D-I-TASSER O95398-D4

D-I-TASSER results for O95398-D4

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

Input Sequence in FASTA format

>O95398 (113 residues)
ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQE
DGWTKGQVLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQVLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHP
Prediction	CCCCCCCCCCCCCCCCCCCCCSCCCCSSSSSSSSCCCCSSSSSSCCCCHHHHHHHHHHHHHCCCCCSSSSSSCCCCCSSSCCCCCSSSSSSCCCCCSSSSSCHHHCCCCCCCC
Confidence	98765446777888878744311688368999925895699997155439999999998627788728999804896676188765787530525459997045512268999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQVLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHP
Prediction	85523411153746366453404564402030023443312041424330440152026415366321001033545434045733021422434120100347326524648
	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

CCCCCCCCCCCCCCCCCCCCCSCCCCSSSSSSSSCCCCSSSSSSCCCCHHHHHHHHHHHHHCCCCCSSSSSSCCCCCSSSCCCCCSSSSSSCCCCCSSSSSCHHHCCCCCCCC
ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKGQVLVKVNSAGDAIGLQPDARGVATSLGLNERLFVVNPQEVHELIPHP

6hftA

0.14

0.12

4.23

1.00

DEthreader

--R-I--PELLNEGK---IRLEDS--IYPALIMYPTQDEFDFVGEVSTTVQELVDLVLEGQFTPKKVLVFMETKAGGLIKA---GKLTFDILVPLFKIYIVPKVESEWIWKKA

2dhzA

0.29

0.25

7.53

2.04

SPARKS-K

------------------GSSGSSGDEIFCRVYMPDHSYVTIRSRLSASVQDILGSVTEKLQYSDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFACTRDSYEALVPLP

4gxbA1

0.09

0.07

2.71

0.66

MapAlign

----------------------VPTEEVSLEVLLSNGQKVLVNVLTSDQTEDVLEAVAAKLDLIGYFSLFLVREFSFVRKLQEFELPYVSVRSQEYKIVLRKSYAQTVSDIE-

2dhzA

0.29

0.25

7.53

0.46

CEthreader

------------------GSSGSSGDEIFCRVYMPDHSYVTIRSRLSASVQDILGSVTEKLQYEDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFACTRDSYEALVPLP

2byvE

0.34

0.32

9.53

1.55

MUSTER

MAAFKEQLPEL-EKIVKKRQPIRGSDEVLFKVYCIDHTYTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFA-------SLTPLP

2dhzA

0.29

0.25

7.53

4.00

HHsearch

------------------GSSGSSGDEIFCRVYMPDHSYVTIRSRLSASVQDILGSVTEKLQYSDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFACTRDSYEALVPLP

2dhzA

0.30

0.25

7.52

1.48

FFAS-3D

-------------------SSGSSGDEIFCRVYMPDHSYVTIRSRLSASVQDILGSVTEKLQYSDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFACTRDSYEALVPLP

1d4bA

0.13

0.12

3.98

0.63

EigenThreader

----MEYLSALNPSDLLRVWTSAPPPQRPFRVCDHRTIRKGLTAATRQ---ELLAKALETLLLNGVLTLVLEE---DGTAVDSEDFFQ--LLEDDTCLMVLQSG--QSWSPTR

4f7zA

0.34

0.29

8.75

1.83

CNFpred

---------------AQKRQPIRGSDEVLFKVYCIDHTYTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFACPREQFDSLTPLP

6hftA2

0.12

0.11

3.73

1.00

DEthreader

--------LLNEG-K--I-RLEDSQLIYPALIMYPTDEFDFVGEVSLTTVQELVDLVLEGQFTPKKVLVFMETKAGGLIKA---GKLTFDILDVPLKIYIVPKVESGWIWKKA

(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	0.685

(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	2dhzA	0.74	1.54	0.295	0.796	model1_2dhzA.pdb.gz
2	2byvE4	0.70	1.70	0.352	0.770	model1_2byvE4.pdb.gz
3	4gxbA	0.66	2.20	0.100	0.761	model1_4gxbA.pdb.gz
4	1wgyA	0.62	2.47	0.160	0.752	model1_1wgyA.pdb.gz
5	2m4nA	0.59	2.35	0.111	0.717	model1_2m4nA.pdb.gz
6	1x3dA	0.35	4.32	0.127	0.602	model1_1x3dA.pdb.gz
7	4jgwA	0.34	5.00	0.070	0.637	model1_4jgwA.pdb.gz
8	4l9mA	0.33	5.24	0.043	0.637	model1_4l9mA.pdb.gz
9	4yixA3	0.32	4.37	0.086	0.540	model1_4yixA3.pdb.gz
10	2diaA	0.32	3.75	0.085	0.478	model1_2diaA.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:0005085	1.00	guanyl-nucleotide exchange factor activity
GO:0005088	0.94	Ras guanyl-nucleotide exchange factor activity
GO:0017034	0.71	Rap guanyl-nucleotide exchange factor activity
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0036094	0.54	small molecule binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032559	0.50	adenyl ribonucleotide 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:0050794	1.00	regulation of cellular process
GO:0007165	0.88	signal transduction
GO:0051049	0.81	regulation of transport
GO:0044699	0.81	single-organism process
GO:0009987	0.81	cellular process
GO:0048856	0.74	anatomical structure development
GO:0048518	0.72	positive regulation of biological process
GO:0044763	0.72	single-organism cellular process
GO:0048522	0.71	positive regulation of cellular process
GO:0051239	0.70	regulation of multicellular organismal process
GO:0048519	0.70	negative regulation of biological process
GO:0048523	0.69	negative regulation of cellular process
GO:0044767	0.69	single-organism developmental process
GO:0042221	0.69	response to chemical
GO:0035556	0.69	intracellular signal transduction
GO:2000026	0.68	regulation of multicellular organismal development
GO:0071495	0.68	cellular response to endogenous stimulus
GO:0071310	0.68	cellular response to organic substance
GO:0051240	0.68	positive regulation of multicellular organismal process
GO:0051128	0.68	regulation of cellular component organization
GO:0014070	0.68	response to organic cyclic compound
GO:0051050	0.67	positive regulation of transport
GO:0080090	0.65	regulation of primary metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0051246	0.63	regulation of protein metabolic process
GO:0031325	0.63	positive regulation of cellular metabolic process
GO:0019220	0.63	regulation of phosphate metabolic process
GO:0065008	0.62	regulation of biological quality
GO:0050790	0.62	regulation of catalytic activity
GO:0045937	0.62	positive regulation of phosphate metabolic process
GO:0010604	0.62	positive regulation of macromolecule metabolic process
GO:0007264	0.62	small GTPase mediated signal transduction
GO:0001932	0.62	regulation of protein phosphorylation
GO:1901701	0.61	cellular response to oxygen-containing compound
GO:0071417	0.61	cellular response to organonitrogen compound
GO:0071407	0.61	cellular response to organic cyclic compound
GO:0051336	0.61	regulation of hydrolase activity
GO:0051130	0.61	positive regulation of cellular component organization
GO:0051094	0.61	positive regulation of developmental process
GO:0048869	0.61	cellular developmental process
GO:0045765	0.61	regulation of angiogenesis
GO:0044087	0.61	regulation of cellular component biogenesis
GO:0043085	0.61	positive regulation of catalytic activity
GO:0007265	0.61	Ras protein signal transduction
GO:0001934	0.61	positive regulation of protein phosphorylation
GO:2000249	0.60	regulation of actin cytoskeleton reorganization
GO:0071320	0.60	cellular response to cAMP
GO:0061028	0.60	establishment of endothelial barrier
GO:0051496	0.60	positive regulation of stress fiber assembly
GO:0045766	0.60	positive regulation of angiogenesis
GO:0043547	0.60	positive regulation of GTPase activity
GO:0032486	0.60	Rap protein signal transduction
GO:0051223	0.55	regulation of protein transport
GO:0023051	0.53	regulation of signaling
GO:0010646	0.52	regulation of cell communication

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	0.99	cell part
GO:0016020	0.94	membrane
GO:0044424	0.90	intracellular part
GO:0005886	0.88	plasma membrane
GO:0044444	0.86	cytoplasmic part
GO:0043226	0.83	organelle
GO:0042995	0.79	cell projection
GO:0044422	0.76	organelle part
GO:0043229	0.76	intracellular organelle
GO:0044446	0.75	intracellular organelle part
GO:0044430	0.72	cytoskeletal part
GO:0030864	0.71	cortical actin cytoskeleton
GO:0030175	0.71	filopodium
GO:0030027	0.71	lamellipodium
GO:0005902	0.71	microvillus
GO:0043227	0.57	membrane-bounded organelle
GO:0044421	0.50	extracellular region part
GO:0031988	0.50	membrane-bounded vesicle

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	0.066	2nptD	0.519	2.77	0.136	0.681	2.7.11.25	79
2	0.060	1r58A	0.462	4.76	0.045	0.850	3.4.11.18	NA
3	0.060	1eqwC	0.462	3.80	0.098	0.726	1.15.1.1	NA
4	0.060	2zxqA	0.450	4.63	0.113	0.823	3.2.1.97	NA
5	0.060	1z9pB	0.456	3.78	0.098	0.717	1.15.1.1	106

	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	0.02	2z0d1	0.552	3.22	0.115	0.770	0.65	III	complex1.pdb.gz	35,54,58,65,66,68,80,84,101,102,105
2	0.01	1mk9D	0.284	5.65	0.078	0.637	0.52	III	complex2.pdb.gz	11,12,91
3	0.01	1y19F	0.292	5.15	0.043	0.584	0.41	III	complex3.pdb.gz	69,70,71,72,73,77

	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.