D-I-TASSER Q9NRA1-D2

D-I-TASSER results for Q9NRA1-D2

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

Input Sequence in FASTA format

>Q9NRA1 (182 residues)
MPQFTEAVSPSVLPPSALPLDLLNNAITAFSTLEDLIRYLEPERWQLDLEDLYRPTWQLL
GKAFVFGRKSRVVDLNLLTEEVRLYSCTPRNFSVSIREELKRTDTIFWPGCLLVKRCGGN
CACCLHNCNECQCVPSKVTKKYHEVLQLRPKTGVRGLHKSLTDVALEHHEECDCVCRGST
GG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MPQFTEAVSPSVLPPSALPLDLLNNAITAFSTLEDLIRYLEPERWQLDLEDLYRPTWQLLGKAFVFGRKSRVVDLNLLTEEVRLYSCTPRNFSVSIREELKRTDTIFWPGCLLVKRCGGNCACCLHNCNECQCVPSKVTKKYHEVLQLRPKTGVRGLHKSLTDVALEHHEECDCVCRGSTGG
Prediction	CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCSSSSSSSSCCCCCCCCCSSSSCCCSSSSSCCCCCCCCCCCCCSSSSSCCSSSSSSSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCSSSCCCCCCC
Confidence	98755578888688653626789999874156999998718760233466531455555655444455555555320122200254168769998643699875688368079873236777777888625877888999999999998158987520135898620003327182899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MPQFTEAVSPSVLPPSALPLDLLNNAITAFSTLEDLIRYLEPERWQLDLEDLYRPTWQLLGKAFVFGRKSRVVDLNLLTEEVRLYSCTPRNFSVSIREELKRTDTIFWPGCLLVKRCGGNCACCLHNCNECQCVPSKVTKKYHEVLQLRPKTGVRGLHKSLTDVALEHHEECDCVCRGSTGG
Prediction	75544545536435545233731453154153043015204164154235414364454455444474454545354145404414043353305035527524120203113032001204234454440403545344242311303245645434441440304305504241476688
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCSSSSSSSSCCCCCCCCCSSSSCCCSSSSSCCCCCCCCCCCCCSSSSSCCSSSSSSSSSSSSSSCCCCCCCSSSSSSSSSSCCCCCSSSCCCCCCC
MPQFTEAVSPSVLPPSALPLDLLNNAITAFSTLEDLIRYLEPERWQLDLEDLYRPTWQLLGKAFVFGRKSRVVDLNLLTEEVRLYSCTPRNFSVSIREELKRTDTIFWPGCLLVKRCGGNCACCLHNCNECQCVPSKVTKKYHEVLQLRPKTGVRGLHKSLTDVALEHHEECDCVCRGSTGG

6rutB

0.04

0.03

1.74

0.83

DEthreader

NGQQKVEYHVVKELEVQRLQKD--LLQTT-FF-NPRRHPEWFGQLPFEAYFANIGNMFIF-VFRIKYTDNFS-------VKWVG-Q---AGTLLRLGTIPVESTLVGNWTSQDGGWFI-TFTDFI--RPRYGITLSSLQQIWADSFQLYQAATN--LKLTTKIKL---SQTINTITTTN---

3mjkA

0.28

0.19

5.87

2.01

SPARKS-K

---------------EAEIPREVIERLAQIHSIRDLQRLLEIDS---------------------VRRKRI--------EEAVPAVCKTRTVIYEIPRDPTSANFLIWPPCVEVKRCTGCC-----NTSSVKCQPSRVHHRSVKVAKVEYVRKKP--KLKEVQVRLEEHLECACA-------

5aejA

0.11

0.06

2.18

0.82

MapAlign

-----------------------------LESSQEALHVT-------------------------------------ERKYLKRDWCKTQPLKQTIH------EEGCNSRTIINRFCYGQCNSFGSFQSCSFCKPKKFTTMMVTLNCPEL-------QPPTKKKRVTRVKQCRCISIDL---

1wq8A

0.24

0.13

4.10

0.82

CEthreader

--------------------------------------------------------------------------VRPFLEVHERSACQARETLVPILQEYDEISDIFRPSCVAVLRCSGCCTDE-----SLKCTPVGKHTVDIQIMRVNP----RTQSSKMEVMKFTEHTACECRPRRKQG-

3mjkA

0.29

0.20

6.03

1.71

MUSTER

--------------EAEIPREVIERLARQIHSIRDLQRLLEIDSV---------------------RRKRI--------EEAVPAVCKTRTVIYEIPRSQTSANFLIWPPCVEVKRCTG---CCNTSS--VKCQPSRVHHRSVKVAKVEYVRKKPKL--KEVQVRLEEHLECACA-------

3mjkA

0.27

0.18

5.58

3.81

HHsearch

---------------EAEIPREVIERLAQIHSIRDLQRLLEIDSV---------------RR------KR--------IEEAVPAVCKTRTVIYEIPRSQTSANFLIWPPCVEVKRCTGCC---NTSS--VKCQPSRVHHRSVKVAKVEYVRKK--PKLKEVQVRLEEHLECACA-------

3mjkA

0.27

0.19

5.73

1.49

FFAS-3D

--------------EAEIPREVIERARSQIHSIRDLQRLLEIDS-----------------------------VRRKRIEEAVPAVCKTRTVIYEIPRSQTSANFLIWPPCVEVKRCTGCC-----NTSSVKCQPSRVHHRSVKVAKVEYVRKKP--KLKEVQVRLEEHLECAC--------

