D-I-TASSER Q8IWZ5-D1

D-I-TASSER results for Q8IWZ5-D1

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

Input Sequence in FASTA format

>Q8IWZ5 (120 residues)
METAMCVCCPCCTWQRCCPQLCSCLCCKFIFTSERNCTCFPCPYKDERNCQFCHCTCSES
PNCHWCCCSWANDPNCKCCCTASSNLNCYYYESRCCRNTIITFHKGRLRSIHTSSKTALR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| METAMCVCCPCCTWQRCCPQLCSCLCCKFIFTSERNCTCFPCPYKDERNCQFCHCTCSESPNCHWCCCSWANDPNCKCCCTASSNLNCYYYESRCCRNTIITFHKGRLRSIHTSSKTALR
Prediction	CCCCCSSSCCCCCHHHHCHHHCCCCCSSSSSSCCCCCCSSCCCCCCCCCCCSSSCSCCCCCCCCSSSCCCCCCCCCSSSSSCCCCCSSSSSSCCCCCCCSSSCCCCCCCCSSSCCCCCCC
Confidence	998842641787423104221132001266615878605338876687863364014899993068624569999517875799942799714446651330111666413635764459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| METAMCVCCPCCTWQRCCPQLCSCLCCKFIFTSERNCTCFPCPYKDERNCQFCHCTCSESPNCHWCCCSWANDPNCKCCCTASSNLNCYYYESRCCRNTIITFHKGRLRSIHTSSKTALR
Prediction	855620302212305400343031200310033655041110226675514102031573340200002137444041102236514032244411542314245443553355764548
	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                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSCCCCCHHHHCHHHCCCCCSSSSSSCCCCCCSSCCCCCCCCCCCSSSCSCCCCCCCCSSSCCCCCCCCCSSSSSCCCCCSSSSSSCCCCCCCSSSCCCCCCCCSSSCCCCCCC
METAMCVCCPCCTWQRCCPQLCSCLCCKFIFTSERNCTCFPCPYKDERNCQFCHCTCSESPNCHWCCCSWANDPNCKCCCTASSNLNCYYYESRCCRNTIITFHKGRLRSIHTSSKTALR

