D-I-TASSER P0DP75-D1

D-I-TASSER results for P0DP75-D1

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

Input Sequence in FASTA format

>P0DP75 (135 residues)
MRSSSLPGARSPRRNGSGQSRHRLPPGRLRTGSRAPTAEARPHVARSPPTPGTGARGGGR
RGWGGSRAAPQRGSCASANAQKQLRQTAATYMLTARGGSRSAERKGDLQRTFRQVGQTMP
MVPPLDFTMNAASVE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRSSSLPGARSPRRNGSGQSRHRLPPGRLRTGSRAPTAEARPHVARSPPTPGTGARGGGRRGWGGSRAAPQRGSCASANAQKQLRQTAATYMLTARGGSRSAERKGDLQRTFRQVGQTMPMVPPLDFTMNAASVE
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	987778888888999976555589999888788897511088645689999988778887789999878755414667899999999888743215786304542028999998624577788753323443359
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRSSSLPGARSPRRNGSGQSRHRLPPGRLRTGSRAPTAEARPHVARSPPTPGTGARGGGRRGWGGSRAAPQRGSCASANAQKQLRQTAATYMLTARGGSRSAERKGDLQRTFRQVGQTMPMVPPLDFTMNAASVE
Prediction	855662644543555456545453454424446534525434543653444444554644543546442444441343434541453123120214334543645441451144145424323324233534638
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
MRSSSLPGARSPRRNGSGQSRHRLPPGRLRTGSRAPTAEARPHVARSPPTPGTGARGGGRRGWGGSRAAPQRGSCASANAQKQLRQTAATYMLTARGGSRSAERKGDLQRTFRQVGQTMPMVPPLDFTMNAASVE

4z28A

0.13

0.12

4.13

0.44

CEthreader

MSPDMKLLAGASNWVNQSGSVAQFVFTPSPTQPQTYEVSGNYINAQGTGCKGTPYPLSGAYYSGNQIISFSVVWSNASANCQ----SATGWTGYFDFSGSQAVLKTDWNLAFYSGSTPAIQQGQDDFMQS-----

3b5xA

0.08

3.20

0.55

EigenThreader

MILGLMFVRGLSGFASSYCLSWVSGNVVMQRITYDSEQVAGATSRALVSIVREGASIIGLELTPGTFTVAMFGLMRPLKALTSVTSEFQRGMAACQTLFGLGEVDVKDVTFTVSFSIPDVDSGSICLDGHDVRDY

4wceC

0.13

0.12

4.09

0.48

FFAS-3D

--------------DGTKSGSIELSDARQGTHAVKNRSAVSGGGRKPWKQKGTGRARQGTIRAGGGIVFGPTPRSYAYKMPKKMRRLALRSALSFKAQENGLTVVDAFNFEAPKTKEFKNVLSTLEQPKKVLVV-

7jjvA

0.19

0.17

5.52

1.13

SPARKS-K

MQCDGLDGADGTSNGQAGASGLAGGPNCN--GGKGGK--GAPGVGTAGGAGGVGGAGGTGNTNGGAGGSG--GNSDVAAGG-----AGAAGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTTV

4ad7A

0.16

0.04

1.48

0.38

CNFpred

-------------------------------------------------------------------------TCCTSEMEENLANRSHAELETA-----LRDSSRVLQAMLATQL-------------------

1hkgA1

0.03

0.02

1.41

0.83

DEthreader

MV-PGGDSHIL--------GIKMGIIFGVNAAYCGIVCGQDSFESGANGGSLRDVLMGYKGG-----G-QGHMKVRRGLFLIAAYAFRLVVCGIGAICQGYSSGHIAA---SGRDYSGFSGNTGNGIY-------

2j0kB

0.08

3.18

0.68

MapAlign

--RFDKECFKCALGSSWIISVELAEGISYLTDKGANPTHLADFTIQYSNSEDKDRKGMLQLKIAGAPEPLTVTAPSLTIAENMADLIDGYCRLVGRCIGEGQFGDVHQGIYMSPENPAMAVAIKTCKNCTSDSV-

5y6pC1

0.13

4.36

0.73

MUSTER

LPPPGIPSGQDPLDN---APLRHYVPRPVETYEDRGFATILPRTWEGETN--TIGAGDIEPVTKEEVEESRKVPVDAASTGAFVEYARMMKEERAQALADQARRNSAPTSGRPTCGEGTEFVSNARPILGVKVVE

