D-I-TASSER Q9Y2T1-D3

D-I-TASSER results for Q9Y2T1-D3

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

Input Sequence in FASTA format

>Q9Y2T1 (132 residues)
KQRCCVASQQRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFC
GEEIPYRRMLKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMY
EGRILGKVERID

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KQRCCVASQQRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFCGEEIPYRRMLKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMYEGRILGKVERID
Prediction	CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCSSSSCCCCCCCHHHHHHHHCCCCCSSSSSSCCCCCCCCCCSSSSSCCCCCCCCCCCCSSSSSSSSCC
Confidence	964323342123356888899888777766686544556788998878876069999808987646863588878899999984789855899832386679970899974798523453887999999669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KQRCCVASQQRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFCGEEIPYRRMLKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMYEGRILGKVERID
Prediction	854346544547544554464544434545344774564564564554444301000114754121315147650314403630656441402023417637252032103447430012543010304748
	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

CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCSSSSCCCCCCCHHHHHHHHCCCCCSSSSSSCCCCCCCCCCSSSSSCCCCCCCCCCCCSSSSSSSSCC
KQRCCVASQQRDRNHSATVQTGATPFSNPSLAPEDHKEPKKLAGVHALQASELVVTYFFCGEEIPYRRMLKAQSLTLGHFKEQLSKKGNYRYYFKKASDEFACGAVFEEIWEDETVLPMYEGRILGKVERID

2d5gB

0.58

0.37

10.66

1.00

DEthreader

--------------P----------------------------------CDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.67

2.35

SPARKS-K

-----------------------------------------------PPCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.66

0.92

MapAlign

------------------------------------------------PCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.67

0.95

CEthreader

-----------------------------------------------PPCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.67

1.89

MUSTER

-----------------------------------------------PPCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.67

4.60

HHsearch

-----------------------------------------------PPCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2d5gB

0.58

0.37

10.66

1.81

FFAS-3D

------------------------------------------------PCDSIVVAYYFCGEPIPYETLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

1z2mA

0.08

0.07

2.73

0.75

EigenThreader

SSSMSVSELKAQITQKIGVHAFQGVALQDRVPLASQGLGPLLV--VDKSDEPLSILVRN--NKGRSSYEVRL-TQTVAHLKQQVVQDDLFWLTFEG----------KPLEDQLPLGEYGLKPLSTVFMNLRL

1wspA

0.61

0.38

10.85

2.17

CNFpred

--------------------------------------------------DSIVVAYYFCGEPIPYRTLVRGRAVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILPVFEEKIIGKVEKVD

2kmaA

0.07

0.05

2.15

0.83

DEthreader

---------PPNDFGLFLSDPK----------------------KGIMEYRKRPLKIRM-LDGTVKTIMVD-DSKTVTDMLMTCINHDEYSLVRELMEEKK---DELNWLD-HGRTLQGVEEHETLLLRRKF