5jqmC

0.10

3.66

0.62

CEthreader

-----MVLLHKSTHIFPTDFASVSRAFFNRYPNPYSIDTISRNVDQEGNLRTTRLLKKSITETWIIEVSVPANSTMKTYTRNLDHKVEEYTTYQFDSATSSTIADSRVKFSSIKSKVEDW

3s8vA3

0.03

1.62

0.70

EigenThreader

PEAFLLFSRRADPLTGVK-----EASALDFDVTDNRIYWTSLKNGSALFGLDYPMAVDWLGKNLYWADTGTKDLDSPLALDPAE--GFMYWTEWGFHSSRQSGWNECAVPGSLNADNRTC

3bwnB1

0.11

0.05

1.82

0.25

FFAS-3D

------------------GREMMKNRWEKLREVVKESDAFTLPKYPEAFCNYFGKSLESYPAFAWLGT--KEETDLV-------------------------------------------

7kzwA

0.11

0.10

3.59

0.62

SPARKS-K

--------QARELPLLKHGYSKKNTAYNFGFCCDNTPSGIFNI--DKKPTEFVNIYVGDNQGCKFIYAADTKGKQGEIAYLSGRNEKLECYKVIAYANAIEYDRVGNLSYLVESGGL---

4gdiA

0.18

0.05

1.62

0.54

CNFpred

-------------------------------------------------------------NFEYSTCYTIN-NLIKCTGTNLNDAKRPLLRFTK-------------------------

5d16A

0.00

0.79

0.83

DEthreader

----------YNSI--FA--NRFAAFDELLSITACRVFEETLVLPHLCPRVIKAVGVQRNSEFVLLEVDVSDGVMLSTKVLSGVYGGHRGVNHPLGEQVNGWAERVVRE-----------

3s8vA

0.02

1.27

0.76

MapAlign

----LRNVRAID---YDPLDKQLYWIDSKAQEDGSQGPYDLSIDIYSRYIYWTCENVIKGEQDRPRAIVNPEKGYMYFTNLQE--RSPKIERAALDGTEREVLFFSGL------------

2m74A

0.17

0.15

4.96

1.06

MUSTER

GSRYNAYCCPGWKGNQCIVPICRHSCGDGFCSRPNMCTCPSGQIAPSCGSRSCNIRCMNGGSCSDDHCLCQKGYIGTHCGQPVCESGCL-NGGRCVAPNRCACTYG-----PQCE-----

6rsnA

0.20

0.06

1.87

0.59

HHsearch

-----------------------------------------------------------------------------------RIVPVVYYLSRN--GRLDHPHHNGLYLKDVINRLNDR

5edfA2

0.08

0.07

2.97

0.48

CEthreader

-------RKDACSLSTTGERLLTYGVKKPSAYPEYEAYEDKRHIPENPYFHEFYYIKKGENPAIITHRNNREEDSYSTSVGSCINTVQYYPFIREKQQLTQQELVGYHQQVEQLVQSFVN

(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	0.6131

(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	4iglA2	0.54	3.88	0.019	0.817	model1_4iglA2.pdb.gz
2	2fr6A	0.53	4.49	0.061	0.942	model1_2fr6A.pdb.gz
3	1r5tA	0.52	4.52	0.061	0.942	model1_1r5tA.pdb.gz
4	3b8fB	0.51	4.55	0.054	0.900	model1_3b8fB.pdb.gz
5	1cttA1	0.47	4.60	0.037	0.867	model1_1cttA1.pdb.gz
6	3ijfX	0.47	4.54	0.029	0.850	model1_3ijfX.pdb.gz
7	4eg2A1	0.47	4.67	0.056	0.858	model1_4eg2A1.pdb.gz
8	3r2nA	0.46	4.69	0.040	0.833	model1_3r2nA.pdb.gz
9	4diqA1	0.42	4.16	0.000	0.650	model1_4diqA1.pdb.gz
10	1k38A	0.39	4.56	0.010	0.658	model1_1k38A.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:0046872	0.60	metal ion binding
GO:0046914	0.57	transition metal ion binding
GO:0003824	0.56	catalytic activity
GO:0016787	0.51	hydrolase activity
GO:0019239	0.50	deaminase activity
GO:0016814	0.50	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines

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	0.94	cellular process
GO:0044699	0.92	single-organism process
GO:0044763	0.91	single-organism cellular process
GO:0065007	0.89	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0048522	0.83	positive regulation of cellular process
GO:0010468	0.83	regulation of gene expression
GO:2001141	0.82	regulation of RNA biosynthetic process
GO:0023051	0.82	regulation of signaling
GO:0016043	0.82	cellular component organization
GO:1902533	0.81	positive regulation of intracellular signal transduction
GO:0065008	0.81	regulation of biological quality
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:0006355	0.81	regulation of transcription, DNA-templated
GO:0090316	0.80	positive regulation of intracellular protein transport
GO:0051491	0.80	positive regulation of filopodium assembly
GO:0043406	0.80	positive regulation of MAP kinase activity
GO:0033138	0.80	positive regulation of peptidyl-serine phosphorylation
GO:0030838	0.80	positive regulation of actin filament polymerization
GO:0006359	0.80	regulation of transcription from RNA polymerase III promoter
GO:0008152	0.62	metabolic process
GO:0071704	0.60	organic substance metabolic process
GO:0044238	0.60	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0006139	0.55	nucleobase-containing compound metabolic process
GO:0044710	0.53	single-organism metabolic process
GO:0044281	0.52	small molecule metabolic process
GO:1901575	0.51	organic substance catabolic process
GO:1901564	0.51	organonitrogen compound metabolic process
GO:0044248	0.51	cellular catabolic process
GO:0006216	0.50	cytidine catabolic 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:0044424	1.00	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043226	0.89	organelle
GO:0043229	0.88	intracellular organelle
GO:0043227	0.88	membrane-bounded organelle
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0005634	0.86	nucleus
GO:0016020	0.85	membrane
GO:0044422	0.84	organelle part
GO:0005737	0.84	cytoplasm
GO:0044446	0.83	intracellular organelle part
GO:0005886	0.83	plasma membrane
GO:0005829	0.83	cytosol
GO:0044425	0.82	membrane part
GO:0048471	0.81	perinuclear region of cytoplasm
GO:0044428	0.81	nuclear part
GO:0043232	0.81	intracellular non-membrane-bounded organelle
GO:0016607	0.80	nuclear speck
GO:0016363	0.80	nuclear matrix
GO:0005887	0.80	integral component of plasma membrane
GO:0005856	0.80	cytoskeleton
GO:0005794	0.80	Golgi apparatus
GO:0005783	0.80	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	0.060	2d30A	0.483	4.49	0.019	0.867	3.5.4.5	NA
2	0.060	1ui7A	0.483	3.89	0.036	0.758	1.4.3.21	NA
3	0.060	2ow6A	0.497	4.33	0.037	0.800	3.2.1.114	NA
4	0.060	2wgqB	0.493	4.40	0.034	0.858	1.4.3.21	NA
5	0.060	1galA	0.484	4.79	0.043	0.850	1.1.3.4	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.