D-I-TASSER Q8IX04-D3

D-I-TASSER results for Q8IX04-D3

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

Input Sequence in FASTA format

>Q8IX04 (177 residues)
PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKV
LTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSAL
AKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL
Prediction	CCHHHHHHHHHHHCCCCCCSSSCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSSCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	916899999999798901288237706999999999999699854550799944899726630377412357789987335665444158662379999999999998099935578985066337878679974068669962788469999899999999999999999997399
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL
Prediction	700000100242160445200010030001001320253143435422000001346220000233641354234541462023103333222200020003002000444530100002233434264000000013024500352161703661245205500620361176278
	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                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHCCCCCCSSSCCCHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSSCCCCSSSSSCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL

4q3nA

0.25

7.71

1.50

DEthreader

PVDVLAYVAWKESGLHHSRVIGSGTSLDTARLRYEISQYIHIDSRNVHAYILGEHGDSEFVCWSNAPIAVISFDLEHIYLKVRDAAEIIKATYYGIGMALVRITAAIFNNENRILPISVLNNGVYDCEDQVYIGLPAVLNKDGVHHIVKLKL-NEKENSQLNNSANILRKNLDDMSY

3d4pB2

0.29

0.28

8.60

2.28

SPARKS-K

PVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEE-DVYIGVPAVINRNGIRNVVEIPLN-DEEQSKFAHSAKTLKDIMAEA--

4q3nA

0.26

0.25

7.86

0.87

MapAlign

PVDVLAYVAWKESGLHHSRVIGSGTSLDTARLRYEISQYIHIDSRNVHAYILGEHGDSEFVCWSNANVGISFEDLEHIYLKVRDAAYRKKATYYGIGMALVRITAAIFNNENRILPISVLNNGVYDCEDQVYIGLPAVLNKDGVHHIVKLKLN-EKENSQLNNSANILRKNLDDMSY

4q3nA

0.26

8.01

0.57

CEthreader

PVDVLAYVAWKESGLHHSRVIGSGTSLDTARLRYEISQYIHIDSRNVHAYILGEHGDSEFVCWSNANVGAKPHIYLKVRDAAYEIISRKKATYYGIGMALVRITAAIFNNENRILPISVLNNGVYDCEDQVYIGLPAVLNKDGVHHIVKLKL-NEKENSQLNNSANILRKNLDDMSY

3dl2A

0.98

0.97

27.07

1.76

MUSTER

PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGEEVVS-HTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTL--DTVTEKLQSSASSIHSLQQQLKL

2d4aD2

0.22

6.94

1.40

HHsearch

PVDAMTYVMYKKTGFPRERVIGFSGILDSARMAYYISQKLGVSFKSVNAIVLGMHGQKMFPVPRLSSVGGVPLVVSETVNAGAKITELGYSSNYGPAAGLVLTVEAIKRDSKRIYPYSLYLQGEYGYN-DIVAEVPAVIGKSGIERIIELPLT-EDEKRKFDEAVQAVKKLVETLPP

6or9A2

0.41

11.98

2.43

FFAS-3D

PVDILTYVSWKLSGLPKHRVIGSGTNLDSARFRYLLSEKLGIATTSCHGYIIGEHGDSSVPVWSGVNIAGWKETHTMVVKSAYEVIKLKGYTSWAIGLSLSQLARAILSNANSVHAVSTYLKGEHDINDEVFLSLPCVLGRSGVCDVIRQPLTQTE-RSQLHQSADLMAKVQAGIKF

6or9A2

0.40

11.82

1.15

EigenThreader

PVDILTYVSWKLSGLPKHRVIGSGTNLDSARFRYLLSEKLGIATTSCHGYIIGEHGDSSVPVWSGVNIAGKINWKETHTMVVKEVIKLKGYTSWAIGLSLSQLARAILSNANSVHAVSTYLKGEHDINDEVFLSLPCVLGRSGVCDVIRQPLTQT-ERSQLHQSADLMAKVQAGIKF

2i6tA

1.00

0.99

27.84

2.12

CNFpred

PVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTL-EDTVTEKLQSSASSIHSLQQQLKL

