D-I-TASSER Q92974-D3

D-I-TASSER results for Q92974-D3

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

Input Sequence in FASTA format

>Q92974 (165 residues)
RRLGEERATEAGSLEARLRESEQARALLEREAEEARRQLAALGQTEPLPAEAPWARRPVD
PRRRSLPAGDALYLSFNPPQPSRGTDRLDLPVTTRSVHRNFEDRERQELGSPEERLQDSS
DPDTGSEEEGSSRLSPPHSPRDFTRMQDIPEETESRDGEAVASES

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| RRLGEERATEAGSLEARLRESEQARALLEREAEEARRQLAALGQTEPLPAEAPWARRPVDPRRRSLPAGDALYLSFNPPQPSRGTDRLDLPVTTRSVHRNFEDRERQELGSPEERLQDSSDPDTGSEEEGSSRLSPPHSPRDFTRMQDIPEETESRDGEAVASES
Prediction	CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCHHHHHHCCCCCCCCCC
Confidence	922678872113225899999999999767788875448876214520122111025689877889988430024689876667655689887212127776433201489568876168999874223688999999930578875334877632466554579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| RRLGEERATEAGSLEARLRESEQARALLEREAEEARRQLAALGQTEPLPAEAPWARRPVDPRRRSLPAGDALYLSFNPPQPSRGTDRLDLPVTTRSVHRNFEDRERQELGSPEERLQDSSDPDTGSEEEGSSRLSPPHSPRDFTRMQDIPEETESRDGEAVASES
Prediction	865356426644435542441552344244525614541441454563446245445545444573533432222134542553454363534343234425446456435425425735575543555455445464446426405623551664735544678
	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 AttentionPotential. 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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCHHHHHHCCCCCCCCCC
RRLGEERATEAGSLEARLRESEQARALLEREAEEARRQLAALGQTEPLPAEAPWARRPVDPRRRSLPAGDALYLSFNPPQPSRGTDRLDLPVTTRSVHRNFEDRERQELGSPEERLQDSSDPDTGSEEEGSSRLSPPHSPRDFTRMQDIPEETESRDGEAVASES

4rsiB

0.05

2.31

0.49

CEthreader

EKNFTSAHLKLKEMQKVLNAHRQRAMEARSSLSKAQNKSKVLTALSRLQKSGRINGRLGDLGVIDDSFDVAISTACPRLDDVVVDTVRFILLDRLRQFNLQPISTPENVPRLFDLVKPRDTLVANVAYGKKRFRVVTVDGKLIDISGTMSGGGNHVAKGLMKLKV

7ko4P

0.06

2.64

0.50

EigenThreader

LEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNN

7abiK

0.18

0.13

4.32

0.58

FFAS-3D

NDEEEYEAWKVRELK-RIKRDREDREALEKEKAEIERMRN-LTEEERRAELRANGKVITNKAVKGK-------YKFLQKYYHRGAFFMD------------------------------------EDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNGRSGRTK-

4epoG

0.06

0.05

2.07

1.09

SPARKS-K

NRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDILVLDNCINKMVNNLSSEVKERRIVLIRERKAKRLF----------------------------------------

1d7mA

0.33

0.08

2.55

0.55

CNFpred

LKNLELEKLARMELEARLAKTEKDRAILELKLAEAIDEKSKLE--------------------------------------------------------------------------------------------------------------------------

3g61A1

0.05

0.04

1.98

1.00

DEthreader

RYRLMLVGTLAAIIHGVALPLMMLIFGDMTDSFASVGNVSKNSMSEADFAKLEEEMTTYAYYYTGGGLIVAYIQVSCLGRHKQKFH---NGIGKIGMNGVEMKMSG--------KKELEGSGYASLQIPYRNKKHVFITFSFTQAMMY-----------------

6zu9p

0.04

2.15

0.97

MapAlign

IPSAKVPVLKKALTSLFMEGFLFVECGMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSPSSSLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVRFSPKGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTF

5goxA

0.15

4.88

0.60

MUSTER

RDRLAKLNKELASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIEKSSRALAGATAVYSQF---TQLTDENQSCCPVCQRVFQTEAELQEQSKLRLAPDKLKSESELKKKEKRRDELGLVP----QSIIDLKEIPELRNKLQNVNRDIQR

1d7mA

0.36

0.09

2.71

0.62

HHsearch

KNLELEKLAR-MELEARLAKTEKDRAILELKLAEAIDEKSKLE--------------------------------------------------------------------------------------------------------------------------