2pffA

0.21

6.57

0.60

HHsearch

MKATSFEHGRTPAEMSRPATTTRNGMGVPIYGIVAMAATATDKIGRSVPAPGKGILTTAREHHSSVKASPNL-NMKYVTREAQIKDWVENELLKNEAESQLRAAQQQWGNDFYKR---DPRIAPLRLTIDDLGVA

7bqx5

0.13

4.40

0.44

CEthreader

HNFITPVGPLVENIKSTYLNKITTVVHGPVVSKAIPRSTVKVTVPSQPCPADARLYVALTYEEAGPRFTFFQSSRGHCQIMNILRIYYSPSIMAVACLGTFSATDGWRRSAFNYRGSSLPVVEIDSFYSNVSDWE

(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	0.5046

(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	7ctpA	0.46	4.57	0.035	0.756	model1_7ctpA.pdb.gz
2	5lpcA	0.46	4.83	0.052	0.822	model1_5lpcA.pdb.gz
3	3nfhA	0.46	4.08	0.017	0.726	model1_3nfhA.pdb.gz
4	6ifkA	0.46	4.72	0.057	0.800	model1_6ifkA.pdb.gz
5	6xs4A	0.45	5.34	0.069	0.867	model1_6xs4A.pdb.gz
6	4bwpA	0.45	4.50	0.074	0.711	model1_4bwpA.pdb.gz
7	3tshA	0.45	4.48	0.068	0.778	model1_3tshA.pdb.gz
8	4qiwB	0.45	5.28	0.060	0.881	model1_4qiwB.pdb.gz
9	5jm7A2	0.45	5.33	0.061	0.837	model1_5jm7A2.pdb.gz
10	6wppA	0.45	4.38	0.084	0.704	model1_6wppA.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:1901265	0.47	nucleoside phosphate binding
GO:0036094	0.47	small molecule binding
GO:0050662	0.37	coenzyme binding
GO:0016491	0.37	oxidoreductase 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:0044710	0.37	single-organism 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:0044464	1.00	cell part
GO:0044424	0.93	intracellular part
GO:0044444	0.79	cytoplasmic part
GO:0043229	0.79	intracellular organelle
GO:0005737	0.79	cytoplasm
GO:0044446	0.71	intracellular organelle part
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0043234	0.64	protein complex
GO:0005634	0.64	nucleus
GO:0043232	0.50	intracellular non-membrane-bounded organelle

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	1jqiA	0.436	5.29	0.055	0.785	1.3.99.2	NA
2	0.060	2ix6E	0.429	4.82	0.040	0.756	1.3.3.6	NA
3	0.060	1ui7A	0.431	4.87	0.048	0.756	1.4.3.21	NA
4	0.060	2p3gX	0.398	4.99	0.039	0.689	2.7.11.1	NA
5	0.060	1av4A	0.428	4.90	0.048	0.756	1.4.3.21 1.4.3.6	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:

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	1j1cA	0.439	4.70	0.060	0.704	0.23	ADP	complex1.pdb.gz	8,27,28,29,34,38,40
2	0.01	3i4bB	0.442	4.51	0.068	0.696	0.26	Z48	complex2.pdb.gz	8,10,22,24,126,129
3	0.01	1j1cB	0.444	4.57	0.060	0.704	0.29	ADP	complex3.pdb.gz	11,25,26,28,31,40
4	0.01	1i09A	0.436	4.35	0.044	0.667	0.21	PO4	complex4.pdb.gz	10,27,39
5	0.01	3e7eA	0.442	4.25	0.068	0.674	0.24	ATP	complex5.pdb.gz	8,29,128,129,131
6	0.01	3q3bA	0.441	4.56	0.052	0.689	0.19	55E	complex6.pdb.gz	26,29,96,97,98
7	0.01	1q3dB	0.436	4.52	0.044	0.681	0.26	STU	complex7.pdb.gz	8,28,40
8	0.01	3f88B	0.440	4.72	0.068	0.711	0.27	3HT	complex8.pdb.gz	7,26,27,28,29,31,34,39
9	0.01	2ix5A	0.441	4.83	0.041	0.756	0.35	FAD	complex9.pdb.gz	7,26,31,64,65
10	0.01	1gngB	0.430	4.70	0.060	0.696	0.23	III	complex10.pdb.gz	5,9,59

	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.