D-I-TASSER A6NDE4-D2

D-I-TASSER results for A6NDE4-D2

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

Input Sequence in FASTA format

>A6NDE4 (123 residues)
TNDGNHPSCQETRDYAPPSRGYAYRDNGHSNRDEHSSRGYRNHRSSRETRDYAPPSRGHA
YRDYGHSRRDESYSRGYRNRRSSRETREYAPPSRGHGYRDYGHSRRHESYSRGYRNHPSS
RET

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TNDGNHPSCQETRDYAPPSRGYAYRDNGHSNRDEHSSRGYRNHRSSRETRDYAPPSRGHAYRDYGHSRRDESYSRGYRNRRSSRETREYAPPSRGHGYRDYGHSRRHESYSRGYRNHPSSRET
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	987778776677888888767777777888777777777788888778888899888887777887877778888877787778777878788888767776666777888887888876779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TNDGNHPSCQETRDYAPPSRGYAYRDNGHSNRDEHSSRGYRNHRSSRETRDYAPPSRGHAYRDYGHSRRDESYSRGYRNRRSSRETREYAPPSRGHGYRDYGHSRRHESYSRGYRNHPSSRET
Prediction	866564644564764444674453465544576445547464354555456344455635446333446554444444546635765634546655534443534655544544554565667
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
TNDGNHPSCQETRDYAPPSRGYAYRDNGHSNRDEHSSRGYRNHRSSRETRDYAPPSRGHAYRDYGHSRRDESYSRGYRNRRSSRETREYAPPSRGHGYRDYGHSRRHESYSRGYRNHPSSRET

3t8sA2

0.09

0.07

2.83

0.49

CEthreader

------------------DDILKGGDVVRLFHAEQEKFLTCDEHRKKQHVFLRTTSATSSKALRFKHLATGHYLAAEVVLVSVPEGNDISSIFELDPTTLRGGDSLVPRNSYVRLRHLCTNTW

5cwsC

0.07

2.98

0.48

EigenThreader

TRWATDLAKYQKEFKEQAAKVMEWDRLLVENGEKIQKLYTSTYEAERASNEIERQLSNVESQQEELTAWLDRYERELDELYAKQMGLTDQLDEMGKDLAKMIKEINDMSNTLSKGSKPDDPLT

2ftcC

0.06

0.05

2.19

0.35

FFAS-3D

KTVSRFRKATSILEFYRELGLPPKQKPGTPLYAAHFRPGYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRPGAVATGDIGRVWPGTKMPGKMGNIYRTEYG----------------

7jjvA

0.05

2.31

1.72

SPARKS-K

-MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTT

5x0mA

0.05

0.04

1.97

0.83

DEthreader

TMALDLRNYIFTSIIVEAV-K--ALSPKFYFKNVFDFIIVAILELFRSRLRVFRLALVIFFWVFFIFGSLKLFVCILIDIFRQQRRDRQLYR--V----TM--SA-KPV--KR--IPKPLRHH

3m7pA

0.06

2.54

0.71

MapAlign

PPPYGHCVTDSGVVYSVGMQWLKTQGNKQMLCTQETAVTQTYGGNSNGEPCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSFCTDHTVLVQTRGGNSNGALCHFPFLYNNHNYT

1zvoC

0.11

4.07

0.73

MUSTER

QPQRTFPEIQRRDSYYMTSTPLQQWRQGQHTASKSKKEIFRWPESPKAQASSVPTAQPQAEGSLAKATTAPATTRNGGEEKKKEKEKEEQEERETKTPECPSHTQPLGVYLLTPAVQDWLRDK

2i0sD

0.17

0.10

3.22

0.45

HHsearch

----------------------------HISLNP-----------------DLANEDEVNSCDYWR----HCAVDGFLCSCC-GGT-TTTCPPDGKSYHDCGKTCGRCQCNTQTRERPGYEFF

1s1dA

0.11

3.85

0.46

CEthreader

KDHGVLESHLAEKGRGMELSDLIVFNGKLYSVDDRTGVVYQIEGSKAVPWVILSDGDGGFKAEWLAVKDERLYVGGLGKEWTTTTGDVVNENPEWVKVVGYKGSVDHENWVSNYNALRAAAGI

6c3iA

0.01

1.22

0.48

EigenThreader

ATNIEGGARYGYSLAANLMAMVIQNLSANLGIASGRNLPELIRERWPRPLVWFYWIQAELVAMATDLAEFLGAALAIQLLTGLPMFWGAVVTGVVTFWLLNLPLELAVGAFVLMIGVAYLVQV

