D-I-TASSER P09467-D2

D-I-TASSER results for P09467-D2

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

Input Sequence in FASTA format

>P09467 (138 residues)
VKIKKKGKIYSLNEGYARDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYG
GIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILG
SPDDVLEFLKVYEKHSAQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VKIKKKGKIYSLNEGYARDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKHSAQ
Prediction	CSCCCCCCSSCCCCHHHHHCCHHHHHHHHHHHCCCCCCCCSSSSSSCCCHHHHHHHHHCCCSSSCCCCCCCCCCCSSSSSSCCCHHHHHHHHCCSCCCCCCCCSCCCCCCCCCCCCSSSCCHHHHHHHHHHHHHHCCC
Confidence	905999975636652023289999999999973878897435666032002577664215379638999999960899963261899999839820479965230145755445447981999999999999975259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VKIKKKGKIYSLNEGYARDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKHSAQ
Prediction	762376242100120124313620440053044457455313121112103412310131000001334733512000101131101003304130243543015241662243000000046105302510663688
	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

CSCCCCCCSSCCCCHHHHHCCHHHHHHHHHHHCCCCCCCCSSSSSSCCCHHHHHHHHHCCCSSSCCCCCCCCCCCSSSSSSCCCHHHHHHHHCCSCCCCCCCCSCCCCCCCCCCCCSSSCCHHHHHHHHHHHHHHCCC
VKIKKKGKIYSLNEGYARDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKHSAQ

7k74A

0.40

11.76

1.50

DEthreader

MQIPAATQEFAINMSNQRHWEAPMQAYVGDLLAGKEGGKNFNMRWIASMVADVHRILTRGGIFIYPWDKKDPKGKLRLMYEANPMGLLVEQAGGAAWTGRERILDIQPDQLHQRVPVFLGSREEVAEAVRYHHAHDNA

1fsaA2

0.86

24.08

3.92

SPARKS-K

-KIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK

7k74A

0.40

11.75

1.32

MapAlign

MQIPAATQEFAINMSNQRHWEAPMQAYVGDLLGKGTRGKNFNMRWIASMVADVHRILTRGGIFIYPWDKKSKAGKLRLMYEANPMGLLVEQAGGAAWTGRERILDIQPDQLHQRVPVFLGSREEVAEAVRYHHAHD--

7k74A

0.39

11.57

1.11

CEthreader

MQIPAATQEFAINMSNQRHWEAPMQAYVGDLLAGKEGTKNFNMRWIASMVADVHRILTRGGIFIYPWDKKDKAGKLRLMYEANPMGLLVEQAGGAAWTGRERILDIQPDQLHQRVPVFLGSREEVAEAVRYHHAHDNA

1fsaA2

0.86

24.08

3.27

MUSTER

-KIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK

1d9qB2

0.51

0.49

14.27

4.13

HHsearch

LQIPKSGKIYSFNEGNYKLWDENLKKYIDDLKEPGPSGKPYSARYIGSLVGDFHRTLLYGGIYGYPRDKKSKNGKLRLLYECAPMSFIVEQAGGKGSDGHQRVLDIQPTEIHQRVPLYIGSTEEVEKVEKYLA-----

1fsaA2

0.86

24.08

2.43

FFAS-3D

-KIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK

1fsaA2

0.86

24.08

1.53

EigenThreader

-KIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK

2fhyA

0.99

0.97

27.20

2.36

CNFpred

VKIKKKGKIYSLNEGYAKDFDPAVTEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFLYPANKKSPNGKLRLLYECNPMAYVMEKAGGMATTGKEAVLDVIPTDIHQRAPVILGSPDDVLEFLKVYEKH---

