D-I-TASSER Q15303-D2

D-I-TASSER results for Q15303-D2

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

Input Sequence in FASTA format

>Q15303 (280 residues)
GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILN
GGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENH
CQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQ
TFVYANTLGKAEYLKNNILSMPEKAKKAFDNPDYWNHSLPPRSTLQHPDYLQEYSTKYFY
KQNGRIRPIVAENPEYLSEFSLKPGTVLPPPPYRHRNTVV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYANTLGKAEYLKNNILSMPEKAKKAFDNPDYWNHSLPPRSTLQHPDYLQEYSTKYFYKQNGRIRPIVAENPEYLSEFSLKPGTVLPPPPYRHRNTVV
Prediction	CSSSSSSCCCCCSCCCCCSSSSCCCCCCCCSSSSSSSCCCCCCCCCCSSSCCCCHHHHCSCCSSSSSCCCCCCCCCSCHHHHHCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCSCCCCCSSCCCCCCSSSSCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9599862553400278813880761116852299996147787777247436872132217679985776566654327886247777854873699865468886656788789998764325788545668876546788887473213778899977672345643398213669998333588883623763010479875556677246432577511136973200179842661688642345799542150236777535888744466659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYANTLGKAEYLKNNILSMPEKAKKAFDNPDYWNHSLPPRSTLQHPDYLQEYSTKYFYKQNGRIRPIVAENPEYLSEFSLKPGTVLPPPPYRHRNTVV
Prediction	3000002130540405302002033014540000001024445343043030440430240201012034032320020210044544422213345444314303530453021324533431364203640444323444421025414540523366303202413266432654153221254433144137104403452445141251022214333234335225614541124361604134074351035232451412313425445436
	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                 200                 220                 240                 260                 280

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSSCCCCCSCCCCCSSSSCCCCCCCCSSSSSSSCCCCCCCCCCSSSCCCCHHHHCSCCSSSSSCCCCCCCCCSCHHHHHCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCSCCCCCSSCCCCCCSSSSCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYANTLGKAEYLKNNILSMPEKAKKAFDNPDYWNHSLPPRSTLQHPDYLQEYSTKYFYKQNGRIRPIVAENPEYLSEFSLKPGTVLPPPPYRHRNTVV

5yz0A

0.07

0.06

2.47

0.83

DEthreader

LVLSQALTPCQDKQVAHRELNTL--I----FDFPLNRLTRT--LQVLLPDAAASASALIRLGLNNEINFKYIFSHLCCSKDEL--ERALHYLKETEIEL-SLL---GPRDIISPE--LMADLQLLGILAMLMKLMGPKVVRVKMTTLRTGLRFLKRQRLMLCEETSYRLLSLNKV-RKAGHH---------LYVERAKWGGLCFPENETPPKNMLIHGRAMLLVGFM---------ACLPEWEHYLAYYDMVLIRYILHFGRSLQYG-----D-------

2ahxB1

0.78

0.68

19.19

5.41

SPARKS-K

GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYNPTTFQLEHNFNAK----------YTYGAFCVKKCPHNFVVDSSSCVRACPSSKMEVEEKMCKPCTDICP--------------------------

1n8yC

0.34

0.30

8.97

1.18

MapAlign

GYMLIAHNQVKRVPLQRLRIVRGTQLFEDKYALAVLDNRD-PQPEGLRELQLRSLTEILKGGVLIRGNPQLCYQDMVLWKDVFRKNNQAPVDIDTNRSR-ACPPCAPACKDHCWGESPEDCQILTGTICTSGC-ARCKGRLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALRYTF--GASCVTT------------------------CPYNYLSTVGSCTLVCPPNNQEVGTQRCEKCGLGMEHLRGARAITSDNVQEFDGC-------

2ahxB1

0.78

0.68

19.19

0.82

CEthreader

GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYNPTTFQLEHNFNAK----------YTYGAFCVKKCPHNFVVDSSSCVRACPSSKMEVEEKMCKPCTDICP--------------------------

2ahxB

0.71

0.69

19.57

2.79

MUSTER

GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYNPTTFQLEHNFNAK----------YTYGAFCVKKCPHNFVVDSSSCVRACPSSKMEVEEKMCKPCTDICPKAIGTGSLMSAQTVDSSNIFINCTKI

