D-I-TASSER O15195-D1

D-I-TASSER results for O15195-D1

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

Input Sequence in FASTA format

>O15195 (120 residues)
MDISKGLPGMQGGLHIWISENRKMVPVPEGAYGNFFEEHCYVILHVPQSPKATQGASSDL
HYWVGKQAGAEAQGAAEAFQQRLQDELGGQTVLHREAQGHESDCFCSYFRPGIIYRKGGL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDISKGLPGMQGGLHIWISENRKMVPVPEGAYGNFFEEHCYVILHVPQSPKATQGASSDLHYWVGKQAGAEAQGAAEAFQQRLQDELGGQTVLHREAQGHESDCFCSYFRPGIIYRKGGL
Prediction	CCCCCCCCCCCCSSSSSSSSCCSSSSCCHHHCCSSSCCCSSSSSSSSSCCCCCCCSSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSSSCCCCCCHHHHHHCCCCSSSSCCCC
Confidence	986536898646189999969887887988878241798299999776168887426899999668899667668999999999984999618985179999999996089749961789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDISKGLPGMQGGLHIWISENRKMVPVPEGAYGNFFEEHCYVILHVPQSPKATQGASSDLHYWVGKQAGAEAQGAAEAFQQRLQDELGGQTVLHREAQGHESDCFCSYFRPGIIYRKGGL
Prediction	543457445553403002047263451457422411554000011024357655523120000104504564322023203402641776222212335421630252155403135458
	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

CCCCCCCCCCCCSSSSSSSSCCSSSSCCHHHCCSSSCCCSSSSSSSSSCCCCCCCSSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHHCCCCCSSSSCCCCCCHHHHHHCCCCSSSSCCCC
MDISKGLPGMQGGLHIWISENRKMVPVPEGAYGNFFEEHCYVILHVPQSPKATQGASSDLHYWVGKQAGAEAQGAAEAFQQRLQDELGGQTVLHREAQGHESDCFCSYFRPGIIYRKGGL

3ffkA1

0.43

0.41

11.98

1.33

DEthreader

-PELKAGK--EPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQLR-NG-NLQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

1j72A1

0.42

0.38

11.27

3.22

SPARKS-K

---PFPGSVQDPGLHVWRVEKLKPVPVAQENQGVFFSGDSYLVLHNG------PEEVSHLHLWIGQQSSRDEQGACAVLAVQLDDYLGGRPVQHREVQGNESDLFMSYFPRGLKYQEGG-

2vilA

0.43

0.42

12.21

1.11

MapAlign

--VTGKLDKTTPGIQIWRIENMEMVPVPTKSYGNFYEGDCYVLLSTRKT---GSGFSYNIHYWLGKNSSQDEQGAAAIYTTQMDEYLGSVAVQHREVQGHESETFRAYFKQGLIYKQGGV

2vilA

0.43

0.42

12.22

0.80

CEthreader

KKVTGKLDKTTPGIQIWRIENMEMVPVPTKSYGNFYEGDCYVLLSTRK---TGSGFSYNIHYWLGKNSSQDEQGAAAIYTTQMDEYLGSVAVQHREVQGHESETFRAYFKQGLIYKQGGV

3ffkA1

0.42

0.41

12.01

2.81

MUSTER

EHPEFLKAGKEPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQL--RNGNLQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

1d0nA

0.44

0.42

12.20

2.64

HHsearch

----VEHPEFLGGLQIWRVEKFDLVPVPPNLYGDFFTGDAYVILKTVQLR--NGILQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

4pkiG1

0.42

12.23

2.07

FFAS-3D

MVVEHPEAGKEPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQL--RNGNLQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

1d0nA1

0.42

0.41

12.01

1.25

EigenThreader

EHPEFLKAGKEPGLQIWRVEKFDLVPVPPNLYGDFFTGDAYVILKTVQLRN--GILQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

5a1kA

0.40

0.35

10.32

1.99

CNFpred

------------GLQVWRIEKLELVPVPQSAHGDFYVGDAYLVLHTAKTS---RGFTYRLHFWLGKECSQDESTAAAIFTVQMDDYLGGKPVQNRELQGYESNDFVSYFKGGLKYKAGGV

3ffkA

0.43

0.41

11.98

1.33

DEthreader

-PELKAGK--EPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQLR-NG-NLQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGV

