D-I-TASSER Q9NPJ1-D2

D-I-TASSER results for Q9NPJ1-D2

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

Input Sequence in FASTA format

>Q9NPJ1 (169 residues)
GLTPTTVIRLNKHLLSLCISYLKSETCGCRIPWALLGGGCTETHLAAYIRHKTHNDPESI
LKDDECTQTELQLIAEAFCSALESVVGSLEHDGGEILTDMKYGHLWSVQADSPCVANWPD
LLSQCGCGLYNSQEELNWSFLRSTRRPFVPQSCLPHEAVGSASNLTLDC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GLTPTTVIRLNKHLLSLCISYLKSETCGCRIPWALLGGGCTETHLAAYIRHKTHNDPESILKDDECTQTELQLIAEAFCSALESVVGSLEHDGGEILTDMKYGHLWSVQADSPCVANWPDLLSQCGCGLYNSQEELNWSFLRSTRRPFVPQSCLPHEAVGSASNLTLDC
Prediction	CCCCCSSSHHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCSSSCCCCCCSSSCCCCCCCCCCHHHHCCCCCCCCSCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCSSSCC
Confidence	9986212134499999999999999974368726427871899999999998505862455413776899999999999999999988641487544306776255258998776771554363455220277776502217878998998887532457655514429
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GLTPTTVIRLNKHLLSLCISYLKSETCGCRIPWALLGGGCTETHLAAYIRHKTHNDPESILKDDECTQTELQLIAEAFCSALESVVGSLEHDGGEILTDMKYGHLWSVQADSPCVANWPDLLSQCGCGLYNSQEELNWSFLRSTRRPFVPQSCLPHEAVGSASNLTLDC
Prediction	8344333241353024204412401321153120021122121101221333335446521563513433033004100400330022043532320213421120113463444351451244010011555761413203343541317423656336435413152
	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

CCCCCSSSHHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCHHHHHHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCSSSCCCCCCSSSCCCCCCCCCCHHHHCCCCCCCCSCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCSSSCC
GLTPTTVIRLNKHLLSLCISYLKSETCGCRIPWALLGGGCTETHLAAYIRHKTHNDPESILKDDECTQTELQLIAEAFCSALESVVGSLEHDGGEILTDMKYGHLWSVQADSPCVANWPDLLSQCGCGLYNSQEELNWSFLRSTRRPFVPQSCLPHEAVGSASNLTLDC

5x9uA1

0.15

0.13

4.36

0.66

CEthreader

GVPVSKVLAGMNRALNHALFLIRKNAIGV-----LPGGGAFFLYLSREVESLKNRLPG-----------MESYGVMAFSEALKVPFRVMAENAGFNGLEKLGDLMTL-----------QVQKNNYALGLDFETGEFIDMIAGGVVDPAEVVYQAVKNASEVAISLLKIN

1s5jA

0.08

3.22

0.68

EigenThreader

NDLTMKLIVLFSRISRWVKNLYYWEHRKRNWLIIVCMRPGITAVITGLLRDFRVKIYKKKAKNPNNSYDVVQRAMKVFINATYGVFGAETFPEGLTYGDT--DSLFLNPPKNSLENIIKWVKTTFNLDNYFQDGKVD-IKGMLVVKKKLKIDAEKYSTFEQILRAFGVS

3iyeP3

0.15

0.11

3.76

0.57

FFAS-3D

AKTEHVIEEVARAV----DDAVGVVGCTIEDGRIVSGGGSTEVELSMKLREYAEGI-------SGREQLAVRAFADALEVIPRTLAENAGLDAIEILVKVRAAHASNGNKCAGLNVFTGAVEDMCENGVVEPLR-----------------------------------

1a6eB4

0.11

0.08

2.99

0.77

SPARKS-K

--HPTVISEGYRMASEEAKRVIDEIS-----TAYAAGGGATAAEIAFRLRSYAQKIGGR-------QQLAIEKFADAIEDILLKLRAEHAKGNKTYGINVFTG-EIEDMVKNGVIEPIRVGKQAIESATEAAIMILRIDDVIA--------------------------

1q2vA

0.19

0.08

2.49

0.73

CNFpred

---------VIDEVERALEDAVKVVKDVMEDGAVLPAGGAPEIELAIRLDEYAKQV-----------GGKEALAIENFADALKIIPKTLA-------------------------------------------------------------------------------

6wxrA3

0.08

0.06

2.38

0.83

DEthreader

-ENYRRHIGCVAVFYTITGALFLERAYYYAHTIILSRGTAASISFMFSYILLTMCRLIFLRTLNRIPFDAAVDFHRLIASTAIILTVLHSAG-HVV----------NVYLFSISP-L--VLSCL---FPGLFHQWFQTLVLLLAYV------------------LIQMP

3p9dF2

0.10

0.09

3.46

0.92

MapAlign

-VHPRIITDGFEIARKESMKFLDEFANVLKDKNIIPGAGAFYIALSRYLRSAN----MNKLGAKGK----TKTGIEAFAEALLVIP-------KLVKNGFDPLDVLAEDELDQDSDETRYVGVDLNIGDSCDPTIEGIWDSYRVLRNAITGATGIASNLLLCDELLRAG

1a6eB4

0.20

0.15

4.92

0.71

MUSTER

--HPTVISEGYRMASEEAKRVIDEIS-----TAYAAGGGATAAEIAFRLRSYAQKIGG-----------RQQLAIEKFADAIEEIPRALAENAGDILLKLRAEHA-KGNKTYVFTGEIEDMVKN---GV--------IEPIRVGKQAI-------ESATEAA--LRIDD

