D-I-TASSER Q8NFH3-D2

D-I-TASSER results for Q8NFH3-D2

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

Input Sequence in FASTA format

>Q8NFH3 (107 residues)
QWTTAHYHTGPGSPSYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIDNADSS
TLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| QWTTAHYHTGPGSPSYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPL
Prediction	CCCCCCCCCCCCCCCCCCCCCSSSSCCCCSSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCSSSSSCCCCCSSSSSCCCCCCCCCSSSSSCCCCCCC
Confidence	96433323456666788644269954899699997798399997799825999817888737999971799599964899199958379998762678624663469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| QWTTAHYHTGPGSPSYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPL
Prediction	82662242445444645402010004445300000443301003175552133145246120200312455200002442301000124757523323424465347
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCSSSSCCCCSSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCCSSSSSSCCCCSSSSSCCCCCSSSSSCCCCCCCCCSSSSSCCCCCCC
QWTTAHYHTGPGSPSYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPL

6b3xA

0.16

5.27

1.33

DEthreader

EGDFILYFVSCNPQDQHTDAICSVNYNSNMYVTGSKDGCIKLWDGVSNRCITTFEKAHGAEVCSAIFSKNKYILSSGKDSVAKLWEISTG-R-TLVRYTAGDERLCI

4j87A1

0.14

4.77

1.59

SPARKS-K

-MAMLTKFESRSSRAGHDRGVNWCAFHLPLILSAGDDRLVKLWRMTKAWEVDTCRG-HFNNVSCCLFHPHELILSASEDKTIRVWDLNRRTNDRFWFITVHPKLNLF

5yzvA

0.11

0.09

3.36

0.34

MapAlign

--------------EGHTHYVLDIAFSGSMVASGSRDGTARLWNVATGTEHAVLK-GHTDYVYAVAFSDGSMVASGSRDGTIRLWDVA--TGKERDVLQPAENVHLW

5nnzB

0.16

5.26

0.23

CEthreader

KLWDATNGKCVATLTGHDDEILDSCFDGKLIATASADGTARIFSAATRKCIAKLE-GHEGEISKISFNPGNHLLTGSSDKTARIWDAQT--GQCLQVLEGHTDEIFS

4i79A

0.85

23.96

1.18

MUSTER

NNQTLSVNQQWTTAHYHTAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPL

6t9iD

0.12

0.11

3.96

0.62

HHsearch

THYPLRIFA------GHLNDVDCVSFHGCYVFTGSSDKTCRMWDVSTGDSVRLFLG-HTAPVISIAVCPGRWLSTGSEDGIINVWDIGTGKGNAIYSLSYSKEGNVL

5cvlA1

0.11

0.09

3.38

1.24

FFAS-3D

-----------EKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKPYIASMEHHTDWVNDIVLCNGKTLISASSDTTVKVWNAHK--GFCMSTLRTHKDYV--

5wlcSG

0.12

0.11

4.00

0.43

EigenThreader

VFRYFGDKLLISEARVGENNLTCISCFQLFAYTVSKDLQLTKYDIKRPKKLKYAKGGHYDEILTVAASPDGYVVTGGRDRKLIVWST---ESLSPVKVIPTKDRRGE

1nexB

0.10

0.09

3.45

1.46

CNFpred

FVPQRTTLRGHM-----TSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGH-DGGVWALKYAHGGILVSGSTDRTVRVWDIKKG--CCTHVFEGHNSTVRC

