D-I-TASSER A1L4K1-D3

D-I-TASSER results for A1L4K1-D3

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

Input Sequence in FASTA format

>A1L4K1 (94 residues)
SPPIIKTKEIRSCEEAVLICWESGNLNPVDSYTVELTQAESPEASGVTESVVGIPTCESV
VQLQPGRSYIIYVRALNMGGPSVRSEPATVHTIG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SPPIIKTKEIRSCEEAVLICWESGNLNPVDSYTVELTQAESPEASGVTESVVGIPTCESVVQLQPGRSYIIYVRALNMGGPSVRSEPATVHTIG
Prediction	CCCSSCCCSSSSSCCSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCSSSSSSCCCCCSSSSSCCCCCCSSSSSSSSSSCCCCCCCCCCSSSSSCC
Confidence	9881401010675785999993799997217999998678998741788761776279985688994399999999367799998637888179
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SPPIIKTKEIRSCEEAVLICWESGNLNPVDSYTVELTQAESPEASGVTESVVGIPTCESVVQLQPGRSYIIYVRALNMGGPSVRSEPATVHTIG
Prediction	8444255651433543010204168653143020102444367445134424627424232604254403010202154362641443434268
	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

                   |                   |                   |                   |

SS
Seq

CCCSSCCCSSSSSCCSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCSSSSSSCCCCCSSSSSCCCCCCSSSSSSSSSSCCCCCCCCCCSSSSSCC
SPPIIKTKEIRSCEEAVLICWESGNLNPVDSYTVELTQAESPEASGVTESVVGIPTCESVVQLQPGRSYIIYVRALNMGGPSVRSEPATVHTIG

1fnfA

0.16

0.15

4.98

1.33

DEthreader

DPPTDLRFTNI-GPDTMRVTWAPPPSIDLTNFLVRYSPVKNEED-VAELSI-SPSDNAVVLTLLPGTEYVVSVSSVYEQHESTPL-RGRQKTGL

5e53A2

0.19

6.16

1.55

SPARKS-K

EVP-TDVSVKVLSSSEISVSWHHVTEKSVEGYQIRYWAAHDKEAAAQRVQVSNQEYSTKLENLKPNTRYHIDVSAFNSAGYGPPSRTIDIITRK

2jllA

0.22

0.21

6.69

0.37

MapAlign

SSPYVKIIEL-S-QTTAKVSFNKPGGVPIHHYQVDVKEVA--SEIWKIVRSHGV-QTMVVLNLEPNTTYEIRVAAVNGKGQGDYSKIEIFQTLP

4lsdA

0.16

5.28

0.26

CEthreader

PSAPVNVTVRHLKANSAVVSWDVLEDEVVIGFAISQQKKD---VRLRFIQEVNTTTRSCALDLEEDTEYIVHVQAISIQGQSPASEPVLFKTPR

2ee2A

0.20

6.46

1.09

MUSTER

SEAPTEVGVKVLSSSEISVHWEHVLEKIVESYQIRYWAAHDKEEAANRVQVTSQEYSARLENLLPDTQYFIEVGACNSAGCGPPSDMIEAFTKK

6rpxA

0.19

0.18

5.84

0.88

HHsearch

SRPPVQIEELIEKPGGIIVRWCKVDDFTAQDYRLQFRKCTANHFEDVY---VGSETEFIVLHIDPNVDYQFRVCA-RGDGRQEWSPWSVPQTGH

2ha1A1

0.16

5.30

1.59

FFAS-3D

SGPVVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGR-WKEATIPGHLNSYTIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTST

