIQAHGGTVDPTFTSRCTHLLCESQVSSA
YAQAIRERKRCVTAHWLNTVLKKKKMVPPHRALHFPVAFPPGGKPCSQHIISVTGFVDSD
RDDLKLMAYLAGAKYTGYLCRSNTVLICKEPTGLKYEKAKEWRIPCVNAQWLGDILLGNF
EALRQIQYSRYTAFSLQDPFAPTQHLVLNLLDAWRVPLKVSAELLMSIRLPPKLKQNEVA
NVQPSSKRARIEDVPPPTKKLTPELTPFVLFTGFEPVQVQQYIKKLYILGGEVAESAQKC
THLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRCQKFIDEQNYILRDAEAEVLFSFSL
EESLKRAHVSPLFKAKYFYITPGICPSLSTMKAIVECAGGKVLSKQPSFRKLMEHKQNSS
LSEIILISCENDLHLCREYFARGIDVHNAEFVLTGVLTQTLDYESYKFN

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	Q6ZW49-D1	1-1069	1069		MSDQAPKVPEEMFREVKYYAVGDIDPQVIQLLKAGKAKEVSYNALASHIISEDGDNPEVGEAREVFDLPVVKPSWVILSVQCGTLLPVNGFSPESCQIFFGITACLSQVSSEDRSALWALVTFYGGDCQLTLNKKCTHLIVPEPKGEKYECALKRASIKIVTPDWVLDCVSEKTKKDEAFYHPRLIIYEEEEEEEEEEEEVENEEQDSQNEGSTDEKSSPASSQEGSPSGDQQFSPKSNTEKSKGELMFDDSSDSSPEKQERNLNWTPAEVPQLAAAKRRLPQGKEPGLINLCANVPPVPGNILPPEVRGNLMAAGQNLQSSERSEMIATWSPAVRTLRNITNNADIQQMNRPSNVAHILQTLSAPTKNLEQQVNHSQQGHTNANAVLFSQVKVTPETHMLQQQQQAQQQQQQHPVLHLQPQQIMQLQQQQQQQISQQPYPQQPPHPFSQQQQQQQQAHPHQFSQQQLQFPQQQLHPPQQLHRPQQQLQPFQQQHALQQQFHQLQQHQLQQQQLAQLQQQHSLLQQQQQQQIQQQQLQRMHQQQQQQQMQSQTAPHLSQTSQALQHQVPPQQPPQQQQQQQPPPSPQQHQLFGHDPAVEIPEEGFLLGCVFAIADYPEQMSDKQLLATWKRIIQAHGGTVDPTFTSRCTHLLCESQVSSAYAQAIRERKRCVTAHWLNTVLKKKKMVPPHRALHFPVAFPPGGKPCSQHIISVTGFVDSDRDDLKLMAYLAGAKYTGYLCRSNTVLICKEPTGLKYEKAKEWRIPCVNAQWLGDILLGNFEALRQIQYSRYTAFSLQDPFAPTQHLVLNLLDAWRVPLKVSAELLMSIRLPPKLKQNEVANVQPSSKRARIEDVPPPTKKLTPELTPFVLFTGFEPVQVQQYIKKLYILGGEVAESAQKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRCQKFIDEQNYILRDAEAEVLFSFSLEESLKRAHVSPLFKAKYFYITPGICPSLSTMKAIVECAGGKVLSKQPSFRKLMEHKQNSSLSEIILISCENDLHLCREYFARGIDVHNAEFVLTGVLTQTLDYESYKFN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4604

(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	3jb9A	0.26	8.96	0.037	0.394	model1_3jb9A.pdb.gz
2	7abiA	0.24	8.77	0.044	0.365	model1_7abiA.pdb.gz
3	4o9xA	0.24	8.79	0.046	0.363	model1_4o9xA.pdb.gz
4	6bq1A	0.24	8.77	0.014	0.358	model1_6bq1A.pdb.gz
5	6u5vB	0.24	9.06	0.032	0.369	model1_6u5vB.pdb.gz
6	6ez8A	0.24	9.30	0.023	0.371	model1_6ez8A.pdb.gz
7	6l7eA	0.23	9.44	0.021	0.370	model1_6l7eA.pdb.gz
8	2uvcG	0.23	9.14	0.011	0.357	model1_2uvcG.pdb.gz
9	6xreA	0.23	9.00	0.034	0.353	model1_6xreA.pdb.gz
10	6bcuA	0.23	8.98	0.035	0.350	model1_6bcuA.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:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0003676	0.52	nucleic acid binding

