D-I-TASSER Q96BQ5-D1

D-I-TASSER results for Q96BQ5-D1

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

Input Sequence in FASTA format

>Q96BQ5 (101 residues)
MNNLNDPPNWNIRPNSRADGGDGSRWNYALLVPMLGLAAFRWIWSRESQKEVEKEREAYR
RRTAAFQQDLEAKYHAMISENRRAVAQLSLELEKEQNRTAS

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MNNLNDPPNWNIRPNSRADGGDGSRWNYALLVPMLGLAAFRWIWSRESQKEVEKEREAYRRRTAAFQQDLEAKYHAMISENRRAVAQLSLELEKEQNRTAS
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	99889999877677888899876502356898888889888875343499999999999999999999999999999988788899999899998721159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MNNLNDPPNWNIRPNSRADGGDGSRWNYALLVPMLGLAAFRWIWSRESQKEVEKEREAYRRRTAAFQQDLEAKYHAMISENRRAVAQLSLELEKEQNRTAS
Prediction	86547534514243465476653430210101223333312211345356405623551464254146514442453146444323404241455564458
	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

CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
MNNLNDPPNWNIRPNSRADGGDGSRWNYALLVPMLGLAAFRWIWSRESQKEVEKEREAYRRRTAAFQQDLEAKYHAMISENRRAVAQLSLELEKEQNRTAS

