D-I-TASSER Q8NFP4-D5

D-I-TASSER results for Q8NFP4-D5

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

Input Sequence in FASTA format

>Q8NFP4 (100 residues)
TVPPTISVPKGRAVVTVREGSPAELQCEVRGKPRPPVLWSRVDKEAALLPSGLPLEETPD
GKLRLERVSRDMSGTYRCQTARYNGFNVRPREAQVQLNVQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| TVPPTISVPKGRAVVTVREGSPAELQCEVRGKPRPPVLWSRVDKEAALLPSGLPLEETPDGKLRLERVSRDMSGTYRCQTARYNGFNVRPREAQVQLNVQ
Prediction	CCCCSSSCCCCCCSSSSSCCCCSSSSSSSSSSCCCSSSSSSCCCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSSSSC
Confidence	9898798068982199977941999999964159889999899410115798569992996899931486778799999992898605799999999759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| TVPPTISVPKGRAVVTVREGSPAELQCEVRGKPRPPVLWSRVDKEAALLPSGLPLEETPDGKLRLERVSRDMSGTYRCQTARYNGFNVRPREAQVQLNVQ
Prediction	8340404365664403043456040434054534240363267663443675442443654454456144544444333040533654440403030428
	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

CCCCSSSCCCCCCSSSSSCCCCSSSSSSSSSSCCCSSSSSSCCCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCCSSSSSSSSSSSSC
TVPPTISVPKGRAVVTVREGSPAELQCEVRGKPRPPVLWSRVDKEAALLPSGLPLEETPDGKLRLERVSRDMSGTYRCQTARYNGFNVRPREAQVQLNVQ

