D-I-TASSER O60895-D1

D-I-TASSER results for O60895-D1

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

Input Sequence in FASTA format

>O60895 (175 residues)
MASLRVERAGGPRLPRTRVGRPAALRLLLLLGAVLNPHEALAQPLPTTGTPGSEGGTVKN
YETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERII
FETHQIHFANCSLVQPTFSDPPEDVLLAMIIAPICLIPFLITLVVWRSKDSEAQA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASLRVERAGGPRLPRTRVGRPAALRLLLLLGAVLNPHEALAQPLPTTGTPGSEGGTVKNYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQPTFSDPPEDVLLAMIIAPICLIPFLITLVVWRSKDSEAQA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCCCC
Confidence	9976556789998885337897235789886332287201134578776543335638899999999999999999862675557388999899999999999977189999788999999999999536999998888997137888999999999999987302325765579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASLRVERAGGPRLPRTRVGRPAALRLLLLLGAVLNPHEALAQPLPTTGTPGSEGGTVKNYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQPTFSDPPEDVLLAMIIAPICLIPFLITLVVWRSKDSEAQA
Prediction	7561456447444344563753410202311122243442224323353134452343630342044015403530551655114165025205302400441054250402242044102300331054053765436222630000002313331332210000104357558
	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

CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCCCC
MASLRVERAGGPRLPRTRVGRPAALRLLLLLGAVLNPHEALAQPLPTTGTPGSEGGTVKNYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAELFDLGFPNPLAERIIFETHQIHFANCSLVQPTFSDPPEDVLLAMIIAPICLIPFLITLVVWRSKDSEAQA

6qp6A

0.06

2.49

1.00

DEthreader

-----PRSIYKKQPFAWLGYYTMLLLAAVGVACFLYGYLDQDCSKEVGGILMPCPWITTPQMATSITASIISFIIIMINT-E-MFLFQFVNYYSSCFYIAFKGKVEECDPGGCLLELTTQLTIIMGGKAINN-ELYEYEMIWMQGIAILAVVTNAMIAFTSD-IPTRDFRNPHEY

6e3yE

0.29

0.19

5.74

1.86

SPARKS-K

--------------------------------------------------------EANYGALLRELCLTQFQVDMEAVGTLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSILYPFIVVPITVTLLVTALVVWQSKR-----

6lfpA1

0.08

0.07

2.96

0.79

MapAlign

DVIQKGISVVGDLLGVVGFPFGGALVSFYTNFLNTIWPSEDPEALMDQKIADYAKNKALAELQGLQNNVEDYVSALSSWQKNSRNPHSIRELFSQAESHFRNSMPSFLFLTTYAQAANTHLFLLKDAQIYGEEWGYEKEDI-AEFYKRQLKLTQEYTDHCVKWYNVGL-------

1dlcA1

0.08

3.16

0.66

CEthreader

VIQKGISVVGDLLGVVGFPFGGALVSFYTNFLNTIWPSEDPWKAFMEQVEALMDQKIADYAKNKALAELQGLQNNVEDYVSALSSRELFSQAESHFRNSMPSFAIEVLFLTTYAQAANTHLFLLKDAQIYGEEWGYEKEDIAEFYKRQLKLTQEYTDHCVKWYNVGLDKLRGSSY

6e3yE

0.30

0.19

5.90

1.96

MUSTER

--------------------------------------------------------EANYGALLRELCLTQFQVDMEAVETLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSILYPFIVVPITVTLLVTALVVWQSKR-----

6e3yE

0.32

0.21

6.20

5.59

HHsearch

---------------------------------------------------------EANYGALLELCLTQFQVDMEAVETLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSILYPFIVVPITVTLLVTALVVWQSKR-----

6e3yE

0.31

0.20

6.05

2.14

FFAS-3D

---------------------------------------------------------EANYGALLRLCLTQFQVDMEAVGELWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSILYPFIVVPITVTLLVTALVVWQSKR-----

6lfpA1

0.08

0.07

2.98

0.72

EigenThreader

IQKGISVVGDLLGVVGFPFGGALVSFYTNFLNTIWPSEDPWKAFMEQVEALMDQKIAKNKALAELQGLQNNVEDYVSALSSWQKNRELFSQAESHFRNSMPSFAYEVLFLTTYAQAANTHLFLLKDAQIYGE-----EWGYEKEDIAEFYKRQLKLTQEYTDHCVKWYNVGLDKL

6e3yE

0.30

0.19

5.73

1.10

CNFpred

-----------------------------------------------------------YGALLRELCLTQFQVDMEAVGTLWCDWGRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSILYPFIVVPITVTLLVTALVVWQSKR-----

6qp6A2

0.04

2.04

1.00

DEthreader

-----FRLYRELIRYGE-KIGIYFAWLGYYTQMLLLAAVGVAFLYQCESSLTPQMASITASIISFIIIMILNTIYEKVAI-QYELTMKMFLFQFVYYSSCFYIAFKGCCLLTTLTIIMGGKAWNNEYEYLEDLRMVPEKAQDIGAWQPIMQGIAILAVVTNAMIIAFSDMIPVDF

