D-I-TASSER Q8N584-D2

D-I-TASSER results for Q8N584-D2

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

Input Sequence in FASTA format

>Q8N584 (127 residues)
APSMVDRLQRQIIIADCQVYLAVLSFVKQELSAYIKGGWILRKAWKIYNKCYLDINALQE
LYQKKLTEESLTSDAANDNHIVAEGVSEESLNRLKGAVSFGYGLFHLCISMVPPNLLKII
NLLGFPG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| APSMVDRLQRQIIIADCQVYLAVLSFVKQELSAYIKGGWILRKAWKIYNKCYLDINALQELYQKKLTEESLTSDAANDNHIVAEGVSEESLNRLKGAVSFGYGLFHLCISMVPPNLLKIINLLGFPG
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHCCHHHHHHHHHCCCCC
Confidence	9629999999999999999999999998589999999999999999999999999999864125665444456677766666556651368898888997346999999976669999997628889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| APSMVDRLQRQIIIADCQVYLAVLSFVKQELSAYIKGGWILRKAWKIYNKCYLDINALQELYQKKLTEESLTSDAANDNHIVAEGVSEESLNRLKGAVSFGYGLFHLCISMVPPNLLKIINLLGFPG
Prediction	8643254031200201020130002014540321131023024014204401520552454366445664445645445544554356633530310031021321021023243323202234368
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHCCHHHHHHHHHCCCCC
APSMVDRLQRQIIIADCQVYLAVLSFVKQELSAYIKGGWILRKAWKIYNKCYLDINALQELYQKKLTEESLTSDAANDNHIVAEGVSEESLNRLKGAVSFGYGLFHLCISMVPPNLLKIINLLGFPG

1bg1A1

0.06

2.46

1.33

DEthreader

MEQHLQDVRKRVQDLEQKMKVVENLQDDFLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDELADWKRQQACIPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKV---SYKGDP-IVQHR

2e2aA

0.05

0.04

1.84

0.77

CEthreader

MTLLGFEIVAYAGDARSKLLEALKAAENGD---FAKADSLVVEAGSCIAEAHSSQTGMLAREASGEELPYS-----------------VTMMHGQLHLMTTILLKDVIHHLIELYKRGA--------

6h2dP

0.09

3.34

0.73

EigenThreader

LPQNAVNIQQNVGEVVAALLPQVQTMQQEIAPIQTLTAQTLTASQSANDRITQDNIALQRIGVELQATIAGLQEGQVNQIEGQIQRQQGFLGQTTAFSQQFGSLIDRVSKVGNTISLLTEVRTLQVD

4zi2C

0.12

0.11

3.87

0.66

FFAS-3D

--AAEEEDEVE------WVVESIAGFLRGPILDFVEQKCEVFTYTEIHQEYKELVEKLLESYLKEIGINEDQFQEACTSPLAKTRTSQAILQPVLAAEDF-TIFKAMMVQKNIEMQLQAIRII----

7by5A

0.07

0.06

2.67

0.74

SPARKS-K

KEKIIKTIDNFLEKRYEKWIEVYKLVKAKWLGTNTQFQKRSYQMYRSLEYQVDAIKKIIDYEYKI----YSGPDKEQIADEINNLKNEEKANKAMININIFMRESSRSFLVMINEAKKQLLEFDTQS

5gpjA

0.12

0.10

3.59

0.63

CNFpred

SLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGLAANGLLVLYIAINLFKIYYGDD----------------------WGGLFEAITGYGLGGSSMALFGRVGGGIYTKAADVGADLV

5oenB

0.09

3.28

1.33

DEthreader

EENRIQGLHVDIEFLVRSIRQLKDEQDVFVQATANKVDRMRKEVLDISKGLVGRLTTLVDLLLPKLDEWKQQAASC--QLEQLE-QWLTAGAKFLFHLRQLLKQLKEMS-HMLRYKGD--M-FGQGD

2e2aA

0.06

0.05

2.05

0.84

MapAlign

MTLLGFEIVAYAGDARSKLLEALKAAENG---DFAKADSLVVEAGSCIAEAHSSQTGMLAREA------------------SGEELPSVTMMHGQLHLMTTILLKDVIHHL----IELYKRGA----

