D-I-TASSER Q9Y4K0-D3

D-I-TASSER results for Q9Y4K0-D3

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

Input Sequence in FASTA format

>Q9Y4K0 (154 residues)
IPGFKFDNSLINQIENLNIQVEDIRIRAILSTYRKRTPVMEGYVEVKEGKTWKQICDKHW
TAKNSRVVCGMFGFPGERTYNTKVYKMFASRRKQRYWPFSMDCTGTEAHISSCKLGPQVS
LDPMKNVTCENGLPAVVSCVPGQVFSPDGPSRFR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| IPGFKFDNSLINQIENLNIQVEDIRIRAILSTYRKRTPVMEGYVEVKEGKTWKQICDKHWTAKNSRVVCGMFGFPGERTYNTKVYKMFASRRKQRYWPFSMDCTGTEAHISSCKLGPQVSLDPMKNVTCENGLPAVVSCVPGQVFSPDGPSRFR
Prediction	CCCCCCCCCCCCCCCCCCSSSCCCCSSSSCCCCCCCCCCCCSSSSSSSCCSSSCSSCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCC
Confidence	9887566775666677632625751897146789998775559999989988625389888668899999849995322455421135678887388873066377498777978776555887566899998679997489744899998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| IPGFKFDNSLINQIENLNIQVEDIRIRAILSTYRKRTPVMEGYVEVKEGKTWKQICDKHWTAKNSRVVCGMFGFPGERTYNTKVYKMFASRRKQRYWPFSMDCTGTEAHISSCKLGPQVSLDPMKNVTCENGLPAVVSCVPGQVFSPDGPSRFR
Prediction	4263434443123366251426724010120326644441101000236441010004414363032002222143144333323322244432201023030424153034043444443542343405253200233364534247365538
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCSSSCCCCSSSSCCCCCCCCCCCCSSSSSSSCCSSSCSSCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCC
IPGFKFDNSLINQIENLNIQVEDIRIRAILSTYRKRTPVMEGYVEVKEGKTWKQICDKHWTAKNSRVVCGMFGFPGERTYNTKVYKMFASRRKQRYWPFSMDCTGTEAHISSCKLGPQVSLDPMKNVTCENGLPAVVSCVPGQVFSPDGPSRFR

5ze3A

0.24

0.18

5.66

1.00

DEthreader

-----------------EQP----LVRLR-GGA----YIGEGRVEVLKNGEWGTVCDDKWDLVSASVVCRELGFGSAKEAVTG-SRLGQ--GIGPIHLNEIQCTGNEKSIIDCKFNAES------QG-CNHEEDAGVRCNTPAM-ELSAHCR-V

1by2A

0.24

0.18

5.46

3.32

SPARKS-K

-------------------AVNDGDMRLADGGAT-----NQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAA---FGQGSGPIMLDEVQCTGTEASLADCKSLG------WLKSNCRHERDAGVVCTNETTL---------

5a2eA

0.23

0.16

5.08

1.26

MapAlign

--------------------AENRALRLVDGG-----GACAGRVEMLEHGEWGSVCDDTWDLEDAHVVCRQLGCGWAVQALP--GLHF-TPGRGPIHRDQVNCSGAEAYLWDCPGLPGQ-------HYCGHKEDAGVVCSEH------------

1by2A

0.24

0.18

5.46

1.08

CEthreader

-------------------AVNDGDMRLADGGA-----TNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAF---GQGSGPIMLDEVQCTGTEASLADCKSLGWLK------SNCRHERDAGVVCTNETTL---------

1by2A

0.24

0.18

5.46

2.15

MUSTER

-------------------AVNDGDMRLA-----DGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAA---FGQGSGPIMLDEVQCTGTEASLADCKS------LGWLKSNCRHERDAGVVCTNETTL---------

5ze3A

0.19

0.16

5.25

3.19

HHsearch

FNA---ESQGCNHEEDAGVRCNTPKLRLNGGRNP-----YEGRVEVLVSLVWGMVCGQNWGIVEAMVVCRQLGLGFASNAFQETW--Y-WHGDNKVVMSGVKCSGTELSLAHCRHDG------ED-VACPQQYGAGVACSETAPD---LVLNAE

1by2A

0.24

0.17

5.27

1.43

FFAS-3D

---------------------NDGDMRLA-----DGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAA---FGQGSGPIMLDEVQCTGTEASLADCKSLG------WLKSNCRHERDAGVVCTNETTL---------

5a2eA

0.16

0.13

4.32

1.13

EigenThreader

HACRSDG----------RRARVTNRALRLVDGG----GACAGRVEMLEHGEWGSVCDDTWDLEDAHVVCRQLGCGWAVQALPGLH---FTPGRGPIHRDNCS-----------GAEAYLWDCPGGQHYCGHKEDAGVVCSEHQPKGLPHSLSGR

5a2eA

0.20

0.16

5.19

2.67

CNFpred

---------------RARVTCAENALRLVDGG-----GACAGRVEMLEHGEWGSVCDDTWDLEDAHVVCRQLGCGWAVQALP---GLHFTPGRGPIHRDQVNCSGAEAYLWDCPGLP-------GQHYCGHKEDAGVVCSEHQSWRLTGGADRC

