D-I-TASSER Q9Y2W1-D4

D-I-TASSER results for Q9Y2W1-D4

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

Input Sequence in FASTA format

>Q9Y2W1 (149 residues)
VPKPSPPLSSTSQMGSTLPSGAGYQSGTHQGQFDHGSGSLSPSKKSPVGKSLARPSGLLA
QERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGM
TLHERFTKYLKRGTEQEAAKNKKSPEIHR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VPKPSPPLSSTSQMGSTLPSGAGYQSGTHQGQFDHGSGSLSPSKKSPVGKSLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIHR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCC
Confidence	99999999885112554655434445564111355555533212114544456776542135665335775167631145599872154446797589999999999999886368889756799999985123466651268953379
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VPKPSPPLSSTSQMGSTLPSGAGYQSGTHQGQFDHGSGSLSPSKKSPVGKSLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIHR
Prediction	87567344554574556453565445436545153637635153435255535444633455442333003125547503300431534546644444014201300330364215557140343045147544546435556446448
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCC
VPKPSPPLSSTSQMGSTLPSGAGYQSGTHQGQFDHGSGSLSPSKKSPVGKSLARPSGLLAQERKLCRDLVHSNKKEQEFRSIFQHIQSAQSQRSPSELFAQHIVTIVHHVKEHHFGSSGMTLHERFTKYLKRGTEQEAAKNKKSPEIHR

4c2mA1

0.07

2.81

0.46

CEthreader

GAFLRNLCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRASCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITLSSTLLNELKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGKCDN

4xgcA

0.05

2.45

0.50

EigenThreader

MRLTELDILCNRRQDVVYNLLDWPTKLVVVTIANTMDLPYSHKQLQEIVTARLGKGEAVQLVARKVAAVSGDARRALDICRRATEIADTAAVKCVTMLHVQQALAEMIAAEVTRTGVEETTFMGVYQQVETIAAFMGRLCSKLGAERLI

5flzA1

0.09

0.06

2.31

0.52

FFAS-3D

------------------------------------IGLEGTYIRYFNDIEFKIAKKMDPSFKTFSRRIVRYGK---QYMILTRAYEKWSDTSFGLQRFAYEIRRLVERLERDFNKVPNFSIRELEQIINETEVNKQMEL---------

5yfpE5

0.08

0.07

2.88

0.79

SPARKS-K

------------KKKDFVPKSQELLDQDTLIEIVNILNLIFEQSSKFLKGKNL-QTFLTLIGEELYGLLLSHYSHTKDIIGYQTAIEDWGVASLIDKATLRELANLF-TVQPELLES---LTKEGHLADIGRDIIQSYISNREDFNHDN

2ijqA

0.13

0.07

2.34

0.47

CNFpred

--------------------------------------------------------ETLRRAVVHGVRLYNSG-EFHESHDCFEDEWYNYGRGNTESKFLHGMVQVAAGAYKHFDFEDDDGMRSLFRTSLQYFRGV-------------

6i33A

0.12

0.11

3.79

0.83

DEthreader

-HIG----------GYYNCSVPQTRENSGITQYTPYNASLLDEGGGHPFVPLDQAQGYQQLFRELEKDLCELTGGSDVGVKLAPLNLKACP-VGTVSA-PWGSSSILPISWA-YI--KMMG-GKGLKQATETAILNANYMAKRLTHYIR

3q3uA

0.06

0.05

2.11

0.71

MapAlign

--------------------MVSCGGGRSVKNAACCAWFPVLDDIQANLFNGGKCEEEAHEAVRLTFHILPNFGLEFTTEGFIPFAL---AHGVSFGDFVQFAGAVGAAKILARMADIGFSPTEVVHLLAMVNNFEAVMSRLAVIGQIP

1td6A1

0.06

0.05

2.31

0.56

MUSTER

-------------------PNQFVNHLSALKKHFASYKELREAFNDYHKHNGDELTTFFLHQFDKVMELVKQKDFKTAQSRCEEELAAPYLPKPLVSFFQSLLQLVNHDLLEQQNAAASLPAAKIIELVLQDYPNMIHYLLPKTKAF--

