D-I-TASSER P20073-D1

D-I-TASSER results for P20073-D1

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

Input Sequence in FASTA format

>P20073 (169 residues)
MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPYPSGFPPMGGGAYPQVPSSGYPGAGGY
PAPGGYPAPGGYPGAPQPGGAPSYPGVPPGQGFGVPPGGAGFSGYPQPPSQSYGGGPAQV
PLPGGFPGGQMPSQYPGGQPTYPSQINTDSFSSYPVFSPVSLDYSSEPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPYPSGFPPMGGGAYPQVPSSGYPGAGGYPAPGGYPAPGGYPGAPQPGGAPSYPGVPPGQGFGVPPGGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTYPSQINTDSFSSYPVFSPVSLDYSSEPA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9989989999999999899998999999999999999999999888999989999999999999999999989999999999999999999999999999989989999999899999899999999998999999998999988888888888888987888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPYPSGFPPMGGGAYPQVPSSGYPGAGGYPAPGGYPAPGGYPGAPQPGGAPSYPGVPPGQGFGVPPGGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTYPSQINTDSFSSYPVFSPVSLDYSSEPA
Prediction	8744633463434442213446644324444434444334444444344444443444343446343445443443434444433243344444434444444242433445444434443444523454424443444333244453643453343423426366668
	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                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPYPSGFPPMGGGAYPQVPSSGYPGAGGYPAPGGYPAPGGYPGAPQPGGAPSYPGVPPGQGFGVPPGGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQPTYPSQINTDSFSSYPVFSPVSLDYSSEPA

2h1tA

0.09

0.08

2.96

0.49

CEthreader

WEALRLEDDQAESQLRAPDERSGLPYQLDYRLRWDADWHLRESETGVRKLHLLADGRGHWQDGDGEALPAFDGCLDIDIWLGLADGQRAEIRALYIEAPALEPRSRQAYTRLDASHYLYENLEGSAFKAVLLVDEQGLVIDYPGLFQRL--------------------

5wtlA

0.05

2.44

0.68

EigenThreader

TDKDGIPDNKDACPEVPGLKEFNGCPDTDGDGIACPQVKGPKEFNGCPDTDGDGIPDKDDACPEVAGPKEFNGCPDTDGDGIPDKDDKCPDVAGPAENGGCPWPDTDGDGVLDKDDLCPEVAGPASNKGCPEPDLNQYAKTILIINVLKKYPNSRAVKVYLIQGGIDAG

6edoA

0.25

0.22

6.99

0.61

FFAS-3D

MGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--------------

7jjvA

0.21

0.15

4.89

1.62

SPARKS-K

----------------------MQCDGLDGADGTSNG---QAGASGLAGGPNCNGGKGG----KGAPGVGTAGGAGGVGGAGGTGNTNGGAG-GSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGT-PAGSAGSPGQTTVL-------------

2mqsB

0.25

0.05

1.65

0.01

CNFpred

-------------------------------------------------------------------------GPMGPMGPMGPQGIAGQRGVVGLMGPMGPMGPMGPM------------------------------------------------------------

6kidA

0.04

0.03

1.60

0.67

DEthreader

-YMNGR-LHHTFSLKCELFPFGLHCGPICKHDRQTGEGVGPQ----------QGNGVALCDQWYLDYGWLQEHA------CSRTY-----G--LGTHLPWDE----SDSTIYMAFYA--RVSGKVPNH--GHL-MSKNFLTAMLALDAGKELKTGFAAISQLVLMVKFE

5hy7A

0.07

2.67

0.87

MapAlign

QQMGEEGLIQIHPKGIRHIVQGRVNEWPAPQHRSIVAATTNENQVVVPEGLRRSSFLAVGCDDCTVRILSAAPSSLLIMSMEDSTGGTTLYLHIGLHSGVYLRTVPTKLFQVTVQNQTCVLALSSRPWLGYTAPITRNFVMTPLSYTELGYTWS---------------