(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	0.6952

(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	4a01A	0.58	4.86	0.029	0.926	model1_4a01A.pdb.gz
2	5gupl	0.58	4.90	0.055	0.931	model1_5gupl.pdb.gz
3	6y795	0.58	5.09	0.053	0.954	model1_6y795.pdb.gz
4	6tjvD	0.57	4.59	0.084	0.920	model1_6tjvD.pdb.gz
5	3rkoM	0.57	4.82	0.066	0.937	model1_3rkoM.pdb.gz
6	7lkpA3	0.57	4.10	0.038	0.829	model1_7lkpA3.pdb.gz
7	6nbqD	0.57	4.87	0.065	0.954	model1_6nbqD.pdb.gz
8	5xtcl	0.57	4.91	0.042	0.926	model1_5xtcl.pdb.gz
9	3rkoL	0.57	4.92	0.065	0.931	model1_3rkoL.pdb.gz
10	5o31L	0.57	5.25	0.036	0.943	model1_5o31L.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:0004872	1.00	receptor activity
GO:0038023	0.99	signaling receptor activity
GO:0015026	0.96	coreceptor activity
GO:0008565	0.83	protein transporter 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:0009987	1.00	cellular process
GO:0050794	0.99	regulation of cellular process
GO:0048518	0.98	positive regulation of biological process
GO:0044699	0.96	single-organism process
GO:0071310	0.95	cellular response to organic substance
GO:0044763	0.95	single-organism cellular process
GO:0016043	0.93	cellular component organization
GO:0044237	0.91	cellular metabolic process
GO:0043170	0.91	macromolecule metabolic process
GO:0006810	0.91	transport
GO:0031623	0.90	receptor internalization
GO:0001525	0.90	angiogenesis
GO:0048523	0.89	negative regulation of cellular process
GO:0032501	0.88	multicellular organismal process
GO:0003008	0.87	system process
GO:0051094	0.86	positive regulation of developmental process
GO:0043116	0.86	negative regulation of vascular permeability
GO:0022603	0.86	regulation of anatomical structure morphogenesis
GO:2000352	0.85	negative regulation of endothelial cell apoptotic process
GO:0097084	0.85	vascular smooth muscle cell development
GO:0070831	0.85	basement membrane assembly
GO:0045766	0.85	positive regulation of angiogenesis
GO:0035924	0.85	cellular response to vascular endothelial growth factor stimulus
GO:0008217	0.85	regulation of blood pressure
GO:0007507	0.85	heart development
GO:0002040	0.85	sprouting angiogenesis
GO:0009893	0.82	positive regulation of metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0015031	0.81	protein transport
GO:0072659	0.80	protein localization to plasma membrane
GO:0010604	0.80	positive regulation of macromolecule metabolic process
GO:0006816	0.80	calcium ion transport
GO:0001570	0.80	vasculogenesis
GO:0010468	0.77	regulation of gene expression
GO:0044238	0.75	primary metabolic process
GO:1901576	0.73	organic substance biosynthetic process
GO:0044711	0.73	single-organism biosynthetic process
GO:0044281	0.73	small molecule metabolic process
GO:0010628	0.73	positive regulation of gene expression
GO:0006807	0.73	nitrogen compound metabolic process
GO:0070830	0.72	bicellular tight junction assembly
GO:0034333	0.72	adherens junction assembly
GO:0006171	0.72	cAMP biosynthetic 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	0.99	cell part
GO:0005886	0.98	plasma membrane
GO:0043235	0.92	receptor complex
GO:0009986	0.92	cell surface
GO:0044424	0.91	intracellular part
GO:0005737	0.84	cytoplasm

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	1xfkA	0.468	4.59	0.065	0.720	3.5.3.8	NA
2	0.060	1zcjA	0.472	4.07	0.115	0.680	1.1.1.35	NA
3	0.060	1uokA	0.461	4.94	0.081	0.766	3.2.1.10	NA
4	0.060	1hrkA	0.459	4.80	0.021	0.726	4.99.1.1	NA
5	0.060	1z0hB	0.304	6.08	0.038	0.589	3.4.24.69	157

	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	0.01	3rkoN	0.558	5.01	0.089	0.909	0.17	LFA	complex1.pdb.gz	58,59,110,113
2	0.01	2np0A	0.446	5.25	0.098	0.783	0.18	III	complex2.pdb.gz	53,55,56,57,105,120
3	0.01	2fh8A	0.529	5.09	0.078	0.846	0.16	UUU	complex3.pdb.gz	55,57,105
4	0.01	2vu9A	0.274	5.76	0.007	0.509	0.16	UUU	complex4.pdb.gz	57,58,111,115
5	0.01	3fi8A	0.432	5.21	0.040	0.771	0.15	ADP	complex5.pdb.gz	60,109,110,114
6	0.01	2x58B	0.494	4.67	0.100	0.771	0.12	COA	complex6.pdb.gz	103,110,166
7	0.01	3mesB	0.500	5.47	0.049	0.909	0.21	ADP	complex7.pdb.gz	57,113,117,118,119

	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.