D-I-TASSER Q8NFH4-D1

D-I-TASSER results for Q8NFH4-D1

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

Input Sequence in FASTA format

>Q8NFH4 (149 residues)
MKQDASRNAAYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEG
IQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVL
VGSGLSWHRTLPLCVIGGDHKLLFWVTEV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKQDASRNAAYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEGIQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVLVGSGLSWHRTLPLCVIGGDHKLLFWVTEV
Prediction	CCCCCCCCCCSSSSCCCSSSSSSSCCCCCCCCCCSSSSSCCCCSSSSSSSSCCCCCCCCCSSSSSSSSSCCCCCSSSSSSCCCCCCCCCCCCSSSSSSCCCCSSSSSSCCCCCCCSSSSSCCSSSSSCCCCSSSSSSCCCSSSSSSSSC
Confidence	98556799738983488289999814557998777999839946999999125766643147665677258997038998899865458872599996379728999578998827998625257313997799981898899997409
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKQDASRNAAYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEGIQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVLVGSGLSWHRTLPLCVIGGDHKLLFWVTEV
Prediction	66656745441415174302001010243654230000027431000103044565625523243045151744020000137342543353020001134340201234176563242143340324564300001423202113376
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSSSCCCSSSSSSSCCCCCCCCCCSSSSSCCCCSSSSSSSSCCCCCCCCCSSSSSSSSSCCCCCSSSSSSCCCCCCCCCCCCSSSSSSCCCCSSSSSSCCCCCCCSSSSSCCSSSSSCCCCSSSSSSCCCSSSSSSSSC
MKQDASRNAAYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEGIQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVLVGSGLSWHRTLPLCVIGGDHKLLFWVTEV

4xfvA

0.15

0.13

4.52

1.17

DEthreader

YGEIKPALWELFKNPHRIIWDADWAPLE--F-GNVFVTASRKTVKVWRHQ-K-------ADDYVLEASIKHTKAVTAISIHDSMI---R-EKILISVGLENGEIYLYSYTLGKFELITQLTPIRLRWSHLLFLGVGSSDLSTRIYSL-A

5wjcA

0.12

0.11

4.01

1.29

SPARKS-K

ALTTGEALPQAVLKHTAEGFGLCWNP---NLPGNLATGAEDQVICLWDVQT-QSFTSSETKVISPIAKYHHTDIVNDVQFHPQHE-------ALLASVSDDCTLQIHDTRLNEEEAPKVIQAHAVAINPFNDLATASADKTVALWDLRN

4xfvA

0.14

0.12

4.11

0.45

MapAlign

--------PEAIFIGTRIIWDADWA---PLEFGNVFVTASRKTVKVWRHQ------KEPADDYVLEASIKHTKAVTAISIHDSM----IREKILISVGLENGEIYLYSYTLGKFELITQLTPKILRWSHKLFLGVGSSDLSTRIYSL--

4fhlA

0.14

0.13

4.58

0.31

CEthreader

-GSMTLSSNQYQLPLNVRPYTTTWCSQSPS-CSNLLAIGHDTGITIYCASEEST-----GLTLQELFTIQTGLPTLHLSFSSSCSYSENSYSLFLACVCQDNTVRLIITKNETIITQHVLFVNDIDIADVQVIASVGDDCTLIIWRLTD

5a9q2

0.84

0.80

22.51

1.19

MUSTER

--------AAYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEGIQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVLEGNGLVFDPGQEIASVSDDHTCRIWNLEG

5ch1A

0.17

0.16

5.30

0.61

HHsearch

EWELPRLRTSFIFQDLAEFFDVKFYPYSPPGAPPVFAATSKKHAVICRLTQTTDKDANNVTEGKLYRTLVHGGGINDLATSPANY--------IIASASDDTTIRIWSLAPEHQPCVCILEGHSVAFHDNGRVLSAGHDQVINLWALPE

5a9q2

0.85

0.79

22.32

1.48

FFAS-3D

---------AYTVDCEDYVHVVEFNPFENGDSGNLIAYGGNNYVVIGTCTFQEEEADVEGIQYKTLRTFHHGVRVDGIAWSPETRLDSLPPVIKFCTSAADMKIRLFTSDLQDKNEYKVLEGHGLVFDPKEEIASVSDDHTCRIWNLE-

4xfvA1

0.21

0.17

5.55

0.52

EigenThreader

---------------FFYPLCLSLSKVE--EKKYLLAIGGNVNVFIASFILSD---SGIEKCRVVAELEGHEDWVKSLAFRHQET----PGDYLLCSGSQDRYIRLWRINDLILSNEALIMDWILQWHERLQLLAATADTSLMVWEPDS

3iiyA

0.19

0.17

5.42

1.64

CNFpred

-KCKYSFKCVNSLKENQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHS--------QGEIRLLQSYVD-ENFYTCAWTYDSN----TSHPLLAVAGSRGIIRIINPIT--MQCIKHYVGNELKFHPPNLLLSVSKDHALRLWNIQT