3p9dF2

0.15

0.13

4.36

1.08

HHsearch

NLTHY----ALAQTKDAVRDGLRAVANVLKDKNIIPGAGAFYIALSRYLRSANKLG----------AKGKTKTGIEAFAEALLVIPKTLVKDPLDVLAMVEDELDDAQDS-----------DETRYVGVDLNTIEGIWDSYRVLRNAITGAGIAS-NLL-LCDELLRAG

1a6eB4

0.16

0.13

4.34

0.61

CEthreader

--HPTVISEGYRMASEEAKRVIDEIS-----TAYAAGGGATAAEIAFRLRSYAQKIGG-----------RQQLAIEKFADAIEEIPRALAENAGL------------DPIDILLKLRAEHAKGNKTYGINVFTGEIEDMVKNGVIEPIRVGKQAIESATEAAIMILRID

(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	0.581

(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	7k3zA	0.50	4.22	0.081	0.746	model1_7k3zA.pdb.gz
2	5hsjA	0.49	4.90	0.037	0.793	model1_5hsjA.pdb.gz
3	5xbjA	0.48	4.78	0.046	0.757	model1_5xbjA.pdb.gz
4	3b4rA	0.48	4.26	0.053	0.728	model1_3b4rA.pdb.gz
5	6sgwB2	0.48	3.89	0.046	0.651	model1_6sgwB2.pdb.gz
6	1mn1A	0.48	4.89	0.086	0.793	model1_1mn1A.pdb.gz
7	6larB	0.47	4.00	0.039	0.651	model1_6larB.pdb.gz
8	6lnaA	0.47	5.07	0.027	0.751	model1_6lnaA.pdb.gz
9	2d4yA	0.47	4.59	0.038	0.722	model1_2d4yA.pdb.gz
10	2hi4A	0.47	5.04	0.058	0.757	model1_2hi4A.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:0001103	1.00	RNA polymerase II repressing transcription factor binding
GO:0051082	0.57	unfolded protein 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:1902589	1.00	single-organism organelle organization
GO:0070925	1.00	organelle assembly
GO:0048513	0.99	animal organ development
GO:0044707	0.99	single-multicellular organism process
GO:0042384	0.99	cilium assembly
GO:0009653	0.99	anatomical structure morphogenesis
GO:0048869	0.87	cellular developmental process
GO:0060271	0.86	cilium morphogenesis
GO:0030154	0.74	cell differentiation
GO:0060296	0.73	regulation of cilium beat frequency involved in ciliary motility
GO:0050910	0.73	detection of mechanical stimulus involved in sensory perception of sound
GO:0048854	0.73	brain morphogenesis
GO:0045494	0.73	photoreceptor cell maintenance
GO:0045444	0.73	fat cell differentiation
GO:0038108	0.73	negative regulation of appetite by leptin-mediated signaling pathway
GO:0035176	0.73	social behavior
GO:0021987	0.73	cerebral cortex development
GO:0021766	0.73	hippocampus development
GO:0021756	0.73	striatum development
GO:0007608	0.73	sensory perception of smell
GO:0007286	0.73	spermatid development
GO:0060027	0.68	convergent extension involved in gastrulation
GO:0051877	0.68	pigment granule aggregation in cell center
GO:0046907	0.68	intracellular transport
GO:0032402	0.68	melanosome transport
GO:0007368	0.68	determination of left/right symmetry
GO:0001947	0.68	heart looping

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:0044430	1.00	cytoskeletal part
GO:0043232	1.00	intracellular non-membrane-bounded organelle
GO:0031514	0.99	motile cilium
GO:0005813	0.99	centrosome
GO:0005622	0.99	intracellular

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	3fjwA	0.451	4.78	0.085	0.740	1.11.1.16	NA
2	0.060	2rfcA	0.446	4.98	0.057	0.710	1.14.14.1	22
3	0.060	3eqmA	0.457	4.93	0.067	0.722	1.14.14.1	NA
4	0.060	1egyA	0.431	4.79	0.096	0.698	1.14.-.-	NA
5	0.060	1ly8A	0.451	5.02	0.060	0.763	1.11.1.7	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	0.14	2h7sC	0.451	4.93	0.089	0.722	0.19	HEM	complex1.pdb.gz	19,22,26,27,38
2	0.01	1mn1A	0.476	4.89	0.086	0.793	0.18	HEM	complex2.pdb.gz	17,18,20,21,26,36,37,38,39
3	0.01	1phfA	0.449	4.99	0.089	0.722	0.15	UUU	complex3.pdb.gz	21,22,24,25,29
4	0.01	3oiaA	0.453	4.95	0.049	0.722	0.14	A31	complex4.pdb.gz	38,92,93,115
5	0.01	7cppA	0.460	4.77	0.068	0.722	0.14	HEM	complex5.pdb.gz	38,96,109,124,126
6	0.01	3p6pA	0.454	4.88	0.056	0.710	0.19	A6B	complex6.pdb.gz	38,86,87,91
7	0.01	1gebA	0.450	4.94	0.075	0.710	0.12	HEM	complex7.pdb.gz	83,84,87,88
8	0.01	1mnpA	0.473	5.09	0.092	0.811	0.17	HEM	complex8.pdb.gz	14,15,17,19,24,25,36,37
9	0.01	1cp4A	0.460	4.71	0.069	0.716	0.13	UUU	complex9.pdb.gz	22,26,30
10	0.01	3p3oA	0.452	4.80	0.069	0.710	0.19	HEM	complex10.pdb.gz	15,22,39

	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.