D-I-TASSER P35408-D3

D-I-TASSER results for P35408-D3

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

Input Sequence in FASTA format

>P35408 (155 residues)
KTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDSQRTSSAMSGHSRSFISRELKEISSTSQ
TLLPDLSLPDLSENGLGGRNLLPGVPGMGLAQEDTTSLRTLRISETSDSSQGQDSESVLL
VDEAGGSGRAGPAPKGSSLQVTFPSETLNLSEKCI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDSQRTSSAMSGHSRSFISRELKEISSTSQTLLPDLSLPDLSENGLGGRNLLPGVPGMGLAQEDTTSLRTLRISETSDSSQGQDSESVLLVDEAGGSGRAGPAPKGSSLQVTFPSETLNLSEKCI
Prediction	CHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCC
Confidence	53899999985722112157767778876753320101221678431122334331122213324668761115789876688887666677776311010244345655566655136640578888888899999624654732323112359
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDSQRTSSAMSGHSRSFISRELKEISSTSQTLLPDLSLPDLSENGLGGRNLLPGVPGMGLAQEDTTSLRTLRISETSDSSQGQDSESVLLVDEAGGSGRAGPAPKGSSLQVTFPSETLNLSEKCI
Prediction	74103400540320002115544745443136344333313542443135415533531312023363461365525454224324435156644542541445446545535544422233435655655435764414131454325256528
	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

CHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCC
KTVLSKAIEKIKCLFCRIGGSRRERSGQHCSDSQRTSSAMSGHSRSFISRELKEISSTSQTLLPDLSLPDLSENGLGGRNLLPGVPGMGLAQEDTTSLRTLRISETSDSSQGQDSESVLLVDEAGGSGRAGPAPKGSSLQVTFPSETLNLSEKCI

2cwhB

0.06

2.57

0.48

CEthreader

EPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQ

4xa3A

0.06

0.05

2.31

0.48

EigenThreader

------PLKPEEHEDILNKLLDPELAQSERTEALQQLRVNYGSFVSEYNDLTKSLSKANSEVAQWRTKYETDAIQRTEELEEA----KKKLAQRLQEAEEAVEAVNAKCSSLEKTKHR--LQNEIDFYFGKLRNIELICQENDPVLQRIVDILY-

2du7A2

0.12

0.10

3.62

0.28

FFAS-3D

---VMETIERLRQAYLRMG--------FEEMINPVIVDIYKQFGPE--AMAVLD------RCFYLAGLPRPDVGLGNEKVEIIKNLGIDIDEEKKERLREVLHLYKKGAIDGDDLSNEMGLKVLETAFPEFKDLKPESTTLTLRSHMT-------

6ahfC1

0.07

0.06

2.46

0.87

SPARKS-K

TERALTILTLAQKLASDHQH--PQLQPIHIETPEDGSVPYLQNLIEKGRYDYDLFKKVVNR--NLVRIPQQQPAPAEITPSYALKIQKQQKDSFIAQFNDSSIQQIFKEAQVDIEAIKQQALELRGNTRIDSRGADTNTPLE-------------

4k82A

0.12

0.04

1.36

0.47

CNFpred

-----DLLVELAVIICAYQ-NGKDLQEQDFKE-----------LKELLERTLERAGCALDDIVADL-----------------------------------------------------------------------------------------

3zuxA

0.06

0.05

2.21

0.83

DEthreader

PKVVIIGVIAQFAIMPATAWCLSLPAIAVVILVCPGGTASMTARGNVLSVAVTSVSTLTSPLLTPAIFLMLA------GEM------------LMS-VKMVLLPIVG--PSVIVLIIGVVSKG--MESGLIFVHNGGYGFAA------PYDAQLT

4gfhA

0.06

2.57

0.79

MapAlign

IFDEILVNAADNKVRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLETADLNVGQKYVQKWENNMSICHDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLIPTILYERINNRWEVAFAV

1f6gA

0.15

0.14

4.59

0.60

MUSTER

LSGLARLV---KLLLGRHGSALHWAAAGAAT-VLLAGSYLERGAPGAQLITYPAALWWSVETATTVGYGDLYPVTLWGRAVVVMVAGITSFGLVTAALATWFVGREQERRGHFVRHSEKAAEEAYTRTTRALHERFDRLE----RMLDDNRR---