6jp6A

0.07

0.06

2.54

1.17

DEthreader

QNFWTPYMIRQALPVSLRIMDFDVKFISQSGD-FLLVTVYSSTIKIWHYREN-----Q--NKFDLIMQGRYKCCLFNVVFIALK----E--ELLVVISPTDGHLVVYNITEYNPAPVAQLPVVKLDYVANATILTGGDDNGLGLSNLKL

(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	0.5892

(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	7wb4f	0.90	1.59	0.699	0.960	model1_7wb4f.pdb.gz
2	4fhlA	0.79	2.50	0.136	0.940	model1_4fhlA.pdb.gz
3	8cliC	0.78	2.75	0.116	0.953	model1_8cliC.pdb.gz
4	5a9q2	0.77	2.62	0.891	0.919	model1_5a9q2.pdb.gz
5	2j04D	0.74	2.64	0.079	0.893	model1_2j04D.pdb.gz
6	1pevA	0.69	2.23	0.118	0.799	model1_1pevA.pdb.gz
7	3jb9L1	0.68	1.97	0.132	0.765	model1_3jb9L1.pdb.gz
8	2h9lA	0.67	2.61	0.144	0.812	model1_2h9lA.pdb.gz
9	2ymuA2	0.65	2.33	0.169	0.765	model1_2ymuA2.pdb.gz
10	1p22A	0.64	2.45	0.167	0.745	model1_1p22A.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:0003824	0.44	catalytic activity
GO:0033558	0.43	protein deacetylase activity
GO:0016811	0.43	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

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:0009987	0.97	cellular process
GO:0044260	0.92	cellular macromolecule metabolic process
GO:0044238	0.92	primary metabolic process
GO:0016043	0.92	cellular component organization
GO:1901360	0.91	organic cyclic compound metabolic process
GO:0046483	0.91	heterocycle metabolic process
GO:0006807	0.91	nitrogen compound metabolic process
GO:0006725	0.91	cellular aromatic compound metabolic process
GO:0065007	0.90	biological regulation
GO:0044699	0.90	single-organism process
GO:0016070	0.90	RNA metabolic process
GO:0051179	0.89	localization
GO:0050794	0.89	regulation of cellular process
GO:0044763	0.89	single-organism cellular process
GO:0006996	0.89	organelle organization
GO:0071702	0.88	organic substance transport
GO:0046907	0.88	intracellular transport
GO:0019538	0.88	protein metabolic process
GO:0010468	0.88	regulation of gene expression
GO:1903047	0.87	mitotic cell cycle process
GO:1902582	0.87	single-organism intracellular transport
GO:0051276	0.87	chromosome organization
GO:0048583	0.87	regulation of response to stimulus
GO:0044249	0.87	cellular biosynthetic process
GO:0010605	0.87	negative regulation of macromolecule metabolic process
GO:0006464	0.87	cellular protein modification process
GO:0006405	0.87	RNA export from nucleus
GO:1900034	0.86	regulation of cellular response to heat
GO:0075733	0.86	intracellular transport of virus
GO:0031047	0.86	gene silencing by RNA
GO:0019083	0.86	viral transcription
GO:0016925	0.86	protein sumoylation
GO:0010827	0.86	regulation of glucose transport
GO:0007077	0.86	mitotic nuclear envelope disassembly
GO:0007062	0.86	sister chromatid cohesion
GO:0006409	0.86	tRNA export from nucleus
GO:0006406	0.86	mRNA export from 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 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:0043229	1.00	intracellular organelle
GO:0044446	0.97	intracellular organelle part
GO:0032991	0.97	macromolecular complex
GO:0043234	0.95	protein complex
GO:0044428	0.94	nuclear part
GO:0031080	0.85	nuclear pore outer ring

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	2vk6A	0.634	3.43	0.045	0.866	3.2.1.18	78,109
2	0.060	2vskC	0.590	3.92	0.052	0.886	3.2.1.18	NA
3	0.060	1rwlA	0.615	2.23	0.074	0.725	2.7.11.1	NA
4	0.060	1c9uB	0.613	3.97	0.075	0.879	1.1.5.2 1.1.99.17	NA
5	0.060	2aeyA	0.525	4.45	0.043	0.873	3.2.1.80	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	0.10	3p4fA	0.674	2.69	0.154	0.819	0.44	III	complex1.pdb.gz	19,21,40,74,75,76,100
2	0.07	3smrA	0.673	2.56	0.146	0.812	0.43	NP7	complex2.pdb.gz	21,22,40,75,76,77
3	0.03	2xl2B	0.673	2.56	0.154	0.812	0.48	III	complex3.pdb.gz	25,26,27,35,67
4	0.02	1a0rB	0.525	2.57	0.122	0.624	0.78	FAR	complex4.pdb.gz	121,122,136,138,139,141,143,145

	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.