D-I-TASSER Q92985-D2

D-I-TASSER results for Q92985-D2

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

Input Sequence in FASTA format

>Q92985 (139 residues)
EAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKGDLLLQAVQQSCLADHLLTASW
GADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGEAAAP
ESPHQAEPYLSPSPSACTA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKGDLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGEAAAPESPHQAEPYLSPSPSACTA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9722278877999986224578766799888887886023899999997412211112246899999999877788998877778877764233445556778999988755666678999977678667899765779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKGDLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGEAAAPESPHQAEPYLSPSPSACTA
Prediction	8436744466444323213466443533531444455433001310342236431142534454334734467374245444255443342442343325435446443331446526447435445424445454258
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
EAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKGDLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGEAAAPESPHQAEPYLSPSPSACTA

2vlcA

0.06

2.75

0.46

CEthreader

QFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSSKAEQKWALYPDGSIRPHQDRDRCLTSTNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATG

4gyoA2

0.04

1.92

0.55

EigenThreader

EAYMIAAAYYNVGHCKYSLG-------DYKEAEGYFKTAAAIFEEHNFQQAVQAVFSLTHIYCKEGKYDKAVEAYDRGIKSAAEWEDDMYLTKFRLIHELYLGLLHDTAERFNQLEHYESAAFFYRRLMNIKKKLAEQR

7abiT

0.15

5.07

0.45

FFAS-3D

KATRNSVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGQEMREALQEKEIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETRLKEKKPGDLSDELRISLGMPVPPPWIAMQRYGPPPSYPNLKIPGLNSPLYGDV-

5jcss

0.05

2.34

1.32

SPARKS-K

GVEIYIDELHSRSTAFDRLTLGFELGENIDFVSIDDGIKKIKLNE-PDMSIPLKHYVPSYLSRPCIFAQVHDILLLSDEEPILAAVIPISHLGEVKWANNVLNCTEYSEKKIAERLYVFITFLTDMGVLEKINNLYK--

3hdqA

0.21

0.04

1.37

0.32

CNFpred

-------------------------------------SEDVVVSKVGRDLYNKGYTRKQWGLDPS--------------------------------------------------------------------------

6kptA

0.09

0.07

2.78

0.83

DEthreader

SFFKSMALFDGGWDKVGLA-----E-HLGGI-P--MPRALQWALIEHILGNPAAYMYAMGPGSAERGWGSSDDFNIMPK-FHFDH---ETGEIGERNGVFVATCARMVGTIAAEG-RAILTALVKDLYEG---------

2nr4A1

0.08

0.05

2.03

0.74

MapAlign

----LSSFGIREGISEIIASTGFEHPNAAPIGIVMLASNVVDPILFVRSTFSDLVPSEFEYVDGEFKFPVLKIAWVVFECINLRNTDQSLVADLVPL------------------------------------------

2nbiA

0.20

0.19

6.24

0.81

MUSTER

ECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPSSAPSDCGEVIEECPLDTCFLPTSDPARPPDCTAVGRPDCDVLPFPNNLGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPTPQP-STPTVITSPAPSSQPS

2pffB

0.17

0.14

4.71

0.56

HHsearch

EAYPNTSLPP-SILEDSLEN--NEGVPSPMLSLTQEQVQDYVNK--TNSHLPAGKQVISLVKNLVVS-GPPQSLYGLN----------------LTLRKAKAPSGLDQSRIPFSERKLKFS--NRFLPVASPFHLLVPA

6pkgA

0.06

2.75

0.41

CEthreader

SDGKLVRNSGGIQNAQFGIRKDGTLVFVQLISGVVWYINESIQAECDKTQETGNFRHFVDVISARTAVGHDKEGKLILFHVDGQTDVRGMNLWQVAKFLKDQNVMNAGSATYVLNGSLASYPSDHCNPSKWRCPRAIST

