D-I-TASSER Q7Z3B3-D4

D-I-TASSER results for Q7Z3B3-D4

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

Input Sequence in FASTA format

>Q7Z3B3 (136 residues)
TRKAEAALRKAASETTTSEGLSNFLKSNSISEELERFTASGIANLRCSEQAFDSDVTDSS
SGGESDIEEEELTRADPEQRHVPLRRRSEWKWAADRAAIVSRWNWLQAHVSDLEYRIRQQ
TDIYKQIRANKGLIVL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TRKAEAALRKAASETTTSEGLSNFLKSNSISEELERFTASGIANLRCSEQAFDSDVTDSSSGGESDIEEEELTRADPEQRHVPLRRRSEWKWAADRAAIVSRWNWLQAHVSDLEYRIRQQTDIYKQIRANKGLIVL
Prediction	CCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	9520356764226776555544456565359999999998899999999853642323578877651444311257421444412457889999999999878999999999999999999999999974387019
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TRKAEAALRKAASETTTSEGLSNFLKSNSISEELERFTASGIANLRCSEQAFDSDVTDSSSGGESDIEEEELTRADPEQRHVPLRRRSEWKWAADRAAIVSRWNWLQAHVSDLEYRIRQQTDIYKQIRANKGLIVL
Prediction	8554554245446544447414433577413530451133044304403752446134324576444745544564454442334442424134420400330220332145144304534511540465544157
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
TRKAEAALRKAASETTTSEGLSNFLKSNSISEELERFTASGIANLRCSEQAFDSDVTDSSSGGESDIEEEELTRADPEQRHVPLRRRSEWKWAADRAAIVSRWNWLQAHVSDLEYRIRQQTDIYKQIRANKGLIVL

3k29A

0.05

0.04

2.03

1.17

DEthreader

------------------L--PVLSIKKDRVDRAEKVVKEKRRLLELEQEKLRERESERDK--KNHYQIRQLREQAILKKAYKVVAIQLSEEEEKVNKQKENVLAASKELERAEVELTKRRKEEEKTRLHKEEWEA

1fxkC

0.05

0.04

1.81

0.51

CEthreader

---------------------AALAEIVAQLNIYQSQVELIQQQMEAVRATISQGKDGSETKAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQAEELLAAVA----

4iloA

0.04

2.19

0.60

EigenThreader

LQSILAIQELDIKMIRLMRVKKEHQNELAKIQALKTDIRRKVEEKEQEMEKLKDQIKGGEKRIQEISDQINKLENQQAAVKKNKERRTLEHQLSDLMDKQAGSEDLLISLKESLSSTENSSSAIEEEIRENIRKIN

2y44A

0.12

0.11

3.93

0.68

FFAS-3D

-ERAEKAVERAKSKKRGVDTATEAAARETVVSDARKHAADLTAASKDAIETTDESLRLLATEADEPIRTAAKKCTGAAAEVTSKSLESAFDALAGADDIREHGAVFVKGLKSLEDDVRTAGEAKYEAEKAE-----

5cwjA

0.14

0.12

4.26

0.74

SPARKS-K

QERIRRILKEARKSGTEEEDVAQLAKKSQDSEVLEEAIRVILRIAKESGSE------------EALRAIRAVAEIAKEAQDS----EVLEEAIRVILRIAKESRQAIRAVAEIAKELEEAIRVIRQIAEESGSEEA

5j1iA

0.14

0.10

3.49

0.56

CNFpred

--------------------LRAQAEAQPTFDALRDELRGAQEVGERLQQRHG----------ERDVEVERWR---------ERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQ

6z9lA4

0.07

0.06

2.40

1.00

DEthreader

-------------------AEKVKA--EKEQAAKEAELANKQKEEAKAKDQKTKDDQVADQ--QT-VVTTSQEKVAKQAAEKSVHKATLANLQAVATKSTTNYEEKVRQTATAEKSLQQTKDQLATINELIQNRA-

1l8dA

0.14

0.10

3.53

0.71

MapAlign

-------------------KLLEELE--TKKTTIEEERNEITQRIGELKNKI----GDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIKRL---------

5cwmA1

0.15

0.12

4.21

0.64

MUSTER

--DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVL----------------EQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQG----

