D-I-TASSER P04626-D4

D-I-TASSER results for P04626-D4

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

Input Sequence in FASTA format

>P04626 (128 residues)
VAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAF
GGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPE
YLGLDVPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
Confidence	98888789832358666688997634588777888876656876678777888877777777678911158889888877888887867889123036788888988876787466683341668899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV
Prediction	74446464355414464564545543654334445564436456446546554464444454335124214665343444465743441232241345513775546532643321412422535568
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC
VAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV

1jb0D

0.08

0.05

2.15

0.39

CEthreader

------------------------------------------TTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVMREGENLVYFARKEQCLALAAQQLRPRKINDYKIYRIFPVLIHPKDGV

3kzsA1

0.03

1.84

0.65

EigenThreader

DGYNFKNINQKGVYGYWDHDYIIRTAAKKGLEPNIIWFIDIRGDVKTAEWEALATSIKAIDAPWLDFNFQSGHRRYGQRFIEENTEEDNVIDGEPIYEEIPHGLHDENELLWKYAYWSVFAGSFHNSI

1jhnA

0.18

0.16

5.35

0.47

FFAS-3D

--PEDQKPKPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPKCESAPGC-------GVWQRPMIDNPNYKGKWKPPMIDNPNGIWKPRKIPNPDFFEDLEP-

6emkG

0.06

2.68

1.03

SPARKS-K

VYLIQLGHDKH-ELIKTFKGNTCVHLALMKGHEQTLHLLLQQFPRFINHRGENGRAPIHIACMNDYYQLLIGVGADLWVMDTNGDTPLHVGSISCMKMLLNEGDNVRDKGNWKPVAEVGNIYSKVLKE

4ufcA

0.09

0.02

0.90

0.27

CNFpred

--------------------------------------------------------------------------------------------AQFYMDFLV--EHPVYKWLVVSPSVSPEHGPITAGC

1a87A

0.05

0.04

1.84

0.83

DEthreader

-------------KG-EKEKNEKE------------ALLASEVMGDGGVKNVAKEVANDIKNFHGNIRSYAMLLV-KIVNAWVEKISLEVAISLFGAVLSLPISLALGVIMTIYLSSFI-DARVNIIV

4nn5B

0.03

0.02

1.56

0.66

MapAlign

------LEFQICGALLRVKCLTLNKLQDIYFIKTSEFLLIGSSNICVKLGQKNLTCKNMAINTIVKAEAPSDLKVVYRKEANDFLVTFNAPVKHDVAYRPARGESKAMYEIKVRSIPHGFWSEWS---

2nbiA2

0.17

0.13

4.38

0.80

MUSTER

-QPSSQPTGPQ--PSSQPSECADVLELCPYDTCFLPFDDSSRPPDTDPSVNRPDCDKLSTAIDFTCPTCCPTQRPDNPMFSPSPDGSPPVCSP---TMMPSPLPSPTE--------------------

2pffB

0.17

0.16

5.42

0.93

HHsearch

MLSISNLTVQDYVNKTNSKQVEISLVNGAKNLVSPPQSTLRKAKAPSGLSERKLKFSNRFLPVASHSHLLVPASDLIVKNNVSFNA-KDIQIPVYDTFDGSDLRVLVDCIIRLPVKHILDFGGLGVLV

2ce8A2

0.06

0.05

2.38

0.39

CEthreader

-----YIRSCKLLPDGCTLIVGGEASTLSIWDLAAPTPRIKAELTSSAPACYALAISPDSKVCFSCCSDGNIAVWDLHNQTLVRQFQGHTDGASCIDIS-------NDGTKLWTGGLDNTVRSWDLRE

