D-I-TASSER Q9NRA1-D1

D-I-TASSER results for Q9NRA1-D1

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

Input Sequence in FASTA format

>Q9NRA1 (163 residues)
MSLFGLLLLTSALAGQRQGTQAESNLSSKFQFSSNKEQNGVQDPQHERIITVSTNGSIHS
PRFPHTYPRNTVLVWRLVAVEENVWIQLTFDERFGLEDPEDDICKYDFVEVEEPSDGTIL
GRWCGSGTVPGKQISKGNQIRIRFVSDEYFPSEPGFCIHYNIV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSLFGLLLLTSALAGQRQGTQAESNLSSKFQFSSNKEQNGVQDPQHERIITVSTNGSIHSPRFPHTYPRNTVLVWRLVAVEENVWIQLTFDERFGLEDPEDDICKYDFVEVEEPSDGTILGRWCGSGTVPGKQISKGNQIRIRFVSDEYFPSEPGFCIHYNIV
Prediction	CSSSSSSSSSCCCCCCSCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCSSSCCCSSSSCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSSSCCSSSCCCCCCCCCCCSSSSSCCCCCCSSSSSSCCCCCCCCSSSSCCSSSSSSSSCCCCCCCCCSSSSSSSC
Confidence	9799877764477663257438982899557660578886425889972895797699799998469899809999995699909999982331311577987447588994599995788871899899848981998999999699856798569999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSLFGLLLLTSALAGQRQGTQAESNLSSKFQFSSNKEQNGVQDPQHERIITVSTNGSIHSPRFPHTYPRNTVLVWRLVAVEENVWIQLTFDERFGLEDPEDDICKYDFVEVEEPSDGTILGRWCGSGTVPGKQISKGNQIRIRFVSDEYFPSEPGFCIHYNIV
Prediction	4321110201033313321332423030323131445463153352324133575040201212566364340303032357423020303330404446533111010103137544201310244433440303134324453124324444134042434
	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

CSSSSSSSSSCCCCCCSCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCSSSCCCSSSSCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSSSCCSSSCCCCCCCCCCCSSSSSCCCCCCSSSSSSCCCCCCCCSSSSCCSSSSSSSSCCCCCCCCCSSSSSSSC
MSLFGLLLLTSALAGQRQGTQAESNLSSKFQFSSNKEQNGVQDPQHERIITVSTNGSIHSPRFPHTYPRNTVLVWRLVAVEENVWIQLTFDERFGLEDPEDDICKYDFVEVEEPSDGTILGRWCGSGTVPGKQISKGNQIRIRFVSDEYFPSEPGFCIHYNIV

3kq4B

0.26

0.20

6.06

1.00

DEthreader

--------------------------IRDGIISHS------SSTGCGGNLTTS-SGTFISPNYPMPYYHSSECYWWLKSSH-GSAFELEFK-DFHLEH--HPNCTLDYLAVYGPSNSHLLTQLCGDE-KPPLIRSSGDSMFIKLRTDEGQ-QGRGFKAEYRQT

6gh8A

0.34

0.25

7.34

1.82

SPARKS-K

-----------------------------------------LGSPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHD---CKYDFIEIRDGDSEDLLGKHCGN-IAPPTIISSGSMLYIRFTSD-YARQGAGFSLRYEIF

2qqmA1

0.29

0.20

6.16

0.95

MapAlign

---------------------------------------------CSQNYTT-PSGVIKSPGFPEKYPNSLECTYIVFAPKM-SEIILEFE-SFDLEPDGGMFCRYDRLEIWDGFVGPHIGRYCGQK-TPGRIRSSSGILSMVFYTDSAI-AKEGFSANYSVL

2qqmA1

0.30

0.21

6.34

0.74

CEthreader

-------------------------------------------PECSQNYT-TPSGVIKSPGFPEKYPNSLECTYIVFAPK-MSEIILEFE-SFDLEPDGGMFCRYDRLEIWDGFPGPHIGRYCGQ-KTPGRIRSSSGILSMVFYTDSAI-AKEGFSANYSVL

3demA

0.20

0.19

6.10

1.41

MUSTER

YMAVDVDECKELSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIEL-EEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPK--VLGPFCGEK-APEPISTQSHSVLILFHSDNS-GENRGWRLSYRAA

2qqmA

0.30

0.21

6.34

2.33

HHsearch

-------------------------------------------PECSQNYT-TPSGVIKSPGFPEKYPNSLECTYIVFAP-KMSEIILEFE-SFDLEPDGGMFCRYDRLEIWDGFPGPHIGRYCGQK-TPGRIRSSSGILSMVFYTDSA-IAKEGFSANYSVL

6f1cA2

0.18

0.13

4.18

1.69

FFAS-3D

-------------------------------------------AECSSELYTEASGYISSLEYPRSYPPDLRCNYSIRVERG-LTLHLKFLEPFDIDDHQQVHCPYDQLQIYANG---KNIGEFCGKQRPPDLDTSSNAVDLLFFTDESG-DSRGWKLRYTTE

3demA2

0.18

0.16

5.18

0.93

EigenThreader

---------------LSCDHYCHNYIGGYYCSCRFGYTDNRTCRVECSDNLFTQRTVITSPDFPNPYPKSSECLYTIEL-EEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVG--PKVLGPFCGEKAPE-PISTQSHSVLILFHS-DNSGENRGWRLSYRAA

