D-I-TASSER Q03468-D5

D-I-TASSER results for Q03468-D5

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

Input Sequence in FASTA format

>Q03468 (162 residues)
RPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGTDYELKPLPKGGKRQKKVPV
QEIDDDFFPSSGEEAEAASVGEGGGGGRKVGRYRDDGDEDYYKQRLRRWNKLRLQDKEKR
LKLEDDSEESDAEFDEGFKVPGFLFKKLFKYQQTGVRWLWEL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| RPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGTDYELKPLPKGGKRQKKVPVQEIDDDFFPSSGEEAEAASVGEGGGGGRKVGRYRDDGDEDYYKQRLRRWNKLRLQDKEKRLKLEDDSEESDAEFDEGFKVPGFLFKKLFKYQQTGVRWLWEL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence	985545555553112676431000110121123566555565544322234302212555566666788843211100122334431222234788738999999999999998745665531689987762204885276289998748889999998629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| RPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGTDYELKPLPKGGKRQKKVPVQEIDDDFFPSSGEEAEAASVGEGGGGGRKVGRYRDDGDEDYYKQRLRRWNKLRLQDKEKRLKLEDDSEESDAEFDEGFKVPGFLFKKLFKYQQTGVRWLWEL
Prediction	857556666656654437665456475555556551655645353554655655555465664655234675556655554675546553653444444630452155135524554654454565664433414541401440163016213300301175
	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                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
RPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGTDYELKPLPKGGKRQKKVPVQEIDDDFFPSSGEEAEAASVGEGGGGGRKVGRYRDDGDEDYYKQRLRRWNKLRLQDKEKRLKLEDDSEESDAEFDEGFKVPGFLFKKLFKYQQTGVRWLWEL

5fmf11

0.11

0.10

3.83

0.54

CEthreader

-SAVIGGDNEREEEDDDIDAVHSFENESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTISVSVMQWRQQFLQWCTLQPENCAVFTSKEMFQTESGLVVSTYSMVANTRNRSH

5mioC

0.04

2.14

0.48

EigenThreader

ETASNEVVYRFTAAPLVQTIFEGGAMASADVFLLKNQPCYRKLGTFANSNAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALGQNKHTPFRESKLTQVLGKKLLEAARAGDEVRVLMANGADVNATD----ASGLTPLHLAATYGHLEIVEVLLKHG

5vvrM1

0.37

0.18

5.31

0.75

FFAS-3D

------------------------------------------------------------------------------------RFRGQPGEAKDDGDELYYQERLKKWVKQRSCGSDLPEWRRPHPNIPDAKLNSQFKIPGEIYSLLFNYQKTCVQWLYEL

5nrlE

0.13

0.08

2.78

0.85

SPARKS-K

LKESSIFDDTDSTEVLENVKAAEENADREKLRLRQMNKKKKILNVKARKSKITDKMEIVKL----------VDEDESLSWMEEEQPVA---------------REIEKARDEEKRRTESILKMR--------------------------------------

5vvrM

0.42

0.19

5.44

0.76

CNFpred

------------------------------------------------------------------------------------------GEAKDDGDELYYQERLKKWVKQRSCGSQRSSDLPE-PNIPDAKLNSQFKIPGEIYSLLFNYQKTCVQWLYEL

6eqoA

0.06

0.05

2.16

0.83

DEthreader

IKLLLEAKALLKLLRIALNMVFGFSDKTDVEEIAILDKDSPVLTQD---------------TVVFTGSFVAG-ADIRQMLEEV-----EALPGYGGTQRLPRLLDAL-AIDADAA-D--TPKPEALIYALLVRPPADLLAG--TL-CNAYEVTMMNEMVAAG

5fmf11

0.07

3.00

0.74

MapAlign

SAVIGGDNEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEVVSTYSMNRSHDSVMDLTGREWG

6etxG

0.09

3.48

0.75

MUSTER

EGESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSGGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIWSFIRIPGK--ESLITD--GKLYALDVL

5vvrM

0.37

0.18

5.32

3.37

HHsearch

-----------------------------------------------------------------------------------LRFRGQPGEAKDDGDELYYQERLKKWVKQRSCGSQRSSDRRPHPNIPDAKLNSQFKIPGEIYSLLFNYQKTCVQWLYEL

5wlcLW

0.05

2.33

0.52

CEthreader

DWRKGQLRAELFLNETCHSATYLQNEQYFAVAQKKYTFIYDHEGTELHRLKQHIEARHLDFLPYHYLLVTAGETGWLKYHDVSTGQLVSELRTKAGPTMAMAQNPWNAVMHLGHSNGTVSKLLSARGPVNSIAISGYYMATTGADRSMKIWDIRNFKQLHSV

