D-I-TASSER Q6PCB7-D1

D-I-TASSER results for Q6PCB7-D1

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

Input Sequence in FASTA format

>Q6PCB7 (69 residues)
MRAPGAGAASVVSLALLWLLGLPWTWSAAAALGVYVGSGGWRFLRIVCKTARRDLFGLSV
LIRVRLELR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MRAPGAGAASVVSLALLWLLGLPWTWSAAAALGVYVGSGGWRFLRIVCKTARRDLFGLSVLIRVRLELR
Prediction	CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHSSSSCCCCCHHHHHHHHHHHHHHHHHSSSSSSSSSCC
Confidence	997325799999999999988985899988851344489610125669876445542002357876519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MRAPGAGAASVVSLALLWLLGLPWTWSAAAALGVYVGSGGWRFLRIVCKTARRDLFGLSVLIRVRLELR
Prediction	744333232201233333237333333232121112333323202000311443141130123133538
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60

                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHSSSSCCCCCHHHHHHHHHHHHHHHHHSSSSSSSSSCC
MRAPGAGAASVVSLALLWLLGLPWTWSAAAALGVYVGSGGWRFLRIVCKTARRDLFGLSVLIRVRLELR

4l8tA

0.06

2.55

1.33

DEthreader

WLIHQFIIIMEKNIQPIIVPGTSVLQQLSYFYTTMCQNGLPELVRQAVKQLFFLIGAVTLNSLFLRKS-

7a23I

0.12

4.13

0.61

CEthreader

TLQQIFFFCSIASMILGALAAMYSSIGHVGYICIGFSCGTIEGIQSLLIGIFIYALMTMDAFAIVLALR

6tjvF

0.10

3.74

0.60

EigenThreader

VALTALLVIGSVTALGGTLIAIALVSAYMGWVFIAVGLKEPGLAFVFILTYSLAMAVLMMSIGSIIWNS

5v6pA2

0.03

1.62

0.44

FFAS-3D

------STSLYLIQVMEFTMLLIDLLNLFLQTCLNFWEFYRKFMYEKAIDVFTRFLKTALHLSM-----

6w2rA1

0.13

4.52

0.72

SPARKS-K

TEDERRELEKVARKAIEAAREGNVREQLQRALEIARESGTKLALDVALRVAQEAAKAIDEAAEVVVRIA

5oglA

0.19

6.09

0.69

CNFpred

MSTFFASLIVVPIILIAREYKLTTYGFIAALLGSIANSYYNRTMSGYYDTDMLVLVLPMLILLTFIRLT

6ku0A

0.09

3.32

1.33

DEthreader

WLIQQLVRVLENILQPMIVSGYSILRQLNSFHSVMCQHGMPELIKQVVKQMFYIVGAITLNNLLLRK--

4he8M2

0.13

4.51

0.68

MapAlign

-QGLLLFLAALSALYGAWVALAYAGLSHMGVAALGVFSGTPEGAMGGLYLLAASGVYTGGLFLLAGRLY

2xndJ

0.15

0.14

4.88

0.72

MUSTER

--IDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYLKQQLFSYAILGFALSEAMGLFCLMVAFLILF

