D-I-TASSER O94985-D4

D-I-TASSER results for O94985-D4

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

Input Sequence in FASTA format

>O94985 (148 residues)
PEEPKISLSGVHHFARAASEFESSEGVFLFPELRIISHDLDTCEVTVEGEELNHEQESLE
VDMARLQQKGIEVSSSELGMTFTGVDTMASYEEVLHLLRYRNWHARSLLDRKFKLICSEL
NGRYISNEFKVEVNVIHTANPMEHANHM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| PEEPKISLSGVHHFARAASEFESSEGVFLFPELRIISHDLDTCEVTVEGEELNHEQESLEVDMARLQQKGIEVSSSELGMTFTGVDTMASYEEVLHLLRYRNWHARSLLDRKFKLICSELNGRYISNEFKVEVNVIHTANPMEHANHM
Prediction	CCCCSSSSSCCCCCCCCHHHHCCCCCCSSCCCSSSSSCCCCSSSSSSSCCCCCCCCSSSSCCHHHHHHCCCSSSSCCCCSSSSCCSHHHHHHHHHHHSSSSSCCCHHHHCCSSSSSSSCCCCSSSSSSSSSSSSSSSCCCCCCCCCCC
Confidence	9998799972444443046541357841167407754146528999863689997169982878875449489985894899912048899999974456636824541527999982348826743689999998348866788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| PEEPKISLSGVHHFARAASEFESSEGVFLFPELRIISHDLDTCEVTVEGEELNHEQESLEVDMARLQQKGIEVSSSELGMTFTGVDTMASYEEVLHLLRYRNWHARSLLDRKFKLICSELNGRYISNEFKVEVNVIHTANPMEHANHM
Prediction	8862403031233234325525364004105504022540440403133671537333042436304736041433432010202531530350043031324434413613030302336331433414030222244644744648
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCSSSSSCCCCCCCCHHHHCCCCCCSSCCCSSSSSCCCCSSSSSSSCCCCCCCCSSSSCCHHHHHHCCCSSSSCCCCSSSSCCSHHHHHHHHHHHSSSSSCCCHHHHCCSSSSSSSCCCCSSSSSSSSSSSSSSSCCCCCCCCCCC
PEEPKISLSGVHHFARAASEFESSEGVFLFPELRIISHDLDTCEVTVEGEELNHEQESLEVDMARLQQKGIEVSSSELGMTFTGVDTMASYEEVLHLLRYRNWHARSLLDRKFKLICSELNGRYISNEFKVEVNVIHTANPMEHANHM

1xezA

0.11

0.09

3.41

1.00

DEthreader

----------V-QFRYGV-T-TLPHVAFYI-SVNSGIHLADYRFVFNAS-N-N--KAQIKTFPVDNIEYTIERNAKNQAVSFTWNLSFVP--KM--DVIYKASATETGSTDFIIDSSVNIRPRRRITKSASFTVDDHPTKLCLDNLLY

2xwxA2

0.10

0.07

2.50

0.82

CEthreader

QPEYSLTVSGLAKEYEIGEQP-------IQLDLTLEAQGEMSAELTVYNHHQK------------------------PLASWSQAMTDGELKSIT--LELSEA---KAGHHMLVSRIKDRDGNLQ-DQQTLDFMLVE-----------

2xdhA

0.09

0.07

2.86

0.77

EigenThreader

-AKTTIIAGS---AEAPQ-----GSDIQVP----VNADKVGSINLILSYPNV---LEVVLQGS-LT--QNSLFDYQNQIVGIADSNGI-SGDGSLFYVKFRVTTL--RNSHALTLIEIYDDGNSVKVATINGTFRIVSQEEAHHHHHH

2x9wA1

0.14

0.12

4.14

0.43

FFAS-3D

EAKPKIDFKGKANPDTPRVDKDTPVNHQVGDVVEYEIVNYATANWSDRTEGLNKGTVKVTVDDVALEAGDYALTEVATGFDLK--LTDAGLAKV------NDQNAEKTVKITYSATLNDIVEVPESNDVTFNYG--------------

4or1A

0.15

0.11

3.89

0.72

SPARKS-K

--STEISLEGLHNMG---EQLFDGD---ILATGRIICREHTGFHIQMNARQVEGRPGHYIVQGSKDTQSKLWVRLGREGIVRSGQEE----------------------QVIFDVMADG-NQWAKPGEYIFSVSGKCLTTAVAKTATS

3lycA

0.11

0.07

2.68

0.85

CNFpred

------------------------------DCLELEGG---GMVVNYTQS---DAPEGLEIKTDRNIFEKYEFNVENHKLKIRPKKEFRKHTNFPTEFMVTANSR-NLKKLAAAGSTHVNNSPLQAEEFEAGLAGSG-----------

3kptB

0.10

0.09

3.26

1.00

DEthreader

-NNEEPTIDKK-LEALPIN--TNY-N--YD--IKTLIPIYKYVVTDTL---DNR-LVIQGPIVKEVNANVVEVAIEGQKVTATVFKKKE-FH--L-QIKSQVKEGVPSEILNTAKIHFTNKNDVIGEKESKPVVVIPTTGQTVKLTIE

