D-I-TASSER Q8NFH3-D1

D-I-TASSER results for Q8NFH3-D1

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

Input Sequence in FASTA format

>Q8NFH3 (185 residues)
MEEIYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIGDFGNLDSDGG
FEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNQSTFLSHS
ISNQANVHQSVISSWLSTDPAKDRIEITSLLPSRSLSVNTLDVLGPCLVCGTDAEAIYVT
RHLFS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MEEIYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIGDFGNLDSDGGFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNQSTFLSHSISNQANVHQSVISSWLSTDPAKDRIEITSLLPSRSLSVNTLDVLGPCLVCGTDAEAIYVTRHLFS
Prediction	CCCSSSSSSSSSSSSSSSCCCCCCCCCCCCSSSSCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSSSCCCSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCCCCSSSCCCCCCCCCCCCSSSSSSSCCCCCCSSSSSCCCCSSSSCCCCSSSSSSCCCCC
Confidence	98434677653333445204884225766558970025899779999834777667876657885225663541632478983499299992798289999727630011101434542246899987025512245654466304777605775334656415872576116537999721059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MEEIYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIGDFGNLDSDGGFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNQSTFLSHSISNQANVHQSVISSWLSTDPAKDRIEITSLLPSRSLSVNTLDVLGPCLVCGTDAEAIYVTRHLFS
Prediction	76414141105202301033456751454420000014366120200314544436566535431322151415240320322365200001340202003235653434354434313333466322101113333444345414033023734220200233442101002100001143138
	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

CCCSSSSSSSSSSSSSSSCCCCCCCCCCCCSSSSCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSSSCCCSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCCCCSSSCCCCCCCCCCCCSSSSSSSCCCCCCSSSSSCCCCSSSSCCCCSSSSSSCCCCC
MEEIYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIGDFGNLDSDGGFEGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNQSTFLSHSISNQANVHQSVISSWLSTDPAKDRIEITSLLPSRSLSVNTLDVLGPCLVCGTDAEAIYVTRHLFS

2p9wA

0.07

0.06

2.51

1.33

DEthreader

TQSHFNVVISQQMSGLSLLT----HDN-SKRLFAVMKNAGASSFHSFNLP-LS------EN--SKPVWSVNFEQFGVVQSAQDRDGNSYVAFLGPAIARVSADKTVSTAWESGPGYGITFDKLIAFGGPRALTAFDVS-KP-YAWPEPVKIDFGTSGTEKIVTVPSVLVGAR-APYAISFRSWDN

5mzhA2

0.13

0.11

3.91

1.65

SPARKS-K

-FTLFKVLRAHPLTNCAFNKSG-------DRFITGSYD---RTCKVWNTFTGE------------EVFTLEGHKNVVYAIAFNYGDKIVTGSFDKTCKLWDAYTGQYTLKGHQTLSFNPQSTIIATGSDNTAKLWDVETGQE-----RATLAGHTDEIFSCAFNGDFIITGSKDNTCRIWKALT-

4wjsA

0.16

0.14

4.47

0.39

MapAlign

----AHRIGHGQILSCQFSPV------SSSRLATGSGD---NTARIWDTDSG-------------TPKFTLGHTGWVLGVSWSDGKYLATCSMDTTVRVWDPSGKQVEFRHAKWVLALAWQARLASASKCTVRIWLV-----NTGRTEHVLSGHKGSVSCVKWGGDLIYTGSHDRSVRVWDAV--

4jspD

0.10

0.09

3.37

0.28

CEthreader

NPNPIISYDGVNIASVGFHEDG-------RWMYTGGED---CTARIWDLRSRN-----------LQCQRIFQVNAPINCVCLHNQAELIVGDQSGAIHIWDLKTDEQLIPEPEVSITSAHIDMAAVNSTGNCYVWNLTGDEVTQLIPKTKIPAHTRYALQCRFDSTLLATCSADQTCKIWRTSNF

4i79A1

0.76

0.67

18.98

1.36

MUSTER

---IYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIEGD------------HQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNQQGVVCNNPEIVTVGEDGRINLFR----ADHKEAVRTIDNADSSN--TLDVLGPCLVCGTDAEAIYVTRHLFS

3dm0A

0.16

0.14

4.50

0.69

HHsearch

YGVAQRRLTGHSVEDVVLSSDG-------QFALSGSWD---GELRLWDLAAGVST------------RRFVGHTKDVLSVAFSDNRQIVSASRDRTIKLWNTLGECYTIEGHRDWRFSPNTLTIVSSWDKTVKVW---NLSNCK-LR-STLAGHTGYVSTVAVSGSLCASGGKDGVVLLWDLAEG

4i79A1

0.61

0.56

16.10

1.76

FFAS-3D

---IYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSIEGDH------------QLLCDIRHHGDVMDLQFFDQERVAASSTGCVTVFLHHPNNQTLSVNQQWTTAHYHTSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTITLDVLGPCLVCGTDAEAIYVTRHLFS

2xzmR

0.09

3.29

0.57

EigenThreader

-SKRGILEGHSDWVTSIVAGFSQKENEDSPVLISGSRD---KTVMIWKLYEEEQN-----GYFGIPHKALTGHNHFVSDLALSENCFAISSSWDKTLRLWDLRTGTTYKRFVGHSAGAEREAEKENHSDWVSCVRSPIMQPFAPYFASVGWDGHESNVNHLSISPKYIATGGKDKKLLIWDILNL

