D-I-TASSER Q8IWU6-D2

D-I-TASSER results for Q8IWU6-D2

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

Input Sequence in FASTA format

>Q8IWU6 (108 residues)
LRKKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKG
PSDLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| LRKKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKGPSDLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLR
Prediction	CCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCHHHCCCCCSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHCC
Confidence	964335663235525685889999999987652332188862477745898657875368753234555654444345688886403588655667455432565409
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| LRKKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKGPSDLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLR
Prediction	755467765436456414535404520545615420654455251265353413245163545334444444423443356645514157752545456454554348
	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

CCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCHHHCCCCCSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHCC
LRKKEESSKNIQQSNHLPKYERVKELCQQARYQTACEQPGQKWQCIEDTSGKLRIHKCKGPSDLLTVRQSTRNLYARGFHDKDKECSCRESGYRASRSQRKSQRQFLR

2k23A

0.04

1.90

0.44

CEthreader

VTSILVRGQGCRYWIRTFVPSSRPGQFTLGNQVADTDYDQFAMVFFQKTSEYFKVTLYGRTKGLSDELKERFVSFAKSLGKDNNIVFSVPTDQCIDN-----------

4qiwC2

0.08

0.07

2.96

0.55

EigenThreader

LIEYNEIQAIIDETVREYQKALKALEVA---RRIEGLSGVGKTIIRKEG-DEYVIYTEGSNFKQVLMLVADMMTLDGVIRPIGRHGIVGEKASVLARAAFHLFAAAER

2x57A

0.15

0.12

4.03

0.34

FFAS-3D

-------ENLYFQSRFHLEIQEEETKCSQTEKHKACSGVWDNITCWRPNVGETVTVPCPYSKAGNISKNCTSDGWSETFPDFVDACGYSDP-----------------

5ygbA1

0.08

0.07

2.89

0.76

SPARKS-K

---------GPQSKKLASMVQEMTSYYSSAENRAKHVYVGQIVAAVFKFDEKWYRAEIVDIMPNQYNPKEQVIDLYFVDYGDSEYISP--ADICELRTDFLTLRFQA-

4x08A

0.11

0.06

1.99

0.72

CNFpred

-------------------FANVVNVCGNQS--IRCPHNRTLNNCHRSR-FRVPLLHCDLINPGAQ---------------NISNCRYAD------------------

4zy8C

0.01

1.03

0.83

DEthreader

-----------------IPLNELKDYIFGSDSDKIKVVANIVLFTRIFYLRIAISCCVTVLVLCWISSFDQCENTLLYLATQFL-------HDWCIAAVLQTFQKIIP

4wj3M

0.03

1.70

0.68

MapAlign

YLVPSRTYPGHFFALPQSPQLFKQLLMVAGFLVDVAVFSGPAVAALRVDGDIVFFGADVCDALGALRIKVGHDLKLLTREWAPMWVVDFPMFEENDDGSLSAL-----

1xu6A

0.15

0.11

3.72

0.60

MUSTER

SHMLEVLTQKHKPAESQQQAAETEGSCNKKD-QNEC-KSPCKWH---DAENK----KCT----LDKEEAKKVADETAKDGKTGNTNTTGSS-----------------

5foeA

0.17

0.15

4.86

0.89

HHsearch

AHAAFIGSYIQREIIGFPISTTFNRLCPDT--EPTCEQP-AKWKIVYSSDSPWSEWTSCSTSCGNGIQQRGRSC-----DSLNNRCEGSSVQTRTCHI------QEC-

6yj1A

0.05

2.25

0.39

CEthreader

NYDEFCGGYHRAFDVYSNETNDVPAVTSGTVIEANDYGNFGGTFVIRDANDNDWIYGHLQRGSMRFQGDIIGLQGNSNYYDNPMSVHLHLQLRPKDAKKDEKSQVCSG

(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	0.4934

(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	3c7nA	0.48	4.43	0.069	0.852	model1_3c7nA.pdb.gz
2	4ixjA	0.48	3.81	0.058	0.759	model1_4ixjA.pdb.gz
3	4wxxA3	0.47	4.31	0.038	0.833	model1_4wxxA3.pdb.gz
4	3zyyX	0.47	4.14	0.032	0.824	model1_3zyyX.pdb.gz
5	5lddB	0.47	3.67	0.109	0.704	model1_5lddB.pdb.gz
6	6kw5f	0.47	3.99	0.019	0.787	model1_6kw5f.pdb.gz
7	1nbwA	0.47	3.86	0.048	0.768	model1_1nbwA.pdb.gz
8	10mhA	0.43	4.34	0.010	0.704	model1_10mhA.pdb.gz
9	1krhA	0.40	4.75	0.054	0.741	model1_1krhA.pdb.gz
