D-I-TASSER Q9P2M4

D-I-TASSER results for Q9P2M4

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

Summary of the Protein

Uniprot ID: Q9P2M4
Protein Name: TBC1 domain family member 14
Gene Name: TBC1D14

Input Sequence in FASTA format

>Q9P2M4 (693 residues)
MTDGKLSTSTNGVAFMGILDGRPGNPLQNLQHVNLKAPRLLSAPEYGPKLKLRALEDRHS
LQSVDSGIPTLEIGNPEPVPCSAVHVRRKQSDSDLIPERAFQSACALPSCAPPAPSSTER
EQSVRKSSTFPRTGYDSVKLYSPTSKALTRSDDVSVCSVSSLGTELSTTLSVSNEDILDL
VVTSSSSAIVTLENDDDPQFTNVTLSSIKETRGLHQQDCVHEAEEGSKLKILGPFSNFFA
RNLLARKQSARLDKHNDLGWKLFGKAPLRENAQKDSKRIQKEYEDKAGRPSKPPSPKQNV
RKNLDFEPLSTTALILEDRPANLPAKPAEEAQKHRQQYEEMVVQAKKRELKEAQRRKKQL
EERCRVEESIGNAVLTWNNEILPNWETMWCSRKVRDLWWQGIPPSVRGKVWSLAIGNELN
ITHELFDICLARAKERWRSLSTGGSEVENEDAGFSAADREASLELIKLDISRTFPNLCIF
QQGGPYHDMLHSILGAYTCYRPDVGYVQGMSFIAAVLILNLDTADAFIAFSNLLNKPCQM
AFFRVDHGLMLTYFAAFEVFFEENLPKLFAHFKKNNLTPDIYLIDWIFTLYSKSLPLDLA
CRIWDVFCRDGEEFLFRTALGILKLFEDILTKMDFIHMAQFLTRLPEDLPAEELFASIAT
IQMQSRNKKWAQVLTALQKDSREMEKGSPSLRH

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	Q9P2M4-D1	1-254	254		MTDGKLSTSTNGVAFMGILDGRPGNPLQNLQHVNLKAPRLLSAPEYGPKLKLRALEDRHSLQSVDSGIPTLEIGNPEPVPCSAVHVRRKQSDSDLIPERAFQSACALPSCAPPAPSSTEREQSVRKSSTFPRTGYDSVKLYSPTSKALTRSDDVSVCSVSSLGTELSTTLSVSNEDILDLVVTSSSSAIVTLENDDDPQFTNVTLSSIKETRGLHQQDCVHEAEEGSKLKILGPFSNFFARNLLARKQSARLDK
2	Q9P2M4-D2	255-544	290		HNDLGWKLFGKAPLRENAQKDSKRIQKEYEDKAGRPSKPPSPKQNVRKNLDFEPLSTTALILEDRPANLPAKPAEEAQKHRQQYEEMVVQAKKRELKEAQRRKKQLEERCRVEESIGNAVLTWNNEILPNWETMWCSRKVRDLWWQGIPPSVRGKVWSLAIGNELNITHELFDICLARAKERWRSLSTGGSEVENEDAGFSAADREASLELIKLDISRTFPNLCIFQQGGPYHDMLHSILGAYTCYRPDVGYVQGMSFIAAVLILNLDTADAFIAFSNLLNKPCQMAFFR
3	Q9P2M4-D3	545-693	149		VDHGLMLTYFAAFEVFFEENLPKLFAHFKKNNLTPDIYLIDWIFTLYSKSLPLDLACRIWDVFCRDGEEFLFRTALGILKLFEDILTKMDFIHMAQFLTRLPEDLPAEELFASIATIQMQSRNKKWAQVLTALQKDSREMEKGSPSLRH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(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	6vr4A	0.37	7.76	0.032	0.566	model1_6vr4A.pdb.gz
2	7a1dA	0.35	7.99	0.038	0.563	model1_7a1dA.pdb.gz
3	5b7iA	0.35	7.88	0.043	0.540	model1_5b7iA.pdb.gz
4	3w5mA	0.34	8.19	0.032	0.554	model1_3w5mA.pdb.gz
5	5jouA	0.34	8.27	0.044	0.560	model1_5jouA.pdb.gz
6	7jptA	0.34	8.58	0.039	0.574	model1_7jptA.pdb.gz
7	4xqkA	0.34	7.93	0.050	0.537	model1_4xqkA.pdb.gz
8	1i8qA	0.34	8.16	0.052	0.550	model1_1i8qA.pdb.gz
9	5wlcLO	0.34	7.84	0.056	0.528	model1_5wlcLO.pdb.gz
10	2x2hA	0.34	8.24	0.026	0.545	model1_2x2hA.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:0005096	1.00	GTPase activator activity
GO:0017137	0.98	Rab GTPase binding
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound 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:0065007	1.00	biological regulation
GO:0050794	0.99	regulation of cellular process
GO:0043087	0.99	regulation of GTPase activity
GO:0060627	0.98	regulation of vesicle-mediated transport
GO:0043547	0.98	positive regulation of GTPase activity
GO:0033043	0.98	regulation of organelle organization
GO:0006810	0.98	transport
GO:0090630	0.97	activation of GTPase activity
GO:0031338	0.97	regulation of vesicle fusion
GO:0006886	0.97	intracellular protein transport

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	0.77	intracellular part
GO:0012505	0.76	endomembrane system
GO:0005622	0.73	intracellular
GO:0044444	0.62	cytoplasmic 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	2gtqA	0.299	8.39	0.040	0.488	3.4.11.2	NA
2	0.060	1z0hB	0.211	7.71	0.032	0.330	3.4.24.69	397,400,412
3	0.060	1j0mA	0.301	7.92	0.052	0.469	4.2.2.12	NA
4	0.060	2pffD	0.311	8.12	0.019	0.493	2.3.1.86	273
5	0.060	3b8cB	0.296	7.90	0.037	0.468	3.6.3.6	416

	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	2x2iB	0.339	8.02	0.044	0.537	0.23	QPS	complex1.pdb.gz	401,404,408
2	0.01	3mdjA	0.284	8.30	0.048	0.462	0.19	BES	complex2.pdb.gz	410,415,418
3	0.01	3b34A	0.281	8.54	0.035	0.463	0.12	PHE	complex3.pdb.gz	375,377,378,410
4	0.01	2uvbA	0.313	7.95	0.036	0.493	0.12	NAP	complex4.pdb.gz	395,408,414,520
5	0.01	2x2iD	0.320	8.32	0.032	0.519	0.28	QPS	complex5.pdb.gz	388,392,396,397,398,406,407,410,414
6	0.01	2x2jA	0.334	8.32	0.029	0.547	0.13	NOJ	complex6.pdb.gz	394,396,410
7	0.01	2dqmA	0.311	8.39	0.056	0.511	0.23	BES	complex7.pdb.gz	270,271,272,395,398,399,402,408
8	0.01	2vsqA	0.321	7.78	0.039	0.502	0.28	LEU	complex8.pdb.gz	397,398,401,410
9	0.01	2fhfA	0.320	8.09	0.052	0.508	0.19	GLC	complex9.pdb.gz	398,407,416

	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.