D-I-TASSER Q03112-D2

D-I-TASSER results for Q03112-D2

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

Input Sequence in FASTA format

>Q03112 (83 residues)
SIKAIASIAEKYFGSTGLVGLQDKKVGALPYPSMFPLPFFPAFSQSMYPFPDRDLRSLPL
KMEPQSPGEVKKLQKGSSESPFD

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| SIKAIASIAEKYFGSTGLVGLQDKKVGALPYPSMFPLPFFPAFSQSMYPFPDRDLRSLPLKMEPQSPGEVKKLQKGSSESPFD
Prediction	CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCC
Confidence	84789999999738876456530135788886557733467899877898841014567788999978854235888889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| SIKAIASIAEKYFGSTGLVGLQDKKVGALPYPSMFPLPFFPAFSQSMYPFPDRDLRSLPLKMEPQSPGEVKKLQKGSSESPFD
Prediction	83532340055333442132145563471424332314222423432221444524523354436446535547655464448
	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

CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCC
SIKAIASIAEKYFGSTGLVGLQDKKVGALPYPSMFPLPFFPAFSQSMYPFPDRDLRSLPLKMEPQSPGEVKKLQKGSSESPFD

1gx3A

0.09

0.08

3.25

0.49

CEthreader

DLEVGSWYVSTHPGSHFVTGLTVAVVTDDARYNLRGRNLAVHRSGATEHIRLDAIVNRFGIDLGDLAGRDVQARVAEVLDT--

4p1mA

0.02

1.63

0.60

EigenThreader

PPDQRDALNQAADDLNQRLQDLKVTN--TEQLVFIAALNISYELAQEKAKTRDYAASMEQRIRMLQQTIEQALLEQGRITEKT

3cnfB

0.15

0.14

4.88

0.30

FFAS-3D

--NWVVDILDIEYQHVDAESIMTAPKGKLFHLQFMDGLLRPEASRLIYPLQPRSMRAIVNHNEVDRPREMDTTLSRNGDLLYS

5lj3Y

0.11

0.10

3.47

1.00

SPARKS-K

NMQRLRVNLFLLFATFGEVLKVSMNFKKQRGQAFITMRTIDQASLAQISLNGERFFGKPLKVEFSKSETKTL-----------

5opxA

0.17

0.04

1.19

0.32

CNFpred

GVNVLADAVKVTLGPKGR-----------------------------------------------------------------

6ql4A

0.01

1.30

1.00

DEthreader

RPQLQTLLKDALDQKVLDQLGVVASRQKTNCVFDAATKLAQTAVLFLNVNDYVRFPREVE-L-FADPKVRHLIRRKELLELIE

3l4rA

0.09

0.08

3.24

0.66

MapAlign

---SNKSDLIKPWGHFRVFIHSMSAKDGNLHGDILIPSLTAFKTATSNKFDLEYWGHNDLYLAEVDPKSYLILYMINQYNDDT

4g6zA2

0.10

3.53

0.55

MUSTER

DDARLAGLAKPFFAALGIDAGAIEQGPDLV-GLMKDASTVKEIAENSAMFYRAPAHTPSIDAVLLLFGRDVVVSRIEA-----

2pffA1

0.16

0.14

4.78

0.56

HHsearch

KSEFAHRIMLTNI---LRMMGCVKKQKSARGIETRPAQVILPMSPNHGTFGGDGMYSSKLSLETLFNR-------WHSESWAN

4p6vC2

0.01

1.33

0.46

CEthreader

ANVGVVYLVKDGDKTSKVILPVHGNGLWSMMYAFVAVTYYEQGETPGLGGEVENPAWRAQKKLFDENHKPAIKIVKGGAPQGS

(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	0.5023

(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	4c2jA	0.48	4.13	0.052	0.892	model1_4c2jA.pdb.gz
2	2hc9A2	0.48	4.14	0.051	0.904	model1_2hc9A2.pdb.gz
3	4efdA	0.47	4.26	0.077	0.916	model1_4efdA.pdb.gz
4	4ecnA	0.47	4.17	0.025	0.807	model1_4ecnA.pdb.gz
5	6bjaA	0.47	4.24	0.128	0.892	model1_6bjaA.pdb.gz
6	4a01A	0.47	4.05	0.048	0.843	model1_4a01A.pdb.gz
7	1gytL2	0.47	4.25	0.077	0.904	model1_1gytL2.pdb.gz
8	2wgeA	0.46	4.11	0.051	0.868	model1_2wgeA.pdb.gz
9	3h8eA2	0.46	4.45	0.114	0.916	model1_3h8eA2.pdb.gz
10	2ewbA1	0.46	4.44	0.037	0.904	model1_2ewbA1.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:0003677	1.00	DNA binding
GO:0046983	0.65	protein dimerization activity
GO:0003700	0.65	transcription factor activity, sequence-specific DNA binding
GO:0042803	0.64	protein homodimerization activity
GO:0003824	0.59	catalytic activity
GO:0016740	0.54	transferase activity
GO:0018024	0.51	histone-lysine N-methyltransferase 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:0065007	0.78	biological regulation
GO:0032502	0.78	developmental process
GO:0048856	0.77	anatomical structure development
GO:0044767	0.77	single-organism developmental process
GO:0050789	0.76	regulation of biological process
GO:0044707	0.76	single-multicellular organism process
GO:0050794	0.75	regulation of cellular process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0009653	0.67	anatomical structure morphogenesis
GO:2000112	0.66	regulation of cellular macromolecule biosynthetic process
GO:0060429	0.66	epithelium development
GO:0019219	0.66	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.66	regulation of gene expression
GO:0009987	0.66	cellular process
GO:0048523	0.65	negative regulation of cellular process
GO:0006355	0.65	regulation of transcription, DNA-templated
GO:0031324	0.64	negative regulation of cellular metabolic process
GO:0010605	0.64	negative regulation of macromolecule metabolic process
GO:0045892	0.63	negative regulation of transcription, DNA-templated
GO:0048518	0.56	positive regulation of biological process
GO:0048522	0.55	positive regulation of cellular process
GO:0031325	0.54	positive regulation of cellular metabolic process
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0048583	0.52	regulation of response to stimulus
GO:0045893	0.52	positive regulation of transcription, DNA-templated
GO:0023051	0.52	regulation of signaling
GO:0010646	0.52	regulation of cell communication
GO:0044763	0.51	single-organism cellular process
GO:0009966	0.51	regulation of signal transduction
GO:0072196	0.50	proximal/distal pattern formation involved in pronephric nephron development
GO:0072073	0.50	kidney epithelium development
GO:0035295	0.50	tube development
GO:0009968	0.50	negative regulation of signal transduction

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044444	0.93	cytoplasmic part
GO:0044446	0.85	intracellular organelle part
GO:0044428	0.83	nuclear part
GO:0005737	0.82	cytoplasm
GO:0005654	0.82	nucleoplasm
GO:0016235	0.81	aggresome
GO:0005794	0.81	Golgi apparatus
GO:0005634	0.61	nucleus
GO:0032991	0.59	macromolecular complex
GO:0043234	0.58	protein complex

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	1o01C	0.364	3.34	0.079	0.602	1.2.1.3	NA
2	0.060	2qfwD	0.432	3.97	0.049	0.735	1.1.1.42	NA
3	0.060	2ewbA	0.458	4.44	0.037	0.904	3.4.11.1 3.4.11.5	NA
4	0.060	2epoA	0.424	4.03	0.079	0.747	3.2.1.52	NA
5	0.060	3g5sA	0.434	4.06	0.080	0.783	2.1.1.74	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:

No Binding sites was predicted

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

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.