D-I-TASSER Q6ZV89-D2

D-I-TASSER results for Q6ZV89-D2

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

Input Sequence in FASTA format

>Q6ZV89 (141 residues)
CLVESEGSLTENIWAFAGISRPCALALLRRDVLGAFLLWPELGASGQWCLSVRTQCGVVP
HQVFRNHLGRYCLEHLPAEFPSLEALVENHAVTERSLFCPLDMGRLNPTYEEQDCGPPGR
PPRTLRPLSHAKSEAELQGLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CLVESEGSLTENIWAFAGISRPCALALLRRDVLGAFLLWPELGASGQWCLSVRTQCGVVPHQVFRNHLGRYCLEHLPAEFPSLEALVENHAVTERSLFCPLDMGRLNPTYEEQDCGPPGRPPRTLRPLSHAKSEAELQGLG
Prediction	CCCCCCCCCCCCCCSCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCCSSSSSSSCCCSSSSSSSSCCCCCSSSCCCCCSCCCHHHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCHHHHHCCC
Confidence	967873221118761899999999999537999738997379999938999997994699999985999599857643209999999998218888616325776587754457888778974334577320224441479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| CLVESEGSLTENIWAFAGISRPCALALLRRDVLGAFLLWPELGASGQWCLSVRTQCGVVPHQVFRNHLGRYCLEHLPAEFPSLEALVENHAVTERSLFCPLDMGRLNPTYEEQDCGPPGRPPRTLRPLSHAKSEAELQGLG
Prediction	744655650573320237041730252057554000000306644310000022774121020343762202044464415204200420363552121304344343425466464664336534526365444534748
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCSCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCCSSSSSSSCCCSSSSSSSSCCCCCSSSCCCCCSCCCHHHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHCHHHHHCCC
CLVESEGSLTENIWAFAGISRPCALALLRRDVLGAFLLWPELGASGQWCLSVRTQCGVVPHQVFRNHLGRYCLEHLPAEFPSLEALVENHAVTERSLFCPLDMGRLNPTYEEQDCGPPGRPPRTLRPLSHAKSEAELQGLG

1qcfA

0.21

0.18

5.63

1.17

DEthreader

------DSLETEEWFFKGISRKDAERQLLAPNMLSFMIRDSETTKGSYSLSVRDYDTVKHYKIRTLDNGGFYI-SPRSTFSTLQELVDHYKKGNDGLQKLSV-PCMSS--KPQ------------QHDKLVKLADFGLARI

1k9aB3

0.18

0.16

5.06

2.56

SPARKS-K

EGVKAGTKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHAS-KLSIDE-EVYFENLMQLVEHYTTDADGLCTRLIKPKVMEGTVAAQDEFYRSG--------------------

2etzA

0.23

0.16

5.11

0.76

MapAlign

------NNLETYEWYNKSISRDKAEKLLLDTKEGAFMVRDSRTP-GTYTVSVFTKPCIKHYHIKETNDKRYYVA-EKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCG----------------------------------

2etzA

0.21

0.15

4.73

0.52

CEthreader

------NNLETYEWYNKSISRDKAEKLLLDTKEGAFMVRDSRTP-GTYTVSVFTKPCIKHYHIKETNDPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCG----------------------------------

2fo0A

0.20

0.19

6.13

1.67

MUSTER

NYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSS-ESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTV---YGVSPNYDKWEMERTDITMK-HKLG

2ozoA

0.19

6.16

1.45

HHsearch

EKLIATTAHERMPWYHSSLTREEAERKLYSQTDGKFLLRPR-KEQGTYALSLIYGKTVYHYLISQDKAGKYCIPE-GTKFDTLWQLVEYLKLKADGLIYCLKEACPNMDTSVFESPFSDPEELKDKKLFLKRDNLLIIELG

1k9aB3

0.21

0.17

5.43

1.64

FFAS-3D

--VKAGTKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASK--LSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVME--------------------GTVAAQDEFYRSG

2ozoA

0.18

0.17

5.54

1.08

EigenThreader

EKLIATTAHERMPWYHSSLTREEAERKLYSGAQTKFLLRPR-KEQGTYALSLIYGKTVYHYLISQDKAGKYCI-PEGTKFDTLWQLVEYLKLKADGLIYCLKEACPNMDTSVFESPFSDPEELKDKKLFLKR------DNL

6amvA

0.23

0.17

5.35

1.72

CNFpred

NYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSS-ESRFNTLAELVHHHSTVADGLITTLHYPAPK----------------------------------