(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	0.8665

(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	4pkiG	0.93	1.23	0.415	0.983	model1_4pkiG.pdb.gz
2	3ffkA1	0.93	1.22	0.415	0.983	model1_3ffkA1.pdb.gz
3	5a1kA	0.92	1.28	0.376	0.975	model1_5a1kA.pdb.gz
4	1j72A	0.86	1.47	0.414	0.925	model1_1j72A.pdb.gz
5	2vilA	0.83	2.08	0.427	0.975	model1_2vilA.pdb.gz
6	3fg6H	0.77	1.47	0.275	0.833	model1_3fg6H.pdb.gz
7	4bwcA	0.41	3.23	0.082	0.567	model1_4bwcA.pdb.gz
8	3iyuX	0.35	4.98	0.041	0.667	model1_3iyuX.pdb.gz
9	4k17A	0.33	4.98	0.082	0.625	model1_4k17A.pdb.gz
10	3d34B	0.33	4.62	0.065	0.575	model1_3d34B.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:0003779	0.80	actin binding
GO:0046872	0.51	metal ion 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:0044699	0.99	single-organism process
GO:0009987	0.97	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0016043	0.95	cellular component organization
GO:0030029	0.90	actin filament-based process
GO:0065007	0.88	biological regulation
GO:0051014	0.88	actin filament severing
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0051128	0.82	regulation of cellular component organization
GO:0048522	0.82	positive regulation of cellular process
GO:0065008	0.80	regulation of biological quality
GO:0048523	0.80	negative regulation of cellular process
GO:0030833	0.79	regulation of actin filament polymerization
GO:0030837	0.78	negative regulation of actin filament polymerization
GO:0007015	0.77	actin filament organization
GO:0051130	0.75	positive regulation of cellular component organization
GO:0051693	0.74	actin filament capping
GO:0051495	0.73	positive regulation of cytoskeleton organization
GO:0051179	0.73	localization
GO:1902578	0.71	single-organism localization
GO:0051125	0.71	regulation of actin nucleation
GO:0032502	0.71	developmental process
GO:0044767	0.70	single-organism developmental process
GO:0022607	0.70	cellular component assembly
GO:0051127	0.67	positive regulation of actin nucleation
GO:0042989	0.67	sequestering of actin monomers
GO:0022411	0.66	cellular component disassembly
GO:0050793	0.65	regulation of developmental process
GO:0030030	0.64	cell projection organization
GO:0048869	0.63	cellular developmental process
GO:0051016	0.62	barbed-end actin filament capping
GO:0048856	0.62	anatomical structure development
GO:0030198	0.62	extracellular matrix organization
GO:0009653	0.62	anatomical structure morphogenesis
GO:0080090	0.61	regulation of primary metabolic process
GO:0050896	0.61	response to stimulus
GO:0032990	0.61	cell part morphogenesis
GO:0032501	0.61	multicellular organismal process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0008152	0.61	metabolic process
GO:0060271	0.60	cilium morphogenesis
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0022617	0.60	extracellular matrix disassembly
GO:0051246	0.59	regulation of protein metabolic process
GO:0032879	0.59	regulation of localization
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010468	0.59	regulation of gene expression
GO:0071704	0.58	organic substance metabolic process
GO:0061024	0.58	membrane organization
GO:0048583	0.58	regulation of response to stimulus
GO:0032270	0.58	positive regulation of cellular protein metabolic process
GO:0030162	0.58	regulation of proteolysis
GO:0010628	0.58	positive regulation of gene expression
GO:0007165	0.58	signal transduction
GO:1903923	0.57	positive regulation of protein processing in phagocytic vesicle
GO:0061041	0.57	regulation of wound healing
GO:0044238	0.57	primary metabolic process
GO:0042221	0.57	response to chemical
GO:0022603	0.57	regulation of anatomical structure morphogenesis
GO:0006911	0.57	phagocytosis, engulfment
GO:0043170	0.56	macromolecule metabolic process
GO:0030334	0.56	regulation of cell migration
GO:0010033	0.56	response to organic substance
GO:0009605	0.56	response to external stimulus
GO:0070887	0.55	cellular response to chemical stimulus
GO:0044710	0.55	single-organism metabolic process
GO:0042981	0.55	regulation of apoptotic process
GO:0009719	0.55	response to endogenous stimulus
GO:0043065	0.54	positive regulation of apoptotic process
GO:0002682	0.54	regulation of immune system process
GO:0019538	0.53	protein metabolic process
GO:0003008	0.53	system process
GO:1903827	0.52	regulation of cellular protein localization
GO:0071801	0.52	regulation of podosome assembly
GO:0050790	0.52	regulation of catalytic activity
GO:0048584	0.52	positive regulation of response to stimulus
GO:0044089	0.52	positive regulation of cellular component biogenesis
GO:0030155	0.52	regulation of cell adhesion
GO:0009966	0.52	regulation of signal transduction
GO:0006915	0.52	apoptotic process
GO:0003012	0.52	muscle system process
GO:2001269	0.51	positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:1990000	0.51	amyloid fibril formation
GO:1903909	0.51	regulation of receptor clustering
GO:1903906	0.51	regulation of plasma membrane raft polarization
GO:1903903	0.51	regulation of establishment of T cell polarity
GO:1903689	0.51	regulation of wound healing, spreading of epidermal cells
GO:1902174	0.51	positive regulation of keratinocyte apoptotic process
GO:0097284	0.51	hepatocyte apoptotic process
GO:0097017	0.51	renal protein absorption
GO:0090527	0.51	actin filament reorganization
GO:0046597	0.51	negative regulation of viral entry into host cell
GO:0035556	0.51	intracellular signal transduction
GO:0031648	0.51	protein destabilization
GO:0014891	0.51	striated muscle atrophy
GO:1901700	0.50	response to oxygen-containing compound
GO:0051239	0.50	regulation of multicellular organismal process
GO:0048468	0.50	cell development
GO:0014070	0.50	response to organic cyclic compound
GO:0009888	0.50	tissue development

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	0.95	cell part
GO:0044424	0.89	intracellular part
GO:0043226	0.60	organelle
GO:0044444	0.52	cytoplasmic part
GO:0044422	0.51	organelle part
GO:0043229	0.51	intracellular organelle

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	2amfE	0.506	3.95	0.049	0.783	1.5.1.2	NA
2	0.060	1tlbA	0.506	4.30	0.026	0.825	1.3.3.3	113
3	0.060	2a96B	0.487	4.48	0.054	0.833	3.1.3.2	NA
4	0.060	1zcjA	0.506	3.79	0.037	0.750	1.1.1.35	NA
5	0.060	3khuB	0.513	4.09	0.044	0.825	1.1.1.22	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	0.16	1d4x1	0.935	1.22	0.415	0.983	1.38	III	complex1.pdb.gz	1,4,22,23,62,70,71,73,74,75,77,78,79,81,82,84,85,91,92,93,95
2	0.14	1c0fS	0.936	1.21	0.415	0.983	0.46	CA	complex2.pdb.gz	40,65,68
3	0.02	3q2bA	0.589	2.98	0.112	0.808	0.46	TAR	complex3.pdb.gz	40,117,119

	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.