D-I-TASSER P54851-D1

D-I-TASSER results for P54851-D1

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

Input Sequence in FASTA format

>P54851 (167 residues)
MLVLLAFIIAFHITSAALLFIATVDNAWWVGDEFFADVWRICTNNTNCTVINDSFQEYST
LQAVQATMILSTILCCIAFFIFVLQLFRLKQGERFVLTSIIQLMSCLCVMIAASIYTDRR
EDIHDKNAKFYPVTREGSYGYSYILAWVAFACTFISGMMYLILRKRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLVLLAFIIAFHITSAALLFIATVDNAWWVGDEFFADVWRICTNNTNCTVINDSFQEYSTLQAVQATMILSTILCCIAFFIFVLQLFRLKQGERFVLTSIIQLMSCLCVMIAASIYTDRREDIHDKNAKFYPVTREGSYGYSYILAWVAFACTFISGMMYLILRKRK
Prediction	CHHHHHHHHHHHHHHHHHHHHHHCCCCSSSCCCCCCCHHHHHCCCCCSSSSCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHSSSCCC
Confidence	93689999999999999999995268079648744664576438984124247754258999999999999999999999999997521137611388999999999999999999874133304776543234442131468999999999999999975122059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLVLLAFIIAFHITSAALLFIATVDNAWWVGDEFFADVWRICTNNTNCTVINDSFQEYSTLQAVQATMILSTILCCIAFFIFVLQLFRLKQGERFVLTSIIQLMSCLCVMIAASIYTDRREDIHDKNAKFYPVTREGSYGYSYILAWVAFACTFISGMMYLILRKRK
Prediction	43331232332132120011000022212334433120013014344343324435444103003111100131133123110112033445431311010133123222200100023345235744523434552300000110120133033113211102448
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHCCCCSSSCCCCCCCHHHHHCCCCCSSSSCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHSSSCCC
MLVLLAFIIAFHITSAALLFIATVDNAWWVGDEFFADVWRICTNNTNCTVINDSFQEYSTLQAVQATMILSTILCCIAFFIFVLQLFRLKQGERFVLTSIIQLMSCLCVMIAASIYTDRREDIHDKNAKFYPVTREGSYGYSYILAWVAFACTFISGMMYLILRKRK

4p79A

0.15

0.14

4.82

1.33

DEthreader

SVAVETFGFF-SALGLL-LGLTLSNSYWRVSTTIFENLWYSCATDSNCWDFPSLALS-GYVQGCRAL-ITAILLGFLGLFLG-VGLTNDLSAKLLAIAGTLHILAGACG-VAISWYAVNITTDFNPLYAGT---K-YELGPALYLGWSASLLSILGGICVFSTAAAS

5vhxE

0.19

6.16

2.37

SPARKS-K

RRGRALLAVALNLLALLFATTAFLTTYWCQGTRFHTGIWYSCEEGEKCRSFIDLAPEKGVLWLSVVSEVLYILLLVVGFSLMCLELLHSSDGKLNAFAAVFTVLSGLLGMVAHMMYTQVFQVTVSLGPEDWR-PHSWDYGWSFCLAWGSFTCCMAASVTTLNSYTK-

6akfA

0.14

0.13

4.52

1.18

MapAlign

SMGLEITGTSLAVLGWLCTIVCCALPMWRVSAITWEGLWMNCVVQMQCKMYDSLLALPQDLQAARALIVVSILLAAFGLLVALATNAVTAKAKITIVAGVLFLLAALLTLVAVSWSANTIIRDF--YNPLVPEAQKREMGAGLYVGWAAAALQLLGGALLAAS----

6akfA

0.14

0.13

4.52

0.97

CEthreader

SMGLEITGTSLAVLGWLCTIVCCALPMWRVSAITWEGLWMNCVVQMQCKMYDSLLALPQDLQAARALIVVSILLAAFGLLVALVGAQATNKAKITIVAGVLFLLAALLTLVAVSWSANTIIRDF--YNPLVPEAQKREMGAGLYVGWAAAALQLLGGALLAAS----

6qkcI

0.18

0.17

5.45

1.81

MUSTER

--VQVLLTTIGAFAAFGLMTIAISTDYWLYTRLTHSGLWRICCLEGVCVKINHFEYLLRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANA-----------GKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIER

5b2gA

0.16

5.16

3.55

HHsearch

AYGLQVMGIALAVLGWLAVMLCCALPMWRVTATIWEGLWMNCVVQMQCKVYDSLLALPQDLQAARALVIISIIVAALGVLLSVVG-DESAKAKTMIVAGVVFLLAGLMVIVPVSWTAHNIIQD--FYNPLVASGQKREMGASLYVGWAASGLLLLGGGLLCCS----

5vhxE

0.20

0.19

6.15

1.86

FFAS-3D

--GRALLAVALNLLALLFATTAFLTTYWCQGTRFHTGIWYSCEEGEKCRSFIDLAPEKGVLWLSVVSEVLYILLLVVGFSLMCLELLHSSDGKLNAFAAVFTVLSGLLGMVAHMMYTQVFQVTVSLGPEDWRP-HSWDYGWSFCLAWGSFTCCMAASVTTLNSYTK-