3rjrA

0.08

0.07

2.65

0.82

EigenThreader

QILSKLRLASPPSQGDVPPG--------PLPEAVLALYNSTRDVTGVVRQWLTRREAIGDLATIHGMNRPFLLLMATPLERAQHALCCVRQLYIDFRKDLGWKWIHEP-KGYHACLGPLYNQHNPGASAAPCCVPQALEPLPI---VYYVG----RKPKVEQLSNMIVRSCKCS--------

3mjkA

0.27

0.18

5.41

2.74

CNFpred

---------------AEIPREVIERLARQIHSIRDLQRLLEIDSV---------------------------------IEEAVPAVCKTRTVIYEIPRSQVDANFLIWPPCVEVKRCTGCCNTS-----SVKCQPSRVHHRSVKVAKVEYVRK--KPKLKEVQVRLEEHLECACA-------

5y9dA

0.07

0.05

2.09

0.83

DEthreader

-------KISIEDPSVTADY-DC--N--L----AR-QTMERVALTRLSIHNNLFIGSIGSGRNFVRQNMLMRYAALDQLVTTKELFAASAMKTCAIIDECRQGSNGFGYDWVQ---NLCSMGRGQPDAFLRCAIHQHIFAFLTFLFINAPYFAKNQQ-------------------------

(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	0.6074

(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	7bwmA	0.46	5.67	0.040	0.819	model1_7bwmA.pdb.gz
2	6rutB	0.45	5.64	0.034	0.791	model1_6rutB.pdb.gz
3	2x1xE	0.44	1.89	0.196	0.483	model1_2x1xE.pdb.gz
4	1katV	0.43	2.29	0.214	0.489	model1_1katV.pdb.gz
5	1iduA	0.43	5.14	0.077	0.720	model1_1iduA.pdb.gz
6	1wq8A	0.43	2.41	0.204	0.489	model1_1wq8A.pdb.gz
7	2xv7A	0.42	2.21	0.243	0.478	model1_2xv7A.pdb.gz
8	2gnnB	0.42	2.26	0.255	0.467	model1_2gnnB.pdb.gz
9	2vweA	0.42	2.81	0.250	0.489	model1_2vweA.pdb.gz
10	3mjkA	0.42	2.24	0.190	0.472	model1_3mjkA.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:0070851	0.99	growth factor receptor binding
GO:0005161	0.94	platelet-derived growth factor receptor 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:0050794	1.00	regulation of cellular process
GO:0048522	0.99	positive regulation of cellular process
GO:0008284	0.98	positive regulation of cell proliferation
GO:0080090	0.97	regulation of primary metabolic process
GO:0031325	0.97	positive regulation of cellular metabolic process
GO:0010604	0.97	positive regulation of macromolecule metabolic process
GO:0048583	0.96	regulation of response to stimulus
GO:0044699	0.96	single-organism process
GO:0001934	0.96	positive regulation of protein phosphorylation
GO:0048584	0.95	positive regulation of response to stimulus
GO:0030335	0.95	positive regulation of cell migration
GO:0007169	0.95	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0031954	0.94	positive regulation of protein autophosphorylation
GO:0023051	0.94	regulation of signaling
GO:0010646	0.94	regulation of cell communication
GO:0009966	0.93	regulation of signal transduction
GO:1902533	0.92	positive regulation of intracellular signal transduction
GO:0070372	0.92	regulation of ERK1 and ERK2 cascade
GO:0065008	0.92	regulation of biological quality
GO:0070374	0.91	positive regulation of ERK1 and ERK2 cascade
GO:0050878	0.91	regulation of body fluid levels
GO:0048008	0.91	platelet-derived growth factor receptor signaling pathway
GO:0043406	0.91	positive regulation of MAP kinase activity
GO:0014068	0.91	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0007596	0.90	blood coagulation

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:0005615	0.99	extracellular space
GO:0044464	0.61	cell 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	1u2zC	0.398	5.15	0.084	0.692	2.1.1.43	25
2	0.060	1vncA	0.433	5.13	0.084	0.714	1.11.1.10	100
3	0.060	1nekA	0.393	5.18	0.038	0.665	1.3.99.1	NA
4	0.060	1jroB	0.400	5.18	0.060	0.681	1.1.1.204	NA
5	0.060	1ti2A	0.349	5.63	0.030	0.626	1.97.1.2	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	0.03	1bj10	0.432	1.91	0.226	0.472	1.14	III	complex1.pdb.gz	88,90,91,93,108,109,110,111,112,113,119,120,122,142,143,144,146
2	0.03	1mjv0	0.433	2.13	0.211	0.478	1.09	III	complex2.pdb.gz	90,93,108,109,111,112,113,118,119,142,143,144,146,163
3	0.03	2xv7A	0.423	2.21	0.243	0.478	0.65	UUU	complex3.pdb.gz	94,96,110,112
4	0.03	2x1wA	0.431	1.89	0.216	0.472	0.59	UUU	complex4.pdb.gz	91,92,93,94,113
5	0.03	1vppV	0.437	1.85	0.221	0.478	0.50	III	complex5.pdb.gz	90,91,92,93,111,112,114,115,116,117,118

	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.