D-I-TASSER Q86UU0-D3

D-I-TASSER results for Q86UU0-D3

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

Input Sequence in FASTA format

>Q86UU0 (126 residues)
ASVLNDPELSEVIRPTPTGIPEFDLSRIIPSEKPSSTLQYFPKSENQPPKAQPPNLHLMN
LQNMMAEQTPSRPPNLPGQQGVQRGLNMSMCHPGQMSLLGRTGVPPQQGMVPHGLHQGVM
SPPQGL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ASVLNDPELSEVIRPTPTGIPEFDLSRIIPSEKPSSTLQYFPKSENQPPKAQPPNLHLMNLQNMMAEQTPSRPPNLPGQQGVQRGLNMSMCHPGQMSLLGRTGVPPQQGMVPHGLHQGVMSPPQGL
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	986789981113478888897423234477889751101277888889999998944222235767789888999999888788888888888888877888999965566888766666898899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ASVLNDPELSEVIRPTPTGIPEFDLSRIIPSEKPSSTLQYFPKSENQPPKAQPPNLHLMNLQNMMAEQTPSRPPNLPGQQGVQRGLNMSMCHPGQMSLLGRTGVPPQQGMVPHGLHQGVMSPPQGL
Prediction	863376552443343444413414244224574244324312545654566534434335245244655354447344443444345362343543434454434445434544334223434777
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
ASVLNDPELSEVIRPTPTGIPEFDLSRIIPSEKPSSTLQYFPKSENQPPKAQPPNLHLMNLQNMMAEQTPSRPPNLPGQQGVQRGLNMSMCHPGQMSLLGRTGVPPQQGMVPHGLHQGVMSPPQGL

6cc7A2

0.09

3.36

0.56

CEthreader

LFYFAPKKVWILAHQWGPTSFSYRTSSDPTNPNGWSSPQPLFTGTISGSSTGVIDQTVIGLFFAGDNGKIYRASMPIGNFPGSFGSSSTVVMSDSTNNLFEAVQVYKLQGQTKYLMIVEAIGSQGR

4p3gA

0.02

1.39

0.67

EigenThreader

LLYGDYATYRTQLSG-----KLLNCRKKLTEYVRLQLLTAERAWAHAAKRSHIVSRLEKGARIAEKLAQALSDASPTDILDARAYAALLRGAALSYAICRIIYTALAGDIFKELLSDTIDPSRFAA

1nwxD

0.14

0.13

4.36

0.32

FFAS-3D

SSVMAVPRIEKIVVNEGLGSSKEDELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTRMYVFLEKLINIGLPRIRDFRGIN---------PNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGM

7jjvA

0.15

0.13

4.56

1.50

SPARKS-K

CDGLDGADGGQAGASGLAGGPNCNGGKGGKG---------APGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGTGGTGGNGGAGKPGGAPGAG--GAGTPAGSAGSPGQT

4mduA

0.20

0.08

2.53

0.40

CNFpred

-------ALMRLLITR----SEIDLQDIMDAYIYGKSLLNAVKDDTSG-------DYRRTLCVLMGE-----------------------------------------------------------

2btqB

0.04

1.98

0.83

DEthreader

-CGNQILHSGGSVPSPLIS-EPAITLQRILDNADGAVLLDALFRKANRS-PNMD-LNNIIA-IVSVT-LDLSFTN---LVPFPGNHFLT-ASFANFTAIWVYLASANMLKLGLALVNHT-GIAAER

1kv9A

0.10

3.56

0.76

MapAlign

-PRVVKGKVIIGNGGAEYGVRGFVSAYDADTGKLAWRFYTVPGDPALPYEHPELREAAKTWQGDQYWKLGGGGTVWYVGTGNGSPWNREVRSPGGGDNLYLSSILAIRPDTGKLAWHYQVTPGDSW

2nbiA2

0.18

0.14

4.67

0.81

MUSTER

-------------QPSSQ--PTGPQPSSQPSEC-ADVLELCPYDTCFLPFDDSSRPPDC--------TDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMPSPLPSP

2vd3A3

0.23

0.06

1.74

0.47

HHsearch

HAVVDEKEVFNLKAVGARDILVVPIERIIP------------------------------------------------------------------------------------------------

6cc7A

0.09

3.36

0.56

CEthreader

LFYFAPKKVWILAHQWGPTSFSYRTSSDPTNPNGWSSPQPLFTGTISGSSTGVIDQTVIGLFFAGDNGKIYRASMPIGNFPGSFGSSSTVVMSDSTNNLFEAVQVYKLQGQTKYLMIVEAIGSQGR