(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	0.4835

(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	1flgA	0.46	4.52	0.038	0.805	model1_1flgA.pdb.gz
2	4aieA	0.45	4.64	0.040	0.797	model1_4aieA.pdb.gz
3	1uokA	0.45	4.87	0.019	0.821	model1_1uokA.pdb.gz
4	1x0uA	0.45	4.98	0.054	0.829	model1_1x0uA.pdb.gz
5	2f9yA	0.44	5.05	0.063	0.837	model1_2f9yA.pdb.gz
6	4w9uB	0.44	4.61	0.097	0.764	model1_4w9uB.pdb.gz
7	1hn0A	0.44	4.29	0.034	0.764	model1_1hn0A.pdb.gz
8	7d6aA	0.44	4.57	0.048	0.764	model1_7d6aA.pdb.gz
9	3ov6A	0.44	4.61	0.000	0.805	model1_3ov6A.pdb.gz
10	6cfwH	0.44	4.71	0.076	0.789	model1_6cfwH.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:0003723	1.00	RNA binding
GO:0044822	0.69	poly(A) RNA binding
GO:0003729	0.64	mRNA binding
GO:0003677	0.51	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	0.87	cellular process
GO:0071704	0.81	organic substance metabolic process
GO:0044238	0.80	primary metabolic process
GO:0044237	0.80	cellular metabolic process
GO:0043170	0.80	macromolecule metabolic process
GO:1901360	0.79	organic cyclic compound metabolic process
GO:0044260	0.79	cellular macromolecule metabolic process
GO:0006807	0.79	nitrogen compound metabolic process
GO:0016070	0.78	RNA metabolic process
GO:0065007	0.76	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0010468	0.72	regulation of gene expression
GO:0080090	0.70	regulation of primary metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0051252	0.69	regulation of RNA metabolic process
GO:0048024	0.62	regulation of mRNA splicing, via spliceosome
GO:0000381	0.61	regulation of alternative mRNA splicing, via spliceosome
GO:0044699	0.59	single-organism process
GO:0034645	0.58	cellular macromolecule biosynthetic process
GO:0006351	0.57	transcription, DNA-templated
GO:2000112	0.56	regulation of cellular macromolecule biosynthetic process
GO:0048522	0.56	positive regulation of cellular process
GO:0051173	0.55	positive regulation of nitrogen compound metabolic process
GO:0031325	0.55	positive regulation of cellular metabolic process
GO:0010628	0.55	positive regulation of gene expression
GO:0006355	0.55	regulation of transcription, DNA-templated
GO:0051254	0.54	positive regulation of RNA metabolic process
GO:0031328	0.54	positive regulation of cellular biosynthetic process
GO:0010557	0.54	positive regulation of macromolecule biosynthetic process
GO:0045893	0.53	positive regulation of transcription, DNA-templated
GO:0016043	0.51	cellular component organization
GO:0043933	0.50	macromolecular complex subunit organization
GO:0022607	0.50	cellular component assembly
GO:0019538	0.50	protein metabolic 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:0005634	1.00	nucleus
GO:0044422	0.74	organelle part
GO:0044446	0.73	intracellular organelle part
GO:0032991	0.73	macromolecular complex
GO:0030529	0.72	intracellular ribonucleoprotein complex
GO:0044428	0.71	nuclear part
GO:0005681	0.69	spliceosomal complex
GO:0071013	0.67	catalytic step 2 spliceosome
GO:0070062	0.66	extracellular exosome
GO:0044530	0.66	supraspliceosomal complex
GO:0005719	0.66	nuclear euchromatin

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	1myrA	0.440	4.32	0.069	0.740	3.2.1.147	95
2	0.060	2f9yA	0.444	5.05	0.063	0.837	6.4.1.2	NA
3	0.060	1kraC	0.427	4.74	0.029	0.764	3.5.1.5	19
4	0.060	2dgaA	0.432	4.52	0.058	0.764	3.2.1.21	NA
5	0.060	2pulA	0.432	4.71	0.018	0.764	2.7.1.100	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1n368	0.219	5.28	0.050	0.415	0.63	III	complex1.pdb.gz	102,103,111
	2	0.01	1xnyA	0.439	5.06	0.082	0.829	0.46	BTN	complex2.pdb.gz	97,98,102,103

	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.