2ahxB

0.70

0.68

19.29

3.16

HHsearch

GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYNPTTFQLEHNFNA----------KYTYGAFCVKKCPHNFVVDSSSCVRACPSSKMEVEIKMCKPCTDICPGIINCTKINGNLIFLVGDPYNAIEAI

2ahxB1

0.78

0.68

19.19

1.87

FFAS-3D

GYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQELGLKNLTEILNGGVYVDQNKFLCYADTIHWQDIVRNPWPSNLTLVSTNGSSGCGRCHKSCTGRCWGPTENHCQTLTRTVCAEQCDGRCYGPYVSDCCHRECAGGCSGPKDTDCFACMNFNDSGACVTQCPQTFVYNPTTFQLEHNFNAKYTYG----------AFCVKKCPHNFVVDSSSCVRACPSSKMEVEENMCKPCTDICP--------------------------

1n8yC

0.26

7.93

1.30

EigenThreader

GYMLIAHNQVKRVPLQRLRIVRGTQLFEDK-YALAVLDNRDPQPEGLRELQLRSLTEILKGGVLIRGNPQLCYQDMVLWKDVFRKNNQLAPVDIDTNRSRACPPCAPACKDNHCWGESPEDCQILTGTICTSGCARCKGRLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELH-CPALVTY--ESMHNPEGRYTFGCNSLCAHGHCWGPGPTQCVNCSHFLRGQECRVWKGLPREYVKRCLPCHPECQPQNSSETCFGSEADQCAACAHDLSYMPI

1m6bA

0.43

0.38

11.11

7.68

CNFpred

GYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVMLNYNTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWRDIVRDR-DAEIVVKDN--GRSCPPCHEVCKGRCWGPGSEDCQTLTKTICAPQCNGHCFGPNPNQCCHDECAGGCSGPQDTDCFACRHFNDSGACVPRCPQPLVYNKLTFQLEPNPHTKYQYG----------GVCVASCPHNFVVDQTSCVRACPPDKMEVDLKMCEPCGGLCP--KACEGTG-----------------

6xjaP

0.04

0.03

1.57

0.83

DEthreader

NDNEATKIKQVHVDGVLAGERGV--------LAKASSIA-----E-SSFKGRIVNTYTDAYNGHLASIAKSKATVTIS--SNTNRSDQTVGLVAHIQNSNVLSDVNANRVS----A-------VDTYGAATDL--FSTLEHY--FVYDRIWKYRNVLLLLVFVISSSLGFGAE-ARETAKRQHLAYAVYYMLDKDQPLKHSKS-D-STEGSRL--Q-------VLDPTERF-NAALQNYVHNMF-------------LAAKGDGMVFKMYQEDQFNLKSS

