D-I-TASSER P52790-D2

D-I-TASSER results for P52790-D2

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

Input Sequence in FASTA format

>P52790 (259 residues)
MLPTYVGSTPHGTEQGDFVVLELGATGASLRVLWVTLTGIEGHRVEPRSQEFVIPQEVML
GAGQQLFDFAAHCLSEFLDAQPVNKQGLQLGFSFSFPCHQTGLDRSTLISWTKGFRCSGV
EGQDVVQLLRDAIRRQGAYNIDVVAVVNDTVGTMMGCEPGVRPCEVGLVVDTGTNACYME
EARHVAVLDEDRGRVCVSVQQTLQVAVATGGRVCERHPRFCSVLQGTVMLLAPECDVSLI
PSVDGGGRGVAMVTAVAAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MLPTYVGSTPHGTEQGDFVVLELGATGASLRVLWVTLTGIEGHRVEPRSQEFVIPQEVMLGAGQQLFDFAAHCLSEFLDAQPVNKQGLQLGFSFSFPCHQTGLDRSTLISWTKGFRCSGVEGQDVVQLLRDAIRRQGAYNIDVVAVVNDTVGTMMGCEPGVRPCEVGLVVDTGTNACYMEEARHVAVLDEDRGRVCVSVQQTLQVAVATGGRVCERHPRFCSVLQGTVMLLAPECDVSLIPSVDGGGRGVAMVTAVAAR
Prediction	CCCCCCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSCCCCCCSSSSSSSSSSCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSCSSSSSCCCCSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSCCHHHHHHHCCCCCCCSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCHHHHHHHHHHHHCCCCCSSSSSCCCCCCHHHHHHHHHHHC
Confidence	9775568899984215899999726985599999998389872599999985358777128789999999999999999718887642257898320366035745999804552478866750789999999982999863899984858888740247999459999927862489987012433577766531144444430222466434567745899999999968998269997468875689999988619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MLPTYVGSTPHGTEQGDFVVLELGATGASLRVLWVTLTGIEGHRVEPRSQEFVIPQEVMLGAGQQLFDFAAHCLSEFLDAQPVNKQGLQLGFSFSFPCHQTGLDRSTLISWTKGFRCSGVEGQDVVQLLRDAIRRQGAYNIDVVAVVNDTVGTMMGCEPGVRPCEVGLVVDTGTNACYMEEARHVAVLDEDRGRVCVSVQQTLQVAVATGGRVCERHPRFCSVLQGTVMLLAPECDVSLIPSVDGGGRGVAMVTAVAAR
Prediction	7400304631526240200001024411200001020427764414344551413641351404400420051025005635277441310101012131341440301301451416412343025204500563622503000000000000001114244010000001213011203054054145755523343544341222244432532240352035005401561504012053111200000000057
	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                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSCCCCCCSSSSSSSSSSCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSCSSSSSCCCCSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSCCHHHHHHHCCCCCCCSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCHHHHHHHHHHHHCCCCCSSSSSCCCCCCHHHHHHHHHHHC
MLPTYVGSTPHGTEQGDFVVLELGATGASLRVLWVTLTGIEGHRVEPRSQEFVIPQEVMLGAGQQLFDFAAHCLSEFLDAQPVNKQGLQLGFSFSFPCHQTGLDRSTLISWTKGFRCSGVEGQDVVQLLRDAIRRQGAYNIDVVAVVNDTVGTMMGCEPGVRPCEVGLVVDTGTNACYMEEARHVAVLDEDRGRVCVSVQQTLQVAVATGGRVCERHPRFCSVLQGTVMLLAPECDVSLIPSVDGGGRGVAMVTAVAAR

3imxA

0.42

0.41

11.90

1.33

DEthreader

MLPTYVRSPEGSEVG-DFLSLDLGG-T-NFRVMLVKVG-EQWSVK-TKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEGRMCV-T-F----GVIRMREEMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACK

1dgkN2

0.49

0.48

14.02

1.58

SPARKS-K

MLPSFVRRTPDGTENGDFLALDLG--GANFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMGQISEVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVR

3imxA

0.45

0.44

12.76

0.87

MapAlign

--PTYVRSTPEGSEVGDFLSLDLGG--TNFRVMLVKVGE--QWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVDEGRMCVNNRMRDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACK

3imxA

0.46

0.45

13.18

0.74

CEthreader

MLPTYVRSTPEGSEVGDFLSLDLG--GTNFRVMLVKVGEQW--SVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACK

1dgkN2

0.49

0.48

14.02

1.13

MUSTER

MLPSFVRRTPDGTENGDFLALDLG--GANFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMLDRLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVR

1dgkN

0.48

13.92

2.24

HHsearch

MLPSFVRRTPDGTENGDFLALDLG--GANFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMRGLDRVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVR

1dgkN2

0.49

0.48

14.02

2.46

FFAS-3D

MLPSFVRRTPDGTENGDFLALDLG--GANFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMLDRLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVR

3imxA

0.41

0.40

11.70

1.13

EigenThreader

MLPTYVRTPEGSEVGD-FLSLDLG--GTNFRVMLVKVGEQWSVKTKHQMYSI--PEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVDI-----DKGILLNWGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACK

4rchA

0.40

0.39

11.49

2.33

CNFpred

MLPTYVRSTPEGSEVGDFLSLDLGG--TNFRVMLVKVGEGGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTE------WGAFGDSGE-LDEFLLEYDRLVDESSAPGQQLYEKLIGGKYMGELVRLVLLRL

1dgkN

0.45

0.44

12.85

1.33

DEthreader

MLPSFVRRPDGTENG-DFLALDLGG-A-NFRVLLVKIRSGKKRTVEMHNKIYAIPIEIMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGILITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEVGLIVGTGSNACYME--EMKNV---EMVIMAVKIRELLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVR

(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	0.846

(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	1dgkN	0.96	1.09	0.479	0.992	model1_1dgkN.pdb.gz
2	3imxA	0.95	1.20	0.455	0.985	model1_3imxA.pdb.gz
3	3hm8A	0.93	1.38	0.522	0.977	model1_3hm8A.pdb.gz
4	1bdgA	0.93	1.38	0.401	0.973	model1_1bdgA.pdb.gz
5	3b8aX	0.92	1.77	0.291	0.981	model1_3b8aX.pdb.gz
6	4qs7A	0.91	1.88	0.336	0.988	model1_4qs7A.pdb.gz
7	5zqtA	0.91	2.00	0.355	0.988	model1_5zqtA.pdb.gz
8	3o08B	0.88	2.20	0.311	0.981	model1_3o08B.pdb.gz
9	1hkgA	0.88	2.09	0.180	0.965	model1_1hkgA.pdb.gz
10	3eo3A	0.59	3.47	0.138	0.718	model1_3eo3A.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:0004396	1.00	hexokinase activity
GO:0004340	0.98	glucokinase activity
GO:0008865	0.96	fructokinase activity
GO:0019158	0.95	mannokinase activity
GO:0005536	0.53	glucose binding
GO:0005524	0.53	ATP 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	0.98	cellular process
GO:0044699	0.97	single-organism process
GO:0016310	0.97	phosphorylation
GO:0005975	0.97	carbohydrate metabolic process
GO:0065007	0.96	biological regulation
GO:0044763	0.96	single-organism cellular process
GO:0065008	0.95	regulation of biological quality
GO:0006096	0.95	glycolytic process
GO:0048878	0.94	chemical homeostasis
GO:0042593	0.93	glucose homeostasis
GO:0055082	0.92	cellular chemical homeostasis
GO:0001678	0.91	cellular glucose homeostasis
GO:0046835	0.53	carbohydrate phosphorylation

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:0044444	0.97	cytoplasmic part
GO:0005829	0.96	cytosol

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	0.559	3hm8A	0.933	1.38	0.522	0.977	2.7.1.1	149
2	0.530	3f9mA	0.944	1.41	0.459	0.985	2.7.1.2	149
3	0.409	1q18A	0.623	3.44	0.089	0.768	2.7.1.2	149
4	0.390	3eo3A	0.586	3.47	0.138	0.718	5.1.3.14 2.7.1.60	149
5	0.380	1xc3A	0.660	3.19	0.117	0.788	2.7.1.4	149

	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	0.52	2nztA	0.929	1.26	0.544	0.965	1.43	BG6	complex1.pdb.gz	22,93,95,149,169,171,172,211,212,245,246
2	0.51	3o5bB	0.859	2.51	0.311	0.981	0.99	BGC	complex2.pdb.gz	148,149,150,173,174,175
3	0.29	3f9mA	0.944	1.41	0.459	0.985	1.49	MRK	complex3.pdb.gz	5,6,7,8,9,10,154,155,158,159,164,179,253,256

	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.