D-I-TASSER O00533-D8

D-I-TASSER results for O00533-D8

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

Input Sequence in FASTA format

>O00533 (97 residues)
PAAPDRNPQNIRVQASQPKEMIIKWEPLKSMEQNGPGLEYRVTWKPQGAPVEWEEETVTN
HTLRVMTPAVYAPYDVKVQAINQLGSGPDPQSVTLYS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PAAPDRNPQNIRVQASQPKEMIIKWEPLKSMEQNGPGLEYRVTWKPQGAPVEWEEETVTNHTLRVMTPAVYAPYDVKVQAINQLGSGPDPQSVTLYS
Prediction	CCCCCCCCCSSSSSSCCCCSSSSSSSCCCHHHCCCCCSSSSSSSSSCCCCCCSSSSSSCCCSSSSCCCCCCCSSSSSSSSSSCCCCCCCCCCSSSSC
Confidence	9899999921799956899899999679913289971569999997899864399980774899879889908999999991897198998666319
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PAAPDRNPQNIRVQASQPKEMIIKWEPLKSMEQNGPGLEYRVTWKPQGAPVEWEEETVTNHTLRVMTPAVYAPYDVKVQAINQLGSGPDPQSVTLYS
Prediction	8646744155042443444304035532446444152230202024546755145451753414056155524030201031434733426324437
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSSSCCCCSSSSSSSCCCHHHCCCCCSSSSSSSSSCCCCCCSSSSSSCCCSSSSCCCCCCCSSSSSSSSSSCCCCCCCCCCSSSSC
PAAPDRNPQNIRVQASQPKEMIIKWEPLKSMEQNGPGLEYRVTWKPQGAPVEWEEETVTNHTLRVMTPAVYAPYDVKVQAINQLGSGPDPQSVTLYS

