D-I-TASSER P51160-D3

D-I-TASSER results for P51160-D3

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

Input Sequence in FASTA format

>P51160 (141 residues)
CERYSIGLLDMTKEKEFYDEWPIKLGEVEPYKGPKTPDGREVNFYKIIDYILHGKEEIKV
IPTPPADHWTLISGLPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIV
NKKEDIVGVATFYNRKDGKPF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CERYSIGLLDMTKEKEFYDEWPIKLGEVEPYKGPKTPDGREVNFYKIIDYILHGKEEIKVIPTPPADHWTLISGLPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYNRKDGKPF
Prediction	CCCSSSSSSSCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSSSSHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCSSSSCCCCCCCCCCCCCCCCCCCCCSSCSSSSSSSSCCCCCSSSSSSSSSCCCCCCC
Confidence	960588877367540121012210124444457888776536777542122224554311578710001158870234432398697376323988675542010259865227888546699979999996866899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CERYSIGLLDMTKEKEFYDEWPIKLGEVEPYKGPKTPDGREVNFYKIIDYILHGKEEIKVIPTPPADHWTLISGLPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYNRKDGKPF
Prediction	653000000234655622542324237245464463663442302421432364565253354465241324421012005344303052027364153745326624132210000002157440000000002575658
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSSSSSSCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSSSSHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCSSSSCCCCCCCCCCCCCCCCCCCCCSSCSSSSSSSSCCCCCSSSSSSSSSCCCCCCC
CERYSIGLLDMTKEKEFYDEWPIKLGEVEPYKGPKTPDGREVNFYKIIDYILHGKEEIKVIPTPPADHWTLISGLPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYNRKDGKPF

3lfvA1

0.27

0.20

6.11

1.00

DEthreader

ADRYSLFLVCENDKFLISR-L----------EGST-----LEEV------------------SNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRF--NAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGGTF

6x88A2

0.96

0.79

22.28

1.44

SPARKS-K

CERYSVGLLDMTPD------------------------GREVNFYKIIDYILHGKEEIKVIPTPPADHWCLISGLPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEEIVGVATFYNRKDGKPF

1ykdA

0.16

0.12

3.99

0.76

MapAlign

ADRSTLWLIDRDRHELWT------------------------------KITQDNGSTK-------ELRVPIGKGFAGIVAASGQKLNIFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKCFQASF

3trcA

0.14

0.10

3.39

0.67

CEthreader

ADACSLFICDDVHGEYVLATQGLNSKQ------------------------------------VGKLRLKFGEGLIGLVGEREEPINLADAPLHPAYKHRPELGE---EDYHGFLGIPIIEQ-GELLGILVIQQ-LESHHF

6mzbB

0.74

0.67

19.10

1.25

MUSTER

CDRYSVGLLDMTKEKEFFDVWPVLMGEAQAYSGPRTPDGREILFYKV-----------KVIPSPPADHWALASGLPTYVAESGFICNIMNAPADEMFN--FQEGPDSGWIVKNVLSMPIVNKKEEIVGVATFYNRKDGKPF

3ibjA

0.28

0.19

5.86

2.02

HHsearch

AEICSVFLLDQ--NELVAKVFDGGVVDD----------------------------------ESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLF--------STGFRTRNILCFPIKNENQEVIGVAELVNKINGPWF

2k31A

0.27

0.21

6.54

1.33

FFAS-3D

ADRYSLFLVCEDSSKD------------------------KFLISRLFDVAEGSTLE---EASNNCIRLEWNKGIVGHVAAFGEPLNIKDAYEDPRFN--AEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNTF

6x88A1

0.15

0.12

4.04

0.82

EigenThreader

LARCSMFICRSGIPEVATRLLNVT--------PTSK------------------FEDNLV-NPDKETVFPLDIGIAGWVAHTKKFFNIPDVKKNNHF--SDYLDKKTGYTTVNMMAIPITQK--EVLAVVMALKLNASEFS

2zmfA

0.25

0.19

5.95

1.33

CNFpred

ADRCALFQVDHKNKELYSDLFDI-----------GEEKEGKPVFKKTK-----------------EIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNR--EVDLYTGYTTRNILCMPIVSR-GSVIGVVQMVNKISGSAF

3lfvA

0.27

0.20

6.11

1.00

DEthreader

ADRYSLFLVCENDKFLISR-L----------EGST-----LEEV------------------SNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRF--NAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGGTF

(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	0.7018

(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	7jsnA	0.67	1.84	0.250	0.766	model1_7jsnA.pdb.gz
2	2zmfA	0.67	2.06	0.215	0.759	model1_2zmfA.pdb.gz
3	6x88A1	0.67	1.85	0.159	0.759	model1_6x88A1.pdb.gz
4	6mzbB	0.66	1.88	0.215	0.759	model1_6mzbB.pdb.gz
5	3lfvA	0.66	2.12	0.248	0.745	model1_3lfvA.pdb.gz
6	1ykdA2	0.64	2.25	0.183	0.738	model1_1ykdA2.pdb.gz
7	2k31A	0.62	2.41	0.243	0.759	model1_2k31A.pdb.gz
8	3trcA	0.60	2.38	0.140	0.702	model1_3trcA.pdb.gz
9	3ibjA	0.59	1.95	0.280	0.660	model1_3ibjA.pdb.gz
10	3mmhA	0.57	2.47	0.108	0.660	model1_3mmhA.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:0004114	1.00	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0097367	0.71	carbohydrate derivative binding
GO:0017076	0.71	purine nucleotide binding
GO:0032555	0.70	purine ribonucleotide binding
GO:0032561	0.65	guanyl ribonucleotide binding
GO:0030551	0.62	cyclic nucleotide binding
GO:0030553	0.60	cGMP binding
GO:0047555	0.55	3',5'-cyclic-GMP phosphodiesterase activity
GO:0004118	0.52	cGMP-stimulated cyclic-nucleotide phosphodiesterase 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:0044699	0.84	single-organism process
GO:0009987	0.83	cellular process
GO:0065007	0.78	biological regulation
GO:0050794	0.77	regulation of cellular process
GO:0032501	0.76	multicellular organismal process
GO:0007165	0.70	signal transduction
GO:0008152	0.68	metabolic process
GO:0071704	0.66	organic substance metabolic process
GO:0044238	0.66	primary metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0044763	0.64	single-organism cellular process
GO:0034641	0.64	cellular nitrogen compound metabolic process
GO:0006139	0.63	nucleobase-containing compound metabolic process
GO:0050896	0.61	response to stimulus
GO:0044710	0.56	single-organism metabolic process
GO:0044281	0.55	small molecule metabolic process
GO:0032502	0.55	developmental process
GO:1901564	0.53	organonitrogen compound metabolic process
GO:0055086	0.53	nucleobase-containing small molecule metabolic process
GO:0019637	0.53	organophosphate metabolic process
GO:0006796	0.53	phosphate-containing compound metabolic process
GO:0009150	0.52	purine ribonucleotide metabolic process
GO:0009628	0.51	response to abiotic stimulus
GO:0009605	0.50	response to external stimulus
GO:0003008	0.50	system 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:0016020	0.92	membrane
GO:0044424	0.78	intracellular part
GO:0005886	0.73	plasma membrane
GO:0097458	0.68	neuron part
GO:0043226	0.63	organelle
GO:0044425	0.61	membrane part
GO:0044422	0.59	organelle part
GO:0044444	0.57	cytoplasmic part
GO:0044459	0.56	plasma membrane part
GO:0043229	0.56	intracellular organelle
GO:0098590	0.55	plasma membrane region
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0005634	0.52	nucleus

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	3dbaB	0.664	1.84	0.159	0.759	3.1.4.35	84
2	0.067	2zmfB	0.664	2.28	0.215	0.759	3.1.4.17	80,83,90
3	0.060	1iqqA	0.426	5.47	0.058	0.759	3.1.27.1	124
4	0.060	3by9B	0.460	3.14	0.071	0.582	2.7.13.3	76,78
5	0.060	3kvnX	0.444	5.04	0.031	0.808	3.1.1.1	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	0.24	1mc0A	0.649	1.66	0.294	0.723	0.85	PCG	complex1.pdb.gz	3,4,5,74,75,97,103,104,109,111,114,131
2	0.21	2k31A	0.618	2.41	0.243	0.759	1.07	35G	complex2.pdb.gz	5,7,21,22,67,75,76,97,133
3	0.02	2o99B	0.486	3.12	0.084	0.638	0.87	GOA	complex3.pdb.gz	78,79,80,85,117,128,130

	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.