D-I-TASSER Q04771-D1

D-I-TASSER results for Q04771-D1

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

Input Sequence in FASTA format

>Q04771 (116 residues)
MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSIN
DGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPG
Prediction	CCCCSSSHHHHHHHCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSCCCSSSSSSSSCCCSSSSSCCCCCCCCCCCSSCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCC
Confidence	96631103222222147888654555678844799838998999986983516899998199299986576677898645379999982688479643589996402799988999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPG
Prediction	74412131313232235244365744537552130203347076633040320010033576543243211545762403143464652314004431015614252346666488
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |

SS
Seq

CCCCSSSHHHHHHHCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSCCCSSSSSSSSCCCSSSSSCCCCCCCCCCCSSCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCC
MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPG

4faoC

0.27

0.17

5.29

2.15

SPARKS-K

------------------------------PLVTCTCESPHCKGP-TCRGAWCTVVLVREEGRPQEHRGCG---NLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------

4faoC

0.26

0.16

5.06

1.58

MUSTER

------------------------------PLVTCTCESPHC-KGPTCRGAWCTVVLVREGRHPQEHRGCGNLH---RELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------

4faoC

0.26

0.16

5.06

2.12

HHsearch

------------------------------PLVTCTCESPHCK-GPTCRGAWCTVVLVREGRHPQEHRGCGNLH---RELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------

