D-I-TASSER O95398-D1

D-I-TASSER results for O95398-D1

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

Input Sequence in FASTA format

>O95398 (224 residues)
MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLL
EHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRK
YHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQ
FYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLLEHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRKYHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQFYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCSCCSSCCSSCCCCSSHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCC
Confidence	97666787641135677788766776567887655898615667776258877403454215776411255566788744345631113445327999999999999851577521102356677365034179999999825667899999999999998198442788754202890599867888885433105677888888751358734444330289
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLLEHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRKYHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQFYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKP
Prediction	65243444532515232464443443445435533467432430243143244123323454434331452543425447554634442564434402400420242035634410321334443043002022002001531651532630140033015421020135533044442100002353554454453453145004203733042203302448
	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                 120                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCSCCSSCCSSCCCCSSHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCSSSCCCCCCCCCCCCSSSSSCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCC
MKVGWPGESCWQVGLAVEDSPALGAPRVGALPDVVPEGTLLNMVLRRMHRPRSCSYQLLLEHQRPSCIQGLRWTPLTNSEESLDFSESLEQASTERVLRAGRQLHRHLLATCPNLIRDRKYHLRLYRQCCSGRELVDGILALGLGVHSRSQVVGICQVLLDEGALCHVKHDWAFQDRDAQFYRFPGPEPEPVRTHEMEEELAEAVALLSQRGPDALLTVALRKP

6ei3A

0.03

1.53

0.83

DEthreader

DFGKYTILVSFMDQFRAVV------LGRKRYVRVPLP---D-HGFGAVVRSALLAHGRPGLALAAISGIGGWWLERARGTHPDAVDGVRALLRVLVIFALVTPFFSLFD---QKASWVASQM--Q---NPLLVMLINRMSGAFS-F--VLVSATGIEAYVMSFWYL----------------TTTGNLWLSAF-FLAALAFGLYARRY-RMV---D-N-YRPAN

2byvE2

0.50

0.29

8.55

1.64

SPARKS-K

------------------------------------------------------------------------------------------NVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKY-LFYRFLDDEREDAPKKECDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE

0.30

0.29

8.93

1.39

MapAlign

--WIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCYAVLAGSLDVKVSETSSHQDAVTICTLGIGLLAPPYGVMETGSNNVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQD-KYLFYRFLDDLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILR--

2byvE

0.31

9.43

1.00

CEthreader

YAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKY-LFYRFLDDEREDAPKKECDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE

0.35

0.32

9.46

1.07

MUSTER

VKVSETSSHQDAVTIGIGTAILDNTPRHATIVTRESEQEDFKALWEKYRQYMAGLL----------------------APPYGVMETGSNNVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYL-FYRFLDDEREDAPLPTCDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE

0.38

0.33

9.93

5.21

HHsearch

FRQGDI-GTNWYAQDAVTICLGIGTAFGESILDNTPEQEDFKALWEKYRQYM--------AGLLAPPY-G-----VM--------ETGSNNVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDK-YLFYRFLDDEREDEEKKECDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE

0.34

0.33

10.04

1.54

SPARKS-K

ITLFRQGDTNWYAVLAVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKY-LFYRFLDDEREDAPKKECDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE2

0.50

0.29

8.55

1.70

FFAS-3D

------------------------------------------------------------------------------------------NVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYL-FYRFLDDEREDAPKKECDEELQDTMLLLSQMGPDAHMRMILRKP

2byvE2

0.45

0.27

7.83

0.75

EigenThreader

--------------------------------------------------------------------------------------NVP----SEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTECDEELQDTMLLLSQMGPDAHMRMILRKP

4f7zA

0.51

0.29

8.54

1.83

CNFpred

---------------------------------------------------------------------------------------------SEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDK-YLFYRFLDDEPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKP

(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	0.6297

(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	2byvE	0.73	3.31	0.345	0.857	model1_2byvE.pdb.gz
2	6h7eA	0.52	1.47	0.984	0.554	model1_6h7eA.pdb.gz
3	1it7A	0.44	5.64	0.049	0.746	model1_1it7A.pdb.gz
4	7ckqC	0.44	6.12	0.063	0.799	model1_7ckqC.pdb.gz
5	6vvsC	0.43	6.16	0.042	0.790	model1_6vvsC.pdb.gz
6	7khbC	0.43	6.14	0.026	0.786	model1_7khbC.pdb.gz
7	4qiwB	0.43	6.26	0.035	0.804	model1_4qiwB.pdb.gz
8	3hkzJ	0.43	6.23	0.035	0.804	model1_3hkzJ.pdb.gz
9	6pd1A	0.43	6.30	0.032	0.790	model1_6pd1A.pdb.gz
10	6gykB	0.43	6.14	0.056	0.786	model1_6gykB.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:0005088	0.97	Ras guanyl-nucleotide exchange factor activity
GO:0017034	0.71	Rap guanyl-nucleotide exchange factor activity