5a2eA

0.19

0.14

4.60

1.00

DEthreader

------------------GSSSNRALRLVDGGG-----ACAGRVEMLEHGEWGSVCDDTWDLEDAHVVCRQLGCGWAVQALPG-LHFTP--GRGPIHRDQVNCSGAEAYLWDCPGL-PG-Q----HY-CGHKEDAGVVCSEH-F------EELT

(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	0.7004

(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	1by2A	0.67	1.51	0.232	0.714	model1_1by2A.pdb.gz
2	5a2eA	0.67	1.79	0.180	0.727	model1_5a2eA.pdb.gz
3	7bzzA	0.67	1.58	0.275	0.708	model1_7bzzA.pdb.gz
4	6sa4A	0.66	1.46	0.202	0.708	model1_6sa4A.pdb.gz
5	5ze3A	0.65	2.16	0.229	0.721	model1_5ze3A.pdb.gz
6	6j02A	0.64	1.07	0.243	0.669	model1_6j02A.pdb.gz
7	6h8mA	0.63	1.87	0.280	0.688	model1_6h8mA.pdb.gz
8	5jfbA	0.60	1.94	0.231	0.675	model1_5jfbA.pdb.gz
9	2xrcA2	0.56	2.91	0.175	0.688	model1_2xrcA2.pdb.gz
10	2oyaA	0.56	2.20	0.225	0.617	model1_2oyaA.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	0.81	catalytic activity
GO:0016491	0.67	oxidoreductase activity
GO:0004720	0.66	protein-lysine 6-oxidase activity
GO:0070492	0.57	oligosaccharide 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	0.96	single-organism process
GO:0009987	0.87	cellular process
GO:0044763	0.83	single-organism cellular process
GO:0065007	0.78	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0050794	0.71	regulation of cellular process
GO:0016043	0.69	cellular component organization
GO:0032502	0.67	developmental process
GO:0050896	0.65	response to stimulus
GO:0044767	0.65	single-organism developmental process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0009653	0.64	anatomical structure morphogenesis
GO:0048523	0.62	negative regulation of cellular process
GO:0010468	0.62	regulation of gene expression
GO:0080090	0.61	regulation of primary metabolic process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0006950	0.61	response to stress
GO:0008152	0.60	metabolic process
GO:0048869	0.59	cellular developmental process
GO:0031324	0.59	negative regulation of cellular metabolic process
GO:0030198	0.59	extracellular matrix organization
GO:0010605	0.59	negative regulation of macromolecule metabolic process
GO:0006355	0.59	regulation of transcription, DNA-templated
GO:0071822	0.58	protein complex subunit organization
GO:0071704	0.58	organic substance metabolic process
GO:0051239	0.58	regulation of multicellular organismal process
GO:0045892	0.58	negative regulation of transcription, DNA-templated
GO:0001837	0.58	epithelial to mesenchymal transition
GO:0048518	0.57	positive regulation of biological process
GO:0044238	0.57	primary metabolic process
GO:0043170	0.56	macromolecule metabolic process
GO:0048522	0.55	positive regulation of cellular process
GO:0009628	0.55	response to abiotic stimulus
GO:2000026	0.54	regulation of multicellular organismal development
GO:0045595	0.54	regulation of cell differentiation
GO:0051240	0.53	positive regulation of multicellular organismal process
GO:0045597	0.53	positive regulation of cell differentiation
GO:0030199	0.53	collagen fibril organization
GO:0019538	0.53	protein metabolic process
GO:0008283	0.53	cell proliferation
GO:0001666	0.53	response to hypoxia
GO:0001525	0.53	angiogenesis
GO:0043542	0.52	endothelial cell migration
GO:0032332	0.52	positive regulation of chondrocyte differentiation
GO:0002040	0.52	sprouting angiogenesis
GO:0001935	0.52	endothelial cell proliferation
GO:0044237	0.50	cellular 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:0044464	0.82	cell part
GO:0044421	0.77	extracellular region part
GO:0044424	0.67	intracellular part
GO:0043226	0.62	organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0005604	0.61	basement membrane
GO:0043229	0.50	intracellular organelle
GO:0005615	0.50	extracellular space

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	1yqwR	0.385	5.09	0.041	0.701	1.12.2.1	41
2	0.060	1p9bA	0.400	5.39	0.047	0.760	6.3.4.4	70
3	0.060	1nrgA	0.432	5.03	0.040	0.773	1.4.3.5	NA
4	0.060	3h0lA	0.401	5.22	0.063	0.727	6.3.5.-	NA
5	0.060	1z8lA	0.402	5.22	0.033	0.701	3.4.17.21	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	1t9mA	0.438	4.94	0.024	0.773	0.46	FMN	complex1.pdb.gz	46,55,67,69,105
2	0.01	3hy8A	0.428	5.07	0.057	0.766	0.47	FMN	complex2.pdb.gz	42,55,56,84,85
3	0.01	1ty9A	0.434	5.08	0.032	0.773	0.43	FMN	complex3.pdb.gz	27,28,29,70,71,72

	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.