D-I-TASSER P33121-D3

D-I-TASSER results for P33121-D3

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

Input Sequence in FASTA format

>P33121 (141 residues)
HIFKLAQGEYIAPEKIENIYMRSEPVAQVFVHGESLQAFLIAIVVPDVETLCSWAQKRGF
EGSFEELCRNKDVKKAILEDMVRLGKDSGLKPFEQVKGITLHPELFSIDNGLLTPTMKAK
RPELRNYFRSQIDDLYSTIKV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| HIFKLAQGEYIAPEKIENIYMRSEPVAQVFVHGESLQAFLIAIVVPDVETLCSWAQKRGFEGSFEELCRNKDVKKAILEDMVRLGKDSGLKPFEQVKGITLHPELFSIDNGLLTPTMKAKRPELRNYFRSQIDDLYSTIKV
Prediction	CSSSCCCCCSSCHHHHHHHHHHCCCCSSSSSSSCCCCCCSSSSSSCCHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCCCSCHHHHHCHHHHHHHHHHHHHHHHHHCCC
Confidence	928858995436699999997398801799996599972899996299999999999199999999961999999999999999998099963447579996799887789325545441899999999999999987469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| HIFKLAQGEYIAPEKIENIYMRSEPVAQVFVHGESLQAFLIAIVVPDVETLCSWAQKRGFEGSFEELCRNKDVKKAILEDMVRLGKDSGLKPFEQVKGITLHPELFSIDNGLLTPTMKAKRPELRNYFRSQIDDLYSTIKV
Prediction	633322744313124015304714202100000375351000000033720450067372744253016275025202620561166570552030440202456433744302322433364036304720550376268
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSCCCCCSSCHHHHHHHHHHCCCCSSSSSSSCCCCCCSSSSSSCCHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSSSCCCCCCCCCCSCHHHHHCHHHHHHHHHHHHHHHHHHCCC
HIFKLAQGEYIAPEKIENIYMRSEPVAQVFVHGESLQAFLIAIVVPDVETLCSWAQKRGFEGSFEELCRNKDVKKAILEDMVRLGKDSGLKPFEQVKGITLHPELFSIDNGLLTPTMKAKRPELRNYFRSQIDDLYSTIKV

5mssA

0.30

0.27

8.18

1.33

DEthreader

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALA-KY-----------GDG-EAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLET

5mssA2

0.30

0.27

8.18

2.27

SPARKS-K

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTP----EALAKYG---------DGEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLAE

5mssA2

0.30

0.27

8.17

0.89

MapAlign

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKY------------GDG-EAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQL--

5mssA

0.30

0.27

8.18

0.74

CEthreader

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKYG-------------DGEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLAE

5mssA2

0.30

0.27

8.18

1.89

MUSTER

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKYG-------------DGEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLAE

6oz1A

0.31

0.28

8.36

1.50

HHsearch

NVLKLAQGEFVAVSKLEAAYTGSPLVRQIFVYGNSERSYLLAVVVPTPEALERY------------ADSPDALKPLIQDSLQQVAKGAELQSYEIPRDFIVETVPFTVESGLLSDARKLLRPKLKEHYGERLEALYAD---

5mssA2

0.29

0.26

7.99

2.26

FFAS-3D

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEA-------------LAKYGDGEAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLA-

5mssA2

0.30

0.27

8.18

1.18

EigenThreader

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALAKYG----DG---------EAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLAE

5mscA

0.30

0.27

8.18

1.28

CNFpred

NVLKLSQGEFVTVAHLEAVFASSPLIRQIFIYGSSERSYLLAVIVPTDDALRGR--------------DTATLKSALAESIQRIAKDANLQPYEIPRDFLIETEPFTIANGLLSGIAKLLRPNLKERYGAQLEQMYTDLAT

