D-I-TASSER P35558-D3

D-I-TASSER results for P35558-D3

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

Input Sequence in FASTA format

>P35558 (190 residues)
FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKIIMHDPFAMRPFFGYNFGK
YLAHWLSMAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWMFNRIDGKASTKL
TPIGYIPKEDALNLKGLGHINMMELFSISKEFWEKEVEDIEKYLEDQVNADLPCEIEREI
LALKQRISQM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKIIMHDPFAMRPFFGYNFGKYLAHWLSMAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWMFNRIDGKASTKLTPIGYIPKEDALNLKGLGHINMMELFSISKEFWEKEVEDIEKYLEDQVNADLPCEIEREILALKQRISQM
Prediction	CCCCCCCCCCCSSSSCCCCCCSSSSSCHHHHHHHHHHCCCCCSSCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCSSSSSCSSSCCCCCSCCCCCCCHHHHHHHHHHHHCCCCCSSSCCCSSCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHC
Confidence	9997899997478835888724775211146777875566628608753576678998999999999716577999947997314547999841789763247999999995397762764643037954478778985479999668999999999999999998714567699999999999999839
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKIIMHDPFAMRPFFGYNFGKYLAHWLSMAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWMFNRIDGKASTKLTPIGYIPKEDALNLKGLGHINMMELFSISKEFWEKEVEDIEKYLEDQVNADLPCEIEREILALKQRISQM
Prediction	8643357310002003315200000122334323145365431341120234226241030041004015564641120000000243772410134344422004000410536451351010100446504163145730440150437304620550461047303750152036115503620676
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSCCCCCCSSSSSCHHHHHHHHHHCCCCCSSCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCSSSSSCSSSCCCCCSCCCCCCCHHHHHHHHHHHHCCCCCSSSCCCSSCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHC
FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKIIMHDPFAMRPFFGYNFGKYLAHWLSMAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWMFNRIDGKASTKLTPIGYIPKEDALNLKGLGHINMMELFSISKEFWEKEVEDIEKYLEDQVNADLPCEIEREILALKQRISQM

2fahA2

0.56

16.06

1.50

DEthreader

AFGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

2zciA2

0.44

0.42

12.32

3.68

SPARKS-K

FGGRRADTVPLVTQTYDWEHGTMVGALLASG-------QVGTLRHDPMAMLPFIGYNAGEYLQNWIDMGNKGGDKMPSIFLVNWFRRGEDGRFLWPGFGDNSRVLKWVIDRIEGHVGADETVVGHTAKAEDLDLDGLPIEDVKEALTAPAEQWANDVEDNAEYLTFL-GPRVPAEVHSQFDALKARIS--

2fahA

0.57

16.35

1.71

MapAlign

FGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

2fahA

0.57

16.35

1.59

CEthreader

FGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

3dt7A

0.89

25.16

2.66

MUSTER

FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM

2fahA2

0.57

16.35

5.00

HHsearch

FGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

2zciA2

0.44

0.42

12.32

2.74

FFAS-3D

FGGRRADTVPLVTQTYDWEHGTMVGALLAS-------GQVGTLRHDPMAMLPFIGYNAGEYLQNWIDMGNKGGDKMPSIFLVNWFRRGEDGRFLWPGFGDNSRVLKWVIDRIEGHVGADETVVGHTAKAEDLDLDGLDIEDVKEALTAPAEQWANDVEDNAEYLTF-LGPRVPAEVHSQFDALKARIS--

2fahA2

0.42

0.41

11.92

2.07

EigenThreader

FGGRRPRGVPLVVEAFGWRHGVFMGSAMSEATAAAEHKGGRLMHDPFAMRPFF-GYNAGRYLEHWLSTGLRS--NARLPRLFHVNLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVEGD--LDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