(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	0.502

(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	7ay1A	0.41	4.29	0.038	0.676	model1_7ay1A.pdb.gz
2	6h02A	0.41	4.81	0.065	0.691	model1_6h02A.pdb.gz
3	5t8vA	0.40	4.91	0.051	0.712	model1_5t8vA.pdb.gz
4	1uf2B	0.39	4.91	0.058	0.662	model1_1uf2B.pdb.gz
5	5jcss	0.39	4.69	0.036	0.669	model1_5jcss.pdb.gz
6	7banA	0.39	5.12	0.072	0.691	model1_7banA.pdb.gz
7	5julA	0.39	5.03	0.061	0.698	model1_5julA.pdb.gz
8	7enjW3	0.38	5.00	0.029	0.698	model1_7enjW3.pdb.gz
9	8earA	0.38	5.05	0.050	0.676	model1_8earA.pdb.gz
10	6ltaA	0.38	4.74	0.051	0.647	model1_6ltaA.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:0000982	1.00	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000979	1.00	RNA polymerase II core promoter sequence-specific DNA 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:0045944	1.00	positive regulation of transcription from RNA polymerase II promoter
GO:0045089	1.00	positive regulation of innate immune response
GO:0044238	1.00	primary metabolic process
GO:0043170	1.00	macromolecule metabolic process
GO:0034127	1.00	regulation of MyD88-independent toll-like receptor signaling pathway
GO:0034124	1.00	regulation of MyD88-dependent toll-like receptor signaling pathway
GO:0032728	1.00	positive regulation of interferon-beta production
GO:0032727	1.00	positive regulation of interferon-alpha production
GO:0032608	1.00	interferon-beta production
GO:0032607	1.00	interferon-alpha production
GO:0006955	1.00	immune response
GO:0002819	1.00	regulation of adaptive immune response
GO:0009987	0.82	cellular process
GO:0007165	0.80	signal transduction
GO:0044237	0.78	cellular metabolic process
GO:0019221	0.78	cytokine-mediated signaling pathway
GO:0051704	0.77	multi-organism process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:0060337	0.76	type I interferon signaling pathway
GO:0048519	0.76	negative regulation of biological process
GO:0016032	0.76	viral process
GO:0006950	0.76	response to stress
GO:0006351	0.76	transcription, DNA-templated
GO:2000113	0.75	negative regulation of cellular macromolecule biosynthetic process
GO:2000026	0.75	regulation of multicellular organismal development
GO:0051716	0.75	cellular response to stimulus
GO:0051172	0.75	negative regulation of nitrogen compound metabolic process
GO:0045595	0.75	regulation of cell differentiation
GO:0045087	0.75	innate immune response
GO:0035556	0.75	intracellular signal transduction
GO:0010629	0.75	negative regulation of gene expression
GO:0009615	0.75	response to virus
GO:0002224	0.75	toll-like receptor signaling pathway
GO:2000110	0.74	negative regulation of macrophage apoptotic process
GO:0060333	0.74	interferon-gamma-mediated signaling pathway
GO:0045655	0.74	regulation of monocyte differentiation
GO:0039530	0.74	MDA-5 signaling pathway
GO:0035666	0.74	TRIF-dependent toll-like receptor signaling pathway
GO:0019043	0.74	establishment of viral latency
GO:0006974	0.74	cellular response to DNA damage stimulus
GO:0006366	0.74	transcription from RNA polymerase II promoter
GO:0000122	0.74	negative regulation of transcription 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:0005737	1.00	cytoplasm
GO:0005654	1.00	nucleoplasm
GO:0044444	0.53	cytoplasmic part
GO:0043226	0.50	organelle

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	2np0A	0.235	5.30	0.043	0.453	3.4.24.69	NA
2	0.060	2vdcF	0.348	4.49	0.017	0.590	1.4.1.13	NA
3	0.060	1t7nA	0.292	4.56	0.043	0.482	2.3.1.7	NA
4	0.060	3f2bA	0.305	4.68	0.036	0.540	2.7.7.7	NA
5	0.060	2pdaA	0.271	4.14	0.058	0.424	1.2.7.1	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:

No Binding sites was predicted

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

	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.