5y9hA2

0.09

0.07

2.82

0.95

MapAlign

---QDLTVSLI-PVGLKAGKNA--PSAKIA-KLVVNSLKEFGVRGIVAGK-NTGKEIGVGLSSDSL-RRSDSTEKWNGVNWMTF-NSN---DTL--DIVLTGQNV-TADTYPITLDVVGYQGFLPEQQKSVDIVFSS-----------

5n8pA

0.11

0.10

3.68

0.56

MUSTER

GAGQNLTATTAAQAANNVA-------VDGGANVTVASTGVTSGTTTVGANSAASGTVSVSVANSSTTTTGAIAVTGGTAVTVAQTAGNAV-NTTLTQADVTVTGNSSTTAVTVTQTAAATAGATVAGRVNGAVTITDSAAASATTAGK

4a2lA

0.18

0.16

5.28

0.66

HHsearch

PETEKFRNFGINGITTFRPEL--LLDNPYTPPVVITKLQLFNKVVRPDDGILTSETKSITLKSWQT-AFSIEFVVSHNAYKLEGYDKEWYYLTDSRTVSYSNLPQGTY---QFLVKAANSDGKWNPIPTALEIIVLPIW---------

(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	0.7709

(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	3f83A	0.63	3.89	0.081	0.912	model1_3f83A.pdb.gz
2	1xezA	0.62	3.73	0.035	0.905	model1_1xezA.pdb.gz
3	6kg8A	0.62	3.75	0.091	0.878	model1_6kg8A.pdb.gz
4	3qe5A	0.62	3.61	0.078	0.851	model1_3qe5A.pdb.gz
5	3pf2A	0.61	3.80	0.061	0.878	model1_3pf2A.pdb.gz
6	3uxfA	0.61	3.76	0.084	0.872	model1_3uxfA.pdb.gz
7	3kptB	0.61	3.75	0.096	0.878	model1_3kptB.pdb.gz
8	4ofqA	0.61	3.71	0.047	0.865	model1_4ofqA.pdb.gz
9	2x9wA	0.61	3.59	0.046	0.885	model1_2x9wA.pdb.gz
10	2xtlA	0.60	3.66	0.099	0.878	model1_2xtlA.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:0008092	0.71	cytoskeletal protein binding
GO:0001540	0.71	beta-amyloid binding
GO:0042988	0.70	X11-like protein binding
GO:0019894	0.70	kinesin binding
GO:0046872	0.62	metal ion binding
GO:0005509	0.57	calcium 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:0007155	0.73	cell adhesion
GO:0065007	0.66	biological regulation
GO:0050789	0.66	regulation of biological process
GO:0050794	0.65	regulation of cellular process
GO:0098742	0.63	cell-cell adhesion via plasma-membrane adhesion molecules
GO:0007156	0.60	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0051128	0.55	regulation of cellular component organization
GO:0051960	0.54	regulation of nervous system development
GO:0044699	0.52	single-organism process
GO:0009987	0.52	cellular 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	0.92	cell part
GO:0016020	0.80	membrane
GO:0044425	0.76	membrane part
GO:0044459	0.74	plasma membrane part
GO:0043226	0.72	organelle
GO:0045211	0.68	postsynaptic membrane
GO:0043227	0.63	membrane-bounded organelle
GO:0044421	0.60	extracellular region part
GO:0044424	0.59	intracellular part
GO:0031988	0.55	membrane-bounded vesicle
GO:0070062	0.54	extracellular exosome

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	1ohzA	0.543	3.94	0.074	0.797	3.2.1.8	99
2	0.060	1hyoB	0.345	5.75	0.040	0.696	3.7.1.2	NA
3	0.060	1l9mB	0.527	3.57	0.109	0.723	2.3.2.13	NA
4	0.060	1g0dA	0.511	4.15	0.052	0.743	2.3.2.13	NA
5	0.060	2g8eA	0.297	5.66	0.078	0.588	3.4.22.52	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	2ahiC	0.584	3.57	0.061	0.804	0.29	QNA	complex1.pdb.gz	84,86,90,93
2	0.01	1xezA	0.623	3.73	0.035	0.905	0.36	BOG	complex2.pdb.gz	42,84,86
3	0.01	3qymB	0.580	3.57	0.046	0.804	0.23	QNA	complex3.pdb.gz	80,82,83,84
4	0.01	2ac0C	0.585	3.68	0.061	0.811	0.20	QNA	complex4.pdb.gz	98,100,101
5	0.01	2jix9	0.434	4.16	0.059	0.669	0.29	III	complex5.pdb.gz	83,120,123
6	0.01	1sxj4	0.301	5.05	0.068	0.547	0.20	III	complex6.pdb.gz	117,118,119,120,121
7	0.01	3d0aA	0.583	3.58	0.061	0.804	0.24	QNA	complex7.pdb.gz	42,84,118
8	0.01	1ycs0	0.586	3.64	0.062	0.811	0.16	III	complex8.pdb.gz	120,124,125
9	0.01	2jix2	0.435	4.12	0.069	0.669	0.36	III	complex9.pdb.gz	79,81,84,96,97
10	0.01	2jix7	0.450	4.58	0.067	0.716	0.20	III	complex10.pdb.gz	87,98,131

	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.