1fsaA

0.86

24.28

1.50

DEthreader

VKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK

(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	0.974

(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	1fsaA	0.97	0.94	0.862	1.000	model1_1fsaA.pdb.gz
2	7k74A	0.94	1.37	0.399	1.000	model1_7k74A.pdb.gz
3	7ns5A	0.93	1.29	0.485	0.986	model1_7ns5A.pdb.gz
4	5oeyA	0.92	0.81	0.458	0.949	model1_5oeyA.pdb.gz
5	1d9qB	0.91	1.33	0.511	0.964	model1_1d9qB.pdb.gz
6	2qvrA	0.91	1.75	0.441	0.986	model1_2qvrA.pdb.gz
7	3uksA	0.87	1.68	0.321	0.949	model1_3uksA.pdb.gz
8	5eq7A	0.68	2.37	0.123	0.826	model1_5eq7A.pdb.gz
9	1dk4A	0.64	2.48	0.118	0.797	model1_1dk4A.pdb.gz
10	1vmeA	0.48	4.53	0.080	0.797	model1_1vmeA.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:0016791	1.00	phosphatase activity
GO:0042132	0.99	fructose 1,6-bisphosphate 1-phosphatase activity
GO:1901363	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0043167	0.65	ion binding
GO:0046872	0.64	metal ion binding
GO:0036094	0.59	small molecule binding
GO:0032555	0.58	purine ribonucleotide binding
GO:0032550	0.58	purine ribonucleoside binding
GO:0032559	0.57	adenyl ribonucleotide binding
GO:0048029	0.53	monosaccharide binding
GO:0016208	0.52	AMP 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:0008152	0.96	metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0044238	0.94	primary metabolic process
GO:0044699	0.91	single-organism process
GO:1901576	0.90	organic substance biosynthetic process
GO:0044710	0.90	single-organism metabolic process
GO:0044723	0.88	single-organism carbohydrate metabolic process
GO:0009987	0.88	cellular process
GO:0044281	0.84	small molecule metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0016051	0.83	carbohydrate biosynthetic process
GO:0006006	0.79	glucose metabolic process
GO:0006094	0.78	gluconeogenesis
GO:0050896	0.73	response to stimulus
GO:0042221	0.69	response to chemical
GO:1901135	0.60	carbohydrate derivative metabolic process
GO:0019637	0.60	organophosphate metabolic process
GO:0006796	0.60	phosphate-containing compound metabolic process
GO:0065007	0.58	biological regulation
GO:0051716	0.57	cellular response to stimulus
GO:0050789	0.57	regulation of biological process
GO:0050794	0.56	regulation of cellular process
GO:0080090	0.54	regulation of primary metabolic process
GO:0070887	0.54	cellular response to chemical stimulus
GO:0031323	0.54	regulation of cellular metabolic process
GO:0051289	0.53	protein homotetramerization
GO:0019219	0.53	regulation of nucleobase-containing compound metabolic process
GO:0009889	0.53	regulation of biosynthetic process
GO:0048519	0.52	negative regulation of biological process
GO:0048583	0.51	regulation of response to stimulus
GO:0031324	0.51	negative regulation of cellular metabolic process
GO:0023051	0.51	regulation of signaling
GO:0010646	0.51	regulation of cell communication
GO:0071286	0.50	cellular response to magnesium ion
GO:0046580	0.50	negative regulation of Ras protein signal transduction
GO:0045820	0.50	negative regulation of glycolytic process
GO:0035690	0.50	cellular response to drug
GO:0030308	0.50	negative regulation of cell growth
GO:0016311	0.50	dephosphorylation
GO:0006111	0.50	regulation of gluconeogenesis
GO:0006002	0.50	fructose 6-phosphate metabolic 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.95	cytoplasmic part
GO:0005829	0.84	cytosol
GO:0043226	0.74	organelle
GO:0043227	0.72	membrane-bounded organelle
GO:0043229	0.64	intracellular organelle
GO:0005737	0.63	cytoplasm
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0005634	0.52	nucleus

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	1g0iA	0.645	2.40	0.118	0.797	3.1.3.25	NA
2	0.060	2cziA	0.620	2.93	0.107	0.797	3.1.3.25	NA
3	0.060	2gi3A	0.490	4.25	0.074	0.790	6.3.5.-	8
4	0.060	2v4uA	0.502	3.93	0.066	0.783	6.3.4.2	NA
5	0.060	2qvrA	0.924	1.72	0.442	1.000	3.1.3.11	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	0.93	1frpA	0.968	0.60	0.868	0.986	1.28	FDP	complex1.pdb.gz	13,16,45,47,48,49,65,75,76,77,81
2	0.16	2wbbH	0.975	0.46	0.993	0.986	1.13	RO3	complex2.pdb.gz	86,89,90,92,94,95,96,119,120
3	0.15	2vt5G	0.967	0.64	0.993	0.986	0.99	ROK	complex3.pdb.gz	86,88,89,90,94,120
4	0.14	1bk40	0.971	0.97	0.877	1.000	0.92	III	complex4.pdb.gz	13,14,15,17,18,32,33,40,41,42,43,44,45,46,55,59

	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.