D-I-TASSER P48723

D-I-TASSER results for P48723

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

Summary of the Protein

Uniprot ID: P48723
Protein Name: Heat shock 70 kDa protein 13
Gene Name: HSPA13

Input Sequence in FASTA format

>P48723 (471 residues)
MAREMTILGSAVLTLLLAGYLAQQYLPLPTPKVIGIDLGTTYCSVGVFFPGTGKVKVIPD
ENGHISIPSMVSFTDNDVYVGYESVELADSNPQNTIYDAKRFIGKIFTAEELEAEIGRYP
FKVLNKNGMVEFSVTSNETITVSPEYVGSRLLLKLKEMAEAYLGMPVANAVISVPAEFDL
KQRNSTIEAANLAGLKILRVINEPTAAAMAYGLHKADVFHVLVIDLGGGTLDVSLLNKQG
GMFLTRAMSGNNKLGGQDFNQRLLQYLYKQIYQTYGFVPSRKEEIHRLRQAVEMVKLNLT
LHQSAQLSVLLTVEEQDRKEPHSSDTELPKDKLSSADDHRVNSGFGRGLSDKKSGESQVL
FETEISRKLFDTLNEDLFQKILVPIQQVLKEGHLEKTEIDEVVLVGGSTRIPRIRQVIQE
FFGKDPNTSVDPDLAVVTGVAIQAGIDGGSWPLQVSALEIPNKHLQKTNFN

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P48723-D1	1-202	202		MAREMTILGSAVLTLLLAGYLAQQYLPLPTPKVIGIDLGTTYCSVGVFFPGTGKVKVIPDENGHISIPSMVSFTDNDVYVGYESVELADSNPQNTIYDAKRFIGKIFTAEELEAEIGRYPFKVLNKNGMVEFSVTSNETITVSPEYVGSRLLLKLKEMAEAYLGMPVANAVISVPAEFDLKQRNSTIEAANLAGLKILRVIN
2	P48723-D2	203-259,366-471	163		EPTAAAMAYGLHKADVFHVLVIDLGGGTLDVSLLNKQGGMFLTRAMSGNNKLGGQDFSRKLFDTLNEDLFQKILVPIQQVLKEGHLEKTEIDEVVLVGGSTRIPRIRQVIQEFFGKDPNTSVDPDLAVVTGVAIQAGIDGGSWPLQVSALEIPNKHLQKTNFN
3	P48723-D3	260-365	106		NQRLLQYLYKQIYQTYGFVPSRKEEIHRLRQAVEMVKLNLTLHQSAQLSVLLTVEEQDRKEPHSSDTELPKDKLSSADDHRVNSGFGRGLSDKKSGESQVLFETEI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.83

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5tkyA	0.78	2.12	0.398	0.817	model1_5tkyA.pdb.gz
2	3c7nA	0.77	2.01	0.232	0.813	model1_3c7nA.pdb.gz
3	5e84A	0.77	2.28	0.387	0.820	model1_5e84A.pdb.gz
4	6gfaA	0.74	1.94	0.294	0.779	model1_6gfaA.pdb.gz
5	4j8fA	0.72	3.17	0.404	0.815	model1_4j8fA.pdb.gz
6	3iucC	0.72	3.04	0.421	0.811	model1_3iucC.pdb.gz
7	1yuwA	0.71	3.27	0.379	0.811	model1_1yuwA.pdb.gz
8	4gniA	0.70	2.86	0.263	0.783	model1_4gniA.pdb.gz
9	5obuA	0.70	2.91	0.346	0.773	model1_5obuA.pdb.gz
10	4kboA	0.70	2.97	0.384	0.786	model1_4kboA.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:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0035639	0.93	purine ribonucleoside triphosphate binding
GO:0032555	0.93	purine ribonucleotide binding
GO:0032550	0.93	purine ribonucleoside binding
GO:0005524	0.92	ATP binding
GO:0051082	0.85	unfolded protein binding
GO:0003824	0.78	catalytic activity
GO:0019899	0.77	enzyme binding
GO:0031625	0.74	ubiquitin protein ligase binding
GO:0016787	0.73	hydrolase activity
GO:0017111	0.72	nucleoside-triphosphatase activity
GO:0016887	0.71	ATPase activity
GO:0031072	0.63	heat shock protein binding
GO:0019904	0.63	protein domain specific binding
GO:0005102	0.62	receptor binding
GO:0055131	0.61	C3HC4-type RING finger domain binding
GO:0001664	0.61	G-protein coupled receptor binding
GO:0042623	0.60	ATPase activity, coupled
GO:0003676	0.54	nucleic acid binding
GO:0003723	0.53	RNA binding
GO:0044183	0.51	protein binding involved in protein folding

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	0.87	cellular process
GO:0050896	0.83	response to stimulus
GO:0006950	0.81	response to stress
GO:0044699	0.79	single-organism process
GO:0008152	0.78	metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044238	0.71	primary metabolic process
GO:0044237	0.71	cellular metabolic process
GO:0044763	0.69	single-organism cellular process
GO:0009628	0.69	response to abiotic stimulus
GO:0009408	0.66	response to heat
GO:0034641	0.65	cellular nitrogen compound metabolic process
GO:0044710	0.64	single-organism metabolic process
GO:0044281	0.62	small molecule metabolic process
GO:1901564	0.61	organonitrogen compound metabolic process
GO:0065007	0.61	biological regulation
GO:0006139	0.61	nucleobase-containing compound metabolic process
GO:0006457	0.60	protein folding
GO:0050789	0.59	regulation of biological process
GO:0050794	0.58	regulation of cellular process
GO:0006796	0.56	phosphate-containing compound metabolic process
GO:1901135	0.55	carbohydrate derivative metabolic process
GO:0055086	0.55	nucleobase-containing small molecule metabolic process
GO:0019637	0.55	organophosphate metabolic process
GO:0061077	0.54	chaperone-mediated protein folding
GO:0046034	0.54	ATP metabolic process
GO:0006458	0.54	'de novo' protein folding
GO:0051085	0.53	chaperone mediated protein folding requiring cofactor
GO:0042221	0.50	response to chemical

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:0044424	0.97	intracellular part
GO:0043226	0.81	organelle
GO:0044444	0.78	cytoplasmic part
GO:0043229	0.76	intracellular organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0044446	0.54	intracellular organelle 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	0.067	2e2oA	0.473	3.91	0.104	0.567	2.7.1.1	NA
2	0.066	2ch5A	0.490	4.61	0.099	0.620	2.7.1.59	172
3	0.060	3gbtA	0.466	5.12	0.108	0.622	2.7.1.12	NA
4	0.060	3flcX	0.474	6.43	0.112	0.705	2.7.1.30	39,41
5	0.060	3cjcA	0.552	4.11	0.119	0.667	3.1.21.1	68,80,103

	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	0.62	3iucA	0.711	2.84	0.418	0.792	1.23	ADP	complex1.pdb.gz	39,40,41,42,227,228,256,293,296,297,300
2	0.39	3ldpA	0.707	3.00	0.416	0.796	0.84	3P1	complex2.pdb.gz	42,228,256,294,408,409,433
3	0.14	3i33A	0.711	2.77	0.419	0.790	1.14	PO4	complex3.pdb.gz	39,40,100,175,203,230
4	0.06	1dkg2	0.693	3.15	0.366	0.790	0.93	III	complex4.pdb.gz	79,83,86,87,89,90,161,162,163,164

	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.