7ndgB3

0.18

5.87

0.42

EigenThreader

SPPKDVTVVKEGKPRTIIVNWQPPSEANITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQLTLDTPYYFKIQARNSKGMGPMSEAVQFRTP-

4pbxA

0.14

4.70

1.46

CNFpred

PGQPMNLRAEARSETSITLSWSPPRQESIIKYELLFREGD--HGREVGRTFDP-TTSYVVEDLKPNTEYAFRLAARSPQGLGAFTPVVRQRTLG

1x5hA

0.18

0.17

5.56

1.33

DEthreader

AAPQNLSLEVR-NSKSIMIHWQPPPQGQITGYKIRYRKASRKSDV-TETLV-SGTQLSQLIELDRGTEYNFRVAALTINGTGPATDWLSAETFE

(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	0.8935

(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	1x5hA	0.87	1.36	0.141	0.979	model1_1x5hA.pdb.gz
2	4n68A	0.87	1.45	0.183	0.989	model1_4n68A.pdb.gz
3	5e4sA2	0.86	1.53	0.183	0.989	model1_5e4sA2.pdb.gz
4	1x4yA	0.86	1.52	0.194	0.989	model1_1x4yA.pdb.gz
5	1va9A	0.86	1.92	0.117	1.000	model1_1va9A.pdb.gz
6	4hljA1	0.85	1.83	0.128	1.000	model1_4hljA1.pdb.gz
7	1uenA	0.85	1.83	0.140	0.989	model1_1uenA.pdb.gz
8	1i1rA3	0.84	1.55	0.176	0.968	model1_1i1rA3.pdb.gz
9	2djuA	0.83	1.59	0.253	0.968	model1_2djuA.pdb.gz
10	1ujtA	0.82	2.01	0.194	0.989	model1_1ujtA.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	0.74	catalytic activity
GO:0008307	0.50	structural constituent of muscle

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	0.93	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0032502	0.84	developmental process
GO:0065007	0.77	biological regulation
GO:0050789	0.76	regulation of biological process
GO:0016043	0.76	cellular component organization
GO:0008152	0.76	metabolic process
GO:0071704	0.75	organic substance metabolic process
GO:0050794	0.74	regulation of cellular process
GO:0044238	0.74	primary metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0044767	0.72	single-organism developmental process
GO:0043170	0.71	macromolecule metabolic process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0019538	0.68	protein metabolic process
GO:0006464	0.66	cellular protein modification process
GO:0048869	0.62	cellular developmental process
GO:0006796	0.62	phosphate-containing compound metabolic process
GO:0048856	0.59	anatomical structure development
GO:0051239	0.58	regulation of multicellular organismal process
GO:0009653	0.58	anatomical structure morphogenesis
GO:0006928	0.58	movement of cell or subcellular component
GO:0051128	0.55	regulation of cellular component organization
GO:2000026	0.53	regulation of multicellular organismal development
GO:0048519	0.53	negative regulation of biological process
GO:0045595	0.53	regulation of cell differentiation
GO:0007411	0.53	axon guidance
GO:0007165	0.53	signal transduction
GO:0051960	0.52	regulation of nervous system development
GO:0048523	0.52	negative regulation of cellular process
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0010975	0.51	regulation of neuron projection development
GO:0022604	0.50	regulation of cell morphogenesis

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	0.94	intracellular part
GO:0016020	0.77	membrane
GO:0044444	0.75	cytoplasmic part
GO:0044425	0.73	membrane part
GO:0043226	0.73	organelle
GO:0044422	0.71	organelle part
GO:0043227	0.70	membrane-bounded organelle
GO:0044421	0.65	extracellular region part
GO:0043229	0.59	intracellular organelle
GO:0044459	0.58	plasma membrane part
GO:0043231	0.55	intracellular membrane-bounded organelle
GO:0032991	0.54	macromolecular complex
GO:0043234	0.53	protein complex
GO:0044446	0.52	intracellular organelle part
GO:0031224	0.50	intrinsic component of membrane
GO:0005886	0.50	plasma membrane

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	0.220	2dlhA	0.821	1.84	0.187	0.968	3.1.3.48	1,85
2	0.077	2gg1A	0.608	2.82	0.150	0.851	2.7.7.48 3.4.21.91	NA
3	0.067	1zvhA	0.683	2.94	0.088	0.968	3.2.1.17	80
4	0.067	2bk8A	0.611	2.89	0.108	0.883	2.7.11.1	17,82,86
5	0.067	1zv5A	0.639	3.30	0.079	0.947	3.2.1.17	80

	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	0.04	2b5i6	0.816	1.96	0.140	0.989	0.70	III	complex1.pdb.gz	30,31,58,59,60,61,62,78
	2	0.01	2rd58	0.395	3.17	0.125	0.606	0.40	III	complex2.pdb.gz	76,77,78,79,80,81

	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.