(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	0.5091

(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	6vm1A	0.44	4.44	0.058	0.766	model1_6vm1A.pdb.gz
2	2y8nA	0.43	4.55	0.103	0.734	model1_2y8nA.pdb.gz
3	5i2aA1	0.43	4.39	0.071	0.727	model1_5i2aA1.pdb.gz
4	3j9tB	0.43	4.39	0.087	0.758	model1_3j9tB.pdb.gz
5	6q45A2	0.43	4.53	0.096	0.766	model1_6q45A2.pdb.gz
6	5bn3B	0.43	4.50	0.067	0.766	model1_5bn3B.pdb.gz
7	6radA	0.43	4.56	0.076	0.773	model1_6radA.pdb.gz
8	5a0uA	0.43	4.48	0.051	0.734	model1_5a0uA.pdb.gz
9	1r8wA	0.43	4.41	0.061	0.727	model1_1r8wA.pdb.gz
10	5dn6A2	0.43	4.49	0.048	0.766	model1_5dn6A2.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:0001042	1.00	RNA polymerase I core binding
GO:0003824	0.66	catalytic activity
GO:0016740	0.63	transferase activity
GO:0046983	0.62	protein dimerization activity
GO:0016773	0.62	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.62	kinase activity
GO:0046982	0.61	protein heterodimerization activity
GO:0004713	0.61	protein tyrosine kinase 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:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0048518	0.87	positive regulation of biological process
GO:0080090	0.86	regulation of primary metabolic process
GO:0050896	0.86	response to stimulus
GO:0048583	0.86	regulation of response to stimulus
GO:0031325	0.86	positive regulation of cellular metabolic process
GO:0010604	0.86	positive regulation of macromolecule metabolic process
GO:0070887	0.85	cellular response to chemical stimulus
GO:0070372	0.85	regulation of ERK1 and ERK2 cascade
GO:0051130	0.85	positive regulation of cellular component organization
GO:0051049	0.85	regulation of transport
GO:0045893	0.85	positive regulation of transcription, DNA-templated
GO:0032270	0.85	positive regulation of cellular protein metabolic process
GO:0010033	0.85	response to organic substance
GO:0009719	0.85	response to endogenous stimulus
GO:0006417	0.85	regulation of translation
GO:0090314	0.84	positive regulation of protein targeting to membrane
GO:0071364	0.84	cellular response to epidermal growth factor stimulus
GO:0045945	0.84	positive regulation of transcription from RNA polymerase III promoter
GO:0045943	0.84	positive regulation of transcription from RNA polymerase I promoter
GO:0045727	0.84	positive regulation of translation
GO:0032886	0.84	regulation of microtubule-based process
GO:0030307	0.84	positive regulation of cell growth
GO:0044699	0.76	single-organism process
GO:0044763	0.72	single-organism cellular process
GO:0008152	0.60	metabolic process
GO:0071704	0.58	organic substance metabolic process
GO:0044238	0.58	primary metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0043170	0.57	macromolecule metabolic process
GO:0044260	0.56	cellular macromolecule metabolic process
GO:0048584	0.53	positive regulation of response to stimulus
GO:0044267	0.53	cellular protein metabolic process
GO:1902533	0.52	positive regulation of intracellular signal transduction
GO:0042127	0.52	regulation of cell proliferation
GO:0032502	0.52	developmental process
GO:0006950	0.52	response to stress
GO:0006796	0.52	phosphate-containing compound metabolic process
GO:0006464	0.52	cellular protein modification process
GO:0001934	0.52	positive regulation of protein phosphorylation
GO:0046777	0.51	protein autophosphorylation
GO:0044767	0.51	single-organism developmental process
GO:0043410	0.51	positive regulation of MAPK cascade
GO:0009611	0.51	response to wounding
GO:0008284	0.51	positive regulation of cell proliferation
GO:0048856	0.50	anatomical structure development

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:0005886	1.00	plasma membrane
GO:0044424	0.94	intracellular part
GO:0043226	0.90	organelle
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0005634	0.88	nucleus
GO:0005737	0.61	cytoplasm
GO:0044444	0.57	cytoplasmic part

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	1h16A	0.395	4.86	0.028	0.727	2.3.1.54	NA
2	0.060	3i4zA	0.405	4.82	0.036	0.719	2.5.1.34	NA
3	0.060	2gblA	0.409	4.94	0.029	0.750	2.7.11.1	NA
4	0.060	1c7gA	0.413	4.47	0.016	0.719	4.1.99.2	NA
5	0.060	1tplA	0.329	5.42	0.035	0.641	4.1.99.2	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:

Click to view	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	3kqzL	0.328	5.20	0.024	0.641	0.22	CO3	complex1.pdb.gz	49,50,53,98
	2	0.01	1tf7F	0.339	4.78	0.058	0.625	0.20	ATP	complex2.pdb.gz	50,51,52,53,54,55,96,112,113

	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.