D-I-TASSER Q4KMG9-D1

D-I-TASSER results for Q4KMG9-D1

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

Input Sequence in FASTA format

>Q4KMG9 (183 residues)
MGVRVHVVAASALLYFILLSGTRCEENCGNPEHCLTTDWVHLWYIWLLVVIGALLLLCGL
TSLCFRCCCLSRQQNGEDGGPPPCEVTVIAFDHDSTLQSTITSLQSVFGPAARRILAVAH
SHSSLGQLPSSLDTLPGYEEALHMSRFTVAMCGQKAPDLPPVPEEKQLPPTEKESTRIVD
SWN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MGVRVHVVAASALLYFILLSGTRCEENCGNPEHCLTTDWVHLWYIWLLVVIGALLLLCGLTSLCFRCCCLSRQQNGEDGGPPPCEVTVIAFDHDSTLQSTITSLQSVFGPAARRILAVAHSHSSLGQLPSSLDTLPGYEEALHMSRFTVAMCGQKAPDLPPVPEEKQLPPTEKESTRIVDSWN
Prediction	CCCCCCSHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCSCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	985431102346666641786422357888222888761335689999999999999977999999998504788888899983589997279974100100133314875442468889888777899878999967888752553102578889999999887789998889986678999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MGVRVHVVAASALLYFILLSGTRCEENCGNPEHCLTTDWVHLWYIWLLVVIGALLLLCGLTSLCFRCCCLSRQQNGEDGGPPPCEVTVIAFDHDSTLQSTITSLQSVFGPAARRILAVAHSHSSLGQLPSSLDTLPGYEEALHMSRFTVAMCGQKAPDLPPVPEEKQLPPTEKESTRIVDSWN
Prediction	753433011010011002034352775155673245241230121212333333333123202001100243436467454231301001034443133233323223323323022234474355342443632442631152443535435653571563457764544765556456578
	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

CCCCCCSHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCSCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MGVRVHVVAASALLYFILLSGTRCEENCGNPEHCLTTDWVHLWYIWLLVVIGALLLLCGLTSLCFRCCCLSRQQNGEDGGPPPCEVTVIAFDHDSTLQSTITSLQSVFGPAARRILAVAHSHSSLGQLPSSLDTLPGYEEALHMSRFTVAMCGQKAPDLPPVPEEKQLPPTEKESTRIVDSWN

5x5yF

0.09

3.36

0.44

CEthreader

FRIPGFLQLILPLGLFLGILLAYGRLYLESEMTVLSATGMSQKRLLGYTMAPALLVAILVAWLSLFLAPQGINQFALLLRDGTRVTYTEELSKDRGELAGIFISQKDQERGISILVAEKGTQNIQADGSRYLILHNGYRYDGNPGQANYRAIQYDTYGVMLPKPDAVPTADLFGSDNPRYQAE

6af0A2

0.06

2.62

0.48

EigenThreader

HDRYALVGMGNLHLMAAREAYNRAVEFFDKALQLDPKNAYAAQGIAIALVEDRNMGHIYAELAIESYEIALSKEGKANDAGIISCLGRTWLNLDAYKMALDQAKKAVAVAFKFNVAFVQIQIALVLHSMRESERAAEGLEEAIKILDEIAASPSPPYPRHDIEQRANMARNTQRKQLERALAS

5doqA2

0.09

0.06

2.32

0.41

FFAS-3D

----AHVLATSYMTSAFVLASIAA-------WHLWKGNRHIYHRMKTAFIFSVASALVGDLSGKEKLAAAEWHFETSSHAP----LILFGTLEEDNEVKYALEIPYA---LSILAHNHPAAVVTGLNDIPEDERPPLFDVMVTIG--------------------------------------

3ixzA1

0.10

0.09

3.27

0.85

SPARKS-K

QTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVID---------ASETALLKFSELAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAP-----ERVLERCSSILIKGQELPLDE---QWREAFQTAYERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLSFA

5ldwM

0.17

0.04

1.44

0.76

CNFpred

------SVSHMALVIVAILIQT------------------PWSYMGATALMIAHGLTSSMLFCLANSNYERI---------------------------------------------------------------------------------------------------------------

6jxaA

0.06

0.05

2.16

0.83

DEthreader

SFDEQAQKLRSN--GEIEDREHYTTKALELIRHYNRVLLQYNRDS-EVLKALLLQKEKFLWHALHFYLNTLVFS-NRYDNDIIKFLWDDNS---QLYKEIG-IPSWKFLPWVQSKIEQKPLQL-----------KRLLYKPSLSVKQAV-K--------QD-LGIFDQGK-PELVPVIYMPF-

5x5yF

0.10

3.66

0.66

MapAlign

VLVTMSAVSAVLLVIIMSGRFIKYLAQAAQGLLDPGSLFLIMAFRIPGFLQLILPLGLFLGILLAYGRLYLESEMTQAMRDGTRVTYTEELSKDRGELAGIFISQKDRGISILVAEKGTQNIQADGSRYLILHNGYRYDGNPGQANYRAIQYDTYGVMLPKPDAVPTADLFGSDNPRYQAELQ