2b3oA

0.20

0.18

5.67

1.17

DEthreader

HRDL-CSDPTSERWYHGHMSGGQAETLLQAKEPWTFLVRESLSQPGDFVLSVLSDLRVTHIKVMCEG-GRYTVG-GLETFDSLTDLVEHFKKTGIEEVYLR-QPYYATRV--E--LQKQE-QYKYV--AQ-IET--KK---

(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	0.681

(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	6md7A	0.73	3.38	0.203	0.894	model1_6md7A.pdb.gz
2	2b3oA	0.72	2.78	0.201	0.837	model1_2b3oA.pdb.gz
3	2ozoA	0.71	2.17	0.170	0.794	model1_2ozoA.pdb.gz
4	2dlyA	0.70	2.35	0.235	0.794	model1_2dlyA.pdb.gz
5	4fl2A1	0.70	2.26	0.165	0.794	model1_4fl2A1.pdb.gz
6	2c9wA	0.69	2.68	0.169	0.830	model1_2c9wA.pdb.gz
7	6pbcA	0.69	2.30	0.141	0.780	model1_6pbcA.pdb.gz
8	4tziA	0.69	1.25	0.204	0.731	model1_4tziA.pdb.gz
9	2ptkA	0.69	1.54	0.173	0.738	model1_2ptkA.pdb.gz
10	2eo6A	0.68	2.17	0.193	0.787	model1_2eo6A.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	0.82	catalytic activity
GO:1901363	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0016740	0.80	transferase activity
GO:0004715	0.79	non-membrane spanning protein tyrosine kinase activity
GO:0005102	0.69	receptor binding
GO:0097367	0.67	carbohydrate derivative binding
GO:0035639	0.66	purine ribonucleoside triphosphate binding
GO:0032555	0.66	purine ribonucleotide binding
GO:0032550	0.66	purine ribonucleoside binding
GO:0005524	0.65	ATP binding
GO:0016787	0.53	hydrolase activity
GO:0030674	0.51	protein binding, bridging
GO:0035591	0.50	signaling adaptor activity
GO:0019899	0.50	enzyme 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	0.95	biological regulation
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.94	cellular process
GO:0044699	0.90	single-organism process
GO:0008152	0.89	metabolic process
GO:0071704	0.88	organic substance metabolic process
GO:0044238	0.87	primary metabolic process
GO:0007165	0.87	signal transduction
GO:0044763	0.86	single-organism cellular process
GO:0044237	0.86	cellular metabolic process
GO:0044260	0.84	cellular macromolecule metabolic process
GO:0007166	0.83	cell surface receptor signaling pathway
GO:0006796	0.83	phosphate-containing compound metabolic process
GO:0016310	0.82	phosphorylation
GO:0006464	0.82	cellular protein modification process
GO:0018193	0.81	peptidyl-amino acid modification
GO:0006468	0.81	protein phosphorylation
GO:0038083	0.80	peptidyl-tyrosine autophosphorylation
GO:0050896	0.76	response to stimulus
GO:0007167	0.76	enzyme linked receptor protein signaling pathway
GO:0002376	0.75	immune system process
GO:0007169	0.73	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0048869	0.72	cellular developmental process
GO:0006950	0.72	response to stress
GO:0030154	0.71	cell differentiation
GO:0048583	0.68	regulation of response to stimulus
GO:0048518	0.65	positive regulation of biological process
GO:0019222	0.63	regulation of metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0016043	0.62	cellular component organization
GO:0048523	0.61	negative regulation of cellular process
GO:0048522	0.61	positive regulation of cellular process
GO:0006955	0.61	immune response
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0042127	0.60	regulation of cell proliferation
GO:0023051	0.60	regulation of signaling
GO:0010646	0.60	regulation of cell communication
GO:0044710	0.59	single-organism metabolic process
GO:0009966	0.59	regulation of signal transduction
GO:0065009	0.57	regulation of molecular function
GO:0048584	0.57	positive regulation of response to stimulus
GO:0042325	0.57	regulation of phosphorylation
GO:0032879	0.57	regulation of localization
GO:0032268	0.57	regulation of cellular protein metabolic process
GO:0022607	0.57	cellular component assembly
GO:1902531	0.56	regulation of intracellular signal transduction
GO:0050790	0.56	regulation of catalytic activity
GO:0032502	0.56	developmental process
GO:0023057	0.56	negative regulation of signaling
GO:0010648	0.56	negative regulation of cell communication
GO:0002682	0.56	regulation of immune system process
GO:0065008	0.55	regulation of biological quality
GO:0051049	0.55	regulation of transport
GO:0050776	0.55	regulation of immune response
GO:0009968	0.55	negative regulation of signal transduction
GO:0006629	0.55	lipid metabolic process
GO:0001932	0.55	regulation of protein phosphorylation
GO:0048856	0.54	anatomical structure development
GO:0044767	0.54	single-organism developmental process
GO:0043549	0.54	regulation of kinase activity
GO:0031324	0.54	negative regulation of cellular metabolic process
GO:0010605	0.54	negative regulation of macromolecule metabolic process
GO:0002684	0.54	positive regulation of immune system process
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0051239	0.53	regulation of multicellular organismal process
GO:0051171	0.53	regulation of nitrogen compound metabolic process
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0010468	0.53	regulation of gene expression
GO:1901576	0.52	organic substance biosynthetic process
GO:1900076	0.52	regulation of cellular response to insulin stimulus
GO:0051716	0.52	cellular response to stimulus
GO:0051128	0.52	regulation of cellular component organization
GO:0051050	0.52	positive regulation of transport
GO:0050865	0.52	regulation of cell activation
GO:0045859	0.52	regulation of protein kinase activity
GO:0044281	0.52	small molecule metabolic process
GO:0043086	0.52	negative regulation of catalytic activity
GO:0032269	0.52	negative regulation of cellular protein metabolic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0006810	0.52	transport
GO:0002768	0.52	immune response-regulating cell surface receptor signaling pathway
GO:0060627	0.51	regulation of vesicle-mediated transport
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0050793	0.51	regulation of developmental process
GO:0045321	0.51	leukocyte activation
GO:0044249	0.51	cellular biosynthetic process
GO:0042981	0.51	regulation of apoptotic process
GO:0042221	0.51	response to chemical
GO:0032270	0.51	positive regulation of cellular protein metabolic process
GO:0030155	0.51	regulation of cell adhesion
GO:0016042	0.51	lipid catabolic process
GO:0006650	0.51	glycerophospholipid metabolic process
GO:0006355	0.51	regulation of transcription, DNA-templated
GO:0002694	0.51	regulation of leukocyte activation
GO:0002252	0.51	immune effector process
GO:1903530	0.50	regulation of secretion by cell
GO:0060548	0.50	negative regulation of cell death
GO:0051249	0.50	regulation of lymphocyte activation
GO:0051173	0.50	positive regulation of nitrogen compound metabolic process
GO:0046649	0.50	lymphocyte activation
GO:0046488	0.50	phosphatidylinositol metabolic process
GO:0038093	0.50	Fc receptor signaling pathway
GO:0033554	0.50	cellular response to stress
GO:0032386	0.50	regulation of intracellular transport
GO:0031328	0.50	positive regulation of cellular biosynthetic process
GO:0022407	0.50	regulation of cell-cell adhesion
GO:0010557	0.50	positive regulation of macromolecule biosynthetic process
GO:0010033	0.50	response to organic substance
GO:0002521	0.50	leukocyte differentiation

