D-I-TASSER P35228-D3

D-I-TASSER results for P35228-D3

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

Input Sequence in FASTA format

>P35228 (156 residues)
RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVV
TSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLG
ASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD
Prediction	CCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHCCCCCSSSCCCCCCHHHCCCCCSSSSSSSCCCCCCCCHHHHHHHHHHHCCCCCCCCCCSSSSCCCCCCHHHHCHHHHHHHHHHHHHCCCSSSCCSSSSCCCCCHHHHHHHHHHHHHHHHHHHC
Confidence	987678996899997396079999999999998099968962333997676348749999814799999810999999996145445898289972798753777188999999999819926353353327998179999999999999999849
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD
Prediction	754557734010000112420330053005107562614023176152750572410000000223121143033014104445541541310100022431540140043015105724043015204013544346404500540052027428
	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

CCCCCCCCCSSSSSSCCCHHHHHHHHHHHHHHHCCCCCSSSCCCCCCHHHCCCCCSSSSSSSCCCCCCCCHHHHHHHHHHHCCCCCCCCCCSSSSCCCCCCHHHHCHHHHHHHHHHHHHCCCSSSCCSSSSCCCCCHHHHHHHHHHHHHHHHHHHC
RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

7ddzA

0.21

6.51

1.50

DEthreader

---KNHVAKALIVYGSTTGNTEYTAETIARELAAGYEVDSRDAASVEGGLFEGFDLVLLGCSTWGDIELQDDFIPLFDSLE-ET-GAQGRKVACFGCGDSSWEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPAARDDIVGWAHDVRGAIDHYHQ

4h2dA

0.27

0.26

7.88

1.55

SPARKS-K

-------PQLLVLFGSQTGTAQDVSERLGREARRRLGCRVQALDSYPVVNLINEPLVIFVCATTGQGDPPDNMKNFWRFIFRPSTALCQMDFAVLGLGDSSYAKFNFVAKKLHRRLLQLGGSALLPVCLGDDQLGPDAAVDPWLRDLWDRVLGLYP

3hr4A

1.00

0.96

26.74

0.74

MapAlign

------RVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETF-

3hr4A

1.00

28.00

0.57

CEthreader

RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

3hr4A

1.00

28.00

1.48

MUSTER

RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

1tllA

0.53

0.52

14.99

1.50

HHsearch

----AKRVKATILYATETGKSQAYAKTLCEIFKHAFDAKAMSMEEYDIVHLEHEALVLVVTSTFGNGDPPENGEKFGCALMEMRGPLANVRFSVFGLGSRAYPHFCAFGHAVDTLLEELGGERILKMREGDELCGQEEAFRTWAKKVFKAACDVFC

3hr4A

1.00

28.00

2.33

FFAS-3D

RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

3hr4A

1.00

28.00

0.68

EigenThreader

RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

3hr4A

1.00

28.00

1.58

CNFpred

RKTMASRVRVTILFATETGKSEALAWDLGALFSCAFNPKVVCMDKYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPRFCAFAHDIDQKLSHLGASQLTPMGEGDELSGQEDAFRSWAVQTFKAACETFD

2mt9A

0.18

0.17

5.44

1.50

DEthreader

-------MNMGLFYGSSTCYTEMAAEKIRDIIGP-ELVTLHNLKDDSPKLMEQYDVLILGIPTWDFGEIQEDWEAVWDQLDDL--NLEGKIVALYGLGDQLYGWFLDALGMLHDKLSTKGVKFVGYGLALDENQLSDERIQSWCEQILNEMAEHYA

(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	0.9077

(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	3hr4A	0.96	0.98	1.000	1.000	model1_3hr4A.pdb.gz
2	1tllA	0.93	1.14	0.533	0.974	model1_1tllA.pdb.gz
3	4h2dA	0.89	1.39	0.262	0.955	model1_4h2dA.pdb.gz
4	1ja0A1	0.89	1.63	0.266	0.968	model1_1ja0A1.pdb.gz
5	2bf4A1	0.87	1.77	0.218	0.962	model1_2bf4A1.pdb.gz
6	1ykgA	0.87	1.27	0.319	0.923	model1_1ykgA.pdb.gz
7	4oxxA	0.86	1.66	0.262	0.942	model1_4oxxA.pdb.gz
8	2m6rA	0.82	1.99	0.243	0.923	model1_2m6rA.pdb.gz
9	1bu5A	0.81	1.99	0.232	0.910	model1_1bu5A.pdb.gz
10	2fcrA	0.80	2.17	0.200	0.929	model1_2fcrA.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:0016491	0.97	oxidoreductase activity
GO:0016705	0.52	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0004497	0.52	monooxygenase activity
GO:0004517	0.51	nitric-oxide synthase 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:0065007	0.81	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0007165	0.66	signal transduction
GO:0048518	0.65	positive regulation of biological process
GO:0009987	0.65	cellular process
GO:0035556	0.64	intracellular signal transduction
GO:0065009	0.62	regulation of molecular function
GO:0019222	0.62	regulation of metabolic process
GO:0007263	0.62	nitric oxide mediated signal transduction
GO:0080090	0.61	regulation of primary metabolic process
GO:0050790	0.61	regulation of catalytic activity
GO:0048522	0.61	positive regulation of cellular process
GO:0044699	0.61	single-organism process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0009893	0.61	positive regulation of metabolic process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0065008	0.59	regulation of biological quality
GO:0051239	0.59	regulation of multicellular organismal process
GO:0051171	0.59	regulation of nitrogen compound metabolic process
GO:0031326	0.59	regulation of cellular biosynthetic process
GO:0051339	0.58	regulation of lyase activity
GO:0045935	0.58	positive regulation of nucleobase-containing compound metabolic process
GO:0043085	0.58	positive regulation of catalytic activity
GO:0031328	0.58	positive regulation of cellular biosynthetic process
GO:0019220	0.58	regulation of phosphate metabolic process
GO:1900373	0.57	positive regulation of purine nucleotide biosynthetic process
GO:0051349	0.57	positive regulation of lyase activity
GO:0031281	0.57	positive regulation of cyclase activity
GO:0030804	0.57	positive regulation of cyclic nucleotide biosynthetic process
GO:0008152	0.57	metabolic process
GO:0050896	0.56	response to stimulus
GO:0031284	0.56	positive regulation of guanylate cyclase activity
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0045776	0.55	negative regulation of blood pressure
GO:0032501	0.55	multicellular organismal process
GO:1903522	0.54	regulation of blood circulation
GO:0003008	0.54	system process
GO:0045909	0.53	positive regulation of vasodilation

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	0.96	cell part
GO:0044424	0.93	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0043226	0.74	organelle
GO:0043229	0.73	intracellular organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0005829	0.50	cytosol

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	0.412	1b1cA	0.887	1.68	0.260	0.968	1.6.2.4	22,72,97,107,113
2	0.081	1cb7A	0.582	3.58	0.096	0.795	5.4.99.1	97
3	0.073	1y80A	0.554	3.33	0.068	0.744	2.1.1.13	NA
4	0.067	2yxbA	0.578	3.38	0.083	0.776	5.4.99.2	NA
5	0.067	1bdjA	0.557	3.60	0.058	0.769	2.7.13.3	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	0.98	3hr4C	0.954	1.09	1.000	1.000	2.01	FMN	complex1.pdb.gz	16,17,18,20,21,62,63,64,65,66,67,98,99,102,104,105,106,132,136

	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.