7d6dA2

0.11

3.90

1.33

DEthreader

ALNTALFAKSLALGEDNT---ALSRALSQLAEVEEKIEQHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLL-WAN

6vbu72

0.08

3.14

0.46

CEthreader

FYFQNTFLDTQLESTYRKGEGVFKSDNISTISILKDVLSKEATKRKINLNISYEINEVSVKHTLKLIHPKLEYQLLLAKKVQLIDALKELQVHEGNTNFLI

6yjdA

0.09

3.41

0.48

EigenThreader

MPLKPEEHEDILNKLLDLAQSERTEALQQLRVNYGSCVSEYNDLTKSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLL

6yipA

0.15

0.10

3.32

0.72

FFAS-3D

------------------------------------MQQREQWCSEHLDTQKELLEEMYEEKLNILKESLTSFYQEEIQERDEKIEELEALLQEARQQSVA

5cwqA2

0.08

3.14

0.79

SPARKS-K

KAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVAEAERAYEDARRVEEEARKVKESAEEQGDSEVKRLAEEAEQLAREARRHVQECRGGWLE

5iuyA

0.19

0.14

4.49

0.54

CNFpred

--------------------------LQVSLIAELVDAYGQLRGAQLREKIALSNLENQKESRQLTEQLRVLRADARLAATAASVPQLQAEAERARHRIAT

7d6dA

0.11

3.90

1.33

DEthreader

ALNTALFAKSLALGEDNT---ALSRALSQLAEVEEKIEQHQEQANNDFFLLAELLSDYIRLLAIVRAAFDQRMKTWQRWQDAQATLQKKRESEARLL-WAN

4ev6A

0.03

1.79

0.71

MapAlign

VEEDEDFYLIIYKAPLFEEDITTTSLGIFHKSLIANRDVLVLLKREDRENFEDLYYDTLQLIDMSATYREVLTSMMDITLSLENIKMNQIMKILTMVTTI-

5cwpA1

0.16

5.28

0.67

MUSTER

MSDEEEARELIERAKEAERTGDPRVRELARELKRLAQEAAEEVKRDPSSSDVNEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEVQR

3kltA

0.24

0.12

3.70

0.45

HHsearch

----------------------------------------------DLTAALRDVRQQYESVAAKNLQEAEEWYKSKSTEYRRQVQSLTCEVDALK-----

(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	0.5708

(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	6z9lA	0.75	2.40	0.041	0.960	model1_6z9lA.pdb.gz
2	6ewyA	0.75	2.89	0.101	0.980	model1_6ewyA.pdb.gz
3	6sihA2	0.73	2.71	0.061	0.980	model1_6sihA2.pdb.gz
4	6h7wB	0.73	2.48	0.061	0.970	model1_6h7wB.pdb.gz
5	1ciiA	0.72	2.64	0.051	0.970	model1_1ciiA.pdb.gz
6	6el1O	0.72	3.01	0.040	0.980	model1_6el1O.pdb.gz
7	2eflA	0.71	2.80	0.061	0.970	model1_2eflA.pdb.gz
8	5wlqA	0.71	2.56	0.082	0.960	model1_5wlqA.pdb.gz
9	6gy6B	0.71	3.01	0.071	0.970	model1_6gy6B.pdb.gz
10	3qweA	0.70	2.57	0.031	0.941	model1_3qweA.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	0.72	heterocyclic compound binding
GO:0097159	0.72	organic cyclic compound binding
GO:0003676	0.68	nucleic acid binding
GO:0003677	0.61	DNA binding
GO:0003700	0.57	transcription factor activity, sequence-specific DNA binding
GO:0000977	0.57	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0098811	0.56	transcriptional repressor activity, RNA polymerase II activating transcription factor binding
GO:0044877	0.56	macromolecular complex binding
GO:0001134	0.56	transcription factor activity, transcription factor recruiting
GO:0001083	0.56	transcription factor activity, RNA polymerase II basal transcription factor binding
GO:0000987	0.56	core promoter proximal 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	0.79	cellular process
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0065007	0.71	biological regulation
GO:0044238	0.71	primary metabolic process
GO:0044237	0.71	cellular metabolic process
GO:0050794	0.70	regulation of cellular process
GO:0044699	0.68	single-organism process
GO:0006807	0.68	nitrogen compound metabolic process
GO:0044763	0.65	single-organism cellular process
GO:1901576	0.63	organic substance biosynthetic process
GO:0044249	0.63	cellular biosynthetic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0048518	0.61	positive regulation of biological process
GO:0080090	0.60	regulation of primary metabolic process
GO:0051171	0.60	regulation of nitrogen compound metabolic process
GO:0048583	0.60	regulation of response to stimulus
GO:0031326	0.60	regulation of cellular biosynthetic process
GO:0010556	0.60	regulation of macromolecule biosynthetic process
GO:0010468	0.60	regulation of gene expression
GO:1902680	0.59	positive regulation of RNA biosynthetic process
GO:0048584	0.59	positive regulation of response to stimulus
GO:0048523	0.59	negative regulation of cellular process
GO:0044710	0.59	single-organism metabolic process
GO:0010628	0.59	positive regulation of gene expression
GO:0080134	0.58	regulation of response to stress
GO:0044281	0.58	small molecule metabolic process
GO:0031324	0.58	negative regulation of cellular metabolic process
GO:0010646	0.58	regulation of cell communication
GO:2000112	0.57	regulation of cellular macromolecule biosynthetic process
GO:0010647	0.57	positive regulation of cell communication
GO:2000144	0.56	positive regulation of DNA-templated transcription, initiation
GO:1903832	0.56	regulation of cellular response to amino acid starvation
GO:1901566	0.56	organonitrogen compound biosynthetic process
GO:0090294	0.56	nitrogen catabolite activation of transcription
GO:0046394	0.56	carboxylic acid biosynthetic process
GO:0045944	0.56	positive regulation of transcription from RNA polymerase II promoter
GO:0045898	0.56	regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0032109	0.56	positive regulation of response to nutrient levels
GO:0010688	0.56	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter
GO:0006520	0.56	cellular amino acid metabolic process
GO:0001079	0.56	nitrogen catabolite regulation of transcription from RNA polymerase II promoter

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	0.97	cell part
GO:0044424	0.93	intracellular part
GO:0043229	0.82	intracellular organelle
GO:0044446	0.70	intracellular organelle part
GO:0044444	0.70	cytoplasmic part
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0016020	0.68	membrane
GO:0032991	0.62	macromolecular complex
GO:0043234	0.61	protein complex
GO:0005737	0.61	cytoplasm
GO:0043232	0.57	intracellular non-membrane-bounded organelle
GO:0044425	0.50	membrane part

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	0.067	1z56A	0.582	2.26	0.080	0.733	6.5.1.1	NA
2	0.066	2h8nA	0.478	2.86	0.061	0.614	3.5.1.98	NA
3	0.060	2hc8A	0.255	3.43	0.027	0.366	3.6.3.-	NA
4	0.060	2ahmE	0.282	2.52	0.030	0.346	2.7.7.48	NA
5	0.060	3btaA	0.508	3.20	0.042	0.743	3.4.24.69	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	0.320	3.13	0.156	0.446	0.44	III	complex1.pdb.gz	14,19,20,23,26,27,30

	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.