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:0044464	0.87	cell part
GO:0044424	0.82	intracellular part
GO:0043226	0.50	organelle
GO:0043229	0.48	intracellular organelle
GO:0044425	0.39	membrane part
GO:0043232	0.35	intracellular non-membrane-bounded organelle
GO:0014069	0.34	postsynaptic density
GO:0030054	0.32	cell junction
GO:0016020	0.31	membrane
GO:0005925	0.31	focal adhesion
GO:0044444	0.30	cytoplasmic 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	0.282	1csyA	0.645	2.35	0.167	0.752	2.7.10.2	14,19,21,58,83,87,97
2	0.258	2hdxF	0.632	1.85	0.202	0.702	2.7.10.2	14,21,27,36
3	0.224	2pldA	0.551	2.64	0.183	0.681	3.1.4.11	14,27,36,83,101
4	0.212	1luiA	0.602	1.89	0.235	0.695	2.7.10.2	19,21,82
5	0.211	2yu7A	0.619	2.04	0.260	0.702	3.1.3.48	14,71,83

	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	0.53	1a09A	0.673	0.99	0.242	0.702	1.01	III	complex1.pdb.gz	21,39,41,42,43,48,49,59,60,61,62,76
2	0.32	1a07A	0.669	0.93	0.245	0.695	0.80	III	complex2.pdb.gz	21,49,60,61,62,63,96
3	0.32	1o4oA	0.665	1.14	0.242	0.702	1.33	HPS	complex3.pdb.gz	20,39,41,42,43,49,60,62

	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.