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	0.99	biological regulation
GO:0050789	0.99	regulation of biological process
GO:0050794	0.98	regulation of cellular process
GO:0007165	0.84	signal transduction
GO:0044699	0.80	single-organism process
GO:0009987	0.80	cellular process
GO:0044763	0.76	single-organism cellular process
GO:0051049	0.68	regulation of transport
GO:0035556	0.66	intracellular signal transduction
GO:0048518	0.63	positive regulation of biological process
GO:0051128	0.61	regulation of cellular component organization
GO:0050793	0.61	regulation of developmental process
GO:0048869	0.61	cellular developmental process
GO:0048522	0.61	positive regulation of cellular process
GO:0051239	0.60	regulation of multicellular organismal process
GO:0019222	0.60	regulation of metabolic process
GO:0080090	0.59	regulation of primary metabolic process
GO:0050790	0.59	regulation of catalytic activity
GO:0044767	0.59	single-organism developmental process
GO:0031323	0.59	regulation of cellular metabolic process
GO:2000026	0.58	regulation of multicellular organismal development
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0048519	0.58	negative regulation of biological process
GO:0043085	0.58	positive regulation of catalytic activity
GO:0022603	0.58	regulation of anatomical structure morphogenesis
GO:0051246	0.57	regulation of protein metabolic process
GO:0051130	0.57	positive regulation of cellular component organization
GO:0051094	0.57	positive regulation of developmental process
GO:0050896	0.57	response to stimulus
GO:0048523	0.57	negative regulation of cellular process
GO:0044087	0.57	regulation of cellular component biogenesis
GO:0043547	0.57	positive regulation of GTPase activity
GO:0032956	0.57	regulation of actin cytoskeleton organization
GO:0031325	0.57	positive regulation of cellular metabolic process
GO:0019220	0.57	regulation of phosphate metabolic process
GO:0010604	0.57	positive regulation of macromolecule metabolic process
GO:0048856	0.56	anatomical structure development
GO:0045937	0.56	positive regulation of phosphate metabolic process
GO:0010033	0.56	response to organic substance
GO:0007264	0.56	small GTPase mediated signal transduction
GO:0001932	0.56	regulation of protein phosphorylation
GO:1901700	0.55	response to oxygen-containing compound
GO:0071310	0.55	cellular response to organic substance
GO:0065008	0.55	regulation of biological quality
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0045765	0.55	regulation of angiogenesis
GO:0014070	0.55	response to organic cyclic compound
GO:0010243	0.55	response to organonitrogen compound
GO:0007265	0.55	Ras protein signal transduction
GO:0001934	0.55	positive regulation of protein phosphorylation
GO:2000249	0.54	regulation of actin cytoskeleton reorganization
GO:0071320	0.54	cellular response to cAMP
GO:0061028	0.54	establishment of endothelial barrier
GO:0051496	0.54	positive regulation of stress fiber assembly
GO:0051050	0.54	positive regulation of transport
GO:0045766	0.54	positive regulation of angiogenesis
GO:0032486	0.54	Rap protein 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	0.96	intracellular part
GO:0044444	0.91	cytoplasmic part
GO:0016020	0.90	membrane
GO:0005886	0.76	plasma membrane
GO:0043226	0.73	organelle
GO:0043229	0.72	intracellular organelle
GO:0044446	0.64	intracellular organelle part
GO:0044430	0.58	cytoskeletal part
GO:0043232	0.58	intracellular non-membrane-bounded organelle
GO:0043227	0.57	membrane-bounded organelle
GO:0030864	0.57	cortical actin cytoskeleton
GO:0030175	0.57	filopodium
GO:0030027	0.57	lamellipodium
GO:0005902	0.57	microvillus

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	1sy7A	0.383	6.00	0.048	0.674	1.11.1.6	NA
2	0.060	2i6qA	0.391	6.17	0.044	0.714	3.4.21.43	NA
3	0.060	3hkzJ	0.431	6.23	0.035	0.804	2.7.7.6	NA
4	0.060	2bklB	0.387	5.80	0.065	0.674	3.4.21.26	NA
5	0.060	1cqzB	0.401	5.81	0.075	0.688	3.3.2.10 3.3.2.3	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	0.01	2nqaA	0.269	6.28	0.020	0.482	0.48	CA	complex1.pdb.gz	130,131,132,137
2	0.01	1j2bA	0.323	6.22	0.051	0.594	0.42	MG	complex2.pdb.gz	133,136,153
3	0.01	1ea0A	0.320	6.63	0.047	0.616	0.64	F3S	complex3.pdb.gz	133,134,135,136,152,155,175

	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.