D-I-TASSER P02679-D1

D-I-TASSER results for P02679-D1

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

Input Sequence in FASTA format

>P02679 (168 residues)
MSWSLHPRNLILYFYALLFLSSTCVAYVATRDNCCILDERFGSYCPTTCGIADFLSTYQT
KVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIM
KYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSWSLHPRNLILYFYALLFLSSTCVAYVATRDNCCILDERFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDT
Prediction	CCCCCCCHHHHHHHHHHHHHCCCCCSSSSCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence	996657308999999999845554223313565535774245668863127899987254055799999999999999858899999999971488987665405799999999999999999998744647999999999978999999999999999961354679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSWSLHPRNLILYFYALLFLSSTCVAYVATRDNCCILDERFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDT
Prediction	743434241001011012313341312133453103337520421111000221044236523520540351054144435415410530354253756645542552355045014303504530243374043035125445530350453145136405632678
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHCCCCCSSSSCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MSWSLHPRNLILYFYALLFLSSTCVAYVATRDNCCILDERFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDT

2dfsA

0.07

0.06

2.48

1.17

DEthreader

-----------------LDPKTKELP-PLRSYAGQVAYLEK--IR-ADKLRAACIRIQKTIRGWLMRKKYMRMRRAAITIQRYVRGHQARCYATFLRRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGW-LARVHRT

1m1jD

0.14

0.12

4.07

4.56

HHsearch

----------------------SCK---YEKNWPICVDDDWGTKCPSGCRMQGIIDDTDQNYSQRIDNIRQQLADSQNKYKTSNRVIVETINILKPGLEGAQQLDENYGHVSTELRRRIVTLKQRVATQVNRIKALQNSIQEQVVEMKRLEVDIDIKIRACKGSCARS

3ghgJ

0.17

0.13

4.33

1.69

FFAS-3D

---------------------------------C--SDEDWNYKCPSGCRMKGLIDEVNQDFTNRINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRA

4cpcA

0.07

0.05

2.23

1.00

DEthreader

-----------------------------------K-ALLAKRKRLEMYTKASLKTSNQKIEHVWKTQQDQRQKLNQEYSQQFLTLFQQWDLDMQKAEEQEEKILNMFRQQQKILQQSRIVQSQRLKTIKQLYEQFIKSMEELEKNHDNLLTGAQNEFKKEMAMLKKM

3ghgJ

0.15

0.13

4.38

0.79

SPARKS-K

--------------------------ACKDSDWPFCSDEDWNYKCPSGCRMKGLIDEVNQDFTNRINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRA

6gmmA1

0.09

3.41

0.71

MapAlign

NDKKNSPAYQAVLLALNAAAGLWQVMSYAISPCGPGKDTSKNGGVCGTTGYEPGPSILSTENYAKINKAYQIIQKAFVLLEQASTIITTLNSACPWILKGDGSACGIFKNEISAIQDMIKNAAIAVEQSKIVAANAQSMFANAKAQAEILNRAQAVVKDFERIPAEFV

6gy6A

0.08

3.09

0.48

CEthreader

VELGNILESMKKDIKRQQENTQKVKTAVSDFKLKLIGGELSDGTIAQGLQPQISSKKKLMDDNNLSTTIKDLQSKIDEKNKEIDQFQKDYNKYVGLAFSGMVGGIISWAITGGIFGDKAEKARKQKNKLIDEVKDLQSQVKDKSALQTSVQNLSLSFAGIHTSMVDAE

3ghgI

1.00

0.84

23.50

0.92

MUSTER

---------------------------VATRDNCCILDERFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDT

3ghgJ

0.16

0.13

4.36

4.37

HHsearch

----------------------ACK----DSDWPFCSDEDWNYKCPSGCRMKGLIDEVNQDFTNRINKLKNSLFQKNNKDSLTTNIMEILRGDFSSAN----NRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRA

1m1jD

0.14

0.11

3.84

1.51

FFAS-3D

------------------------------------VDDDWGTKCPSGCRMQGIIDDTDQNYSQRIDNIRQQLADSQNKYKTSNRVIVETINILKPGLEGAQQLDENYGHVSTELRRRIVTLKQRVATQVNRIKALQNSIQEQVVEMKRLEVDIDIKIRACKGSCARS

