D-I-TASSER P35318-D1

D-I-TASSER results for P35318-D1

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

Input Sequence in FASTA format

>P35318 (185 residues)
MKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVK
AGPAQTLIRPQDMKGASRSPEDSSPDAARIRVKRYRQSMNNFQGLRSFGCRFGTCTVQKL
AHQIYQFTDKDKDNVAPRSKISPQGYGRRRRRSLPEAGPGRTLVSSKPQAHGAPAPPSGS
APHFL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPEDSSPDAARIRVKRYRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGYGRRRRRSLPEAGPGRTLVSSKPQAHGAPAPPSGSAPHFL
Prediction	CCHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	95178999999999860345334665611045561666530123355434566532123226603214401113455788988877655454334566676665556774213206888999999985645557799899999876553335664346543112566334445578777775459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPEDSSPDAARIRVKRYRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGYGRRRRRSLPEAGPGRTLVSSKPQAHGAPAPPSGSAPHFL
Prediction	43212311130000121314236264447144404422343445515436444543444643445412445526555544445447444334433445354464344410301102213004102403564457435445442632144344436754443524555453443534455542457
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPEDSSPDAARIRVKRYRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGYGRRRRRSLPEAGPGRTLVSSKPQAHGAPAPPSGSAPHFL

1vt4I3

0.08

3.18

1.00

MapAlign

-PKYERLVNAILDFLPKLLRIALMAEDEAIFEEAHKQVQGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2l7sA

1.00

0.28

7.87

4.00

HHsearch

----------------------------------------------------------------------------------------------YRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGY---------------------------------------

1vt4I

0.08

3.19

0.48

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6ly9N

0.04

2.17

0.47

EigenThreader

LFYLVGRWLSGYVKRQVIGKLVHILNWMVFWTVVWGVIYGEFFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVLMSRIWLAGLLTDVGFALAERLGLLGVLLGLLVA

2l7sA

1.00

0.28

7.87

0.88

FFAS-3D

----------------------------------------------------------------------------------------------YRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGY---------------------------------------

5yfpD

0.09

3.30

0.85

SPARKS-K

HNIFKTALDFQRLFYNLLNVFNTANTFRDLLNHFYNYYLGLFNSLIGTSDRHLTRKIITAWLQNGILMDQEQK--ILNGDETLFHEESIELFKEIPHFYQAGKGLSKS--DLFNLQFSASVLWILNWLPGLKKAI--NIDEVSQEPMLDADRLRSSWTFSESMDLNYSNPSSSPNSLGNLKILLD

4mmhA

0.10

0.04

1.39

0.59

CNFpred

--LFEAQRNLFAGVSFPEFK---------DSPRWRQTGISVLNTEIKKQ-VYADGMQFELS------------------------------------------------PIYHVAAIDIFLKAYGSAKR--------------------------------------------------------

1z8lA

0.07

0.06

2.43

0.83

DEthreader

-MKAFL-DELKAEN--I-KKFLY-NFTQ--IP-HLAGTELSYPFSAFSPQG--MPEGKIVAGVIL-GNIL-NLNGAGPLGIALSHSTNEVT-IY-GHDSWVFGG-IDPQSGAAVVHEIVRSFGTLKKEG---W-RPRRT-ILFAG-AYINACLVHPRISYTKNWNKFSGPLYH----SH------

1vbgA

0.03

1.73

0.76

MapAlign

ASDLKELVGQYKEVYLSAKGEPFPSDPKKQLELAVLAVFNSYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRGKSAVKIAVDMVNEGLVVGILTERGGMTSHAAVSGCSGIRVNDAEKLVTIGGHVLREGEWLSLNGSTGEVI

2l7sA

1.00

0.28

7.87

0.71

MUSTER

----------------------------------------------------------------------------------------------YRQSMNNFQGLRSFGCRFGTCTVQKLAHQIYQFTDKDKDNVAPRSKISPQGY---------------------------------------

