D-I-TASSER P00533-D11

D-I-TASSER results for P00533-D11

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

Input Sequence in FASTA format

>P00533 (106 residues)
VACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQ
NPVYHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQI
Prediction	CSSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9023368987898888851000257998777643467788777021167789999877668611356775566788123077899865556788544578888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQI
Prediction	7403445355534366743344236333432467425763223442135435554645364443424333563363342144444543463254352145755568
	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

                   |                   |                   |                   |                   |

SS
Seq

CSSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
VACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQI

4luqC

0.08

3.04

0.62

CEthreader

FDKTLTHPNGLVVERPVGFDARRSAEGFRFDEGGKLRNPRQLEVQRQDAPPPPDLASRRLGDGEARYLWAAKPAGARWIVVSASEQSEDGEPTFALAWALLERARL

2dknA

0.08

3.04

0.52

EigenThreader

DLSTPGGRETAVAAVLDRCGGVLDVSALLDGLAEALSRGQQPAAVIAATQPGAAELPMVEAMLAGDQTHLAYAGSKYAVTRGVAVETPLGRGSEPREVAEAIAFLL

6enyG

0.17

0.15

4.98

0.49

FFAS-3D

----LKKIKDPDASKPEDWDEAKIDDPTDSKPEDWDKPEHIPDPDAKKPEDGEWEPPVIQNPEYK--GEWKPRQIDNDY----KGTWIHPEIDNPEYSPDPSIYAY

7jjvA

0.10

0.09

3.50

1.18

SPARKS-K

QAGASGLGGPNCNGGKGGKGAPGVGTAGGAGGVGGATGNTNGGAGGSGGNSD-----VAAGGAGAAGGAAGGAGTGGTGGNKPGGAPGAGGAGTPAGSAGSPGQTT

3hbdA

0.17

0.05

1.56

0.40

CNFpred

------------------------------------------------------------------------GLNNPEKVG----QDSTISFTAVWFWMKNSNCHS

7c76B

0.03

1.63

0.83

DEthreader

-----AASAGLTGVY-GLLQMQ------INVTPMAIVPLASMGFYFHLSFACAQLPMI--FACTGIGGCPLAAALWGSAKTLSLQITIHWWQAVIFTVYGSLMKAA

3ei2A2

0.04

1.96

0.71

MapAlign

FCGNVAHQQLIQISCNSSQVVVAVGRALYYLQIHPQELRQISHCALGDGALFYF----GLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY--

2nbiA2

0.13

0.12

4.25

0.85

MUSTER

------QPSSQPTGPQPSSQPSECADVLELCPYDTFDDSSRP-PDCTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMSPLPSPTE

2pffB

0.17

5.58

0.60

HHsearch

VRCYEAYPNTSLPILEDSLENNEGVPSPMLSISNLTQESHLPAISLVNGALRKPSGLQSRIPFSEFSNRFLPLVEIVNYNVENQQYVAARALDTVTNVLNFIKLQK

1sq9A2

0.07

2.78

0.57

CEthreader

TSVDISERGLIATGFNNGTVQISTLRPLYNFESQHNNSNSIRSVAHDSNSFGCITLYETEFGERIGSLSVPGEFAHSSWVMSLSFNDSGETLCKLRFWDVKTKERI

(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	0.5135

(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	5okmA	0.50	4.27	0.086	0.887	model1_5okmA.pdb.gz
2	6ibdA	0.49	4.24	0.068	0.877	model1_6ibdA.pdb.gz
3	1i9yA	0.48	4.42	0.066	0.877	model1_1i9yA.pdb.gz
4	4cmnA	0.48	4.48	0.047	0.877	model1_4cmnA.pdb.gz
5	1dbiA	0.48	4.27	0.059	0.859	model1_1dbiA.pdb.gz
6	3nr8B	0.48	4.32	0.070	0.887	model1_3nr8B.pdb.gz
7	3i6sA	0.48	4.37	0.059	0.868	model1_3i6sA.pdb.gz
8	7a0vA	0.48	4.40	0.097	0.868	model1_7a0vA.pdb.gz
9	3vtaA	0.48	4.50	0.063	0.868	model1_3vtaA.pdb.gz
10	6n4uA	0.47	4.49	0.095	0.840	model1_6n4uA.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:0044877	1.00	macromolecular complex binding
GO:0004713	1.00	protein tyrosine kinase activity
GO:0004872	0.79	receptor activity
GO:0004871	0.79	signal transducer activity
GO:0046982	0.78	protein heterodimerization activity
GO:0032403	0.78	protein complex binding
GO:0019899	0.78	enzyme binding
GO:0004714	0.78	transmembrane receptor protein tyrosine kinase activity
GO:0005006	0.77	epidermal growth factor-activated receptor activity
GO:0003682	0.64	chromatin binding
GO:0050839	0.59	cell adhesion molecule binding
GO:0048408	0.55	epidermal growth factor 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	0.96	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0048522	0.88	positive regulation of cellular process
GO:0007165	0.88	signal transduction
GO:0009987	0.86	cellular process
GO:0044699	0.85	single-organism process
GO:0080090	0.82	regulation of primary metabolic process