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	0.99	cellular process
GO:0050794	0.94	regulation of cellular process
GO:0050896	0.90	response to stimulus
GO:0033554	0.89	cellular response to stress
GO:0006974	0.88	cellular response to DNA damage stimulus
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0044238	0.80	primary metabolic process
GO:0031323	0.80	regulation of cellular metabolic process
GO:0051171	0.78	regulation of nitrogen compound metabolic process
GO:0060255	0.76	regulation of macromolecule metabolic process
GO:0031326	0.76	regulation of cellular biosynthetic process
GO:0080090	0.75	regulation of primary metabolic process
GO:0019219	0.73	regulation of nucleobase-containing compound metabolic process
GO:0034641	0.72	cellular nitrogen compound metabolic process
GO:0090304	0.71	nucleic acid metabolic process
GO:2000112	0.70	regulation of cellular macromolecule biosynthetic process
GO:0006355	0.69	regulation of transcription, DNA-templated
GO:0048518	0.67	positive regulation of biological process
GO:0006259	0.67	DNA metabolic process
GO:0031325	0.66	positive regulation of cellular metabolic process
GO:0010604	0.66	positive regulation of macromolecule metabolic process
GO:0033044	0.65	regulation of chromosome organization
GO:0031399	0.65	regulation of protein modification process
GO:1902275	0.64	regulation of chromatin organization
GO:0048583	0.64	regulation of response to stimulus
GO:0031401	0.64	positive regulation of protein modification process
GO:0006357	0.64	regulation of transcription from RNA polymerase II promoter
GO:0045935	0.63	positive regulation of nucleobase-containing compound metabolic process
GO:0045893	0.62	positive regulation of transcription, DNA-templated
GO:0045944	0.61	positive regulation of transcription from RNA polymerase II promoter
GO:0035066	0.61	positive regulation of histone acetylation
GO:0016043	0.61	cellular component organization
GO:0006281	0.58	DNA repair
GO:0051052	0.57	regulation of DNA metabolic process
GO:0050776	0.57	regulation of immune response
GO:0002700	0.57	regulation of production of molecular mediator of immune response
GO:0000018	0.54	regulation of DNA recombination
GO:0048584	0.53	positive regulation of response to stimulus
GO:0006302	0.53	double-strand break repair
GO:2000026	0.52	regulation of multicellular organismal development
GO:0051240	0.52	positive regulation of multicellular organismal process
GO:0051054	0.52	positive regulation of DNA metabolic process
GO:0031398	0.52	positive regulation of protein ubiquitination
GO:0002822	0.52	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0002706	0.52	regulation of lymphocyte mediated immunity
GO:0060261	0.51	positive regulation of transcription initiation from RNA polymerase II promoter
GO:0051571	0.51	positive regulation of histone H3-K4 methylation
GO:0045830	0.51	positive regulation of isotype switching
GO:0043933	0.51	macromolecular complex subunit organization
GO:0019538	0.51	protein metabolic process
GO:0000416	0.51	positive regulation of histone H3-K36 methylation
GO:0006464	0.50	cellular protein modification 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:0044424	1.00	intracellular part
GO:0044446	0.92	intracellular organelle part
GO:0044428	0.90	nuclear part
GO:0043229	0.86	intracellular organelle
GO:0032991	0.84	macromolecular complex
GO:0043234	0.77	protein complex
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005634	0.75	nucleus
GO:1990234	0.72	transferase complex
GO:0044451	0.69	nucleoplasm part
GO:0035097	0.60	histone methyltransferase complex
GO:0005654	0.60	nucleoplasm

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	3ixzA	0.184	9.44	0.040	0.295	3.6.3.10	NA
2	0.060	1mo7A	0.076	5.81	0.054	0.095	3.6.3.9	NA
3	0.060	2pdaA	0.158	10.11	0.022	0.269	1.2.7.1	NA
4	0.060	2zxqA	0.194	8.85	0.023	0.294	3.2.1.97	NA
5	0.060	2uv8G	0.243	9.57	0.031	0.392	2.3.1.86	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.