D-I-TASSER Q93063-D1

D-I-TASSER results for Q93063-D1

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

Input Sequence in FASTA format

>Q93063 (50 residues)
MCASVKYNIRGPALIPRMKTKHRIYYITLFSIVLLGLIATGMFQFWPHSI

Predicted Secondary Structure

Sequence	20 40 \| \| MCASVKYNIRGPALIPRMKTKHRIYYITLFSIVLLGLIATGMFQFWPHSI
Prediction	CCCCSSCCCCCCSSCCCCCCCSSSSHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	97430104669710344323203420368999999999971232045679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MCASVKYNIRGPALIPRMKTKHRIYYITLFSIVLLGLIATGMFQFWPHSI
Prediction	73453435351332044344533211032333333313332334334566
	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

                   |                   |

SS
Seq

CCCCSSCCCCCCSSCCCCCCCSSSSHHHHHHHHHHHHHHHHHHHHCCCCC
MCASVKYNIRGPALIPRMKTKHRIYYITLFSIVLLGLIATGMFQFWPHSI

1mztA

0.13

0.10

3.48

1.06

SPARKS-K

----------AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKF-

6xf1A

0.00

0.98

1.33

DEthreader

GSEN-LPHFEKTNQCQNTVVLWENTKALVTECLEQCGRVLELLKQYQNFK

2c3tA

0.10

3.70

0.46

CEthreader

WHKVMFPVFLGEPVSPQTLAATLAELDVTLQLLEDKFLQNKAFLTGPHIS

5nl2A2

0.10

3.70

0.43

EigenThreader

VFFSVFMALWAATFMEHWKRKQMRLNYRIQLSIIMLGKQLIQNNLFEIGI

2xndJ

0.17

0.12

3.96

0.39

FFAS-3D

---------RNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILF-----

3dl8C

0.06

0.04

1.78

0.97

SPARKS-K

--------------KATISVIIFSLAIGVYLWILDLTFTKIISFILSLR-

4he8F

0.07

0.04

1.66

0.50

CNFpred

---------------------YSRFFAYFNLFIAMMLTLVLADSYPVMFI

4fm3A

0.08

3.12

1.33

DEthreader

-ATAES-YKARLEQAELDARLAESKVLTQKSKDQLGELDKSLKRLRKQLG

2b2jA

0.10

3.70

0.79

MapAlign

NPEVNGYAGLLFGNPQLLVSQLIAVASTTAYAFLVTLILAKAVDAAVGLR

1spfA

0.14

0.10

3.40

0.84

MUSTER

------------LRIPCCPVNLKRLLVVVVVVVLVVVVIVGALLMGL---

(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	0.353

(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	6j9fC	0.67	2.23	0.040	1.000	model1_6j9fC.pdb.gz
2	5fvmA	0.67	2.46	0.080	1.000	model1_5fvmA.pdb.gz
3	7ekuA	0.66	2.70	0.061	0.980	model1_7ekuA.pdb.gz
4	4gfhA	0.66	2.77	0.120	0.980	model1_4gfhA.pdb.gz
5	7vf2A	0.66	2.50	0.020	1.000	model1_7vf2A.pdb.gz
6	7f0rC	0.66	2.29	0.040	1.000	model1_7f0rC.pdb.gz
7	8jo2C	0.65	2.21	0.020	1.000	model1_8jo2C.pdb.gz
8	7zu0E	0.65	2.56	0.020	1.000	model1_7zu0E.pdb.gz
9	7ay1A	0.65	2.68	0.060	0.960	model1_7ay1A.pdb.gz
10	5u6oA	0.64	2.68	0.122	0.960	model1_5u6oA.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:0050509	1.00	N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity
GO:0008375	0.54	acetylglucosaminyltransferase 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:1901135	1.00	carbohydrate derivative metabolic process
GO:0043170	0.88	macromolecule metabolic process
GO:0009987	0.88	cellular process
GO:1901576	0.87	organic substance biosynthetic process
GO:0044699	0.87	single-organism process
GO:1901564	0.86	organonitrogen compound metabolic process
GO:1901137	0.86	carbohydrate derivative biosynthetic process
GO:0044237	0.86	cellular metabolic process
GO:0009059	0.86	macromolecule biosynthetic process
GO:0044763	0.85	single-organism cellular process
GO:0044260	0.85	cellular macromolecule metabolic process
GO:0006024	0.85	glycosaminoglycan biosynthetic process
GO:0034645	0.84	cellular macromolecule biosynthetic process
GO:0006790	0.84	sulfur compound metabolic process
GO:0044707	0.83	single-multicellular organism process
GO:0015012	0.83	heparan sulfate proteoglycan biosynthetic process
GO:0001503	0.82	ossification
GO:0065007	0.75	biological regulation
GO:0050789	0.74	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0044767	0.68	single-organism developmental process
GO:0007165	0.68	signal transduction
GO:0048869	0.66	cellular developmental process
GO:0030154	0.65	cell differentiation
GO:0048518	0.53	positive regulation of biological process
GO:0048522	0.52	positive regulation of cellular process
GO:0051239	0.51	regulation of multicellular organismal process
GO:0048856	0.51	anatomical structure development
GO:0048583	0.51	regulation of response to stimulus
GO:2000026	0.50	regulation of multicellular organismal development
GO:0048584	0.50	positive regulation of response to stimulus
GO:0022603	0.50	regulation of anatomical structure morphogenesis
GO:0016043	0.50	cellular component organization
GO:0009966	0.50	regulation of signal transduction
GO:0009653	0.50	anatomical structure morphogenesis
GO:0007166	0.50	cell surface receptor signaling pathway

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:0044425	1.00	membrane part
GO:0044421	1.00	extracellular region part
GO:0044464	0.89	cell part
GO:0044424	0.86	intracellular part
GO:0044444	0.80	cytoplasmic part
GO:0044446	0.78	intracellular organelle part
GO:0016020	0.78	membrane
GO:0098588	0.74	bounding membrane of organelle
GO:0000139	0.73	Golgi membrane
GO:0043226	0.72	organelle
GO:0043229	0.71	intracellular organelle
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0044432	0.68	endoplasmic reticulum part
GO:0032991	0.68	macromolecular complex
GO:0070062	0.67	extracellular exosome
GO:0043234	0.67	protein complex
GO:0005789	0.67	endoplasmic reticulum membrane
GO:0043541	0.66	UDP-N-acetylglucosamine transferase complex
GO:0005794	0.66	Golgi apparatus
GO:0005783	0.66	endoplasmic reticulum

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	0.142	2jwaA	0.533	1.93	0.077	0.720	2.7.10.1	37
2	0.073	3brtA	0.496	1.50	0.100	0.600	2.7.11.10	NA
3	0.068	3brvC	0.521	1.79	0.088	0.680	2.7.11.10	NA
4	0.060	3btaA	0.586	2.76	0.100	0.900	3.4.24.69	NA
5	0.060	2r0nA	0.561	3.12	0.040	0.840	1.3.99.7	41

	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	0.07	3g7fM	0.632	3.07	0.100	0.940	0.57	BCB	complex1.pdb.gz	35,36,39,40,43,44
	2	0.02	7prcM	0.628	3.04	0.120	0.940	0.42	MQ7	complex2.pdb.gz	33,37,38,40

	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.