D-I-TASSER P17813-D3

D-I-TASSER results for P17813-D3

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

Input Sequence in FASTA format

>P17813 (106 residues)
SPAPIQTTPPKDTCSPELLMSLIQTKCADDAMTLVLKKELVAHLKCTITGLTFWDPSCEA
EDRGDKFVLRSAYSSCGMQVSASMISNEAVVNILSSSSPQRKKVHC

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SPAPIQTTPPKDTCSPELLMSLIQTKCADDAMTLVLKKELVAHLKCTITGLTFWDPSCEAEDRGDKFVLRSAYSSCGMQVSASMISNEAVVNILSSSSPQRKKVHC
Prediction	CCCCCCCCCCCCCCCHHHHHCCCCCCCCCCSSSSSSSHHHHCHCCCCSSSSSSCCCCCCCCCCCCSSSSSCCCCCCCCSSCCCSSSCSSSSSSCCCCCCSSSSSCC
Confidence	9989777897557883142001356447985999997233000388535667428974231169679997057778854303178612899955999835766149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SPAPIQTTPPKDTCSPELLMSLIQTKCADDAMTLVLKKELVAHLKCTITGLTFWDPSCEAEDRGDKFVLRSAYSSCGMQVSASMISNEAVVNILSSSSPQRKKVHC
Prediction	8665465434675354401222344515643020104453154262433303232451416646421103132551334346422333211313475433355268
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCHHHHHCCCCCCCCCCSSSSSSSHHHHCHCCCCSSSSSSCCCCCCCCCCCCSSSSSCCCCCCCCSSCCCSSSCSSSSSSCCCCCCSSSSSCC
SPAPIQTTPPKDTCSPELLMSLIQTKCADDAMTLVLKKELVAHLKCTITGLTFWDPSCEAEDRGDKFVLRSAYSSCGMQVSASMISNEAVVNILSSSSPQRKKVHC

4wrnA

0.15

0.14

4.75

1.17

DEthreader

-----QADS-DFNITDISLLE-HRLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNDRDWVSVVTPARPCGTVLTNHTYSNTLYLADIIRDLNIKINFAC

4wrnA3

0.14

0.12

4.19

1.77

SPARKS-K

-------------NITDISLLEHRLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNNRDWVSVVTPARDCGTVLTRNTYSNTLYLADEIRDLNIKINFAC

4wrnA3

0.16

0.14

4.69

0.87

MapAlign

-------------ITDISLL-EHRLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNDRDWVSVVTPAGPCGTVTTHATYSNTLYLAIIIRDLNIKINFAC

4wrnA3

0.16

0.14

4.70

1.03

CEthreader

------------NITDISLL-EHRLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNDRDWVSVVTPARDCGTVLTRNTYSNTLYLAIIIRDLNIKINFAC