6tgbA1

0.16

0.15

4.89

0.75

HHsearch

GGGGFPEIIMPGDV-----RNDIYITLLQ-GDFDKYNKNVEVIMCVCADGKTLNAICVGAGDKPMNEYRSVEDMQRIHLRFMFRHRSSLESKDKGEKNFAMSYVKL--------MKEDGTTLHDGFHDLVVLKKEDASAYLTLPSYRHH

5hpdA

0.08

0.05

2.10

0.41

CEthreader

----------------------------------------------------SPQESRRLSIQRCIQSLVHACPSCQKMKRVVQHTKGCKRKTNGGCPVCKQLIALCCYHAKHCENKCPVPFCLNIKHKLRQQQGSGSGSEEPQSDPSV

(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	0.512

(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	3ecpA	0.51	3.92	0.034	0.725	model1_3ecpA.pdb.gz
2	5xeiA	0.50	5.24	0.063	0.893	model1_5xeiA.pdb.gz
3	2awnB	0.50	4.59	0.055	0.792	model1_2awnB.pdb.gz
4	6wg3B	0.50	5.18	0.056	0.852	model1_6wg3B.pdb.gz
5	7d3uD	0.49	5.06	0.042	0.852	model1_7d3uD.pdb.gz
6	5x7kA	0.49	4.78	0.032	0.799	model1_5x7kA.pdb.gz
7	6z16D	0.49	4.94	0.021	0.812	model1_6z16D.pdb.gz
8	6yufC	0.48	5.42	0.056	0.866	model1_6yufC.pdb.gz
9	4hluD	0.48	4.52	0.089	0.765	model1_4hluD.pdb.gz
10	3ikmD	0.48	4.85	0.042	0.805	model1_3ikmD.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:0003677	1.00	DNA binding
GO:0044822	0.76	poly(A) RNA binding
GO:0051219	0.74	phosphoprotein binding
GO:0003713	0.74	transcription coactivator activity
GO:0001046	0.74	core promoter sequence-specific DNA binding
GO:0046966	0.50	thyroid hormone receptor binding
GO:0004872	0.50	receptor activity
GO:0001104	0.50	RNA polymerase II transcription cofactor 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:0051254	1.00	positive regulation of RNA metabolic process
GO:0010628	1.00	positive regulation of gene expression
GO:0009987	1.00	cellular process
GO:0045893	0.76	positive regulation of transcription, DNA-templated
GO:0048255	0.74	mRNA stabilization
GO:0048026	0.74	positive regulation of mRNA splicing, via spliceosome
GO:0042753	0.74	positive regulation of circadian rhythm
GO:0000956	0.74	nuclear-transcribed mRNA catabolic process
GO:0000381	0.74	regulation of alternative mRNA splicing, via spliceosome
GO:0045944	0.50	positive regulation of transcription from RNA polymerase II promoter
GO:0030521	0.50	androgen receptor signaling pathway
GO:0006367	0.50	transcription initiation from RNA polymerase II promoter

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:0044428	1.00	nuclear part
GO:0005634	1.00	nucleus
GO:0005654	0.90	nucleoplasm
GO:0016607	0.79	nuclear speck
GO:0043234	0.75	protein complex
GO:0035145	0.59	exon-exon junction complex

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	2b0tA	0.466	4.96	0.056	0.799	1.1.1.42	NA
2	0.060	2awnA	0.316	5.61	0.033	0.597	3.6.3.19	NA
3	0.060	3fvqB	0.475	4.89	0.039	0.812	3.6.3.30	NA
4	0.060	2eabA	0.449	5.02	0.060	0.799	3.2.1.63	NA
5	0.060	1ctsA	0.423	5.29	0.051	0.792	2.3.3.1 4.1.3.7	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:

Click to view	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	1f2uA	0.286	5.10	0.045	0.497	0.20	ATP	complex1.pdb.gz	30,36,40,41
	2	0.01	1murA	0.513	3.87	0.034	0.725	0.10	QNA	complex2.pdb.gz	115,118,119,125

	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.