5vhxE

0.17

5.51

1.22

EigenThreader

RRGRALLAVALNLLALLFATTAFLTYWCQGTQRFHTGIWYSCEEKCRSFIDLAPASEKGVLWLSVVSEVLYILLLVVGFSLMCLELLHSSDGKLNAFAAVFTVLSGLLGMVAHMMYTQVFQVTVSLGPEDW-RPHSWDYGWSFCLAWGSFTCCMAASVTTLNSYTK-

4p79A

0.17

5.51

1.27

CNFpred

SVAVETFGFFMSALGLLMLGLTLSNSYWRVSTTIFENLWYSCATVSNCWDFPSMLALSGYVQGCRALMITAILLGFLGLFLGMVGLRATKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDF--FNPLYAG-TKYELGPALYLGWSASLLSILGGICVFSTAAAS

6ov2A

0.13

4.35

1.33

DEthreader

-G-LELLGMTLAVLGWLGTLVSCALPLWKVTAVVWEGLWMSCVVQQCKVYDSLLA-LPQDLQAARALCVIALLLALLGLLVAITGATVEEGARIVLTAGVILLLAGILVLIPVCWTAHAIIQDFNPLVA-EAL-K-RELGASLYLGWAAAALLMLGGGLLCCT--CP

(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	0.8975

(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	5vhxE	0.85	2.11	0.182	0.988	model1_5vhxE.pdb.gz
2	4p79A	0.84	1.86	0.155	0.928	model1_4p79A.pdb.gz
3	6qkcI	0.84	1.83	0.176	0.916	model1_6qkcI.pdb.gz
4	6ov2A	0.83	2.12	0.154	0.934	model1_6ov2A.pdb.gz
5	6akfA	0.82	2.49	0.138	0.946	model1_6akfA.pdb.gz
6	3x29A	0.81	2.11	0.145	0.910	model1_3x29A.pdb.gz
7	5b2gA	0.80	2.46	0.167	0.928	model1_5b2gA.pdb.gz
8	6c14B	0.77	1.97	0.138	0.868	model1_6c14B.pdb.gz
9	5vjsA	0.74	3.06	0.046	0.904	model1_5vjsA.pdb.gz
10	5kk2E	0.74	2.50	0.120	0.898	model1_5kk2E.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:0005102	0.50	receptor binding
GO:0044877	0.49	macromolecular complex binding
GO:0019901	0.49	protein kinase binding
GO:0005178	0.48	integrin binding
GO:0042802	0.36	identical protein 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	0.96	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.93	single-organism cellular process
GO:0022607	0.87	cellular component assembly
GO:0065007	0.82	biological regulation
GO:0008219	0.78	cell death
GO:0032060	0.77	bleb assembly
GO:0050789	0.75	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0032501	0.72	multicellular organismal process
GO:0042127	0.67	regulation of cell proliferation
GO:0051239	0.62	regulation of multicellular organismal process
GO:0048518	0.60	positive regulation of biological process
GO:0007155	0.60	cell adhesion
GO:0048522	0.59	positive regulation of cellular process
GO:0003008	0.59	system process
GO:0008284	0.57	positive regulation of cell proliferation
GO:0003093	0.57	regulation of glomerular filtration
GO:2000026	0.55	regulation of multicellular organismal development
GO:0045595	0.55	regulation of cell differentiation
GO:0008283	0.55	cell proliferation
GO:0065009	0.54	regulation of molecular function
GO:0032879	0.54	regulation of localization
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0050896	0.53	response to stimulus
GO:0031323	0.53	regulation of cellular metabolic process
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0006810	0.52	transport
GO:1902578	0.51	single-organism localization
GO:0050790	0.51	regulation of catalytic activity
GO:0022414	0.51	reproductive process
GO:0001934	0.51	positive regulation of protein phosphorylation
GO:2001212	0.50	regulation of vasculogenesis
GO:0072659	0.50	protein localization to plasma membrane
GO:0070836	0.50	caveola assembly
GO:0070252	0.50	actin-mediated cell contraction
GO:0045765	0.50	regulation of angiogenesis
GO:0045022	0.50	early endosome to late endosome transport
GO:0043534	0.50	blood vessel endothelial cell migration
GO:0034394	0.50	protein localization to cell surface
GO:0032147	0.50	activation of protein kinase activity
GO:0010594	0.50	regulation of endothelial cell migration
GO:0007566	0.50	embryo implantation
GO:0007160	0.50	cell-matrix adhesion
GO:0007015	0.50	actin filament organization
GO:0001913	0.50	T cell mediated cytotoxicity

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	0.86	membrane
GO:0005886	0.84	plasma membrane
GO:0044424	0.76	intracellular part
GO:0044425	0.72	membrane part
GO:0043226	0.64	organelle
GO:0043229	0.63	intracellular organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0044444	0.62	cytoplasmic part
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0005634	0.59	nucleus
GO:0044459	0.57	plasma membrane part
GO:0005737	0.55	cytoplasm
GO:0098590	0.50	plasma membrane region
GO:0031982	0.50	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	0.060	2wpnB	0.616	3.79	0.074	0.862	1.12.7.2	NA
2	0.060	1yfmA	0.560	4.24	0.048	0.844	4.2.1.2	NA
3	0.060	2pnrF	0.585	3.39	0.068	0.766	2.7.11.2	NA
4	0.060	1yqwR	0.629	3.75	0.040	0.868	1.12.2.1	152
5	0.060	2fonB	0.553	4.29	0.093	0.838	1.3.3.6	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.