4wrnA3

0.16

0.14

4.70

1.35

MUSTER

------------NITDISLLEH-RLECGANDMKVSLGKCQLKSLGFDKVFMYLSDSRCSGFNNRDWVSVVTPDGPCGTVLTRNTYSNTLYLAIIIRDLNIKINFAC

3nk3A1

0.11

0.09

3.37

3.65

HHsearch

-------------------YTPVAVQCQEAQLVVTVHRDLFGTRLINAADLTLGPAACKHSSNHNTVTFAAGLHECGSVVQDTLYRTLINYDPSIRTNPAVIPIEC

3nk3A1

0.12

0.09

3.36

1.05

FFAS-3D

--------------------TPVAVQCQEAQLVVTVHRDLFGTRLINAADLTLGPAACKHSSAHNTVTFAAGLHECGSVVQVTIYRTLINYDPIIRTNPAVIPIEC

6h7wJ2

0.12

0.11

3.96

0.82

EigenThreader

--YRIPPELNSSDC----LHIEFEYSYHKDVIVGRIYFLLVR---LKIKHMELSIIRFEIMDGGETIPILFLGGFLTTFRDVNSTRYSLVLIDED-ARRYFKQSEI

5hzvA

1.00

0.89

24.83

1.78

CNFpred

------------TCSPELLMSLIQTKCADDAMTLVLKKELVAHLKCTITGLTFWDPSCEAEDRGDKFVLRSAYSSCGMQVSASMISNEAVVNILSSSSPQRKKVHC

4wrnA3

0.14

0.12

4.18

1.17

DEthreader

----------N--ITDISLLE-HRLECGANDMKVSLGKCQLKS-LGFKVFMYLSDSRCSGFNDRDWVSVVTPARPCGTVLTNHTYSNTLYLADIIRDLNIKINFAC

(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	0.7658

(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	4wrnA3	0.72	2.01	0.141	0.859	model1_4wrnA3.pdb.gz
2	3nk3A1	0.67	2.15	0.116	0.802	model1_3nk3A1.pdb.gz
3	3qd1X1	0.62	3.37	0.065	0.877	model1_3qd1X1.pdb.gz
4	4gaaA1	0.47	3.81	0.097	0.783	model1_4gaaA1.pdb.gz
5	4uicA4	0.45	3.78	0.068	0.689	model1_4uicA4.pdb.gz
6	2gjeD	0.41	3.74	0.045	0.641	model1_2gjeD.pdb.gz
7	5eq2A2	0.40	2.81	0.067	0.547	model1_5eq2A2.pdb.gz
8	1eu8A	0.39	4.20	0.031	0.689	model1_1eu8A.pdb.gz
9	4p7wA1	0.38	4.01	0.025	0.594	model1_4p7wA1.pdb.gz
10	2b3bA	0.38	4.48	0.020	0.708	model1_2b3bA.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:0004871	0.90	signal transducer activity
GO:0005102	0.88	receptor binding
GO:0005160	0.87	transforming growth factor beta receptor binding
GO:0005114	0.84	type II transforming growth factor beta receptor binding
GO:0003824	0.81	catalytic activity
GO:0016740	0.79	transferase activity
GO:0004888	0.79	transmembrane signaling receptor activity
GO:0005024	0.78	transforming growth factor beta-activated receptor activity
GO:0097367	0.71	carbohydrate derivative binding
GO:0005539	0.68	glycosaminoglycan binding
GO:0034713	0.51	type I transforming growth factor beta receptor 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:0050794	1.00	regulation of cellular process
GO:0044699	0.93	single-organism process
GO:0009987	0.93	cellular process
GO:0048518	0.91	positive regulation of biological process
GO:0044763	0.91	single-organism cellular process
GO:0048522	0.90	positive regulation of cellular process
GO:0044767	0.90	single-organism developmental process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0009893	0.86	positive regulation of metabolic process
GO:0048856	0.85	anatomical structure development
GO:0010628	0.85	positive regulation of gene expression
GO:0051239	0.75	regulation of multicellular organismal process
GO:0048583	0.74	regulation of response to stimulus
GO:0009966	0.73	regulation of signal transduction
GO:0080090	0.72	regulation of primary metabolic process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0017015	0.72	regulation of transforming growth factor beta receptor signaling pathway
GO:0031325	0.71	positive regulation of cellular metabolic process
GO:0042327	0.70	positive regulation of phosphorylation
GO:0010557	0.70	positive regulation of macromolecule biosynthetic process
GO:0001932	0.70	regulation of protein phosphorylation
GO:0051240	0.69	positive regulation of multicellular organismal process
GO:0048513	0.69	animal organ development
GO:0001934	0.69	positive regulation of protein phosphorylation
GO:0050896	0.65	response to stimulus
GO:0009628	0.61	response to abiotic stimulus
GO:0007165	0.57	signal transduction
GO:0016043	0.50	cellular component organization

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:0044424	0.79	intracellular part
GO:0044425	0.68	membrane part
GO:0044422	0.65	organelle part
GO:0044446	0.64	intracellular organelle part
GO:0044428	0.60	nuclear part
GO:0005737	0.60	cytoplasm
GO:0044421	0.57	extracellular region part
GO:0005654	0.57	nucleoplasm
GO:0005615	0.55	extracellular space

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	0.067	1k85A	0.487	3.37	0.063	0.736	3.2.1.14	NA
2	0.066	1u2hA	0.498	3.06	0.065	0.726	2.7.11.1	56
3	0.060	1ogmX	0.549	3.54	0.074	0.830	3.2.1.11	NA
4	0.060	1cygA	0.539	3.67	0.066	0.849	2.4.1.19	NA
5	0.060	2biiA	0.520	4.04	0.053	0.877	1.7.1.3	73

	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	1p4uA	0.563	3.46	0.109	0.868	0.27	III	complex1.pdb.gz	32,53,78
2	0.02	3nk3B	0.675	2.08	0.106	0.802	0.12	III	complex2.pdb.gz	24,33,35,51,52,53,55,87,88
3	0.02	1bhgA	0.570	3.36	0.102	0.830	0.21	UUU	complex3.pdb.gz	3,4,41,87
4	0.02	3hn3B	0.579	3.35	0.102	0.830	0.10	UUU	complex4.pdb.gz	50,52,55
5	0.02	1e6j2	0.535	3.26	0.129	0.774	0.14	III	complex5.pdb.gz	4,6,7,47,51,52,53,77,89,91
6	0.01	1na80	0.575	3.41	0.109	0.868	0.20	III	complex6.pdb.gz	25,38,60,62
7	0.01	2q7aA	0.588	3.13	0.075	0.849	0.24	HEM	complex7.pdb.gz	52,53,78
8	0.01	2ivfC	0.591	3.69	0.091	0.924	0.11	HEM	complex8.pdb.gz	52,54,90,99,101
9	0.01	2dwxC	0.568	3.36	0.088	0.859	0.18	III	complex9.pdb.gz	59,60,76
10	0.01	1xwvA	0.553	3.63	0.074	0.868	0.34	PE3	complex10.pdb.gz	5,24,33,35,55,68,70,73,90,100,102

	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.