(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	0.5532

(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	5z9sA	0.45	4.66	0.052	0.833	model1_5z9sA.pdb.gz
2	2vpuA	0.45	4.73	0.046	0.802	model1_2vpuA.pdb.gz
3	3of7A	0.45	4.68	0.074	0.802	model1_3of7A.pdb.gz
4	5yotA	0.45	4.43	0.027	0.786	model1_5yotA.pdb.gz
5	3t68A	0.44	4.63	0.082	0.794	model1_3t68A.pdb.gz
6	3h0lA	0.44	4.80	0.027	0.770	model1_3h0lA.pdb.gz
7	5nbsA	0.44	4.71	0.054	0.802	model1_5nbsA.pdb.gz
8	6jxgA	0.44	4.76	0.063	0.809	model1_6jxgA.pdb.gz
9	3kl9A	0.44	4.71	0.065	0.778	model1_3kl9A.pdb.gz
10	4mmoA	0.44	4.81	0.027	0.809	model1_4mmoA.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:0008013	0.87	beta-catenin 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:0009987	0.91	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0019222	0.78	regulation of metabolic process
GO:0080090	0.77	regulation of primary metabolic process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0048522	0.77	positive regulation of cellular process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0009893	0.77	positive regulation of metabolic process
GO:0051171	0.76	regulation of nitrogen compound metabolic process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0010604	0.76	positive regulation of macromolecule metabolic process
GO:0045893	0.75	positive regulation of transcription, DNA-templated
GO:0045944	0.74	positive regulation of transcription from RNA polymerase II promoter
GO:0044699	0.74	single-organism process
GO:0009966	0.74	regulation of signal transduction
GO:0017015	0.73	regulation of transforming growth factor beta receptor signaling pathway
GO:0032502	0.67	developmental process
GO:0044767	0.66	single-organism developmental process
GO:0051239	0.64	regulation of multicellular organismal process
GO:0048519	0.64	negative regulation of biological process
GO:2000026	0.63	regulation of multicellular organismal development
GO:0048523	0.63	negative regulation of cellular process
GO:0045595	0.63	regulation of cell differentiation
GO:0022603	0.63	regulation of anatomical structure morphogenesis
GO:0030512	0.62	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0010718	0.62	positive regulation of epithelial to mesenchymal transition
GO:0044763	0.53	single-organism cellular process

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:0044422	0.90	organelle part
GO:0044428	0.89	nuclear part
GO:0005634	0.89	nucleus
GO:0005654	0.87	nucleoplasm
GO:0043232	0.75	intracellular non-membrane-bounded organelle
GO:0005730	0.74	nucleolus

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	1yzpA	0.417	4.59	0.038	0.722	1.11.1.13	NA
2	0.060	3eifA	0.434	4.48	0.075	0.746	3.4.21.110	NA
3	0.060	2nliB	0.372	5.29	0.060	0.746	1.13.12.4	NA
4	0.060	2rduA	0.417	5.03	0.036	0.802	1.1.3.15	NA
5	0.060	2j6xH	0.391	5.27	0.050	0.770	1.1.3.2	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	3sqgA	0.421	4.92	0.029	0.778	0.19	M43	complex1.pdb.gz	100,103,113
2	0.01	3h0lV	0.439	4.66	0.027	0.762	0.15	ASN	complex2.pdb.gz	62,100,101,102
3	0.01	3h0rA	0.440	4.85	0.072	0.794	0.15	ASN	complex3.pdb.gz	99,100,101,102
4	0.01	1y0yA	0.444	4.95	0.085	0.809	0.15	ATI	complex4.pdb.gz	98,104,105,106
5	0.01	3fidB	0.424	4.71	0.027	0.754	0.33	CXE	complex5.pdb.gz	95,97,100
6	0.01	1icpA	0.421	5.12	0.063	0.802	0.12	FMN	complex6.pdb.gz	2,3,4,10,100,101
7	0.01	2j6xH	0.391	5.27	0.050	0.770	0.11	FMN	complex7.pdb.gz	2,7,10,41,100,101
8	0.01	2bfgC	0.422	5.11	0.025	0.825	0.14	XYS	complex8.pdb.gz	38,40,99,124
9	0.01	2bfgA	0.424	5.12	0.025	0.825	0.12	UUU	complex9.pdb.gz	34,38,100,126
10	0.01	3sqgD	0.405	4.92	0.038	0.754	0.28	M43	complex10.pdb.gz	105,106,107,110

	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.