4wsaC2

0.09

3.49

0.56

MUSTER

--TTKELVQNTYQWVLKNLVTLKAQFL-LGKEDMFQEAFESIQYSGFARAVLKQMRDQEVTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIEVRKGSPLFYNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDFKTIEELEKLKPGEKANILLYQGKP

2kncA

0.19

0.05

1.77

0.60

HHsearch

------------------------------GAMGSEERAIPIWWVLV-GVLGGLLLLTILVLAMWKVGFFKRNRPPLEEDDEEGE--------------------------------------------------------------------------------------------------

5lp4A

0.08

0.07

2.56

0.39

CEthreader

QDWRVGDTLITASFLATPLQVLAYTGLIATGKLATPHFAINNKQPLKDPLNSFQKKKLQALRVGMYEVCNHKDGTAYTRGSKITLACKTGTAQVVRSHAWITAFLPYEKPKYAITILVEHGEGGSKLGGLLVKMSNKLYELGYL---------------------------------------

(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	0.4286

(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	7kf5A	0.50	4.94	0.099	0.770	model1_7kf5A.pdb.gz
2	4ro5A	0.48	5.20	0.079	0.803	model1_4ro5A.pdb.gz
3	1is2A2	0.48	4.86	0.067	0.765	model1_1is2A2.pdb.gz
4	4mt1A	0.46	4.96	0.058	0.727	model1_4mt1A.pdb.gz
5	4k0eA	0.45	4.79	0.075	0.689	model1_4k0eA.pdb.gz
6	2j8sA3	0.43	5.23	0.051	0.721	model1_2j8sA3.pdb.gz
7	3djlA	0.42	5.31	0.037	0.721	model1_3djlA.pdb.gz
8	1w07B3	0.38	4.76	0.045	0.546	model1_1w07B3.pdb.gz
9	4z29A	0.33	4.36	0.061	0.486	model1_4z29A.pdb.gz
10	2rgzB	0.32	5.65	0.066	0.590	model1_2rgzB.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:0004871	0.47	signal transducer 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:0051179	0.91	localization
GO:2000484	0.87	positive regulation of interleukin-8 secretion
GO:1902715	0.87	positive regulation of interferon-gamma secretion
GO:0050900	0.87	leukocyte migration
GO:0045580	0.87	regulation of T cell differentiation
GO:0042110	0.87	T cell activation
GO:0034113	0.87	heterotypic cell-cell adhesion
GO:0032760	0.87	positive regulation of tumor necrosis factor production
GO:0030887	0.87	positive regulation of myeloid dendritic cell activation
GO:0030101	0.87	natural killer cell activation
GO:0007166	0.87	cell surface receptor signaling pathway
GO:0006915	0.87	apoptotic process
GO:0001766	0.87	membrane raft polarization

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:0070062	1.00	extracellular exosome

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	2v2fF	0.423	5.32	0.006	0.732	3.4.16.4	NA
2	0.060	1w07B	0.434	5.05	0.051	0.667	1.3.3.6	NA
3	0.060	3b8cA	0.437	4.48	0.041	0.650	3.6.3.6	NA
4	0.060	2is4B	0.425	5.40	0.036	0.765	3.6.1.-	NA
5	0.060	3b8eA	0.448	5.29	0.069	0.727	3.6.3.9	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	3kdpC	0.447	4.88	0.064	0.689	0.21	III	complex1.pdb.gz	45,48,49,52,53,56,59,63,104,109
2	0.01	3fpsA	0.448	4.78	0.046	0.678	0.19	CZA	complex2.pdb.gz	59,65,101
3	0.01	2yfyA	0.438	4.51	0.052	0.650	0.38	9TN	complex3.pdb.gz	61,64,65,68,89,100,104
4	0.01	2by4A	0.430	4.66	0.046	0.650	0.15	AD4	complex4.pdb.gz	10,11,52,56,59
5	0.01	3ar9A	0.420	4.52	0.026	0.628	0.21	TM1	complex5.pdb.gz	60,62,63,108,109,110
6	0.01	2eatA	0.436	4.47	0.052	0.650	0.24	CZA	complex6.pdb.gz	59,62,105
7	0.01	3b8eA	0.448	5.29	0.069	0.727	0.12	III	complex7.pdb.gz	107,129,138
8	0.01	1hbmE	0.447	5.20	0.049	0.770	0.26	UUU	complex8.pdb.gz	62,64,65,107,108
9	0.01	2easA	0.440	4.55	0.039	0.650	0.25	CZA	complex9.pdb.gz	62,65,66
10	0.01	2eauA	0.453	5.05	0.053	0.700	0.24	CZA	complex10.pdb.gz	60,63,64

	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.