D-I-TASSER Q5TAA0-D1

D-I-TASSER results for Q5TAA0-D1

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

Input Sequence in FASTA format

>Q5TAA0 (136 residues)
MAELEAVADDLDALIDDLDYLPGHFHLEMQLNFEPRSPAPQRARDLKLQREGLRQELQLA
AAPQRPAVRHLLGAFAFYLEELDEARECFLEVAHEHPGNLNAWANLAHVYGRLGQEEEEE
ACAARLADLMGLAEEP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAELEAVADDLDALIDDLDYLPGHFHLEMQLNFEPRSPAPQRARDLKLQREGLRQELQLAAAPQRPAVRHLLGAFAFYLEELDEARECFLEVAHEHPGNLNAWANLAHVYGRLGQEEEEEACAARLADLMGLAEEP
Prediction	CCCCCCHHHHHHHHHHHHCCCCCCCSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
Confidence	9974312668999998530466510001004777776322233210474999999999854013489999999999997468999999999999582115789999999999801889999999999996455799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAELEAVADDLDALIDDLDYLPGHFHLEMQLNFEPRSPAPQRARDLKLQREGLRQELQLAAAPQRPAVRHLLGAFAFYLEELDEARECFLEVAHEHPGNLNAWANLAHVYGRLGQEEEEEACAARLADLMGLAEEP
Prediction	8554744564143016414323131202020325564445454551424375045415444433431032010101221652640351045006524730311221120254245455244036304512545768
	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

CCCCCCHHHHHHHHHHHHCCCCCCCSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
MAELEAVADDLDALIDDLDYLPGHFHLEMQLNFEPRSPAPQRARDLKLQREGLRQELQLAAAPQRPAVRHLLGAFAFYLEELDEARECFLEVAHEHPGNLNAWANLAHVYGRLGQEEEEEACAARLADLMGLAEEP

2pl2A

0.15

4.95

1.50

DEthreader

GLVNPALENGKTLVARTPRYLGGYMVLSEAYVALRQAEDERGKGYLEQALSVLKDAE-RV-NPRYAPLHLQRGLVYALLGERDKAEASLKQALALED-TPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDV

2hyzA

0.21

0.19

6.06

1.47

SPARKS-K

GDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQ---------GDYDEAIEYYQKALELD--PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRS---

4a1sA

0.18

5.76

0.61

MapAlign

GRFDEAAICCERHLTLARSEGRALYNLGNVYHAKGGKFGDDVKEALTRAVEFYQENLKLMRRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGER

4a1sA

0.18

5.76

0.36

CEthreader

GRFDEAAICCERHLTLARQEGRALYNLGNVYHAKGKHFGDDVKEALTRAVEFYQENLKLMRDGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIARAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGER

4rg6A3

0.16

0.15

4.90

1.28

MUSTER

---YNAWYGLGMIYYKQEKFSLAEMHFQKALDINPQSSVLLCHIGVVQHALTLNKAIVI--DPKNPLCKFHRASVLFANEKYKSALQELEELKQIVPKESLVYFLIGKVYKKLGQTHLALMNFSWAMDLDP-----

3pe3A

0.18

0.16

5.29

0.61

HHsearch

GNIEEAVRLYRKALEVFPEFAAAHSNLASVLQ---------QQGKLQEALMHYKEAIR--ISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDA

2hyzA

0.21

0.18

5.83

1.76

FFAS-3D

----EAIEYYQKALELDPRSAEAWYNLGNAY---------YKQGDYDEAIEY--YQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRS---

6af0A

0.14

4.76

0.57

EigenThreader

GFKDDAKIAWERCLEINPDSKHANILLGLYYLDASPTNSPEFIRLYKKAMTEYTQKSFKLD-KNLPLTCATFAGYFLSRKQFGNVDALAHKAIQYTDVASDGWYLLARKEHYDGNLERASDYYRRADDARGGAERG

3cv0A

0.18

0.16

5.28

1.10

CNFpred

NEYRECRTLLHAALEMNPNDAQLHASLGVLYNLS---------NNYDSAAANLRRAVELR--PDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTT-

5dseA

0.09

3.36

1.50

DEthreader

HWLEEAEKFAKTVV-TSEFKAKGYLALGLTYSLQTDALRGMQEVLQRKALLAFQRAHSL--SPTDHQAAFYLALQLAISRQIPEALGYVRQALQLQGDDANSLHLLALLLSAQKHYHDALNIIDMALSEYPENFIF