3bj4B

0.26

0.07

2.26

0.69

HHsearch

----------------------------------------------------------------------------------------------GSNTIGARLNRVEDKVTQLDQRLALITDMLHQLLSLHG----

(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	0.5389

(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	6z9lA1	0.71	2.72	0.080	0.868	model1_6z9lA1.pdb.gz
2	3k29A	0.71	2.11	0.027	0.801	model1_3k29A.pdb.gz
3	2b5uA	0.71	3.63	0.068	0.934	model1_2b5uA.pdb.gz
4	4mh6A	0.69	2.72	0.099	0.853	model1_4mh6A.pdb.gz
5	3hhmB2	0.69	2.75	0.062	0.860	model1_3hhmB2.pdb.gz
6	3qweA	0.68	2.75	0.104	0.831	model1_3qweA.pdb.gz
7	3l4qC	0.63	3.26	0.053	0.838	model1_3l4qC.pdb.gz
8	3v47C	0.55	3.58	0.097	0.765	model1_3v47C.pdb.gz
9	1rh1A	0.43	3.46	0.060	0.581	model1_1rh1A.pdb.gz
10	4ehiA1	0.35	3.29	0.039	0.478	model1_4ehiA1.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	0.68	heterocyclic compound binding
GO:0097159	0.68	organic cyclic compound binding
GO:0003676	0.63	nucleic acid binding
GO:0003677	0.59	DNA binding
GO:0019899	0.55	enzyme binding
GO:0035035	0.54	histone acetyltransferase binding
GO:0001047	0.54	core promoter 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:0016043	1.00	cellular component organization
GO:0065007	0.72	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0044699	0.70	single-organism process
GO:0044763	0.68	single-organism cellular process
GO:0019222	0.68	regulation of metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0031325	0.67	positive regulation of cellular metabolic process
GO:0050896	0.66	response to stimulus
GO:0048519	0.66	negative regulation of biological process
GO:0045893	0.66	positive regulation of transcription, DNA-templated
GO:0032502	0.66	developmental process
GO:1903047	0.65	mitotic cell cycle process
GO:0048869	0.65	cellular developmental process
GO:0048856	0.65	anatomical structure development
GO:0048523	0.65	negative regulation of cellular process
GO:0044767	0.65	single-organism developmental process
GO:0008152	0.65	metabolic process
GO:0071704	0.64	organic substance metabolic process
GO:0048477	0.64	oogenesis
GO:0044238	0.64	primary metabolic process
GO:0030727	0.64	germarium-derived female germ-line cyst formation
GO:0030718	0.64	germ-line stem cell population maintenance
GO:0030100	0.64	regulation of endocytosis
GO:0007528	0.64	neuromuscular junction development
GO:0007526	0.64	larval somatic muscle development
GO:0007095	0.64	mitotic G2 DNA damage checkpoint
GO:0044237	0.63	cellular metabolic process
GO:0043170	0.63	macromolecule metabolic process
GO:0044260	0.62	cellular macromolecule 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:0000123	1.00	histone acetyltransferase complex
GO:0044427	0.65	chromosomal part
GO:0005737	0.65	cytoplasm
GO:0044545	0.64	NSL complex
GO:0005705	0.64	polytene chromosome interband
GO:0035097	0.52	histone methyltransferase 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	0.060	3errA	0.504	4.35	0.092	0.787	6.1.1.11	NA
2	0.060	2ahmE	0.267	3.35	0.038	0.368	2.7.7.48	NA
3	0.060	2qb0B	0.264	5.08	0.090	0.493	3.2.1.17	NA
4	0.060	1u7lA	0.535	4.27	0.030	0.853	3.6.3.14	NA
5	0.060	1yfeA	0.512	4.07	0.031	0.728	4.2.1.2	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	2hdi1	0.318	3.51	0.033	0.434	0.22	III	complex1.pdb.gz	54,55,56,57,62,63,64,65,95,96
	2	0.01	2j0n0	0.487	2.82	0.057	0.647	0.26	III	complex2.pdb.gz	94,98,100,101,102,104,105,107,108,109,112,115,116,119,122,123,126,127

	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.