5yjeA

0.09

0.08

2.96

0.46

CEthreader

----------------------------KLPIPSPQRAFTLQVPSMYIEVENEVTVVGGVKLSRLKCNREETVLTSRILTAAGSCDVVCVACEKRMLSVFSTCGRRLLLPSPISTLHCTGSYVMALTAAATLSVWDVHRQVVVVKEESLHSILAGSDMTVSQILL

(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	0.531

(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 AttentionPotential, 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	4acrA	0.50	4.73	0.105	0.788	model1_4acrA.pdb.gz
2	6wjlG	0.49	4.65	0.084	0.782	model1_6wjlG.pdb.gz
3	4a01A	0.49	5.24	0.053	0.812	model1_4a01A.pdb.gz
4	1e6yE	0.49	5.33	0.032	0.849	model1_1e6yE.pdb.gz
5	1f31A	0.48	4.67	0.037	0.746	model1_1f31A.pdb.gz
6	3jacA	0.48	4.98	0.050	0.812	model1_3jacA.pdb.gz
7	3odnA2	0.41	4.42	0.062	0.630	model1_3odnA2.pdb.gz
8	2fpqA	0.37	5.26	0.045	0.667	model1_2fpqA.pdb.gz
9	1bkgA	0.36	5.17	0.064	0.612	model1_1bkgA.pdb.gz
10	1xl6A	0.35	5.51	0.071	0.594	model1_1xl6A.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:0048365	1.00	Rac GTPase binding
GO:0098772	0.87	molecular function regulator
GO:0008092	0.84	cytoskeletal protein binding
GO:0005089	0.84	Rho guanyl-nucleotide exchange factor activity
GO:0030676	0.83	Rac guanyl-nucleotide exchange factor activity
GO:0008017	0.83	microtubule 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:0044093	1.00	positive regulation of molecular function
GO:0001934	1.00	positive regulation of protein phosphorylation
GO:0009987	0.88	cellular process
GO:0044699	0.87	single-organism process
GO:0044763	0.86	single-organism cellular process
GO:0048583	0.85	regulation of response to stimulus
GO:0016043	0.85	cellular component organization
GO:2000112	0.84	regulation of cellular macromolecule biosynthetic process
GO:1902531	0.84	regulation of intracellular signal transduction
GO:0051239	0.84	regulation of multicellular organismal process
GO:0051171	0.84	regulation of nitrogen compound metabolic process
GO:0048523	0.84	negative regulation of cellular process
GO:0033043	0.84	regulation of organelle organization
GO:0032989	0.84	cellular component morphogenesis
GO:0010468	0.84	regulation of gene expression
GO:0010033	0.84	response to organic substance
GO:0071225	0.83	cellular response to muramyl dipeptide
GO:0051092	0.83	positive regulation of NF-kappaB transcription factor activity
GO:0050731	0.83	positive regulation of peptidyl-tyrosine phosphorylation
GO:0045944	0.83	positive regulation of transcription from RNA polymerase II promoter
GO:0032760	0.83	positive regulation of tumor necrosis factor production
GO:0032755	0.83	positive regulation of interleukin-6 production
GO:0007026	0.83	negative regulation of microtubule depolymerization
GO:0007015	0.83	actin filament organization
GO:0000902	0.83	cell morphogenesis
GO:0080135	0.68	regulation of cellular response to stress
GO:0046578	0.68	regulation of Ras protein signal transduction
GO:0007165	0.60	signal transduction

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:0043234	1.00	protein complex
GO:0032587	1.00	ruffle membrane
GO:0031982	1.00	vesicle
GO:0005874	1.00	microtubule
GO:0005856	1.00	cytoskeleton
GO:0005737	1.00	cytoplasm
GO:0044444	0.54	cytoplasmic part

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	1dysA	0.415	4.86	0.043	0.673	3.2.1.4	NA
2	0.060	1hbmB	0.469	5.44	0.025	0.842	2.8.4.1	NA
3	0.060	1w27A	0.422	5.61	0.071	0.751	4.3.1.24	NA
4	0.060	1tj7A	0.426	5.23	0.050	0.709	4.3.2.1	NA
5	0.060	2pflA	0.432	5.41	0.038	0.782	2.3.1.54	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	2agvA	0.416	4.97	0.019	0.691	0.40	PTY	complex1.pdb.gz	13,69,73

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.