5fh0A

0.89

25.01

2.77

CNFpred

FGGRRPAGVPLVYEALSWQHGVFVGAAMRSEAT-AAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM

2fahA

0.56

16.06

1.50

DEthreader

AFGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM

(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	0.972

(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	3dt7A	1.00	0.23	0.895	1.000	model1_3dt7A.pdb.gz
2	2fahA	0.98	0.72	0.568	1.000	model1_2fahA.pdb.gz
3	4wieA2	0.89	1.41	0.469	0.942	model1_4wieA2.pdb.gz
4	2zciA2	0.87	1.64	0.444	0.937	model1_2zciA2.pdb.gz
5	4iibA	0.34	5.84	0.030	0.611	model1_4iibA.pdb.gz
6	3d5tC2	0.32	5.24	0.060	0.553	model1_3d5tC2.pdb.gz
7	3ivcA2	0.32	5.20	0.058	0.537	model1_3ivcA2.pdb.gz
8	2c1cA	0.32	5.80	0.058	0.568	model1_2c1cA.pdb.gz
9	2pmlX	0.31	5.56	0.025	0.537	model1_2pmlX.pdb.gz
10	1aylA1	0.31	5.36	0.054	0.542	model1_1aylA1.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:0004611	1.00	phosphoenolpyruvate carboxykinase activity
GO:0004613	0.78	phosphoenolpyruvate carboxykinase (GTP) activity
GO:1901363	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0043167	0.66	ion binding
GO:0000166	0.66	nucleotide binding
GO:0046872	0.65	metal ion binding
GO:0035639	0.65	purine ribonucleoside triphosphate binding
GO:0032555	0.65	purine ribonucleotide binding
GO:0032550	0.65	purine ribonucleoside binding
GO:0046914	0.63	transition metal ion binding
GO:0005525	0.62	GTP binding
GO:0030145	0.61	manganese ion binding

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:0008152	0.87	metabolic process
GO:0009987	0.83	cellular process
GO:0071704	0.82	organic substance metabolic process
GO:0044699	0.82	single-organism process
GO:0044238	0.80	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0065007	0.74	biological regulation
GO:0050896	0.74	response to stimulus
GO:0044710	0.72	single-organism metabolic process
GO:0044281	0.69	small molecule metabolic process
GO:0044763	0.64	single-organism cellular process
GO:0042221	0.64	response to chemical
GO:1901700	0.63	response to oxygen-containing compound
GO:1901576	0.63	organic substance biosynthetic process
GO:0010033	0.63	response to organic substance
GO:0044711	0.59	single-organism biosynthetic process
GO:0006006	0.59	glucose metabolic process
GO:0006094	0.58	gluconeogenesis
GO:0019752	0.54	carboxylic acid metabolic process
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0032787	0.53	monocarboxylic acid metabolic process
GO:0050789	0.52	regulation of biological process
GO:0065008	0.51	regulation of biological quality
GO:0009725	0.51	response to hormone
GO:0006090	0.51	pyruvate metabolic process
GO:0050794	0.50	regulation of cellular 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:0044444	1.00	cytoplasmic part
GO:0043226	0.65	organelle
GO:0043227	0.64	membrane-bounded organelle
GO:0044422	0.55	organelle part
GO:0005829	0.52	cytosol
GO:0043229	0.51	intracellular organelle
GO:0043231	0.50	intracellular membrane-bounded organelle

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	2gepA	0.420	4.83	0.059	0.653	1.8.1.2	NA
2	0.060	1siqA	0.416	5.33	0.019	0.700	1.3.99.7	175
3	0.060	1lpsA	0.412	5.20	0.049	0.684	3.1.1.3	6,138
4	0.060	3ej6D	0.418	5.68	0.039	0.726	1.11.1.6	9
5	0.060	2ix6A	0.422	4.92	0.040	0.679	1.3.3.6	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	0.70	1m51A	0.949	0.55	0.989	0.958	1.22	TSX	complex1.pdb.gz	4,84,85,93,95,96,97,98,101
2	0.68	2rk7A	0.945	0.49	0.890	0.953	1.51	MN	complex2.pdb.gz	84,98,101
3	0.16	2fafA	0.916	0.81	0.551	0.937	1.34	20S	complex3.pdb.gz	16,19,125,186
4	0.03	2pc9A	0.690	2.87	0.110	0.853	0.91	PO4	complex4.pdb.gz	57,58,59,168,171

	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.