D-I-TASSER P27487-D2

D-I-TASSER results for P27487-D2

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

Input Sequence in FASTA format

>P27487 (128 residues)
RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNY
VKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNL
PSYRITWT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT
Prediction	CCCCCCSSSSSSCCCSSSSSCCCCCSSSSSCCCCCCCCCCCSCSSSSCCCCCSSSSSSCCCCCSSCCCSSSSSSSSCCCCCSSCCCCCCCCCSSSSSCCCCCSSSSSSCCCSSSSSCCCCCSSSSSCC
Confidence	97679859999199399998568978999807632457874014799689989999977722302143138999988999393166799860057878999989999787089997899987952189
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT
Prediction	84366540112365402111054653322133443564444144132334232000114345322334413010010546533526657541110201252420000242101024277564331358
	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

CCCCCCSSSSSSCCCSSSSSCCCCCSSSSSCCCCCCCCCCCSCSSSSCCCCCSSSSSSCCCCCSSCCCSSSSSSSSCCCCCSSCCCCCCCCCSSSSSCCCCCSSSSSSCCCSSSSSCCCCCSSSSSCC
RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT

3pe7A

0.10

0.09

3.50

1.33

DEthreader

GFSPDDALFYVKDRNLMRVDLATLEENVVYQVPA--EW-VGYGTWVANSDCTKLVGIEIRDWVPFTKPCCRLMRVDLKTGES-TVILQEQWLGHPIYRPYDDTVAFCHVARMWLINEDGTNMRKVKTH

3g0bB

1.00

28.00

1.40

SPARKS-K

RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT

1n6fA

0.15

0.14

4.76

0.42

MapAlign

GVDRGKFAVVANRFEIMTVDLETGKPTVIERS-----REAMITDFTISDNSRFIAYGFPLKHGETDGVMQAIHVYDMEGRKIFAATTENSHDYAPAFDADSKNLYYLSRSKPFVIPLMYKRSSPIVDP

4ci8A2

0.11

3.91

0.30

CEthreader

YLLPTGETVYFIASVVVLYNVEEQLQRHYAGHND------DVKCLAVHPDRITIATGQVAGTSKDKQLPPHVRIWDSVTLNTLHVIGFDRAVTCIAFSKSGTNLCAVDDHVLSVWDWQKEEKLADVKC

3g0bB

1.00

28.00

1.32

MUSTER

RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT

5oljA

0.25

0.24

7.52

0.70

HHsearch

RSMPDGHYTEMNETAIVRYNYASGKVDTLFSIERAREKQIQ--NYEVSSTGHHILLFTDMESIYRHSYRAAVYDYDVRRNL-VKPLSEHGKVMIPTFSPDGRMVAFVRDNNIFIKKFDFDTEVQVTTD

5oljA1

0.24

7.54

1.23

FFAS-3D

RSMPDGEHYTEERTAIVRYNYASGKAVDTLFSIERECPFKQIQNYEVSSTGHHILLFTDMESIYRHSYRAAVYDYDVRRNLVKPLSEHVGKVMIPTFSPDGRMVAFVRDNNIFIKKFDFDTEVQVTTD

3g0bB

0.97

27.16

0.55

EigenThreader

LRWIDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT

2qt9A

1.00

28.00

1.96

CNFpred

RWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT

6trwA

0.13

0.12

4.37

1.33

DEthreader

KLCPDDWIAFIHSNDIWISNIVTREERRLTYVHN-DARSAGVAGYWWCPKALRILYEENDESVETANPKVTFKMSEIMDVIDKELIFLFVEYIRAGWTPEGKYAWSILLLQIVLISPLVTPLIIYEES