2pffB

0.20

0.18

5.79

0.65

HHsearch

FFV--SVRKAITVLFFIG-V--------RCYEAYPNTSLLNNVPSPLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS-LYGLNL-TLRKAKAPSGLDQSRIPFSERRFLINKDLVKNNVSFNAKDIQIPVTFDGSDLRISERCI

4woyA

0.07

2.89

0.46

CEthreader

EAHVTLAKQLAGDIALELQAYLRSKF-PELPFGALVPGGPLYDGLQAGTAEHVRLLAPLELEPGLWSLVPGVDTVAAEPRCWAVRRTQLEFHPRGCSPWD---RFLVGGYLSSRVLLELLRKALSASVNWPAIGSLLGCLIWPDVASEELLLKVQ

(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	0.4459

(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	3cmmC	0.49	5.29	0.074	0.884	model1_3cmmC.pdb.gz
2	5v96A	0.48	5.16	0.061	0.839	model1_5v96A.pdb.gz
3	4ii2A	0.48	5.36	0.041	0.871	model1_4ii2A.pdb.gz
4	6dc6A	0.48	5.23	0.068	0.865	model1_6dc6A.pdb.gz
5	3p9dD	0.48	4.41	0.063	0.774	model1_3p9dD.pdb.gz
6	7lumL2	0.48	4.32	0.024	0.768	model1_7lumL2.pdb.gz
7	3aq1B	0.48	4.57	0.040	0.787	model1_3aq1B.pdb.gz
8	3ko1A	0.48	4.65	0.063	0.787	model1_3ko1A.pdb.gz
9	7lumO1	0.48	4.58	0.076	0.793	model1_7lumO1.pdb.gz
10	3p9dA2	0.47	4.76	0.084	0.800	model1_3p9dA2.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:0004957	1.00	prostaglandin E receptor 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:0065007	0.99	biological regulation
GO:0050789	0.99	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0007187	0.95	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0007188	0.94	adenylate cyclase-modulating G-protein coupled receptor signaling pathway
GO:0048519	0.76	negative regulation of biological process
GO:0048583	0.75	regulation of response to stimulus
GO:0048523	0.74	negative regulation of cellular process
GO:2000420	0.73	negative regulation of eosinophil extravasation
GO:0050728	0.73	negative regulation of inflammatory response
GO:0033624	0.73	negative regulation of integrin activation
GO:0009987	0.71	cellular process
GO:0044699	0.70	single-organism process
GO:0044763	0.64	single-organism cellular process
GO:0050896	0.62	response to stimulus
GO:0065008	0.57	regulation of biological quality
GO:0098771	0.55	inorganic ion homeostasis
GO:0030003	0.55	cellular cation homeostasis
GO:0010033	0.55	response to organic substance
GO:0006950	0.55	response to stress
GO:1901700	0.54	response to oxygen-containing compound
GO:0051716	0.54	cellular response to stimulus
GO:0009719	0.54	response to endogenous stimulus
GO:0007204	0.54	positive regulation of cytosolic calcium ion concentration
GO:0007189	0.54	adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:0071380	0.53	cellular response to prostaglandin E stimulus

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	0.99	cell part
GO:0044425	0.91	membrane part
GO:0005887	0.90	integral component of plasma membrane

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	1aq6A	0.429	4.58	0.067	0.710	3.8.1.2	NA
2	0.060	1ajsA	0.424	5.16	0.078	0.787	2.6.1.1	NA
3	0.060	1ajrA	0.426	5.20	0.079	0.787	2.6.1.1	NA
4	0.060	1szqA	0.442	5.38	0.107	0.806	4.2.1.79	49
5	0.060	1cf3A	0.433	5.38	0.085	0.813	1.1.3.4	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	2j2pF	0.440	4.56	0.114	0.716	0.72	SC2	complex1.pdb.gz	21,26,28,29
	2	0.01	2j2pC	0.435	5.01	0.082	0.742	0.63	SC2	complex2.pdb.gz	41,57,59

	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.