D-I-TASSER Q9NZF1-D1

D-I-TASSER results for Q9NZF1-D1

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

Input Sequence in FASTA format

>Q9NZF1 (115 residues)
MQAQAPVVVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNE
CCLCGTSVAMRTLYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MQAQAPVVVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNECCLCGTSVAMRTLYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF
Prediction	CCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	9989998253189877788888999757855707981125559866789983177872672489999999999999949999842689999841449999999999997503899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MQAQAPVVVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNECCLCGTSVAMRTLYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF
Prediction	7754544433423444444545655142100102233420110010000110232343220001100122123116426166330200000300220000023321542674767
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
MQAQAPVVVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNECCLCGTSVAMRTLYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF

2uuiA

0.06

2.64

0.59

CEthreader

LLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGARSAQLRLAPLYASALWLLVALAALGLLAHFLPAA

3vskA

0.06

2.61

0.65

EigenThreader

VSQQLSKLDRKYYSRNDRVGKSYRSQGPKNGDILALDIGTFTSQFAVGSSVKGGTLLAGYQNPAQKLRRGLNQVE----PLTNNPGNYLDLSIGQPLQLSQYVSTIANFKMAFND

2el7A1

0.13

0.10

3.62

0.40

FFAS-3D

-NPEAPRVPGIDGKAKMSKSLGNT------IGLLEP----------EESIWQKIQHLPDDPTILFTYLSYFEALKEEYRKAGVGTYVVKRILF---DHLMEALRPIRERAEA---

4nreA2

0.09

3.29

0.92

SPARKS-K

PGCGPLLPLAIQLSQTPGPN-------SPIFLPTDDKWDWLLAKTWVRNAEFSFHEALTHLLHSHLLPEVFTLATLRQLPHCHPLFKLLIPHTRYTLHINTLARELLIVPGQVVD

4rflA

0.03

0.02

1.15

0.62

CNFpred

-------------------------------------NKLVKALVGSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGIGTIMMSYLHEKENKKLSGLHEKI

4a01A

0.05

0.03

1.70

0.83

DEthreader

---VIAIFIT-------------------------LFGRVGGGIYVGIAGMGSDLFGSYILDAAIGKGFAIGSAALVSLLVSGVQIAISASNGLKTSGPSLNILIKLMAVESLVF

3caiA

0.09

0.07

2.63

0.71

MapAlign

-------------------PAGMLIPDSVATTV---STAFRRSSAAVLDAAREAVADNSASGTLGDHSAATVNAHA-WGGPPIGAMVFRDPSVMNFGLLAGVVASIEYLA-----

4didB

0.12

0.11

3.96

0.61

MUSTER

--ARPEIIVLREPGATWGNYLQHQK---------ASNHSLHNLYNLQRDLLTVAATVLGKQDPVLTSMANQMELAKVKADRPATKQEEAAAKALKKNLIELIAARTQQQDGLPAK

1vt4I3

0.09

3.34

0.87

HHsearch

-EYALHRSIVNIPKTFDSDDLIPPYLDQYFYSHLKNIEPERMTLFRMVFLDFRFLEQIHDSALPKYERLVNAILDFLPIEENLICSKYTDLLRIALMADEAIFEEAHKQVQRGGG

2xsdC

0.14

0.09

2.98

0.56

CEthreader

----------------------------------------APSSDDLEQFAKQFKQR--RIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLFKNMCKLKPLLNKWLEETDS

(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	0.6733

(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	6l85A	0.51	4.51	0.036	0.913	model1_6l85A.pdb.gz
2	3vf1A	0.50	4.33	0.027	0.826	model1_3vf1A.pdb.gz
3	3dy5A3	0.50	4.37	0.035	0.826	model1_3dy5A3.pdb.gz
4	6qjaA	0.50	3.57	0.034	0.722	model1_6qjaA.pdb.gz
5	4nreA2	0.49	4.37	0.055	0.809	model1_4nreA2.pdb.gz
6	2pfmA	0.49	3.22	0.071	0.722	model1_2pfmA.pdb.gz
7	2zr3A2	0.49	4.40	0.011	0.817	model1_2zr3A2.pdb.gz
8	3c8tA1	0.49	3.53	0.023	0.730	model1_3c8tA1.pdb.gz
9	1ygpA	0.48	3.53	0.037	0.713	model1_1ygpA.pdb.gz
10	4bxdA	0.48	4.77	0.051	0.852	model1_4bxdA.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:0003682	0.47	chromatin binding
GO:0003824	0.33	catalytic activity

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:0044699	0.85	single-organism process
GO:0009987	0.78	cellular process
GO:0050896	0.76	response to stimulus
GO:0006950	0.74	response to stress
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0044763	0.67	single-organism cellular process
GO:0048518	0.57	positive regulation of biological process
GO:0048522	0.56	positive regulation of cellular process
GO:0010468	0.56	regulation of gene expression
GO:2000112	0.55	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.55	regulation of primary metabolic process
GO:0051171	0.55	regulation of nitrogen compound metabolic process
GO:0048523	0.55	negative regulation of cellular process
GO:0030154	0.55	cell differentiation
GO:0051704	0.54	multi-organism process
GO:0051173	0.54	positive regulation of nitrogen compound metabolic process
GO:0031328	0.54	positive regulation of cellular biosynthetic process
GO:0010628	0.54	positive regulation of gene expression
GO:0010557	0.54	positive regulation of macromolecule biosynthetic process
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0045893	0.53	positive regulation of transcription, DNA-templated
GO:0042127	0.53	regulation of cell proliferation
GO:0006357	0.53	regulation of transcription from RNA polymerase II promoter
GO:0051707	0.52	response to other organism
GO:0045944	0.52	positive regulation of transcription from RNA polymerase II promoter
GO:0045444	0.52	fat cell differentiation
GO:0009628	0.52	response to abiotic stimulus
GO:0006952	0.52	defense response
GO:0042742	0.51	defense response to bacterium
GO:0050873	0.50	brown fat cell differentiation
GO:0043066	0.50	negative regulation of apoptotic process
GO:0040015	0.50	negative regulation of multicellular organism growth
GO:0009409	0.50	response to cold
GO:0008284	0.50	positive regulation of cell proliferation

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:0044464	1.00	cell part
GO:0043226	0.89	organelle
GO:0044424	0.88	intracellular part
GO:0043227	0.88	membrane-bounded organelle
GO:0043229	0.70	intracellular organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0016020	0.67	membrane
GO:0005886	0.57	plasma membrane
GO:0005634	0.55	nucleus

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	1k7wD	0.325	5.02	0.019	0.652	4.3.2.1	NA
2	0.060	2p0mA	0.461	4.12	0.019	0.783	1.13.11.33	NA
3	0.060	2pfmA	0.492	3.22	0.071	0.722	4.3.2.2	NA
4	0.060	1lnsA	0.445	4.28	0.053	0.791	3.4.14.11	NA
5	0.060	1ygeA	0.482	4.53	0.028	0.826	1.13.11.12	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	3fg4C	0.491	4.53	0.045	0.826	0.51	ACD	complex1.pdb.gz	70,73,80,82

	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.