D-I-TASSER Q0IIM8

D-I-TASSER results for Q0IIM8

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

Summary of the Protein

Uniprot ID: Q0IIM8
Protein Name: TBC1 domain family member 8B
Gene Name: TBC1D8B

Input Sequence in FASTA format

>Q0IIM8 (1120 residues)
MWLKPEEVLLKNALKLWLMERSNDYFVLQRRRGYGEEGGGGLTGLLVGTLDSVLDSTAKV
APFRILHQTPDSQVYLSIACGANREEITKHWDWLEQNIMKTLSVFDSNEDITNFVQGKIR
GLIAEEGKHCFAKEDDPEKFREALLKFEKCFGLPEKEKLVTYYSCSYWKGRVPCQGWLYL
STNFLSFYSFLLGSEIKLIISWDEVSKLEKTSNVILTESIHVCSQGENHYFSMFLHINQT
YLLMEQLANYAIRRLFDKETFDNDPVLYNPLQITKRGLENRAHSEQFNAFFRLPKGESLK
EVHECFLWVPFSHFNTHGKMCISENYICFASQDGNQCSVIIPLREVLAIDKTNDSSKSVI
ISIKGKTAFRFHEVKDFEQLVAKLRLRCGAASTQYHDISTELAISSESTEPSDNFEVQSL
TSQRECSKTVNTEALMTVFHPQNLETLNSKMLKEKMKEQSWKILFAECGRGVSMFRTKKT
RDLVVRGIPETLRGELWMLFSGAVNDMATNPDYYTEVVEQSLGTCNLATEEIERDLRRSL
PEHPAFQSDTGISALRRVLTAYAYRNPKIGYCQAMNILTSVLLLYAKEEEAFWLLVAVCE
RMLPDYFNRRIIGALVDQAVFEELIRDHLPQLTEHMTDMTFFSSVSLSWFLTLFISVLPI
ESAVNVVDCFFYDGIKAILQLGLAILDYNLDKLLTCKDDAEAVTALNRFFDNVTNKDSPL
PSNVQQGSNVSDEKTSHTRVDITDLIRESNEKYGNIRYEDIHSMRCRNRLYVIQTLEETT
KQNVLRVVSQDVKLSLQELDELYVIFKKELFLSCYWCLGCPVLKHHDPSLPYLEQYQIDC
QQFRALYHLLSPWAHSANKDSLALWTFRLLDENSDCLINFKEFSSAIDIMYNGSFTEKLK
LLFKLHIPPAYTEVKSKDASKGDELSKEELLYFSQLHVSKPANEKEAESAKHSPEKGKGK
IDIQAYLSQWQDELFKKEENIKDLPRMNQSQFIQFSKTLYNLFHEDPEEESLYQAIAVVT
SLLLRMEEVGRKLHSPTSSAKGFSGTVCGSGGPSEEKTGSHLEKDPCSFREEPQWSFAFE
QILASLLNEPALVRFFEKPIDVKAKLENARISQLRSRTKM

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	Q0IIM8-D1	1-658,756-1120	1023		MWLKPEEVLLKNALKLWLMERSNDYFVLQRRRGYGEEGGGGLTGLLVGTLDSVLDSTAKVAPFRILHQTPDSQVYLSIACGANREEITKHWDWLEQNIMKTLSVFDSNEDITNFVQGKIRGLIAEEGKHCFAKEDDPEKFREALLKFEKCFGLPEKEKLVTYYSCSYWKGRVPCQGWLYLSTNFLSFYSFLLGSEIKLIISWDEVSKLEKTSNVILTESIHVCSQGENHYFSMFLHINQTYLLMEQLANYAIRRLFDKETFDNDPVLYNPLQITKRGLENRAHSEQFNAFFRLPKGESLKEVHECFLWVPFSHFNTHGKMCISENYICFASQDGNQCSVIIPLREVLAIDKTNDSSKSVIISIKGKTAFRFHEVKDFEQLVAKLRLRCGAASTQYHDISTELAISSESTEPSDNFEVQSLTSQRECSKTVNTEALMTVFHPQNLETLNSKMLKEKMKEQSWKILFAECGRGVSMFRTKKTRDLVVRGIPETLRGELWMLFSGAVNDMATNPDYYTEVVEQSLGTCNLATEEIERDLRRSLPEHPAFQSDTGISALRRVLTAYAYRNPKIGYCQAMNILTSVLLLYAKEEEAFWLLVAVCERMLPDYFNRRIIGALVDQAVFEELIRDHLPQLTEHMTDMTFFSSVSLSWFLTLFISVLIRYEDIHSMRCRNRLYVIQTLEETTKQNVLRVVSQDVKLSLQELDELYVIFKKELFLSCYWCLGCPVLKHHDPSLPYLEQYQIDCQQFRALYHLLSPWAHSANKDSLALWTFRLLDENSDCLINFKEFSSAIDIMYNGSFTEKLKLLFKLHIPPAYTEVKSKDASKGDELSKEELLYFSQLHVSKPANEKEAESAKHSPEKGKGKIDIQAYLSQWQDELFKKEENIKDLPRMNQSQFIQFSKTLYNLFHEDPEEESLYQAIAVVTSLLLRMEEVGRKLHSPTSSAKGFSGTVCGSGGPSEEKTGSHLEKDPCSFREEPQWSFAFEQILASLLNEPALVRFFEKPIDVKAKLENARISQLRSRTKM
2	Q0IIM8-D2	659-755	97		PIESAVNVVDCFFYDGIKAILQLGLAILDYNLDKLLTCKDDAEAVTALNRFFDNVTNKDSPLPSNVQQGSNVSDEKTSHTRVDITDLIRESNEKYGN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4