(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	0.948

(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	3g0bB	0.99	0.54	1.000	1.000	model1_3g0bB.pdb.gz
2	4ffvA	0.96	1.01	0.828	1.000	model1_4ffvA.pdb.gz
3	1z68A	0.93	1.13	0.452	0.984	model1_1z68A.pdb.gz
4	1xfdA	0.84	1.96	0.298	0.969	model1_1xfdA.pdb.gz
5	4wjlA	0.83	1.93	0.315	0.969	model1_4wjlA.pdb.gz
6	5oljA1	0.82	2.56	0.234	1.000	model1_5oljA1.pdb.gz
7	7y4fA	0.80	2.51	0.220	0.992	model1_7y4fA.pdb.gz
8	2bklB	0.66	2.88	0.095	0.906	model1_2bklB.pdb.gz
9	2xe4A	0.66	3.16	0.101	0.930	model1_2xe4A.pdb.gz
10	2ecfA	0.64	3.03	0.159	0.883	model1_2ecfA.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:0003824	0.98	catalytic activity
GO:0008233	0.97	peptidase activity
GO:0008239	0.95	dipeptidyl-peptidase activity
GO:0005102	0.62	receptor binding
GO:0046983	0.58	protein dimerization activity
GO:0042802	0.58	identical protein binding
GO:0042803	0.57	protein homodimerization activity
GO:0019899	0.57	enzyme binding
GO:0002020	0.56	protease 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:0065007	0.96	biological regulation
GO:0050794	0.95	regulation of cellular process
GO:0044699	0.95	single-organism process
GO:0009987	0.95	cellular process
GO:0044763	0.94	single-organism cellular process
GO:0048518	0.83	positive regulation of biological process
GO:0048522	0.82	positive regulation of cellular process
GO:0051128	0.77	regulation of cellular component organization
GO:0048519	0.70	negative regulation of biological process
GO:0048523	0.69	negative regulation of cellular process
GO:0042127	0.68	regulation of cell proliferation
GO:0043542	0.67	endothelial cell migration
GO:0010716	0.67	negative regulation of extracellular matrix disassembly
GO:0002376	0.59	immune system process
GO:0002684	0.58	positive regulation of immune system process
GO:0031295	0.57	T cell costimulation
GO:0008284	0.57	positive regulation of cell proliferation

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:0016020	0.95	membrane
GO:0044425	0.88	membrane part
GO:0044459	0.86	plasma membrane part
GO:0044424	0.76	intracellular part
GO:0043226	0.71	organelle
GO:0044444	0.70	cytoplasmic part
GO:0043227	0.70	membrane-bounded organelle
GO:0009986	0.70	cell surface
GO:0071438	0.67	invadopodium membrane
GO:0030027	0.67	lamellipodium
GO:0005886	0.66	plasma membrane
GO:0031988	0.65	membrane-bounded vesicle
GO:0043229	0.64	intracellular organelle
GO:0043231	0.63	intracellular membrane-bounded organelle
GO:0016023	0.58	cytoplasmic, membrane-bounded vesicle
GO:0030139	0.57	endocytic vesicle

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	1k32A	0.629	3.42	0.085	0.914	3.4.21.-	NA
2	0.060	3fsnB	0.611	3.55	0.041	0.914	5.2.1.7	NA
3	0.060	1kb0A	0.588	4.14	0.066	0.945	1.1.99.-	NA
4	0.060	2ebsB	0.610	3.67	0.085	0.891	3.2.1.150	50
5	0.060	2htrA	0.585	3.94	0.100	0.930	3.2.1.18	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	0.28	1u8eA	0.982	0.58	1.000	1.000	0.21	UUU	complex1.pdb.gz	4,47,48
2	0.26	2bucA	0.986	0.52	0.898	1.000	0.27	NDG	complex2.pdb.gz	48,51,52,102
3	0.23	2gbiA	0.960	1.01	0.828	1.000	0.10	XIH	complex3.pdb.gz	8,100,101
4	0.19	1tk3B	0.985	0.54	1.000	1.000	0.23	NDG	complex4.pdb.gz	101,102,103
5	0.19	3kwfA	0.986	0.50	1.000	1.000	0.12	B1Q	complex5.pdb.gz	52,55,100,101
6	0.19	3cccB	0.974	0.44	1.000	0.984	0.17	7AC	complex6.pdb.gz	5,99,100
7	0.19	3h0cA	0.973	0.72	1.000	1.000	0.12	PS4	complex7.pdb.gz	7,52,54
8	0.15	2qjrA	0.982	0.58	1.000	1.000	0.35	UUU	complex8.pdb.gz	101,103,104
9	0.15	2bgn0	0.984	0.56	1.000	1.000	0.18	III	complex9.pdb.gz	51,53,54,101,103
10	0.14	2i03B	0.991	0.41	1.000	1.000	0.12	AXD	complex10.pdb.gz	8,52,100,101

	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.