4i79A

0.62

0.56

15.93

2.21

CNFpred

---IYAKFVSQKISKTRWRPLPPGSLQTAETFATGSWDNEENYISLWSI------------EGDHQLLCDIRHHGDVMDLQFFDQERIVAASSTGCVTVFLHHPNNQTLSVNPCTGVVCNPEIVTVGEDGRINLFRADHK-EAVRTIDNAD---SSTLHAVTFLRPEILTVNSIGQLKIWDFRQQ

1u2vC

0.15

0.14

4.55

1.33

DEthreader

DWWVCKHIKISTVLSLDWH-P------NSVLLAAGSCD---FKCRIFSA-YIKEV-------PFGELMFESSSCGWVHGVCFSAGSRVAWVSHDSTVCLADAKMAVATLASETLPLAVTFISLVAAGHDCFPVLFTYDSAAGKLSFGGRLDSLHKNSVSQISVLSSQFCTTGMDGGMSIWDVRLE

(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	0.7873

(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	7wb4C	0.83	1.61	0.593	0.865	model1_7wb4C.pdb.gz
2	4i79A	0.76	1.18	0.872	0.784	model1_4i79A.pdb.gz
3	8cliC	0.72	3.18	0.124	0.876	model1_8cliC.pdb.gz
4	2xzmR	0.68	2.66	0.082	0.800	model1_2xzmR.pdb.gz
5	6x90B	0.68	2.92	0.070	0.816	model1_6x90B.pdb.gz
6	3zey7	0.63	3.19	0.108	0.778	model1_3zey7.pdb.gz
7	2h9lA	0.63	2.59	0.115	0.730	model1_2h9lA.pdb.gz
8	1erjC	0.63	2.82	0.090	0.735	model1_1erjC.pdb.gz
9	1u2vC	0.61	3.01	0.146	0.757	model1_1u2vC.pdb.gz
10	2aq5A	0.58	3.59	0.082	0.773	model1_2aq5A.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:0003676	0.46	nucleic acid binding
GO:0042623	0.42	ATPase activity, coupled
GO:0031491	0.42	nucleosome binding
GO:0031490	0.42	chromatin DNA binding
GO:0001158	0.42	enhancer sequence-specific DNA binding
GO:0000987	0.42	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.42	RNA polymerase II regulatory region sequence-specific DNA 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:0009987	0.96	cellular process
GO:0016043	0.86	cellular component organization
GO:0006996	0.82	organelle organization
GO:1903047	0.80	mitotic cell cycle process
GO:0065007	0.71	biological regulation
GO:0071704	0.69	organic substance metabolic process
GO:0044238	0.69	primary metabolic process
GO:0034641	0.69	cellular nitrogen compound metabolic process
GO:0090304	0.68	nucleic acid metabolic process
GO:0044260	0.68	cellular macromolecule metabolic process
GO:0050794	0.67	regulation of cellular process
GO:0044699	0.66	single-organism process
GO:0044763	0.65	single-organism cellular process
GO:0019222	0.62	regulation of metabolic process
GO:0016070	0.62	RNA metabolic process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0009892	0.61	negative regulation of metabolic process
GO:0010629	0.60	negative regulation of gene expression
GO:1902582	0.59	single-organism intracellular transport
GO:0044249	0.59	cellular biosynthetic process
GO:0009059	0.59	macromolecule biosynthetic process
GO:0006464	0.59	cellular protein modification process
GO:0048583	0.57	regulation of response to stimulus
GO:0051276	0.54	chromosome organization
GO:0051704	0.53	multi-organism process
GO:0032774	0.53	RNA biosynthetic process
GO:0018205	0.53	peptidyl-lysine modification
GO:0006405	0.53	RNA export from nucleus
GO:1900034	0.51	regulation of cellular response to heat
GO:0075733	0.51	intracellular transport of virus
GO:0031047	0.51	gene silencing by RNA
GO:0019083	0.51	viral transcription
GO:0016925	0.51	protein sumoylation
GO:0010827	0.51	regulation of glucose transport
GO:0007077	0.51	mitotic nuclear envelope disassembly
GO:0007062	0.51	sister chromatid cohesion
GO:0006409	0.51	tRNA export from nucleus
GO:0006406	0.51	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:0044424	1.00	intracellular part
GO:0044446	0.98	intracellular organelle part
GO:0032991	0.98	macromolecular complex
GO:0043234	0.97	protein complex
GO:0044428	0.96	nuclear part
GO:0031080	0.91	nuclear pore outer ring
GO:0043229	0.58	intracellular organelle

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	2agsA	0.593	3.27	0.049	0.778	3.2.1.18	92
2	0.060	1lrwA	0.562	3.70	0.037	0.778	1.1.99.8	NA
3	0.060	1s0kA	0.419	3.75	0.047	0.551	3.2.1.18	92
4	0.060	1aomB	0.539	3.27	0.083	0.686	1.7.99.1 1.7.2.1	NA
5	0.060	2vsmA	0.590	3.86	0.076	0.822	3.2.1.18	100

	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	0.07	2h9pA	0.629	2.54	0.127	0.724	0.66	III	complex1.pdb.gz	12,13,14,37,78,172
2	0.02	2xzkA	0.602	3.84	0.059	0.827	0.79	K99	complex2.pdb.gz	33,34,35,46
3	0.01	2xzjA	0.603	3.84	0.059	0.827	0.62	NA	complex3.pdb.gz	73,74,75,76

	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.