1ez4B

0.25

7.70

1.50

DEthreader

PVDILTYATWKFSGFPKERVIGSGTSLDSSRLRVALGKQFNVDPRSVDAYIMGEHGDSEFAAYSTATPVRAVDLAKLEDGVRNKAYDIIKATFYGIGTALMRISKAILRDENAVLPVGAYMDGQYGLN-DIYIGTPAIIGGTGLKQIIESPL-SADELKKMQDSAATLKKVLNDGLA

(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	0.8535

(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	4q3nA	0.96	0.99	0.250	0.994	model1_4q3nA.pdb.gz
2	1ldnA	0.95	1.10	0.263	0.989	model1_1ldnA.pdb.gz
3	9ldbA	0.94	1.34	0.415	0.994	model1_9ldbA.pdb.gz
4	3d4pB2	0.94	1.08	0.272	0.977	model1_3d4pB2.pdb.gz
5	1ez4B	0.94	1.25	0.257	0.989	model1_1ez4B.pdb.gz
6	2v7pA	0.94	1.27	0.291	0.989	model1_2v7pA.pdb.gz
7	1llcA	0.93	1.40	0.269	0.989	model1_1llcA.pdb.gz
8	3wsvA	0.93	1.40	0.280	0.989	model1_3wsvA.pdb.gz
9	1a5zA	0.93	1.38	0.263	0.989	model1_1a5zA.pdb.gz
10	1pzhA	0.93	1.39	0.229	0.989	model1_1pzhA.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:0016614	0.99	oxidoreductase activity, acting on CH-OH group of donors
GO:0016616	0.92	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0004457	0.91	lactate dehydrogenase activity
GO:0004459	0.89	L-lactate dehydrogenase activity
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	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:0009987	0.94	cellular process
GO:0008152	0.93	metabolic process
GO:0071704	0.92	organic substance metabolic process
GO:0044699	0.91	single-organism process
GO:0044237	0.91	cellular metabolic process
GO:0044763	0.88	single-organism cellular process
GO:0044281	0.86	small molecule metabolic process
GO:0006082	0.82	organic acid metabolic process
GO:0044238	0.81	primary metabolic process
GO:0019752	0.74	carboxylic acid metabolic process
GO:0032787	0.73	monocarboxylic acid metabolic process
GO:0006807	0.71	nitrogen compound metabolic process
GO:0034641	0.70	cellular nitrogen compound metabolic process
GO:0006139	0.69	nucleobase-containing compound metabolic process
GO:0006090	0.68	pyruvate metabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0009117	0.57	nucleotide metabolic process
GO:0006732	0.55	coenzyme metabolic process
GO:0046496	0.54	nicotinamide nucleotide metabolic process
GO:1901135	0.53	carbohydrate derivative metabolic process
GO:0046034	0.52	ATP metabolic process
GO:0044723	0.52	single-organism carbohydrate metabolic process
GO:1901575	0.51	organic substance catabolic process
GO:0044712	0.50	single-organism catabolic process
GO:0006091	0.50	generation of precursor metabolites and energy

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	0.97	cell part
GO:0044424	0.95	intracellular part
GO:0043226	0.86	organelle
GO:0043227	0.85	membrane-bounded organelle
GO:0044444	0.69	cytoplasmic part
GO:0043229	0.64	intracellular organelle
GO:0070062	0.62	extracellular exosome
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0005634	0.53	nucleus

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	0.312	1ez4B	0.938	1.25	0.257	0.989	1.1.1.27	28,31
2	0.312	1gv0A	0.903	1.51	0.312	0.977	1.1.1.37	28,31
3	0.262	3d4pB	0.941	1.08	0.272	0.977	1.1.1.27	56,96
4	0.247	1lldB	0.922	1.50	0.251	0.989	1.1.1.27	27,54,56,89
5	0.198	2ewdA	0.926	1.50	0.217	0.989	1.1.1.27	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	0.42	1t2fA	0.937	1.40	0.409	0.994	0.55	OXQ	complex1.pdb.gz	27,31,55
	2	0.17	2ldbA	0.943	1.15	0.259	0.983	0.66	UUU	complex2.pdb.gz	23,27,31,55,92,96

	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.