(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	0.6756

(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	2ahxB	0.87	1.74	0.696	0.911	model1_2ahxB.pdb.gz
2	1yy9A	0.81	2.51	0.344	0.907	model1_1yy9A.pdb.gz
3	1n8yC	0.80	2.21	0.336	0.868	model1_1n8yC.pdb.gz
4	3i2tA	0.76	2.83	0.306	0.871	model1_3i2tA.pdb.gz
5	1m6bB	0.75	3.07	0.388	0.900	model1_1m6bB.pdb.gz
6	1igrA1	0.38	1.85	0.345	0.404	model1_1igrA1.pdb.gz
7	2dtgE1	0.37	1.77	0.369	0.396	model1_2dtgE1.pdb.gz
8	1hg8A1	0.29	4.04	0.051	0.368	model1_1hg8A1.pdb.gz
9	3mtvA	0.26	5.27	0.049	0.393	model1_3mtvA.pdb.gz
10	3g04C2	0.26	3.90	0.096	0.336	model1_3g04C2.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	0.82	catalytic activity
GO:0016773	0.80	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.80	kinase activity
GO:0004713	0.72	protein tyrosine kinase activity
GO:0004872	0.69	receptor activity
GO:0019838	0.68	growth factor binding
GO:0004888	0.68	transmembrane signaling receptor activity
GO:0004714	0.66	transmembrane receptor protein tyrosine kinase activity
GO:0098772	0.64	molecular function regulator
GO:1901363	0.62	heterocyclic compound binding
GO:0097367	0.62	carbohydrate derivative binding
GO:0097159	0.62	organic cyclic compound binding
GO:0046934	0.61	phosphatidylinositol-4,5-bisphosphate 3-kinase activity
GO:0005088	0.61	Ras guanyl-nucleotide exchange factor activity
GO:0005524	0.59	ATP binding
GO:0046983	0.56	protein dimerization activity
GO:0046982	0.52	protein heterodimerization activity
GO:0042802	0.52	identical protein 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:0044699	0.93	single-organism process
GO:0009987	0.86	cellular process
GO:0044763	0.82	single-organism cellular process
GO:0050794	0.80	regulation of cellular process
GO:0007165	0.76	signal transduction
GO:0007169	0.75	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0071704	0.73	organic substance metabolic process
GO:0044238	0.73	primary metabolic process
GO:0032502	0.72	developmental process
GO:0044767	0.71	single-organism developmental process
GO:0016310	0.71	phosphorylation
GO:0050790	0.67	regulation of catalytic activity
GO:0043085	0.66	positive regulation of catalytic activity
GO:0038127	0.65	ERBB signaling pathway
GO:0048518	0.64	positive regulation of biological process
GO:0043170	0.64	macromolecule metabolic process
GO:0019538	0.63	protein metabolic process
GO:0044710	0.62	single-organism metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0006468	0.61	protein phosphorylation
GO:0038128	0.60	ERBB2 signaling pathway
GO:0051345	0.59	positive regulation of hydrolase activity
GO:0048856	0.59	anatomical structure development
GO:0048583	0.59	regulation of response to stimulus
GO:0046777	0.59	protein autophosphorylation
GO:0044255	0.59	cellular lipid metabolic process
GO:0048869	0.58	cellular developmental process
GO:0043547	0.58	positive regulation of GTPase activity
GO:0009966	0.58	regulation of signal transduction
GO:1902531	0.57	regulation of intracellular signal transduction
GO:0046854	0.57	phosphatidylinositol phosphorylation
GO:0048584	0.56	positive regulation of response to stimulus
GO:1902533	0.55	positive regulation of intracellular signal transduction
GO:0009653	0.55	anatomical structure morphogenesis
GO:0050896	0.52	response to stimulus
GO:0016043	0.52	cellular component organization
GO:0030154	0.51	cell differentiation
GO:0032501	0.50	multicellular organismal 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:0044464	0.93	cell part
GO:0016020	0.86	membrane
GO:0005886	0.78	plasma membrane
GO:0044425	0.73	membrane part
GO:0044459	0.67	plasma membrane part
GO:0044424	0.61	intracellular part
GO:0043226	0.61	organelle
GO:0016021	0.61	integral component of membrane
GO:0043227	0.60	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0032991	0.56	macromolecular complex
GO:0098590	0.52	plasma membrane region
GO:0043234	0.52	protein complex
GO:0043235	0.50	receptor complex
GO:0005634	0.50	nucleus

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	0.325	2ahxB	0.873	1.74	0.696	0.911	2.7.10.1	22,59,147,160,162,165,168,170,172,174,178
2	0.205	1n8zC	0.799	2.72	0.354	0.893	2.7.10.1	19,24,59,164,169,172,174,178
3	0.066	1m6bB	0.752	3.07	0.388	0.900	2.7.10.1	2,17,19,22,24
4	0.060	1u22A	0.382	6.74	0.032	0.707	2.1.1.14	154,157
5	0.060	3h09B	0.390	6.08	0.044	0.654	3.4.21.72	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	0.09	1igrA	0.640	3.57	0.256	0.793	1.26	UUU	complex1.pdb.gz	57,59,80,81,82,83,85,151,166,167
2	0.06	1ivo0	0.775	3.19	0.345	0.914	0.67	III	complex2.pdb.gz	24,132,143,144,157,168,184,190,191,223,231,232,233
3	0.05	3ltfC	0.705	3.38	0.295	0.843	0.53	UUU	complex3.pdb.gz	48,98,104
4	0.04	2hr7A	0.621	3.75	0.266	0.786	0.55	UUU	complex4.pdb.gz	153,155,163

	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.