4faoC

0.26

0.16

5.04

1.72

CNFpred

-------------------------------LVTCTCESPHCKG-PTCRGAWCTVVLVREGRHPQEHRGCGNLH---RELCRGRPTEFVNHYCCDSHLCNHNVSLVL---------

2qjbD

0.27

0.19

5.83

1.00

DEthreader

---------------------------TLPF-LKCYC-SHHCPDANTCITNHCFTMIEEDDGETTLTSGCLGLE-GSDFQCDTPPHQRRSIECCRTNLCNQYLQPTLPPV--VI--

2qjbD

0.23

0.16

5.14

2.05

SPARKS-K

----------------------------TLPFLKCYCS-HHCPINNTCITNHCFTMIEEDDQGTTLTSGCLG-LEGSDFQCRDTPIQRRSIECCRTNLCNQYLQPTLPPVVIG---

2qjbD

0.20

0.14

4.41

0.87

MapAlign

-----------------------------LPFLKCYCSHHCPEDANTCITGHCFTMIEEDQGETTLTSGCLGLEGSDFQCDTPIPHQRRSIECCRTNLCNQYLQPTLP--------

2qjbD

0.21

0.16

4.92

0.75

CEthreader

----------------------------TLPFLKCYCSHHCPAINNTCITGHCFTMIEEDQGETTLTSGCLGLEGSDFQCRDTPPHQRRSIECCRTNLCNQYLQPTLPPVVIG---

2qjbD

0.24

0.17

5.38

1.52

MUSTER

----------------------------TLPFLKCYCSHHEDAINNTCITNHCFTMIEEDQGETTLTSGCLGL-EGSDFQCRDTPIPRRSIECCRTNLCNQYLQPTLPPVV---IG

2qjbD

0.22

0.16

4.90

2.10

HHsearch

----------------------------TLPFLKCYCSHH-CPINNTCITGHCFTMIEEDQGETTLTSGCLGLEG-SDFQCRDTPIQRRSIECCRTNLCNQYLQPTLPPVVG----

(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	0.6119

(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 AttentionPotential, 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	2qjbD	0.59	2.40	0.217	0.716	model1_2qjbD.pdb.gz
2	4faoC	0.57	1.70	0.257	0.638	model1_4faoC.pdb.gz
3	3bt1U	0.50	3.37	0.104	0.664	model1_3bt1U.pdb.gz
4	2pjyC	0.50	2.46	0.200	0.603	model1_2pjyC.pdb.gz
5	3laqV	0.49	4.36	0.106	0.716	model1_3laqV.pdb.gz
6	1ploA	0.48	3.08	0.120	0.612	model1_1ploA.pdb.gz
7	7bprA	0.47	3.45	0.162	0.647	model1_7bprA.pdb.gz
8	1ks6A	0.46	3.03	0.132	0.612	model1_1ks6A.pdb.gz
9	6gbiA	0.46	2.84	0.134	0.603	model1_6gbiA.pdb.gz
10	1bteB	0.46	3.22	0.189	0.638	model1_1bteB.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	0.79	catalytic activity
GO:0004872	0.78	receptor activity
GO:0004871	0.78	signal transducer activity
GO:0004672	0.78	protein kinase activity
GO:0016361	0.77	activin receptor activity, type I
GO:1901363	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound binding
GO:0097367	0.61	carbohydrate derivative binding
GO:0050431	0.61	transforming growth factor beta binding
GO:0046332	0.60	SMAD binding
GO:0032555	0.60	purine ribonucleotide binding
GO:0035639	0.59	purine ribonucleoside triphosphate binding
GO:0032559	0.59	adenyl ribonucleotide binding
GO:0032550	0.59	purine ribonucleoside binding
GO:0005524	0.58	ATP 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:0065007	1.00	biological regulation
GO:0032502	1.00	developmental process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.93	cellular process
GO:0007165	0.91	signal transduction
GO:0044699	0.90	single-organism process
GO:0007178	0.90	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0044767	0.88	single-organism developmental process
GO:0048856	0.86	anatomical structure development
GO:0044763	0.78	single-organism cellular process
GO:0048731	0.74	system development
GO:0044707	0.71	single-multicellular organism process
GO:0008152	0.71	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0007389	0.70	pattern specification process
GO:0007179	0.70	transforming growth factor beta receptor signaling pathway
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0044238	0.69	primary metabolic process
GO:0050896	0.67	response to stimulus
GO:0048869	0.67	cellular developmental process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0080090	0.66	regulation of primary metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0044267	0.66	cellular protein metabolic process
GO:0006468	0.65	protein phosphorylation
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0009653	0.62	anatomical structure morphogenesis
GO:0006357	0.62	regulation of transcription from RNA polymerase II promoter
GO:0030509	0.61	BMP signaling pathway
GO:0007368	0.60	determination of left/right symmetry
GO:0051716	0.56	cellular response to stimulus
GO:0010033	0.56	response to organic substance
GO:0009719	0.56	response to endogenous stimulus
GO:2000026	0.55	regulation of multicellular organismal development
GO:0071495	0.55	cellular response to endogenous stimulus
GO:0071310	0.55	cellular response to organic substance
GO:0048583	0.53	regulation of response to stimulus
GO:0048523	0.53	negative regulation of cellular process
GO:0048518	0.52	positive regulation of biological process
GO:0009966	0.52	regulation of signal transduction
GO:0090092	0.51	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0048513	0.50	animal organ development
GO:0016477	0.50	cell migration
GO:0003143	0.50	embryonic heart tube 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:0098802	1.00	plasma membrane receptor complex
GO:1902554	0.78	serine/threonine protein kinase complex
GO:0048179	0.77	activin receptor complex
GO:0016021	0.73	integral component of membrane
GO:0005887	0.72	integral component of plasma membrane
GO:0044424	0.60	intracellular 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	3cf4A	0.417	4.87	0.063	0.793	1.2.99.2	37
2	0.060	1fmiA	0.428	4.77	0.020	0.767	3.2.1.113	NA
3	0.060	2hlqA	0.435	3.30	0.147	0.612	2.7.11.30	68,70,93,97,99
4	0.060	2bp7G	0.415	4.46	0.071	0.698	1.2.4.4	NA
5	0.060	1g0dA	0.410	4.65	0.036	0.776	2.3.2.13	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:

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	0.08	2h622	0.563	2.09	0.260	0.664	1.02	III	complex1.pdb.gz	40,50,54,70,72,75,76,80,89,91
	2	0.06	1ywhI	0.492	3.88	0.106	0.716	1.20	III	complex2.pdb.gz	34,47,49,97,98

	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.