D-I-TASSER P02788-D3

D-I-TASSER results for P02788-D3

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

Input Sequence in FASTA format

>P02788 (194 residues)
RRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVY
TAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYMAPNHAVVSRMDKVERLKQVLLHQQ
AKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKC
STSPLLEACEFLRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| RRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYMAPNHAVVSRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK
Prediction	CCCCSSSSSCCHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHCCCCSSSSCCCCSSSSCCCCCSSHHHHHCCCCCCCCCCCCCCCCCCCCCSSCCSSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCHHHHHCHHHHHHHHHHHCCCCHHHHHHHHHHCC
Confidence	99716997559899999999998638965884169989999999809983999664011210335966434553243234334656664564442111237995364479999999999999654678888873222699987551457311033599997899825999999999851894689999998519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| RRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYMAPNHAVVSRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK
Prediction	85540300022651450055016424340413447336401530475402000034521240451402000243144553444347446443641442320103355335202410340043125534635640401417342000332052035147734145112540140053046144650250043158
	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

CCCCSSSSSCCHHHHHHHHHHHHHCCCCSSSSSCCCHHHHHHHHHHCCCCSSSSCCCCSSSSCCCCCSSHHHHHCCCCCCCCCCCCCCCCCCCCCSSCCSSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCHHHHHCHHHHHHHHHHHCCCCHHHHHHHHHHCC
RRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYMAPNHAVVSRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK

1b1xA

0.65

18.68

1.33

DEthreader

AAERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSEGYLAVAVAFLCLDCHLARAPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA

2hauA2

0.58

0.54

15.40

3.26

SPARKS-K

ECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKI-NGEADA-SLDGGFVYIAGKCGLVPVLAENYDKSD-NCED-----------TPENHAVVTRKDKEACVHKILRQQQHLFGSDVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

1b1xA

0.68

0.64

18.35

1.08

MapAlign

--ERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSQSCAPGADPQSSLCALAPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLE-------

1b1xA

0.68

19.37

0.85

CEthreader

RRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSVGNNENENKCMPNSEERYYAPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA

1b1xA2

0.72

0.70

19.90

2.24

MUSTER

RRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPD--CVHRPP---EGPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA

1b1xA2

0.70

0.69

19.48

2.82

HHsearch

RRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPDC--VH-RPPE--GPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA

1b1xA2

0.70

0.68

19.20

2.37

FFAS-3D

-RERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPDCV-----HRPPEGPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLR-

1b1xA2

0.70

0.68

19.35

1.28

EigenThreader

RRERVVWCAVGPEEERKCKQWSDVSNRKVACASASTTEECIALVLKGEADALNLDGGFIYVAGKCGLVPVLAENQKSQNSNAPDCVHR-----PPEGPNHAVVSQSDRAQHLKKVLFLQQDQFGGNGPDCPGKFCLFKSETKNLLFNDNTECLAELQGKTTYEQYLGSEYVTSITNLRRCSSSPLLEACAFLRA

3s9lC

0.60

0.56

16.11

3.00

CNFpred

ECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYDKSD------NCEDTPEAG---PNHAVVTRKDKEACVHKILRQQQHLFGSDVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFR--

1ryxA

0.44

0.43

12.69

1.33

DEthreader

RENRIQWCAVGKDEKSKCDRWSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDASYFAVVYAAFILLCYNAEVPTHAVVVRPEKANKIRDLLERQEKRFGVNG-SEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEK

(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	0.962

(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	1b1xA	0.97	0.74	0.724	0.990	model1_1b1xA.pdb.gz
2	3mc2A	0.94	1.47	0.539	0.990	model1_3mc2A.pdb.gz
3	2hauA2	0.87	1.86	0.594	0.928	model1_2hauA2.pdb.gz
4	1ryxA2	0.87	1.52	0.480	0.923	model1_1ryxA2.pdb.gz
5	1d4nA	0.78	2.18	0.355	0.861	model1_1d4nA.pdb.gz
6	3i6vA	0.43	3.86	0.066	0.603	model1_3i6vA.pdb.gz
7	1zcjA	0.36	4.77	0.039	0.562	model1_1zcjA.pdb.gz
8	3h2zA	0.34	5.72	0.024	0.588	model1_3h2zA.pdb.gz
9	2nuyA	0.33	5.49	0.029	0.557	model1_2nuyA.pdb.gz
10	2x58A	0.32	5.50	0.040	0.557	model1_2x58A.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:0005506	0.92	iron ion binding
GO:0005102	0.59	receptor binding
GO:0030234	0.54	enzyme regulator activity
GO:1990459	0.51	transferrin receptor binding
GO:0008198	0.51	ferrous iron binding
GO:0008199	0.50	ferric iron 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:0050896	0.94	response to stimulus
GO:0043207	0.84	response to external biotic stimulus
GO:0065007	0.83	biological regulation
GO:0051707	0.82	response to other organism
GO:0044699	0.82	single-organism process
GO:0009617	0.80	response to bacterium
GO:0048522	0.78	positive regulation of cellular process
GO:0009987	0.72	cellular process
GO:0060284	0.69	regulation of cell development
GO:0051240	0.69	positive regulation of multicellular organismal process
GO:0042127	0.68	regulation of cell proliferation
GO:0006952	0.68	defense response
GO:0006826	0.68	iron ion transport
GO:0010721	0.66	negative regulation of cell development
GO:0009966	0.66	regulation of signal transduction
GO:2000026	0.65	regulation of multicellular organismal development
GO:0051094	0.65	positive regulation of developmental process
GO:0045597	0.65	positive regulation of cell differentiation
GO:0019730	0.65	antimicrobial humoral response
GO:0008284	0.65	positive regulation of cell proliferation
GO:0065008	0.64	regulation of biological quality
GO:0044767	0.64	single-organism developmental process
GO:2001205	0.63	negative regulation of osteoclast development
GO:2000308	0.63	negative regulation of tumor necrosis factor (ligand) superfamily member 11 production
GO:1902732	0.63	positive regulation of chondrocyte proliferation
GO:1900229	0.63	negative regulation of single-species biofilm formation in or on host organism
GO:1900159	0.63	positive regulation of bone mineralization involved in bone maturation
GO:0060349	0.63	bone morphogenesis
GO:0045669	0.63	positive regulation of osteoblast differentiation
GO:0043066	0.63	negative regulation of apoptotic process
GO:0033690	0.63	positive regulation of osteoblast proliferation
GO:0032680	0.63	regulation of tumor necrosis factor production
GO:0031665	0.63	negative regulation of lipopolysaccharide-mediated signaling pathway
GO:0019732	0.63	antifungal humoral response
GO:0019731	0.63	antibacterial humoral response
GO:0002227	0.63	innate immune response in mucosa
GO:0042592	0.58	homeostatic process
GO:0044763	0.57	single-organism cellular process
GO:0043170	0.57	macromolecule metabolic process
GO:0001895	0.55	retina homeostasis
GO:0042221	0.52	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	0.91	cell part
GO:0044424	0.87	intracellular part
GO:0043227	0.85	membrane-bounded organelle
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0044444	0.81	cytoplasmic part
GO:0031988	0.77	membrane-bounded vesicle
GO:0044421	0.73	extracellular region part
GO:0016023	0.73	cytoplasmic, membrane-bounded vesicle
GO:0005615	0.71	extracellular space
GO:0005576	0.63	extracellular region
GO:0042581	0.58	specific granule

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	3ldhA	0.463	4.51	0.067	0.711	1.1.1.27	NA
2	0.060	2mdhA	0.495	4.34	0.060	0.742	1.1.1.37	NA
3	0.060	1guzA	0.465	4.42	0.046	0.711	1.1.1.37	NA
4	0.060	2wj2A	0.505	4.79	0.127	0.768	3.5.1.99	NA
5	0.060	1a5zA	0.476	4.36	0.050	0.717	1.1.1.27	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	0.38	3todA	0.892	1.26	0.708	0.917	1.52	XXB	complex1.pdb.gz	93,94,98,164,165,167
	2	0.33	2h4iA	0.899	1.75	0.690	0.949	0.74	UUU	complex2.pdb.gz	169,172,173,176

	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.