(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	6z2wE	0.36	9.68	0.035	0.578	model1_6z2wE.pdb.gz
2	5x6oC	0.34	9.59	0.045	0.545	model1_5x6oC.pdb.gz
3	5u1sA	0.34	8.98	0.037	0.512	model1_5u1sA.pdb.gz
4	6um1A	0.34	9.43	0.037	0.527	model1_6um1A.pdb.gz
5	7a1dA	0.33	9.13	0.045	0.505	model1_7a1dA.pdb.gz
6	6jxaA	0.33	9.63	0.039	0.520	model1_6jxaA.pdb.gz
7	5a22A	0.32	9.38	0.038	0.507	model1_5a22A.pdb.gz
8	6xjaP	0.32	9.68	0.042	0.519	model1_6xjaP.pdb.gz
9	6wjvA	0.32	9.23	0.051	0.499	model1_6wjvA.pdb.gz
10	6ez8A	0.32	9.17	0.038	0.491	model1_6ez8A.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	0.99	GTPase activator activity
GO:0017137	0.97	Rab GTPase binding
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0000166	0.54	nucleotide binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032550	0.53	purine ribonucleoside 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: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:0012505	0.94	endomembrane system
GO:0005622	0.93	intracellular
GO:0044424	0.66	intracellular 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	2vdcF	0.298	8.80	0.037	0.442	1.4.1.13	NA
2	0.060	1ofdA	0.295	8.93	0.037	0.444	1.4.7.1	NA
3	0.060	2uv8G	0.321	9.42	0.042	0.504	2.3.1.86	NA
4	0.060	2vdcA	0.298	8.70	0.036	0.440	1.4.1.13	NA
5	0.060	2vuaA	0.155	7.38	0.036	0.212	3.4.24.69	490,496,501

	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	0.02	2uvcG	0.315	9.46	0.047	0.497	0.11	FMN	complex1.pdb.gz	454,457,503
2	0.01	3cmvD	0.282	8.96	0.051	0.428	0.28	ANP	complex2.pdb.gz	455,459,460,461,486,492,495,753
3	0.01	3cmvB	0.283	8.98	0.044	0.429	0.21	ANP	complex3.pdb.gz	459,462,463,487
4	0.01	2vdcB	0.275	9.28	0.035	0.429	0.18	FMN	complex4.pdb.gz	503,666,667,682,743
5	0.01	2np0A	0.317	10.00	0.042	0.525	0.13	III	complex5.pdb.gz	487,489,495,496
6	0.01	2vdcA	0.298	8.70	0.036	0.440	0.26	F3S	complex6.pdb.gz	486,487,488
7	0.01	3cmvB	0.283	8.98	0.044	0.429	0.14	ANP	complex7.pdb.gz	460,461,463,464,465
8	0.01	2uvaI	0.326	9.18	0.041	0.502	0.11	FMN	complex8.pdb.gz	458,467,500
9	0.01	3cmvC	0.268	9.02	0.033	0.405	0.28	ANP	complex9.pdb.gz	454,457,458,495,499,753
10	0.01	3cmvD	0.282	8.96	0.051	0.428	0.23	ANP	complex10.pdb.gz	464,465,466,469,470,471,499

	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.