5ztyA

0.09

3.30

0.49

MUSTER

RNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYARM-----RLDVELAKTLGLVLAVLLICWFPVLALMAHSLATTLS

2pffB

0.12

4.19

0.57

HHsearch

EPTTPAELVGKLYQTYHVLVGDLIKFSAETLSELIRTTLDIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHAETDSWESFFVSVRKAITVLFFCYEAYPNTSLPPSILEDLENEGVPS

(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	0.7843

(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	5oenB	0.78	2.73	0.098	0.953	model1_5oenB.pdb.gz
2	2xheB	0.76	3.01	0.063	0.992	model1_2xheB.pdb.gz
3	1yvlB	0.75	2.60	0.059	0.929	model1_1yvlB.pdb.gz
4	1bg1A	0.75	2.63	0.051	0.929	model1_1bg1A.pdb.gz
5	3c98B	0.74	2.69	0.076	0.929	model1_3c98B.pdb.gz
6	1fioA	0.69	2.96	0.086	0.913	model1_1fioA.pdb.gz
7	1y1uA	0.62	2.59	0.058	0.811	model1_1y1uA.pdb.gz
8	3hhmB	0.54	2.84	0.063	0.677	model1_3hhmB.pdb.gz
9	2btpA2	0.48	2.98	0.037	0.614	model1_2btpA2.pdb.gz
10	1a38A2	0.48	2.65	0.038	0.598	model1_1a38A2.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	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0003676	0.59	nucleic acid binding
GO:0003677	0.55	DNA binding
GO:0098531	0.53	transcription factor activity, direct ligand regulated sequence-specific DNA binding
GO:0070491	0.53	repressing transcription factor binding
GO:0048020	0.53	CCR chemokine receptor binding
GO:0043566	0.53	structure-specific DNA binding
GO:0035258	0.53	steroid hormone receptor binding
GO:0019902	0.53	phosphatase binding
GO:0019900	0.53	kinase binding
GO:0004871	0.53	signal transducer activity
GO:0003682	0.53	chromatin binding
GO:0001228	0.53	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001085	0.53	RNA polymerase II transcription factor binding
GO:0000987	0.53	core promoter proximal region sequence-specific DNA binding
GO:0000982	0.53	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000977	0.53	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	1.00	cellular process
GO:0044763	0.98	single-organism cellular process
GO:1902589	0.97	single-organism organelle organization
GO:0044767	0.97	single-organism developmental process
GO:0044707	0.97	single-multicellular organism process
GO:0009653	0.97	anatomical structure morphogenesis
GO:0061371	0.96	determination of heart left/right asymmetry
GO:0042384	0.96	cilium assembly
GO:0032474	0.96	otolith morphogenesis

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:0005634	1.00	nucleus
GO:0044444	0.97	cytoplasmic part
GO:0005829	0.93	cytosol
GO:0044446	0.74	intracellular organelle part
GO:0016020	0.68	membrane
GO:0005737	0.64	cytoplasm
GO:0032991	0.63	macromolecular complex

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	0.074	3k1sA	0.576	2.99	0.040	0.748	2.7.1.69	NA
2	0.067	3eabA	0.510	2.63	0.106	0.653	3.6.4.3	21,50
3	0.067	1cxzB	0.508	3.01	0.095	0.653	2.7.11.13	93,104
4	0.060	2h1nA	0.576	3.25	0.149	0.779	3.4.24.-	102
5	0.060	3e08A	0.584	3.68	0.064	0.866	1.13.11.11	106

	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	0.03	2r5bC	0.334	1.14	0.089	0.354	1.30	III	complex1.pdb.gz	99,102,106,107
2	0.03	3l39A	0.594	2.82	0.170	0.779	0.81	PO4	complex2.pdb.gz	98,101,102,105
3	0.02	1g730	0.622	3.10	0.054	0.866	0.82	III	complex3.pdb.gz	38,45,46,48,49,52,53,56,98
4	0.01	1gzlB	0.334	1.09	0.089	0.354	1.24	III	complex4.pdb.gz	93,96,97,100,103,104,107,111
5	0.01	2r5bA	0.333	1.11	0.089	0.354	1.27	III	complex5.pdb.gz	98,101,102,105

	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.