2eb0B

0.08

0.07

2.90

0.40

HHsearch

ILYYAKPVGSTATVIAELYFAIELKPDLALLSAIISDTVLFKSP----TTTDLDKEMAKKLAEAGINIE

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4794

(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	5yd1A3	0.74	2.17	0.130	1.000	model1_5yd1A3.pdb.gz
2	1rsrB	0.72	2.71	0.043	0.971	model1_1rsrB.pdb.gz
3	4l8tA	0.72	2.15	0.058	0.986	model1_4l8tA.pdb.gz
4	4llsA	0.72	2.45	0.134	0.957	model1_4llsA.pdb.gz
5	6iu3A2	0.72	2.36	0.059	0.986	model1_6iu3A2.pdb.gz
6	5z1fA2	0.72	2.20	0.103	0.986	model1_5z1fA2.pdb.gz
7	4gfqA	0.71	2.37	0.077	0.942	model1_4gfqA.pdb.gz
8	4k1pA	0.71	2.60	0.044	0.986	model1_4k1pA.pdb.gz
9	2v46Y2	0.69	2.43	0.015	0.942	model1_2v46Y2.pdb.gz
10	2f6hX2	0.67	2.46	0.044	0.971	model1_2f6hX2.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:0005215	0.91	transporter activity
GO:0015245	0.90	fatty acid transporter activity
GO:0003824	0.63	catalytic 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:0044699	0.95	single-organism process
GO:0008152	0.94	metabolic process
GO:0044710	0.93	single-organism metabolic process
GO:0009987	0.93	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044763	0.92	single-organism cellular process
GO:0044238	0.92	primary metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044255	0.90	cellular lipid metabolic process
GO:0044765	0.89	single-organism transport
GO:0015909	0.88	long-chain fatty acid transport
GO:0065007	0.72	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:1901576	0.68	organic substance biosynthetic process
GO:0044281	0.68	small molecule metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0044249	0.67	cellular biosynthetic process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0008610	0.66	lipid biosynthetic process
GO:0048523	0.65	negative regulation of cellular process
GO:0045017	0.65	glycerolipid biosynthetic process
GO:0031326	0.65	regulation of cellular biosynthetic process
GO:0019637	0.65	organophosphate metabolic process
GO:0006807	0.65	nitrogen compound metabolic process
GO:0006796	0.65	phosphate-containing compound metabolic process
GO:1901566	0.64	organonitrogen compound biosynthetic process
GO:0046474	0.64	glycerophospholipid biosynthetic process
GO:0031324	0.64	negative regulation of cellular metabolic process
GO:0019220	0.64	regulation of phosphate metabolic process
GO:0019216	0.64	regulation of lipid metabolic process
GO:0071072	0.63	negative regulation of phospholipid biosynthetic process
GO:0032049	0.63	cardiolipin biosynthetic process
GO:0006661	0.63	phosphatidylinositol biosynthetic process
GO:0006659	0.63	phosphatidylserine biosynthetic process
GO:0006656	0.63	phosphatidylcholine biosynthetic process
GO:0006654	0.63	phosphatidic acid biosynthetic process
GO:0006646	0.63	phosphatidylethanolamine biosynthetic process
GO:0032787	0.59	monocarboxylic acid metabolic process
GO:0006631	0.58	fatty acid metabolic process
GO:0001676	0.55	long-chain fatty acid metabolic 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:0005886	1.00	plasma membrane
GO:0044424	0.91	intracellular part
GO:0044444	0.86	cytoplasmic part
GO:0043226	0.70	organelle
GO:0043229	0.69	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0044446	0.66	intracellular organelle part
GO:0044425	0.56	membrane 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	0.066	1wu0A	0.494	2.88	0.076	0.754	3.6.3.14	NA
2	0.060	2wodA	0.651	2.47	0.119	0.899	3.2.2.24	NA
3	0.060	2hc1A	0.618	2.66	0.032	0.899	3.1.3.48	NA
4	0.060	2p6xA	0.696	2.40	0.061	0.957	3.1.3.48	NA
5	0.060	1rsrB	0.722	2.71	0.043	0.971	1.17.4.1	42

	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	0.05	3p41A	0.692	2.85	0.188	0.986	0.19	IPE	complex1.pdb.gz	37,38,39,40,47
2	0.05	3q5eG	0.693	2.12	0.141	0.927	0.28	GDP	complex2.pdb.gz	32,36,40
3	0.02	2o1oA	0.690	3.01	0.103	0.971	0.25	RIS	complex3.pdb.gz	31,34,39
4	0.02	2q58A	0.688	2.84	0.103	0.971	0.21	ZOL	complex4.pdb.gz	32,35,39
5	0.02	2h8o0	0.690	1.99	0.106	0.957	0.20	III	complex5.pdb.gz	17,22,23,25,28,29,32,33,40,41,47,48,51,52,56,57,60
6	0.02	3bm3A	0.615	2.92	0.104	0.957	0.24	QNA	complex6.pdb.gz	32,40,41,43,45
7	0.02	3aklB	0.689	2.86	0.060	0.971	0.16	ANP	complex7.pdb.gz	32,33,38,39,50,51
8	0.01	3bm3B	0.685	2.29	0.030	0.957	0.21	QNA	complex8.pdb.gz	32,35,36,40,41,45
9	0.01	3exfE	0.604	2.82	0.061	0.942	0.19	TPP	complex9.pdb.gz	8,33,38,40,41
10	0.01	1ni4A	0.681	2.55	0.029	0.957	0.18	TPP	complex10.pdb.gz	8,38,40,41

	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.