6vycA

0.18

5.77

1.33

DEthreader

RGASFLWQLQF-SLDPEPIAINCTAFNNNLLVTGAADGVIRLFDMQQHECAMSWR-AHYGEVYSVEFSYENTVYSIGEDGKFIQWNIHKS-GLKVSEYSLPSDATLT

(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	0.8015

(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	6b3xA	0.84	1.93	0.162	0.972	model1_6b3xA.pdb.gz
2	1pevA	0.83	2.17	0.136	0.963	model1_1pevA.pdb.gz
3	3iytA3	0.82	2.09	0.127	0.944	model1_3iytA3.pdb.gz
4	1b9xA	0.82	2.04	0.108	0.944	model1_1b9xA.pdb.gz
5	5vh9B	0.82	2.03	0.118	0.953	model1_5vh9B.pdb.gz
6	3w15A	0.81	1.91	0.137	0.944	model1_3w15A.pdb.gz
7	4lg8A	0.81	2.17	0.107	0.953	model1_4lg8A.pdb.gz
8	1vyhT	0.81	1.87	0.108	0.935	model1_1vyhT.pdb.gz
9	7kqqA	0.81	1.91	0.146	0.944	model1_7kqqA.pdb.gz
10	6n31A	0.81	2.31	0.078	0.953	model1_6n31A.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:1901363	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0003676	0.71	nucleic acid binding
GO:0003824	0.62	catalytic activity
GO:0044877	0.59	macromolecular complex binding
GO:0016787	0.59	hydrolase activity
GO:0019899	0.58	enzyme binding
GO:0003682	0.58	chromatin binding
GO:0003677	0.58	DNA binding
GO:1990837	0.57	sequence-specific double-stranded DNA binding
GO:0032403	0.57	protein complex binding
GO:0017111	0.57	nucleoside-triphosphatase activity
GO:0042623	0.56	ATPase activity, coupled
GO:0033558	0.56	protein deacetylase activity
GO:0031491	0.56	nucleosome binding
GO:0031490	0.56	chromatin DNA binding
GO:0016811	0.56	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0001158	0.56	enhancer sequence-specific DNA binding
GO:0000987	0.56	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.56	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:1903047	1.00	mitotic cell cycle process
GO:0006996	1.00	organelle organization
GO:0008152	0.80	metabolic process
GO:0044238	0.79	primary metabolic process
GO:0044237	0.79	cellular metabolic process
GO:0043170	0.79	macromolecule metabolic process
GO:0090304	0.78	nucleic acid metabolic process
GO:0065007	0.78	biological regulation
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0050794	0.77	regulation of cellular process
GO:0016070	0.77	RNA metabolic process
GO:0044699	0.76	single-organism process
GO:0071702	0.75	organic substance transport
GO:0044763	0.75	single-organism cellular process
GO:0051649	0.74	establishment of localization in cell
GO:0051641	0.74	cellular localization
GO:0051028	0.73	mRNA transport
GO:0048519	0.73	negative regulation of biological process
GO:0044249	0.73	cellular biosynthetic process
GO:0016032	0.73	viral process
GO:0009059	0.73	macromolecule biosynthetic process
GO:0006913	0.73	nucleocytoplasmic transport
GO:1902580	0.72	single-organism cellular localization
GO:0080135	0.72	regulation of cellular response to stress
GO:0051276	0.72	chromosome organization
GO:0044765	0.72	single-organism transport
GO:0032774	0.72	RNA biosynthetic process
GO:0032446	0.72	protein modification by small protein conjugation
GO:0018205	0.72	peptidyl-lysine modification
GO:0010605	0.72	negative regulation of macromolecule metabolic process
GO:0006406	0.72	mRNA export from nucleus
GO:1900034	0.71	regulation of cellular response to heat
GO:0075733	0.71	intracellular transport of virus
GO:0031047	0.71	gene silencing by RNA
GO:0019083	0.71	viral transcription
GO:0016925	0.71	protein sumoylation
GO:0010827	0.71	regulation of glucose transport
GO:0007077	0.71	mitotic nuclear envelope disassembly
GO:0007062	0.71	sister chromatid cohesion
GO:0006409	0.71	tRNA 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:0031080	1.00	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	2aeyA	0.653	3.39	0.085	0.981	3.2.1.80	40
2	0.060	2agsA	0.689	3.19	0.076	0.963	3.2.1.18	36
3	0.060	1st8A	0.690	2.91	0.075	0.972	3.2.1.80	NA
4	0.060	2gc7A	0.732	2.87	0.107	0.963	1.4.99.3	38
5	0.060	1g72A	0.753	2.38	0.109	0.944	1.1.99.8	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	0.08	3p4fA	0.810	2.02	0.186	0.944	0.48	III	complex1.pdb.gz	23,36,61,62,63,78
2	0.05	2ovrB	0.799	2.17	0.087	0.944	0.53	III	complex2.pdb.gz	23,36,63,77
3	0.03	1a0rB	0.815	2.07	0.108	0.944	0.59	FAR	complex3.pdb.gz	55,62,75,77,79,81,83,85
4	0.03	2bcj5	0.815	2.06	0.108	0.944	0.49	III	complex4.pdb.gz	18,20,22,36,37,38,55,58,60,61,63,78,104,106

	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.