5mssA2

0.30

0.27

8.18

1.33

DEthreader

NVLKLSQGEFVALSKLEAAYGTSPLVRQISVYGSSQRSYLLAVVVPTPEALA-KY-----------GDG-EAVKSALGDSLQKIAREEGLQSYEVPRDFIIETDPFTIENGILSDAGKTLRPKVKARYGERLEALYAQLET

(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	0.8267

(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	5mssA	0.86	1.10	0.297	0.908	model1_5mssA.pdb.gz
2	5mscA	0.86	1.08	0.299	0.901	model1_5mscA.pdb.gz
3	6oz1A	0.85	1.18	0.310	0.894	model1_6oz1A.pdb.gz
4	6eqoA	0.65	2.35	0.196	0.794	model1_6eqoA.pdb.gz
5	3e7xA2	0.63	2.36	0.178	0.759	model1_3e7xA2.pdb.gz
6	1ultA2	0.62	2.15	0.206	0.723	model1_1ultA2.pdb.gz
7	5gxdA	0.62	2.67	0.145	0.780	model1_5gxdA.pdb.gz
8	4wv3A	0.62	2.32	0.162	0.745	model1_4wv3A.pdb.gz
9	3l8cB	0.62	2.16	0.154	0.738	model1_3l8cB.pdb.gz
10	5ifiA	0.61	2.51	0.173	0.766	model1_5ifiA.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	0.99	catalytic activity
GO:0015645	0.97	fatty acid ligase activity
GO:0004467	0.95	long-chain fatty acid-CoA ligase activity

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:0044699	1.00	single-organism process
GO:0009987	0.96	cellular process
GO:0008152	0.95	metabolic process
GO:0071704	0.93	organic substance metabolic process
GO:0044763	0.92	single-organism cellular process
GO:0044710	0.92	single-organism metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044238	0.90	primary metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0006629	0.88	lipid metabolic process
GO:0044255	0.86	cellular lipid metabolic process
GO:0006631	0.84	fatty acid 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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.92	cytoplasmic part
GO:0043226	0.86	organelle
GO:0043229	0.85	intracellular organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0016020	0.64	membrane
GO:0044422	0.60	organelle part
GO:0044446	0.59	intracellular organelle 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	0.060	1iq0A	0.457	4.84	0.069	0.780	6.1.1.19	NA
2	0.060	1yrtA	0.498	4.07	0.077	0.759	4.6.1.1	NA
3	0.060	3l8cB	0.615	2.16	0.154	0.738	6.1.1.13	121
4	0.060	1t3nA	0.476	3.80	0.108	0.709	2.7.7.7	NA
5	0.060	1ultA	0.623	2.15	0.206	0.723	6.2.1.3	4

	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	0.05	3gpcB	0.608	2.28	0.223	0.731	0.13	COA	complex1.pdb.gz	28,29,30,31,32,33
2	0.04	3gpcA	0.608	2.23	0.223	0.731	0.17	COA	complex2.pdb.gz	34,85,92
3	0.04	1md9A	0.591	2.54	0.184	0.731	0.17	AMP	complex3.pdb.gz	4,5,6,91
4	0.03	1mdbA	0.591	2.58	0.184	0.731	0.14	UUU	complex4.pdb.gz	29,30,31,32,33,42
5	0.03	1md9A	0.591	2.54	0.184	0.731	0.13	DBH	complex5.pdb.gz	2,4,5
6	0.03	3eq6A	0.603	2.33	0.214	0.731	0.24	BCO	complex6.pdb.gz	6,8,9,86,93,95,97
7	0.03	2qvxX	0.576	2.25	0.216	0.688	0.19	3BZ	complex7.pdb.gz	8,34,37
8	0.03	3lgxA	0.605	2.34	0.154	0.738	0.11	ATP	complex8.pdb.gz	9,39,90
9	0.02	3lgxB	0.608	2.31	0.173	0.738	0.11	ATP	complex9.pdb.gz	121,127,128,129,130
10	0.02	3e7wA	0.614	2.78	0.159	0.759	0.20	AMP	complex10.pdb.gz	3,4,13,39,90

	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.