D-I-TASSER Q9C0B7

D-I-TASSER results for Q9C0B7

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

Summary of the Protein

Uniprot ID: Q9C0B7
Protein Name: Transport and Golgi organization protein 6 homolog
Gene Name: TANGO6

Input Sequence in FASTA format

>Q9C0B7 (1094 residues)
MAARQAVGSGAQETCGLDRILEALKLLLSPGGSGSSSLQVTKHDVLLATLKSNLSALEDK
FLKDPQWKNLKLLRDEIADKAEWPQNSVDVTWSFTSQTLLLLLCLKETMIRLAANFNPGK
PNPRTPEVAPALSPDALSISQQKTVQFVLQFVVTLGICPYLMPGVGVPLRYRTEFGAVVQ
DVVCFDAAPDATRRLYTSCKALLNVAQHTSLGSLIFCHHFGDIAAGLCQLGFCPTKRKLL
TPAEEVLTEEERTLSRGALRDMLDQVYQPLAVRELLILQGGPPQSCTDVKTQMRCRAPAW
LRRLCGQLLSERLMRPNGVQAVVRGILEGAGAGAAGGSDAEVTAADWKKCDLIAKILASC
PQQSLSPENYYRDICPQVLDLFHFQDKLTARQFQRVATTTFITLSRERPHLAAKYLLQPV
LAPLHRCLNTAELSESDMVPGTILVTEEELSRCIEDVFKVYVVGNEPLTVLMDSLLPVLG
VLFLLYCFTKQSVSHIRSLCQEILLWILGKLERKKAIASLKGFAGLDKAVPSLHSLCQFR
VATQGGIMITIKEAISDEDEDEALYQKVSSEQGRVEHLGDLLSHCQECGLAGDFFIFCLK
ELTHVASENETELKTEPFSSKSLLELEQHQTLLVEGQERKLLVLQLMAVLCERMSEQIFT
NVTQVVDFVAATLQRACASLAHQAESTVESQTLSMSMGLVAVMLGGAVQLKSSDFAVLKQ
LLPLLEKVSNTYPDPVIQELAVDLRITISTHGAFATEAVSMAAQSTLNRKDLEGKIEEQQ
QTSHERPTDVAHSHLEQQQSHETAPQTGLQSNAPIIPQGVNEPSTTTSQKSGSVTTEQLQ
EVLLSAYDPQIPTRAAALRTLSHWIEQREAKALEMQEKLLKIFLENLEHEDTFVYLSAIQ
GVALLSDVYPEKILPDLLAQYDSSKDKHTPETRMKVGEVLMRIVRALGDMVSKYREPLIH
TFLRGVRDPDGAHRASSLANLGELCQRLDFLLGSVVHEVTACLIAVAKTDGEVQVRRAAI
HVVVLLLRGLSQKATEVLSAVLKDLYHLLKHVVCLEPDDVAKLHAQLALEELDDIMKNFL
FPPQKLEKKIMVLP

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	Q9C0B7-D1	1-297	297		MAARQAVGSGAQETCGLDRILEALKLLLSPGGSGSSSLQVTKHDVLLATLKSNLSALEDKFLKDPQWKNLKLLRDEIADKAEWPQNSVDVTWSFTSQTLLLLLCLKETMIRLAANFNPGKPNPRTPEVAPALSPDALSISQQKTVQFVLQFVVTLGICPYLMPGVGVPLRYRTEFGAVVQDVVCFDAAPDATRRLYTSCKALLNVAQHTSLGSLIFCHHFGDIAAGLCQLGFCPTKRKLLTPAEEVLTEEERTLSRGALRDMLDQVYQPLAVRELLILQGGPPQSCTDVKTQMRCRA
2	Q9C0B7-D2	298-436	139		PAWLRRLCGQLLSERLMRPNGVQAVVRGILEGAGAGAAGGSDAEVTAADWKKCDLIAKILASCPQQSLSPENYYRDICPQVLDLFHFQDKLTARQFQRVATTTFITLSRERPHLAAKYLLQPVLAPLHRCLNTAELSES
3	Q9C0B7-D3	437-654	218		DMVPGTILVTEEELSRCIEDVFKVYVVGNEPLTVLMDSLLPVLGVLFLLYCFTKQSVSHIRSLCQEILLWILGKLERKKAIASLKGFAGLDKAVPSLHSLCQFRVATQGGIMITIKEAISDEDEDEALYQKVSSEQGRVEHLGDLLSHCQECGLAGDFFIFCLKELTHVASENETELKTEPFSSKSLLELEQHQTLLVEGQERKLLVLQLMAVLCERM
4	Q9C0B7-D4	655-754	100		SEQIFTNVTQVVDFVAATLQRACASLAHQAESTVESQTLSMSMGLVAVMLGGAVQLKSSDFAVLKQLLPLLEKVSNTYPDPVIQELAVDLRITISTHGAF
5	Q9C0B7-D5	755-1094	340		ATEAVSMAAQSTLNRKDLEGKIEEQQQTSHERPTDVAHSHLEQQQSHETAPQTGLQSNAPIIPQGVNEPSTTTSQKSGSVTTEQLQEVLLSAYDPQIPTRAAALRTLSHWIEQREAKALEMQEKLLKIFLENLEHEDTFVYLSAIQGVALLSDVYPEKILPDLLAQYDSSKDKHTPETRMKVGEVLMRIVRALGDMVSKYREPLIHTFLRGVRDPDGAHRASSLANLGELCQRLDFLLGSVVHEVTACLIAVAKTDGEVQVRRAAIHVVVLLLRGLSQKATEVLSAVLKDLYHLLKHVVCLEPDDVAKLHAQLALEELDDIMKNFLFPPQKLEKKIMVLP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.51