(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	0.3296

(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	4mt1A	0.45	5.04	0.062	0.778	model1_4mt1A.pdb.gz
2	6ca8A	0.45	5.06	0.061	0.765	model1_6ca8A.pdb.gz
3	2rgrA	0.45	4.81	0.045	0.741	model1_2rgrA.pdb.gz
4	1n5uA	0.44	5.16	0.099	0.784	model1_1n5uA.pdb.gz
5	2wl2B	0.43	4.99	0.069	0.753	model1_2wl2B.pdb.gz
6	1zvuA	0.40	5.01	0.073	0.728	model1_1zvuA.pdb.gz
7	2xcoA2	0.40	5.12	0.089	0.704	model1_2xcoA2.pdb.gz
8	3k07A	0.38	5.94	0.086	0.759	model1_3k07A.pdb.gz
9	2j8sA2	0.36	5.86	0.048	0.691	model1_2j8sA2.pdb.gz
10	2xkjE1	0.34	5.24	0.085	0.611	model1_2xkjE1.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:0008094	1.00	DNA-dependent ATPase activity
GO:1901363	0.94	heterocyclic compound binding
GO:0097159	0.94	organic cyclic compound binding
GO:0003676	0.93	nucleic acid binding
GO:0003677	0.92	DNA binding
GO:0036094	0.91	small molecule binding
GO:0047485	0.90	protein N-terminus binding
GO:0032403	0.90	protein complex binding
GO:0030296	0.90	protein tyrosine kinase activator activity
GO:0008022	0.90	protein C-terminus binding
GO:0005524	0.90	ATP binding
GO:0003682	0.90	chromatin 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:0006974	1.00	cellular response to DNA damage stimulus
GO:0008152	0.89	metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0044238	0.88	primary metabolic process
GO:1901360	0.87	organic cyclic compound metabolic process
GO:0046483	0.87	heterocycle metabolic process
GO:0034641	0.87	cellular nitrogen compound metabolic process
GO:0006725	0.87	cellular aromatic compound metabolic process
GO:0090304	0.86	nucleic acid metabolic process
GO:0006259	0.83	DNA metabolic process
GO:0006281	0.82	DNA repair
GO:0006289	0.80	nucleotide-excision repair
GO:0006283	0.77	transcription-coupled nucleotide-excision repair
GO:0065007	0.75	biological regulation
GO:0050794	0.74	regulation of cellular process
GO:0016070	0.72	RNA metabolic process
GO:0044271	0.71	cellular nitrogen compound biosynthetic process
GO:0019222	0.71	regulation of metabolic process
GO:0009059	0.71	macromolecule biosynthetic process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0048518	0.70	positive regulation of biological process
GO:0032774	0.70	RNA biosynthetic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0048522	0.69	positive regulation of cellular process
GO:0031326	0.69	regulation of cellular biosynthetic process
GO:0019219	0.69	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.69	regulation of macromolecule biosynthetic process
GO:0010468	0.69	regulation of gene expression
GO:2001141	0.68	regulation of RNA biosynthetic process
GO:2000112	0.68	regulation of cellular macromolecule biosynthetic process
GO:0045935	0.68	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.68	positive regulation of cellular biosynthetic process
GO:0010628	0.68	positive regulation of gene expression
GO:0010557	0.68	positive regulation of macromolecule biosynthetic process
GO:0009314	0.68	response to radiation
GO:1902680	0.67	positive regulation of RNA biosynthetic process
GO:0006355	0.67	regulation of transcription, DNA-templated
GO:0045893	0.66	positive regulation of transcription, DNA-templated
GO:0032786	0.65	positive regulation of DNA-templated transcription, elongation
GO:0009411	0.65	response to UV
GO:0006979	0.65	response to oxidative stress
GO:0006284	0.65	base-excision repair

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:0044446	0.94	intracellular organelle part
GO:0044428	0.93	nuclear part
GO:0043234	0.93	protein complex
GO:0044451	0.92	nucleoplasm part
GO:0043232	0.91	intracellular non-membrane-bounded organelle
GO:0005654	0.91	nucleoplasm
GO:0008023	0.90	transcription elongation factor complex
GO:0005730	0.90	nucleolus

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	1mosA	0.357	5.79	0.051	0.691	2.6.1.16	NA
2	0.060	1hwxA	0.421	5.37	0.047	0.765	1.4.1.3	146
3	0.060	1a3wA	0.417	4.90	0.052	0.716	2.7.1.40	NA
4	0.060	2ajqA	0.417	5.72	0.025	0.790	2.7.7.7	NA
5	0.060	2id0C	0.409	5.42	0.046	0.759	3.1.13.1	150

	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	1e7cA	0.435	5.15	0.081	0.772	0.40	HLT	complex1.pdb.gz	98,103,138,158
	2	0.01	1e7cA	0.435	5.15	0.081	0.772	0.42	HLT	complex2.pdb.gz	101,106,156

	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.