(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	0.4651

(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	4a01A	0.49	5.22	0.046	0.816	model1_4a01A.pdb.gz
2	6y6kA	0.48	5.46	0.036	0.843	model1_6y6kA.pdb.gz
3	4av3A	0.48	5.32	0.046	0.811	model1_4av3A.pdb.gz
4	6vjrA	0.48	5.14	0.060	0.784	model1_6vjrA.pdb.gz
5	3mpiA	0.48	4.50	0.047	0.724	model1_3mpiA.pdb.gz
6	6l42A1	0.47	5.46	0.017	0.805	model1_6l42A1.pdb.gz
7	7dbwC	0.47	5.00	0.039	0.746	model1_7dbwC.pdb.gz
8	4j72A	0.47	4.83	0.043	0.735	model1_4j72A.pdb.gz
9	3mkhA	0.47	5.01	0.090	0.757	model1_3mkhA.pdb.gz
10	6n3tA	0.47	4.83	0.055	0.746	model1_6n3tA.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:0005102	1.00	receptor 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:1903522	1.00	regulation of blood circulation
GO:0051704	1.00	multi-organism process
GO:0050880	1.00	regulation of blood vessel size
GO:0048522	1.00	positive regulation of cellular process
GO:0048519	1.00	negative regulation of biological process
GO:0044765	1.00	single-organism transport
GO:0044763	1.00	single-organism cellular process
GO:0044237	1.00	cellular metabolic process
GO:0043207	1.00	response to external biotic stimulus
GO:0022414	1.00	reproductive process
GO:0006950	1.00	response to stress
GO:0007165	0.76	signal transduction
GO:0080090	0.75	regulation of primary metabolic process
GO:0031323	0.75	regulation of cellular metabolic process
GO:0009893	0.74	positive regulation of metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0045935	0.73	positive regulation of nucleobase-containing compound metabolic process
GO:0044281	0.73	small molecule metabolic process
GO:0044238	0.73	primary metabolic process
GO:0031328	0.73	positive regulation of cellular biosynthetic process
GO:0019220	0.73	regulation of phosphate metabolic process
GO:0010817	0.73	regulation of hormone levels
GO:0043170	0.72	macromolecule metabolic process
GO:0034754	0.72	cellular hormone metabolic process
GO:0030819	0.72	positive regulation of cAMP biosynthetic process
GO:0009611	0.72	response to wounding
GO:0007565	0.72	female pregnancy
GO:0006807	0.72	nitrogen compound metabolic process
GO:1901566	0.71	organonitrogen compound biosynthetic process
GO:1901137	0.71	carbohydrate derivative biosynthetic process
GO:0051241	0.71	negative regulation of multicellular organismal process
GO:0048869	0.71	cellular developmental process
GO:0044711	0.71	single-organism biosynthetic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0034654	0.71	nucleobase-containing compound biosynthetic process
GO:0009150	0.71	purine ribonucleotide metabolic process
GO:0006955	0.71	immune response
GO:0006952	0.71	defense response
GO:0050830	0.70	defense response to Gram-positive bacterium
GO:0050829	0.70	defense response to Gram-negative bacterium
GO:0045906	0.70	negative regulation of vasoconstriction
GO:0019731	0.70	antibacterial humoral response
GO:0006171	0.70	cAMP biosynthetic process
GO:0002031	0.70	G-protein coupled receptor internalization
GO:0001570	0.70	vasculogenesis
GO:0032502	0.61	developmental process
GO:0048856	0.60	anatomical structure development
GO:0044767	0.60	single-organism developmental process
GO:0051240	0.59	positive regulation of multicellular organismal process
GO:0048513	0.58	animal organ development
GO:0042127	0.58	regulation of cell proliferation
GO:0009653	0.58	anatomical structure 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	0.85	cell part
GO:0044424	0.76	intracellular part
GO:0044421	0.71	extracellular region part
GO:0005615	0.70	extracellular space

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	1bi5A	0.448	5.54	0.050	0.789	2.3.1.74	NA
2	0.060	1u8vA	0.451	5.35	0.044	0.746	5.3.3.3	NA
3	0.060	2tysB	0.381	5.38	0.060	0.659	4.2.1.20	NA
4	0.060	1t9gC	0.454	4.83	0.074	0.730	1.3.99.3	NA
5	0.060	1rx0A	0.443	5.02	0.069	0.730	1.3.99.-	42

	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	0.02	2c0uA	0.484	5.09	0.104	0.773	0.43	UUU	complex1.pdb.gz	94,109,112,115,145,146
2	0.01	1egeA	0.357	5.11	0.057	0.568	0.47	FAD	complex2.pdb.gz	96,112,114,144,145
3	0.01	3mddA	0.436	4.81	0.041	0.692	0.49	FAD	complex3.pdb.gz	94,95,111,114,144,145
4	0.01	1so2A	0.459	5.49	0.047	0.805	0.55	HG9	complex4.pdb.gz	114,117,118
5	0.01	1egcD	0.462	4.82	0.068	0.730	0.44	FAD	complex5.pdb.gz	97,112,115,144,145

	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.