(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	5t8vA	0.45	7.25	0.069	0.613	model1_5t8vA.pdb.gz
2	5y81A	0.44	8.10	0.062	0.631	model1_5y81A.pdb.gz
3	3a6pA	0.44	8.04	0.070	0.627	model1_3a6pA.pdb.gz
4	6yvuD	0.43	7.78	0.071	0.602	model1_6yvuD.pdb.gz
5	3s4wA	0.43	8.09	0.061	0.622	model1_3s4wA.pdb.gz
6	6sytA	0.43	8.38	0.059	0.626	model1_6sytA.pdb.gz
7	6yufD	0.43	7.79	0.074	0.593	model1_6yufD.pdb.gz
8	6wg3E	0.43	7.90	0.062	0.597	model1_6wg3E.pdb.gz
9	3s4wB	0.42	8.13	0.071	0.610	model1_3s4wB.pdb.gz
10	6qj3A	0.42	8.03	0.077	0.602	model1_6qj3A.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	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0005215	0.61	transporter activity
GO:0008565	0.59	protein transporter 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:0009987	0.97	cellular process
GO:0044699	0.88	single-organism process
GO:0016043	0.81	cellular component organization
GO:0006810	0.77	transport
GO:0071702	0.75	organic substance transport
GO:0008152	0.74	metabolic process
GO:0008104	0.74	protein localization
GO:0071704	0.71	organic substance metabolic process
GO:0051641	0.70	cellular localization
GO:0065007	0.69	biological regulation
GO:0046907	0.69	intracellular transport
GO:0044238	0.69	primary metabolic process
GO:0050789	0.68	regulation of biological process
GO:0044763	0.68	single-organism cellular process
GO:0033365	0.68	protein localization to organelle
GO:0006913	0.68	nucleocytoplasmic transport
GO:0050794	0.67	regulation of cellular process
GO:0043170	0.67	macromolecule metabolic process
GO:0015031	0.67	protein transport
GO:0050896	0.61	response to stimulus
GO:0044237	0.61	cellular metabolic process
GO:0006886	0.60	intracellular protein transport
GO:0044260	0.58	cellular macromolecule metabolic process
GO:0006996	0.57	organelle organization
GO:1902578	0.55	single-organism localization
GO:0022402	0.55	cell cycle process
GO:0048519	0.54	negative regulation of biological process
GO:0044765	0.54	single-organism transport
GO:0048523	0.53	negative regulation of cellular process
GO:0019538	0.53	protein metabolic process
GO:0006807	0.53	nitrogen compound metabolic process
GO:0006139	0.52	nucleobase-containing compound metabolic process
GO:0090304	0.51	nucleic acid metabolic process
GO:0051726	0.51	regulation of cell cycle
GO:0051716	0.51	cellular response to stimulus
GO:0006950	0.51	response to stress
GO:0006974	0.50	cellular response to DNA damage stimulus

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	0.96	intracellular organelle part
GO:0043229	0.95	intracellular organelle
GO:0043227	0.95	membrane-bounded organelle
GO:0043231	0.94	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0032991	0.88	macromolecular complex
GO:0044428	0.87	nuclear part
GO:0043234	0.86	protein complex
GO:0005737	0.83	cytoplasm
GO:0044444	0.72	cytoplasmic part
GO:0016020	0.72	membrane
GO:0031090	0.57	organelle membrane
GO:0031965	0.51	nuclear membrane

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	2jfdA	0.131	6.36	0.056	0.167	2.3.1.85	NA
2	0.060	2pffD	0.229	9.97	0.026	0.380	2.3.1.86	NA
3	0.060	2zxqA	0.259	9.22	0.028	0.402	3.2.1.97	NA
4	0.060	2vdcF	0.260	8.80	0.044	0.390	1.4.1.13	NA
5	0.060	2qf7B	0.276	9.34	0.035	0.435	6.4.1.1	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:

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
	1	0.01	3b2pA	0.307	8.11	0.051	0.440	0.13	ARG	complex1.pdb.gz	571,572,575
	2	0.01	2dqmA	0.306	8.13	0.048	0.440	0.33	BES	complex2.pdb.gz	572,575,576,579

	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.