(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	0.8346

(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	2pl2A	0.87	1.61	0.158	0.978	model1_2pl2A.pdb.gz
2	5dseA	0.86	1.81	0.083	0.963	model1_5dseA.pdb.gz
3	3cvnA	0.86	1.29	0.176	0.919	model1_3cvnA.pdb.gz
4	4bujB	0.85	2.13	0.089	0.993	model1_4bujB.pdb.gz
5	2hyzA	0.85	1.13	0.205	0.897	model1_2hyzA.pdb.gz
6	6af0A	0.84	2.06	0.112	0.985	model1_6af0A.pdb.gz
7	5o09C	0.84	1.61	0.110	0.934	model1_5o09C.pdb.gz
8	4g1tA	0.84	2.04	0.097	0.985	model1_4g1tA.pdb.gz
9	4eqfA	0.83	1.62	0.152	0.919	model1_4eqfA.pdb.gz
10	6b85J	0.83	1.28	0.205	0.897	model1_6b85J.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:0003824	0.67	catalytic activity
GO:0016740	0.57	transferase activity
GO:0042277	0.55	peptide binding
GO:0034212	0.52	peptide N-acetyltransferase activity
GO:0030234	0.50	enzyme regulator activity
GO:0016758	0.50	transferase activity, transferring hexosyl groups
GO:0005543	0.50	phospholipid 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	0.90	cellular process
GO:0071704	0.75	organic substance metabolic process
GO:0044238	0.74	primary metabolic process
GO:0043170	0.74	macromolecule metabolic process
GO:0044260	0.73	cellular macromolecule metabolic process
GO:0044699	0.72	single-organism process
GO:0065007	0.70	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0044763	0.68	single-organism cellular process
GO:0019222	0.61	regulation of metabolic process
GO:0051179	0.60	localization
GO:0031323	0.60	regulation of cellular metabolic process
GO:0016043	0.60	cellular component organization
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0044767	0.59	single-organism developmental process
GO:0006464	0.59	cellular protein modification process
GO:0080090	0.58	regulation of primary metabolic process
GO:0050896	0.57	response to stimulus
GO:2000112	0.56	regulation of cellular macromolecule biosynthetic process
GO:0051641	0.56	cellular localization
GO:0019219	0.56	regulation of nucleobase-containing compound metabolic process
GO:0048518	0.55	positive regulation of biological process
GO:0018193	0.55	peptidyl-amino acid modification
GO:0051128	0.54	regulation of cellular component organization
GO:0048856	0.54	anatomical structure development
GO:0048522	0.54	positive regulation of cellular process
GO:0048519	0.54	negative regulation of biological process
GO:0031399	0.54	regulation of protein modification process
GO:0022607	0.54	cellular component assembly
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0048523	0.53	negative regulation of cellular process
GO:0044710	0.53	single-organism metabolic process
GO:0032501	0.53	multicellular organismal process
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0007165	0.53	signal transduction
GO:0048583	0.52	regulation of response to stimulus
GO:0044707	0.52	single-multicellular organism process
GO:0031060	0.52	regulation of histone methylation
GO:0019220	0.52	regulation of phosphate metabolic process
GO:0006996	0.52	organelle organization
GO:1901575	0.51	organic substance catabolic process
GO:0051569	0.51	regulation of histone H3-K4 methylation
GO:0045935	0.51	positive regulation of nucleobase-containing compound metabolic process
GO:0043933	0.51	macromolecular complex subunit organization
GO:0043207	0.51	response to external biotic stimulus
GO:0031328	0.51	positive regulation of cellular biosynthetic process
GO:0031324	0.51	negative regulation of cellular metabolic process
GO:0010557	0.51	positive regulation of macromolecule biosynthetic process
GO:0009966	0.51	regulation of signal transduction
GO:0006473	0.51	protein acetylation
GO:0065003	0.50	macromolecular complex assembly
GO:0051130	0.50	positive regulation of cellular component organization
GO:0050790	0.50	regulation of catalytic activity
GO:0035556	0.50	intracellular signal transduction
GO:0031401	0.50	positive regulation of protein modification process
GO:0018022	0.50	peptidyl-lysine methylation
GO:0010941	0.50	regulation of cell death
GO:0010605	0.50	negative regulation of macromolecule metabolic process
GO:0001932	0.50	regulation of protein phosphorylation

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	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0043226	0.85	organelle
GO:0044444	0.83	cytoplasmic part
GO:0043229	0.80	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0043234	0.73	protein complex
GO:0005737	0.72	cytoplasm
GO:0044446	0.71	intracellular organelle part
GO:0005634	0.60	nucleus
GO:0016020	0.58	membrane
GO:0005829	0.52	cytosol

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	0.152	1tjcA	0.578	2.10	0.178	0.654	1.14.11.2	72
2	0.066	1klxA	0.558	3.75	0.105	0.809	3.5.2.6	110,111
3	0.060	2c0lA	0.854	1.30	0.176	0.919	2.3.1.176	57,72,74,84,105
4	0.060	1ia7A	0.653	3.31	0.048	0.897	3.2.1.4	NA
5	0.060	1gxmB	0.652	3.60	0.053	0.963	4.2.2.2	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.23	3cv0A	0.850	1.45	0.168	0.919	0.66	III	complex1.pdb.gz	70,71,74,77,78,89,101,104,105,108,112
2	0.19	3kd7C	0.706	1.22	0.158	0.743	0.86	III	complex2.pdb.gz	77,78,101,105,108,112
3	0.03	2wh0A	0.775	2.69	0.128	0.978	0.50	III	complex3.pdb.gz	29,66,67,70,74,98,99,103

	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.