D-I-TASSER Q16630

D-I-TASSER results for Q16630

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

Summary of the Protein

Uniprot ID: Q16630
Protein Name: Cleavage and polyadenylation specificity factor subunit 6
Gene Name: CPSF6

Input Sequence in FASTA format

>Q16630 (551 residues)
MADGVDHIDIYADVGEEFNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTV
GDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRAN
GQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPCNKQFLSQFEMQSRKTTQSGQM
SGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTPPRPP
LGPPGPPGPPGPPPPGQVLPPPLAGPPNRGDRPPPPVLFPGQPFGQPPLGPLPPGPPPPV
PGYGPPPGPPPPQQGPPPPPGPFPPRPPGPLGPPLTLAPPPHLPGPPPGAPPPAPHVNPA
FFPPPTNSGMPTSDSRGPPPTDPYGRPPPYDRGDYGPPGREMDTARTPLSEAEFEEIMNR
NRAISSSAISRAVSDASAGDYGSAIETLVTAISLIKQSKVSADDRCKVLISSLQDCLHGI
ESKSYGSGSRRERSRERDHSRSREKSRRHKSRSRDRHDDYYRERSRERERHRDRDRDRDR
ERDREREYRHR

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 AttentionPotential. 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	Q16630-D1	1-551	551		MADGVDHIDIYADVGEEFNQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPCNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTPPRPPLGPPGPPGPPGPPPPGQVLPPPLAGPPNRGDRPPPPVLFPGQPFGQPPLGPLPPGPPPPVPGYGPPPGPPPPQQGPPPPPGPFPPRPPGPLGPPLTLAPPPHLPGPPPGAPPPAPHVNPAFFPPPTNSGMPTSDSRGPPPTDPYGRPPPYDRGDYGPPGREMDTARTPLSEAEFEEIMNRNRAISSSAISRAVSDASAGDYGSAIETLVTAISLIKQSKVSADDRCKVLISSLQDCLHGIESKSYGSGSRRERSRERDHSRSREKSRRHKSRSRDRHDDYYRERSRERERHRDRDRDRDRERDREREYRHR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6013

(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 AttentionPotential, 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	5y81A	0.40	7.29	0.042	0.626	model1_5y81A.pdb.gz
2	6h02A	0.39	7.49	0.032	0.626	model1_6h02A.pdb.gz
3	6tntA	0.37	7.26	0.056	0.575	model1_6tntA.pdb.gz
4	7kpxC	0.37	7.49	0.025	0.590	model1_7kpxC.pdb.gz
5	6vr4A	0.36	7.38	0.026	0.566	model1_6vr4A.pdb.gz
6	6xteA	0.35	7.23	0.033	0.541	model1_6xteA.pdb.gz
7	5mpbN	0.35	7.50	0.042	0.555	model1_5mpbN.pdb.gz
8	5yz0A	0.35	8.03	0.035	0.581	model1_5yz0A.pdb.gz
9	4f91B	0.34	7.58	0.036	0.561	model1_4f91B.pdb.gz
10	5l56A	0.34	8.00	0.054	0.586	model1_5l56A.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:0003723	0.99	RNA binding
GO:0044822	0.96	poly(A) RNA binding
GO:0003729	0.91	mRNA 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:0016070	0.95	RNA metabolic process
GO:0016071	0.92	mRNA metabolic process
GO:0006396	0.91	RNA processing
GO:0006397	0.90	mRNA processing
GO:0031124	0.85	mRNA 3'-end processing
GO:0006378	0.83	mRNA polyadenylation

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	0.99	intracellular organelle part
GO:0044428	0.98	nuclear part
GO:0043229	0.93	intracellular organelle
GO:0032991	0.93	macromolecular complex
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0044451	0.90	nucleoplasm part
GO:0043234	0.90	protein complex
GO:0005634	0.89	nucleus
GO:0005849	0.86	mRNA cleavage factor complex

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	2pffB	0.243	6.84	0.044	0.365	2.3.1.86	NA
2	0.060	1qxpB	0.293	8.17	0.051	0.508	3.4.22.53 3.4.22.52	NA
3	0.060	2vumA	0.276	7.86	0.037	0.456	2.7.7.6	NA
4	0.060	2aryA	0.162	6.95	0.030	0.247	3.4.22.52	NA
5	0.060	2g8eA	0.169	6.98	0.028	0.260	3.4.22.52	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	2y0pD	0.214	8.10	0.044	0.368	0.17	ACO	complex1.pdb.gz	180,209,222,223
2	0.01	2uvcG	0.341	7.58	0.052	0.546	0.11	FMN	complex2.pdb.gz	174,196,209,329
3	0.01	2y0pA	0.241	7.94	0.047	0.406	0.16	ACO	complex3.pdb.gz	174,188,192,194,196,257
4	0.01	3fu3A	0.301	7.30	0.031	0.475	0.31	92G	complex4.pdb.gz	197,212,216
5	0.01	3b7rL	0.305	7.26	0.034	0.481	0.10	BIR	complex5.pdb.gz	190,191,327,332
6	0.01	1gw6A	0.304	7.13	0.025	0.475	0.12	BES	complex6.pdb.gz	190,191,193,194,196,328,333
7	0.01	3chrA	0.289	7.57	0.027	0.472	0.14	4BS	complex7.pdb.gz	189,191,332
8	0.01	3ftyA	0.305	7.04	0.035	0.468	0.16	3IP	complex8.pdb.gz	214,217,218
9	0.01	3fu0A	0.305	7.15	0.025	0.477	0.40	22F	complex9.pdb.gz	196,209,218
10	0.01	3chsA	0.306	7.29	0.034	0.483	0.14	4BU	complex10.pdb.gz	189,207,332,333

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.