GO:0060255	0.82	regulation of macromolecule metabolic process
GO:0031323	0.82	regulation of cellular metabolic process
GO:0050896	0.81	response to stimulus
GO:0048584	0.81	positive regulation of response to stimulus
GO:0032501	0.81	multicellular organismal process
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:0009966	0.81	regulation of signal transduction
GO:0001932	0.81	regulation of protein phosphorylation
GO:1901701	0.80	cellular response to oxygen-containing compound
GO:0071495	0.80	cellular response to endogenous stimulus
GO:0071407	0.80	cellular response to organic cyclic compound
GO:0071396	0.80	cellular response to lipid
GO:0044707	0.80	single-multicellular organism process
GO:0043410	0.80	positive regulation of MAPK cascade
GO:0032355	0.80	response to estradiol
GO:0007173	0.80	epidermal growth factor receptor signaling pathway
GO:0008152	0.69	metabolic process
GO:0044763	0.68	single-organism cellular process
GO:0071704	0.67	organic substance metabolic process
GO:0044238	0.67	primary metabolic process
GO:0044237	0.67	cellular metabolic process
GO:0043170	0.66	macromolecule metabolic process
GO:0003008	0.66	system process
GO:0071363	0.65	cellular response to growth factor stimulus
GO:0048519	0.65	negative regulation of biological process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0048523	0.64	negative regulation of cellular process
GO:0019538	0.64	protein metabolic process
GO:0050790	0.63	regulation of catalytic activity
GO:0032879	0.63	regulation of localization
GO:0006796	0.63	phosphate-containing compound metabolic process
GO:0006464	0.63	cellular protein modification process
GO:2000379	0.62	positive regulation of reactive oxygen species metabolic process
GO:0080134	0.62	regulation of response to stress
GO:0051222	0.62	positive regulation of protein transport
GO:0046777	0.62	protein autophosphorylation
GO:0045860	0.62	positive regulation of protein kinase activity
GO:0043405	0.62	regulation of MAP kinase activity
GO:0043066	0.62	negative regulation of apoptotic process
GO:0009628	0.62	response to abiotic stimulus
GO:0008284	0.62	positive regulation of cell proliferation
GO:0007346	0.62	regulation of mitotic cell cycle
GO:0051128	0.58	regulation of cellular component organization
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.53	regulation of gene expression
GO:0045893	0.52	positive regulation of transcription, DNA-templated
GO:0071392	0.51	cellular response to estradiol stimulus
GO:0071364	0.51	cellular response to epidermal growth factor stimulus
GO:0070374	0.51	positive regulation of ERK1 and ERK2 cascade
GO:0045944	0.51	positive regulation of transcription from RNA polymerase II promoter
GO:0044710	0.51	single-organism metabolic process
GO:0030307	0.51	positive regulation of cell growth
GO:0007611	0.51	learning or memory
GO:0035556	0.50	intracellular signal transduction

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	1.00	cell part
GO:0044424	0.92	intracellular part
GO:0044444	0.87	cytoplasmic part
GO:0043226	0.86	organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0016020	0.85	membrane
GO:0005634	0.84	nucleus
GO:0005886	0.83	plasma membrane
GO:0005768	0.82	endosome
GO:0044425	0.67	membrane part
GO:0098590	0.64	plasma membrane region
GO:0045121	0.64	membrane raft
GO:0016323	0.63	basolateral plasma membrane
GO:0009986	0.63	cell surface
GO:0032991	0.53	macromolecular complex
GO:0043234	0.52	protein complex

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	3f7mA	0.469	4.28	0.053	0.840	3.4.21.-	NA
2	0.060	1s2nA	0.458	4.44	0.073	0.840	3.4.21.-	NA
3	0.060	3kzuA	0.441	4.72	0.048	0.849	2.3.1.41	NA
4	0.060	1bh6A	0.458	4.58	0.068	0.877	3.4.21.62	NA
5	0.060	2q2wB	0.436	4.20	0.030	0.764	1.1.1.30	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	0.01	2sic1	0.458	4.60	0.068	0.877	0.12	III	complex1.pdb.gz	32,45,46,47,92,93

	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.