2wv3A

0.19

0.18

5.79

1.33

DEthreader

IAAPDITGH--KRSENKNEGQDAMMYCKSVGYPHPEWMWRKKEFE-EISNSSGRFFIINKTELNIVNLQIEDPGEYECNATN--S--IGSASVSTVLRVR

5oj2A4

0.79

0.76

21.48

1.15

SPARKS-K

TVPPTISVPKGQSTITVREGSRAELQCEVRGKPKPPIIWSRVDKE---TPPSGTTVETYDGKLRLESVSRD-SGTYKCQTARYNGFNIRPREALVQLNVQ

2fboJ

0.22

0.21

6.64

0.58

MapAlign

-SIMTVRTT--HTEVEVHAGGTVELPCSYQLAQPPVISWLKGARSTKVSFGDFRASVANLPTLRLTHVHPQDGGRYWCQVAQWSRTEFGLDAKSVVLKVT

1gl4B

0.22

0.19

6.01

0.34

CEthreader

--PIMVTVEE-QRSQSVRPGADVTFICTAKSKSAYTLVWTRLHNGKL-----PSRAMDFNGILTIRNVQPSDAGTYVCTGSNM----FAMDQGTATLHVQ

6eg0B2

0.27

0.26

7.98

1.21

MUSTER

-VPPDILDYPTSTDMVVREGSNVTLKCAATGSPEPTITWRRESGVPIELATGEEVMSIEGTDLVIPNVRRHHMGAYLCIASNGVPPS---VSKRITLVVH

3p3yA

0.18

0.17

5.52

0.43

HHsearch

KAAPYWLDEPK--NLILAPGEDGRLVCRANGNPKPTVQWMVNGEPLQSAPPNPNR-EVAGDTIIFRDTQISSRAVYQCNTSNEHGY----LLANAFVSVL

5oj2A4

0.76

0.73

20.67

1.74

FFAS-3D

TVPPTISVPKGQSTITVREGSRAELQCEVRGKPKPPIIWSRVDKETP---PSGTTVETYDGKLRLESVS-RDSGTYKCQTARYNGFNIRPREALVQLNVQ

2e7cA

0.23

0.22

6.88

0.30

EigenThreader

AEPPKIRLPRHLRQYIRKVGEQLNLVVPFQGKPRPQVVWTKG--GAPLDTSRVHVRTSDFDVFFVRQAARSDSGEYELSVQIE----NMKDTATIRIRVV

5oj2A

0.76

0.75

21.24

1.69

CNFpred

TVPPTISVPKGQSTITVREGSRAELQCEVRGKPKPPIIWSRVDKETPMPSGTMTVETY-DGKLRLESVSRDMSGTYKCQTARYNGFNIRPREALVQLNVQ

2wv3A2

0.20

0.18

5.78

1.33

DEthreader

-AAPDITGH--KRSENKNEGQDAMMYCKSVGYPHPEWMWRKKEFE-EISNSSGRFFIINKTELNIVNLQIEDPGEYECNATN--S--IGSASVSTVLRVR

(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	0.9176

(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	2wv3A	0.85	1.38	0.194	0.930	model1_2wv3A.pdb.gz
2	6a69B	0.84	1.37	0.174	0.920	model1_6a69B.pdb.gz
3	1e0oB	0.84	1.62	0.158	0.950	model1_1e0oB.pdb.gz
4	5noiA	0.83	1.72	0.266	0.940	model1_5noiA.pdb.gz
5	5o5gA	0.83	1.72	0.280	0.930	model1_5o5gA.pdb.gz
6	6efyA3	0.83	1.63	0.185	0.920	model1_6efyA3.pdb.gz
7	2va4A2	0.82	1.46	0.228	0.920	model1_2va4A2.pdb.gz
8	6iaaA	0.82	1.86	0.266	0.940	model1_6iaaA.pdb.gz
9	1ya5A1	0.82	1.67	0.258	0.930	model1_1ya5A1.pdb.gz
10	6eg0B	0.82	1.47	0.207	0.920	model1_6eg0B.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:0042802	0.63	identical protein binding
GO:0003824	0.62	catalytic activity
GO:1901363	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0016740	0.58	transferase activity
GO:0097367	0.56	carbohydrate derivative binding
GO:0005198	0.56	structural molecule activity
GO:0035639	0.53	purine ribonucleoside triphosphate binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032550	0.53	purine ribonucleoside binding
GO:0004672	0.53	protein kinase activity
GO:0008307	0.52	structural constituent of muscle
GO:0005524	0.50	ATP binding
GO:0004674	0.50	protein serine/threonine kinase 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	0.92	single-organism process
GO:0009987	0.88	cellular process
GO:0044763	0.82	single-organism cellular process
GO:0065007	0.63	biological regulation
GO:0050789	0.61	regulation of biological process
GO:0032502	0.60	developmental process
GO:0050794	0.54	regulation of cellular process
GO:0044767	0.54	single-organism developmental process

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	0.94	cell part
GO:0044424	0.65	intracellular part
GO:0044444	0.50	cytoplasmic part
GO:0044425	0.48	membrane part
GO:0044421	0.45	extracellular region part
GO:0044459	0.44	plasma membrane part
GO:0043226	0.42	organelle
GO:0016020	0.42	membrane
GO:0044422	0.39	organelle part
GO:0031224	0.39	intrinsic component of membrane
GO:0044446	0.35	intracellular organelle part
GO:0031226	0.34	intrinsic component of plasma membrane
GO:0043229	0.33	intracellular organelle
GO:0016021	0.32	integral component of membrane
GO:0005886	0.31	plasma membrane
GO:0043227	0.30	membrane-bounded 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	0.263	2edwA	0.711	1.96	0.238	0.840	2.7.11.1	41,45
2	0.211	1u2hA	0.814	1.64	0.264	0.910	2.7.11.1	NA
3	0.131	2cknA	0.689	2.57	0.169	0.890	2.7.10.1	40
4	0.110	2edhA	0.735	1.82	0.212	0.850	2.7.11.1	NA
5	0.104	2edtA	0.707	2.16	0.188	0.850	2.7.11.1	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	0.07	2p5eD	0.803	1.87	0.211	0.950	0.83	III	complex1.pdb.gz	21,67,68,69,70,71,72,73
2	0.05	1tlk0	0.806	1.62	0.231	0.910	0.76	III	complex2.pdb.gz	2,5,30,32,34,36,37,38
3	0.05	2bnqD	0.789	1.86	0.226	0.930	0.81	III	complex3.pdb.gz	21,67,68,69,70,71,72
4	0.05	1gl41	0.782	1.50	0.227	0.880	0.71	III	complex4.pdb.gz	34,35,37,47,57,58,59,60,80,82,84,85,87,89
5	0.05	2iep0	0.808	1.86	0.204	0.930	0.80	III	complex5.pdb.gz	7,8,22,24,26,28,30,59

	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.