1x5hA

0.21

6.57

1.50

DEthreader

SDVPSAAPQNLSLEVRNSKSIMIHWQPPAPATQNGQITGYKIRYRKASRKSDVTETLVSQLSQLIEGLDRGTEYNFRVAALTINGTGPATDWLSAET

5e55A3

0.21

6.56

1.54

SPARKS-K

-DEPQLAPRGTSVQSFSASEMEVSWNAIAWNRNTGRVLGYEVLYWTDKESMIGKIRVSGVTTKNITGLRANTIYFASVRAYNTAGTGPSSLPVNVTT

1uenA

0.19

6.01

0.39

MapAlign

EDLPMVAPGNVRVNVVNSTLAEVHWDPVPLKSIRGHLQGYRIYYWKTRRHIEKKILTFGKTHGMLPGLEPFSHYTLNVRVVNGKGEGPASPDRVFNT

1uenA

0.19

6.01

0.28

CEthreader

EDLPMVAPGNVRVNVVNSTLAEVHWDPVPLKSIRGHLQGYRIYYWKTQSSIEKKILTFQKTHGMLPGLEPFSHYTLNVRVVNGKGEGPASPDRVFNT

2ed9A

0.22

6.85

1.18

MUSTER

SDVPSAPPQNVSLEVVNSRSIKVSWLPPPSGTQNGFITGYKIRHRKTTRRGEMETLEPNNLWYLFTGLEKGSQYSFQVSAMTVNGTGPPSNWYTAET

4bk4A

0.16

0.15

5.14

0.85

HHsearch

QAAPS-SIALVQAKEVTRYSVALAWLEPD--RPNGVILEYEVKYYEKDQNRSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPLEVTT

5e55A2

0.28

8.52

1.81

FFAS-3D

ASVPNVAPGNINGGGGSRSELVITWEAIPEELQNGEGFGYIVMFRPVGTTAWMKERVASKFIYRNESIMPLSPFEVKVGVYNNEGEGSLSTVTIVYS

7ndgB3

0.26

7.94

0.45

EigenThreader

ELVPTSPPKDVTVVSGKPRTIIVNWQPPS--EANGKITGYIIYYSTDVNAEDWVIEPVVGLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRT

4n5uA

0.18

5.73

1.53

CNFpred

QSTPSAPPQKVMCVSMGSTTVRVSWVPPPADSRNGVITQYSVAYEAVDGRGRHVVDGISHSSWDLVGLEKWTEYRVWVRAHTDVGPGPESSPVLVRT

6xfiA

0.16

0.15

5.16

1.33

DEthreader

VGLYPGKVREARCQASVEARLTVSWQIPWLKYLKVREVKYEVWLQEQGE-NTYVPYILALQNHTFTNIKPFTTYLVWVRCIFNILLGPFADVLVCNT

(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	0.9042

(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	1x5hA	0.93	1.35	0.206	1.000	model1_1x5hA.pdb.gz
2	1uenA	0.91	1.32	0.186	1.000	model1_1uenA.pdb.gz
3	1va9A	0.90	1.41	0.227	1.000	model1_1va9A.pdb.gz
4	4yfeA	0.89	1.68	0.211	0.979	model1_4yfeA.pdb.gz
5	4pbxA	0.89	1.63	0.253	0.979	model1_4pbxA.pdb.gz
6	2ed9A	0.89	1.41	0.208	0.990	model1_2ed9A.pdb.gz
7	6tpwA3	0.89	1.35	0.183	0.959	model1_6tpwA3.pdb.gz
8	2dlhA	0.88	1.37	0.213	0.969	model1_2dlhA.pdb.gz
9	5e4sA	0.88	1.23	0.160	0.969	model1_5e4sA.pdb.gz
10	4n68A	0.88	1.16	0.161	0.959	model1_4n68A.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:0004872	0.76	receptor activity
GO:0099600	0.73	transmembrane receptor activity
GO:0038023	0.73	signaling receptor activity
GO:0004888	0.72	transmembrane signaling receptor activity
GO:0042802	0.70	identical protein binding
GO:0046983	0.68	protein dimerization activity
GO:0042803	0.65	protein homodimerization activity
GO:0008046	0.64	axon guidance receptor activity
GO:0003823	0.64	antigen 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	0.93	single-organism process
GO:0009987	0.92	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0032502	0.83	developmental process
GO:0048856	0.76	anatomical structure development
GO:0044767	0.76	single-organism developmental process
GO:0006928	0.74	movement of cell or subcellular component
GO:0051239	0.71	regulation of multicellular organismal process
GO:0060284	0.70	regulation of cell development
GO:0051960	0.70	regulation of nervous system development
GO:0045664	0.69	regulation of neuron differentiation
GO:0051128	0.67	regulation of cellular component organization
GO:0048869	0.66	cellular developmental process
GO:0048731	0.66	system development
GO:0010975	0.66	regulation of neuron projection development
GO:0007411	0.65	axon guidance
GO:0022603	0.64	regulation of anatomical structure morphogenesis
GO:0050770	0.63	regulation of axonogenesis
GO:0009653	0.63	anatomical structure morphogenesis
GO:0050896	0.62	response to stimulus
GO:0051179	0.61	localization
GO:0051234	0.59	establishment of localization
GO:1902578	0.58	single-organism localization
GO:0048675	0.58	axon extension
GO:0006810	0.57	transport
GO:0048513	0.56	animal organ development
GO:0044765	0.56	single-organism transport
GO:0010033	0.56	response to organic substance
GO:0050773	0.55	regulation of dendrite development
GO:0048468	0.55	cell development
GO:0007422	0.55	peripheral nervous system development
GO:0007413	0.55	axonal fasciculation
GO:0050974	0.54	detection of mechanical stimulus involved in sensory perception
GO:0048814	0.54	regulation of dendrite morphogenesis
GO:0048666	0.54	neuron development
GO:0016319	0.54	mushroom body development
GO:0006897	0.54	endocytosis
GO:0070593	0.53	dendrite self-avoidance
GO:0050976	0.53	detection of mechanical stimulus involved in sensory perception of touch
GO:0048846	0.53	axon extension involved in axon guidance
GO:0032490	0.53	detection of molecule of bacterial origin
GO:0021551	0.53	central nervous system morphogenesis
GO:0007419	0.53	ventral cord development
GO:0006909	0.53	phagocytosis

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	0.97	cell part
GO:0097458	0.78	neuron part
GO:0044425	0.77	membrane part
GO:0044459	0.71	plasma membrane part
GO:0042995	0.71	cell projection
GO:0031224	0.69	intrinsic component of membrane
GO:0043005	0.68	neuron projection
GO:0016021	0.67	integral component of membrane
GO:0031226	0.64	intrinsic component of plasma membrane
GO:0030424	0.64	axon
GO:0043025	0.62	neuronal cell body
GO:0005887	0.62	integral component of plasma membrane
GO:0030425	0.61	dendrite

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	0.300	2dlhA	0.884	1.37	0.213	0.969	3.1.3.48	32,41,77,88
2	0.166	1k85A	0.762	1.85	0.195	0.897	3.2.1.14	30
3	0.093	2dleA	0.719	2.55	0.067	0.897	3.1.3.48	63
4	0.067	2djmA	0.647	2.34	0.045	0.856	3.2.1.3	NA
5	0.067	2hvbB	0.645	3.14	0.088	0.907	1.15.1.2	20

	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	0.09	3d48R	0.811	1.92	0.198	0.928	0.51	CO3	complex1.pdb.gz	37,38,39,81,83
2	0.05	3besR	0.715	2.65	0.097	0.949	0.62	UUU	complex2.pdb.gz	36,38,82,84
3	0.04	2b5i6	0.809	2.06	0.149	0.969	0.85	III	complex3.pdb.gz	38,39,55,57,58,60,62,63,64,65,66,83
4	0.03	1ebpA	0.819	2.35	0.105	0.979	0.41	III	complex4.pdb.gz	37,38,39,85

	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.