(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	0.5516

(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	4ut1A	0.63	4.16	0.069	0.899	model1_4ut1A.pdb.gz
2	4tqlA	0.61	4.24	0.069	0.881	model1_4tqlA.pdb.gz
3	7d6dA	0.60	4.51	0.031	0.869	model1_7d6dA.pdb.gz
4	1ciiA	0.59	3.96	0.083	0.780	model1_1ciiA.pdb.gz
5	1vw1A	0.59	3.15	0.055	0.738	model1_1vw1A.pdb.gz
6	5xbjA	0.59	4.26	0.063	0.875	model1_5xbjA.pdb.gz
7	3qweA	0.58	4.29	0.081	0.827	model1_3qweA.pdb.gz
8	3haiA	0.53	3.79	0.087	0.732	model1_3haiA.pdb.gz
9	3ljbA	0.39	4.60	0.110	0.607	model1_3ljbA.pdb.gz
10	1m1cA	0.36	6.00	0.050	0.696	model1_1m1cA.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:0050839	1.00	cell adhesion molecule binding
GO:0005198	1.00	structural molecule activity
GO:0005102	1.00	receptor 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	1.00	response to stimulus
GO:0008152	0.85	metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0044238	0.84	primary metabolic process
GO:0043170	0.83	macromolecule metabolic process
GO:0019538	0.82	protein metabolic process
GO:0072376	0.81	protein activation cascade
GO:0072378	0.80	blood coagulation, fibrin clot formation
GO:0065007	0.69	biological regulation
GO:0050789	0.67	regulation of biological process
GO:0044699	0.67	single-organism process
GO:0009987	0.64	cellular process
GO:0050794	0.59	regulation of cellular process
GO:0044763	0.58	single-organism cellular process
GO:0048519	0.57	negative regulation of biological process
GO:0048518	0.56	positive regulation of biological process
GO:0065008	0.55	regulation of biological quality
GO:0048583	0.54	regulation of response to stimulus
GO:0022610	0.54	biological adhesion
GO:0019222	0.54	regulation of metabolic process
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0051239	0.53	regulation of multicellular organismal process
GO:0048523	0.53	negative regulation of cellular process
GO:0031323	0.53	regulation of cellular metabolic process
GO:0007155	0.53	cell adhesion
GO:0080134	0.52	regulation of response to stress
GO:0050878	0.52	regulation of body fluid levels
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0048584	0.51	positive regulation of response to stimulus
GO:0048522	0.51	positive regulation of cellular process
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0030193	0.51	regulation of blood coagulation
GO:0016337	0.51	single organismal cell-cell adhesion
GO:0016043	0.51	cellular component organization
GO:0070527	0.50	platelet aggregation
GO:0051241	0.50	negative regulation of multicellular organismal process
GO:0048585	0.50	negative regulation of response to stimulus
GO:0042221	0.50	response to chemical
GO:0032501	0.50	multicellular organismal process
GO:0031325	0.50	positive regulation of cellular metabolic process
GO:0010604	0.50	positive regulation of macromolecule metabolic 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:0072562	1.00	blood microparticle
GO:0044424	1.00	intracellular part
GO:0043227	0.76	membrane-bounded organelle
GO:0044444	0.75	cytoplasmic part
GO:0043229	0.75	intracellular organelle
GO:0044425	0.74	membrane part
GO:0043234	0.74	protein complex
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0044459	0.73	plasma membrane part
GO:0070062	0.72	extracellular exosome
GO:0005615	0.72	extracellular space
GO:0031091	0.71	platelet alpha granule
GO:0009986	0.71	cell surface
GO:0009897	0.71	external side of plasma membrane
GO:0005577	0.71	fibrinogen complex
GO:0005737	0.60	cytoplasm
GO:0005576	0.57	extracellular region
GO:0016020	0.52	membrane

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	1a31A	0.283	5.33	0.038	0.506	5.99.1.2	NA
2	0.060	2ohyB	0.450	4.12	0.034	0.661	5.4.3.6	NA
3	0.060	1yfmA	0.448	4.72	0.053	0.684	4.2.1.2	NA
4	0.060	1q5nA	0.442	4.94	0.043	0.702	5.5.1.2	NA
5	0.060	2b5uA	0.518	3.10	0.037	0.673	3.1.-.-	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	0.01	3b5zD	0.465	4.06	0.034	0.673	0.43	UUU	complex1.pdb.gz	41,42,43,44
2	0.01	2w6dA	0.550	4.64	0.038	0.839	0.41	GDP	complex2.pdb.gz	34,41,50,56
3	0.01	2j9tA	0.502	3.55	0.066	0.691	0.44	BO3	complex3.pdb.gz	33,34,42,51,53

	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.