1kqgA

0.13

4.51

0.75

MUSTER

GVLIAKKGQLLSSFAHLRDDGTTASSCWIYTGSWTEQGNQMANRDNSDPSGLGNTLGWAWAWPLNRRVLYNRASA-DINGKPWDPKRMLIQWNGSKWTGNDIPDFGNAAPGTPTGPFIMQPAINKMAEGPFPEHYEPIETPLGTNPLHPNVVSNPVVRLYEQDALRMGK

6ty2A

0.27

0.04

1.27

0.56

HHsearch

-----------------------------------------------------------------------------------------------------------------------------------------------DEIDREHQERNSEGRPASLVYLSRDA

1kitA1

0.05

2.24

0.44

CEthreader

NTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASF--YFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQ----

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4569

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5jtaA	0.45	4.92	0.049	0.751	model1_5jtaA.pdb.gz
2	5zvs2	0.44	4.91	0.065	0.728	model1_5zvs2.pdb.gz
3	2cse1	0.44	5.12	0.039	0.757	model1_2cse1.pdb.gz
4	1b1xA	0.44	5.41	0.025	0.799	model1_1b1xA.pdb.gz
5	6fopA1	0.43	5.51	0.034	0.805	model1_6fopA1.pdb.gz
6	2zwaB	0.43	5.48	0.062	0.787	model1_2zwaB.pdb.gz
7	3dpuA	0.43	5.64	0.019	0.811	model1_3dpuA.pdb.gz
8	1llwA	0.43	5.04	0.096	0.746	model1_1llwA.pdb.gz
9	3ba6A	0.43	5.64	0.060	0.811	model1_3ba6A.pdb.gz
10	6hluA	0.43	5.46	0.026	0.799	model1_6hluA.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:0048306	0.63	calcium-dependent protein binding
GO:0097159	0.52	organic cyclic compound binding
GO:1901363	0.51	heterocyclic 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:0065007	0.83	biological regulation
GO:0044699	0.82	single-organism process
GO:0050789	0.81	regulation of biological process
GO:0009987	0.71	cellular process
GO:0050794	0.67	regulation of cellular 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:0016020	1.00	membrane
GO:0044424	0.81	intracellular part
GO:0044444	0.71	cytoplasmic part
GO:0005886	0.66	plasma membrane
GO:0044446	0.63	intracellular organelle part
GO:0031090	0.57	organelle membrane
GO:0098588	0.56	bounding membrane of organelle
GO:0098805	0.55	whole membrane
GO:0043226	0.54	organelle
GO:0043229	0.51	intracellular organelle
GO:0043227	0.51	membrane-bounded organelle
GO:0030659	0.51	cytoplasmic vesicle membrane
GO:0042584	0.50	chromaffin granule membrane

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

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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	1jxaA	0.411	5.51	0.053	0.763	2.6.1.16	NA
2	0.060	1llwA	0.432	5.04	0.096	0.746	1.4.7.1	NA
3	0.060	3hinA	0.406	5.68	0.052	0.757	4.2.1.55	65
4	0.060	1cb7B	0.400	5.39	0.043	0.734	5.4.99.1	NA
5	0.060	1mosA	0.304	6.19	0.044	0.621	2.6.1.16	34

	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

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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	0.01	1fckA	0.433	5.49	0.013	0.799	0.41	CO3	complex1.pdb.gz	67,68,69
2	0.01	3kj7A	0.398	5.46	0.032	0.746	0.43	CTR	complex2.pdb.gz	65,66,96
3	0.01	2qjeA	0.399	5.38	0.039	0.734	0.42	CO3	complex3.pdb.gz	92,107,108,113,114
4	0.01	2dojA	0.393	5.41	0.026	0.734	0.57	UUU	complex4.pdb.gz	65,71,94,100,101
5	0.01	3mjnA	0.406	5.45	0.045	0.734	0.45	RNP	complex5.pdb.gz	61,65,66
6	0.01	2ds9A	0.406	5.48	0.045	0.740	0.42	MAN	complex6.pdb.gz	16,60,61

	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.