10	2fu3B1	0.39	4.69	0.031	0.694	model1_2fu3B1.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:0008449	1.00	N-acetylglucosamine-6-sulfatase activity
GO:0004065	1.00	arylsulfatase 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:0051239	1.00	regulation of multicellular organismal process
GO:0048869	1.00	cellular developmental process
GO:0048731	1.00	system development
GO:0048523	1.00	negative regulation of cellular process
GO:0044767	1.00	single-organism developmental process
GO:0044707	1.00	single-multicellular organism process
GO:0007166	1.00	cell surface receptor signaling pathway
GO:0003008	1.00	system process
GO:2000026	0.98	regulation of multicellular organismal development
GO:0032879	0.98	regulation of localization
GO:0045995	0.95	regulation of embryonic development
GO:0030336	0.95	negative regulation of cell migration
GO:0008152	0.95	metabolic process
GO:0071704	0.94	organic substance metabolic process
GO:1901135	0.93	carbohydrate derivative metabolic process
GO:0044237	0.93	cellular metabolic process
GO:0043170	0.93	macromolecule metabolic process
GO:0048513	0.92	animal organ development
GO:0030201	0.92	heparan sulfate proteoglycan metabolic process
GO:0009968	0.92	negative regulation of signal transduction
GO:0009967	0.92	positive regulation of signal transduction
GO:0007169	0.92	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0060384	0.91	innervation
GO:0060348	0.91	bone development
GO:0051216	0.91	cartilage development
GO:0048706	0.91	embryonic skeletal system development
GO:0040037	0.91	negative regulation of fibroblast growth factor receptor signaling pathway
GO:0035860	0.91	glial cell-derived neurotrophic factor receptor signaling pathway
GO:0030177	0.91	positive regulation of Wnt signaling pathway
GO:0014846	0.91	esophagus smooth muscle contraction
GO:0002063	0.91	chondrocyte development
GO:0001822	0.91	kidney development
GO:2000027	0.89	regulation of organ morphogenesis
GO:0050678	0.89	regulation of epithelial cell proliferation
GO:0080090	0.88	regulation of primary metabolic process
GO:0060255	0.88	regulation of macromolecule metabolic process
GO:0031323	0.88	regulation of cellular metabolic process
GO:0060686	0.87	negative regulation of prostatic bud formation
GO:0048010	0.87	vascular endothelial growth factor receptor signaling pathway
GO:0030513	0.87	positive regulation of BMP signaling pathway
GO:0016525	0.87	negative regulation of angiogenesis
GO:0001937	0.87	negative regulation of endothelial cell proliferation
GO:0009653	0.82	anatomical structure morphogenesis
GO:0048661	0.81	positive regulation of smooth muscle cell proliferation
GO:0036022	0.81	limb joint morphogenesis
GO:0007155	0.81	cell adhesion
GO:0001502	0.81	cartilage condensation

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:0016020	1.00	membrane
GO:0009986	1.00	cell surface
GO:0005783	1.00	endoplasmic reticulum
GO:0005615	1.00	extracellular space
GO:0045121	0.95	membrane raft
GO:0005794	0.95	Golgi apparatus

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	1wd4A	0.448	4.44	0.030	0.806	3.2.1.55	NA
2	0.060	3drwA	0.443	5.09	0.019	0.880	2.7.1.146	NA
3	0.060	1odiA	0.440	4.69	0.048	0.806	2.4.2.28	NA
4	0.060	1nbwA	0.465	3.86	0.048	0.768	4.2.1.30	100
5	0.060	1lrwC	0.450	4.74	0.047	0.870	1.1.99.8	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.