4gz9A

0.35

0.25

7.33

2.05

CNFpred

-------------------------------------------DKCGGTIKIENPGYLTSPGYPHSYHPSEKCEWLIQAPEPYQRIMINFNPHFDLED---RDCKYDYVEVIDGE-GRLWGKFCGKIA-PSPVVSSGPFLFIKFVSDYET-HGAGFSIRYEIF

6f1cA

0.22

0.16

5.04

1.00

DEthreader

-----------------------------RP-GYE-------QAECSELYTEA-SGYISSLEYPRSYPPDLRCNYSIRVE-RGLTLHLKFLEPFDIDDHQQVHCPYDQLQIYA-N-GKNIGEFCGKQ-RPPDLDTSSNAVDLLFFTDE-SGDSRGWKLRYTTE

(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	0.7429

(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	3kq4B	0.71	2.96	0.188	0.841	model1_3kq4B.pdb.gz
2	6f1cA	0.67	1.77	0.161	0.730	model1_6f1cA.pdb.gz
3	3demA2	0.66	1.82	0.200	0.724	model1_3demA2.pdb.gz
4	6gh8A	0.66	1.64	0.333	0.718	model1_6gh8A.pdb.gz
5	5fwsA	0.66	3.19	0.190	0.822	model1_5fwsA.pdb.gz
6	4gzaH	0.65	1.55	0.348	0.706	model1_4gzaH.pdb.gz
7	4losA1	0.64	1.89	0.222	0.718	model1_4losA1.pdb.gz
8	2qqmA	0.64	1.90	0.287	0.706	model1_2qqmA.pdb.gz
9	1nt0A2	0.62	1.97	0.199	0.693	model1_1nt0A2.pdb.gz
10	2qqoA	0.62	1.55	0.300	0.675	model1_2qqoA.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:0005102	0.66	receptor binding
GO:0070851	0.53	growth factor receptor binding
GO:0005161	0.51	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:0065007	0.93	biological regulation
GO:0044699	0.93	single-organism process
GO:0050789	0.92	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0048583	0.81	regulation of response to stimulus
GO:0048518	0.74	positive regulation of biological process
GO:0009966	0.74	regulation of signal transduction
GO:0048522	0.68	positive regulation of cellular process
GO:0019222	0.68	regulation of metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0080090	0.66	regulation of primary metabolic process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0048584	0.65	positive regulation of response to stimulus
GO:0031325	0.62	positive regulation of cellular metabolic process
GO:0010604	0.62	positive regulation of macromolecule metabolic process
GO:0007165	0.62	signal transduction
GO:0032268	0.61	regulation of cellular protein metabolic process
GO:0019220	0.61	regulation of phosphate metabolic process
GO:1902531	0.60	regulation of intracellular signal transduction
GO:0045937	0.60	positive regulation of phosphate metabolic process
GO:0007166	0.60	cell surface receptor signaling pathway
GO:0001932	0.60	regulation of protein phosphorylation
GO:0009967	0.59	positive regulation of signal transduction
GO:0007167	0.59	enzyme linked receptor protein signaling pathway
GO:0001934	0.59	positive regulation of protein phosphorylation
GO:0043408	0.58	regulation of MAPK cascade
GO:0032501	0.58	multicellular organismal process
GO:0009987	0.57	cellular process
GO:0044707	0.55	single-multicellular organism process
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:0070372	0.50	regulation of ERK1 and ERK2 cascade
GO:0065008	0.50	regulation of biological quality
GO:0032879	0.50	regulation of localization
GO:0007169	0.50	transmembrane receptor protein tyrosine kinase signaling pathway

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:0044421	0.80	extracellular region part
GO:0005615	0.74	extracellular space
GO:0044464	0.66	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	3ecqB	0.513	3.85	0.029	0.755	3.2.1.97	NA
2	0.060	3ffzA	0.480	4.55	0.034	0.797	3.4.24.69	NA
3	0.060	1nt0A	0.625	1.97	0.178	0.693	3.4.21.104	61,107,124,148
4	0.060	1uwwA	0.471	4.34	0.064	0.724	3.2.1.4	89,94,140
5	0.060	2rfwA	0.505	4.18	0.056	0.736	3.2.1.91	110

	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	0.05	2wnoA	0.646	1.69	0.304	0.706	0.63	CA	complex1.pdb.gz	113,137,139,140
2	0.04	3pobA	0.640	1.38	0.241	0.687	1.07	III	complex2.pdb.gz	97,99,105,106
3	0.04	1szb0	0.592	1.97	0.283	0.656	0.60	III	complex3.pdb.gz	64,84,87,89,91
4	0.04	1nzi0	0.577	1.81	0.269	0.638	0.53	III	complex4.pdb.gz	54,55,63,64,84,89,92
5	0.03	1nt0A	0.625	1.97	0.178	0.693	0.55	CA	complex5.pdb.gz	107,108,110,125
6	0.03	1spp1	0.572	2.44	0.174	0.669	0.74	III	complex6.pdb.gz	87,88,89,130,155,156,157,159

	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.