(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	0.6925

(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	2d5gB	0.62	1.06	0.576	0.644	model1_2d5gB.pdb.gz
2	2kmaA	0.56	3.27	0.086	0.758	model1_2kmaA.pdb.gz
3	3pz7A	0.56	1.54	0.341	0.614	model1_3pz7A.pdb.gz
4	3pz8A	0.54	1.36	0.333	0.591	model1_3pz8A.pdb.gz
5	3jyuA	0.54	3.36	0.078	0.727	model1_3jyuA.pdb.gz
6	1ty2A	0.54	3.37	0.056	0.750	model1_1ty2A.pdb.gz
7	5f3yA	0.53	3.54	0.046	0.727	model1_5f3yA.pdb.gz
8	1ktkC	0.53	3.38	0.085	0.735	model1_1ktkC.pdb.gz
9	3ea6A	0.52	3.48	0.083	0.750	model1_3ea6A.pdb.gz
10	3pvlA	0.52	3.67	0.055	0.727	model1_3pvlA.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:0098772	0.69	molecular function regulator
GO:0008047	0.68	enzyme activator activity
GO:0005096	0.67	GTPase activator activity
GO:0019899	0.66	enzyme binding
GO:0019901	0.65	protein kinase binding
GO:0008013	0.65	beta-catenin binding
GO:0019904	0.63	protein domain specific binding
GO:0070016	0.61	armadillo repeat domain 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:0050794	0.99	regulation of cellular process
GO:0016055	0.96	Wnt signaling pathway
GO:0044699	0.78	single-organism process
GO:0009987	0.78	cellular process
GO:0048583	0.68	regulation of response to stimulus
GO:0009966	0.67	regulation of signal transduction
GO:0080090	0.66	regulation of primary metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0044763	0.66	single-organism cellular process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0051239	0.63	regulation of multicellular organismal process
GO:0048519	0.63	negative regulation of biological process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0030111	0.63	regulation of Wnt signaling pathway
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0048523	0.62	negative regulation of cellular process
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0060828	0.61	regulation of canonical Wnt signaling pathway
GO:0050896	0.61	response to stimulus
GO:0044707	0.61	single-multicellular organism process
GO:0032879	0.60	regulation of localization
GO:0009968	0.60	negative regulation of signal transduction
GO:1903827	0.59	regulation of cellular protein localization
GO:0048869	0.59	cellular developmental process
GO:0042221	0.59	response to chemical
GO:0030178	0.59	negative regulation of Wnt signaling pathway
GO:0090090	0.58	negative regulation of canonical Wnt signaling pathway
GO:0051716	0.58	cellular response to stimulus
GO:0045595	0.58	regulation of cell differentiation
GO:0010033	0.58	response to organic substance
GO:0007389	0.58	pattern specification process
GO:0090244	0.57	Wnt signaling pathway involved in somitogenesis
GO:0071407	0.57	cellular response to organic cyclic compound
GO:0035412	0.57	regulation of catenin import into nucleus
GO:0060070	0.56	canonical Wnt signaling pathway
GO:0045596	0.56	negative regulation of cell differentiation
GO:0009950	0.55	dorsal/ventral axis specification
GO:0008219	0.54	cell death

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:0044424	1.00	intracellular part
GO:0044444	0.95	cytoplasmic part
GO:0043226	0.73	organelle
GO:0043229	0.72	intracellular organelle
GO:0005737	0.70	cytoplasm
GO:0043227	0.69	membrane-bounded organelle
GO:0044446	0.68	intracellular organelle part
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0016020	0.66	membrane
GO:0044430	0.62	cytoskeletal part
GO:0043232	0.62	intracellular non-membrane-bounded organelle
GO:0005886	0.62	plasma membrane
GO:0032991	0.60	macromolecular complex
GO:0043234	0.59	protein complex
GO:0031982	0.57	vesicle
GO:0005938	0.57	cell cortex
GO:0031988	0.56	membrane-bounded vesicle
GO:0031410	0.56	cytoplasmic vesicle
GO:0097458	0.55	neuron part
GO:0016023	0.55	cytoplasmic, membrane-bounded vesicle
GO:0005874	0.55	microtubule
GO:0030877	0.53	beta-catenin destruction complex
GO:0014069	0.53	postsynaptic density
GO:0005881	0.53	cytoplasmic microtubule

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	1pxtB	0.425	4.45	0.030	0.727	2.3.1.16	88
2	0.060	2o2vA	0.424	2.45	0.056	0.530	2.7.12.2	113,130
3	0.060	2ib7D	0.433	4.19	0.041	0.712	2.3.1.9	88
4	0.060	2vz8A	0.438	4.62	0.042	0.758	2.3.1.85	NA
5	0.060	1mdwA	0.344	5.35	0.079	0.667	3.4.22.53	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	0.03	3a9kA	0.425	1.83	0.108	0.492	0.90	III	complex1.pdb.gz	60,91,93,107,127,129
2	0.02	1q0wB	0.422	2.00	0.106	0.500	0.86	III	complex2.pdb.gz	60,91,93,94,107,108,110,127,128,129,130,131,132
3	0.02	3a9kB	0.430	1.97	0.121	0.500	0.78	III	complex3.pdb.gz	119,120,121,122
4	0.02	1aar0	0.426	1.96	0.121	0.500	0.75	III	complex4.pdb.gz	61,94,107,108,109,126,128,129

	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.