D-I-TASSER Q96PB8-D1

D-I-TASSER results for Q96PB8-D1

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

Input Sequence in FASTA format

>Q96PB8 (197 residues)
MNLVDLWLTRSLSMCLLLQSFVLMILCFHSASMCPKGCLCSSSGGLNVTCSNANLKEIPR
DLPPETVLLYLDSNQITSIPNEIFKDLHQLRVLNLSKNGIEFIDEHAFKGVAETLQTLDL
SDNRIQSVHKNAFNNLKARARIANNPWHCDCTLQQVLRSMASNHETAHNVICKTSVLDEH
AGRPFLNAANDADLCNL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNLVDLWLTRSLSMCLLLQSFVLMILCFHSASMCPKGCLCSSSGGLNVTCSNANLKEIPRDLPPETVLLYLDSNQITSIPNEIFKDLHQLRVLNLSKNGIEFIDEHAFKGVAETLQTLDLSDNRIQSVHKNAFNNLKARARIANNPWHCDCTLQQVLRSMASNHETAHNVICKTSVLDEHAGRPFLNAANDADLCNL
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSSCCCCCCSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCSCCCCHHHHHHHHCCSSSCCCCCCCCCCCHHHCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCC
Confidence	97344220368999999999999999841368899964763899937985899987248999988639986889788359574668878988879999486428112233565237814789989865800222550105511877337686199999999857876566457888766698361225898467999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNLVDLWLTRSLSMCLLLQSFVLMILCFHSASMCPKGCLCSSSGGLNVTCSNANLKEIPRDLPPETVLLYLDSNQITSIPNEIFKDLHQLRVLNLSKNGIEFIDEHAFKGVAETLQTLDLSDNRIQSVHKNAFNNLKARARIANNPWHCDCTLQQVLRSMASNHETAHNVICKTSVLDEHAGRPFLNAANDADLCNL
Prediction	53334321131012122221320111114315413641313676434030443403211762254034030444304503550355044034030550304303630054016304402045030431264005604303204701020203013004303653653541425433356244230351365744057
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSSCCCCCCSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCSCCCCHHHHHHHHCCSSSCCCCCCCCCCCHHHCCCCCCCSCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCC
MNLVDLWLTRSLSMCLLLQSFVLMILCFHSASMCPKGCLCSSSGGLNVTCSNANLKEIPRDLPPETVLLYLDSNQITSIPNEIFKDLHQLRVLNLSKNGIEFIDEHAFKGVAETLQTLDLSDNRIQSVHKNAFNNLKARARIANNPWHCDCTLQQVLRSMASNHETAHNVICKTSVLDEHAGRPFLNAANDADLCNL

1p8tA

0.24

0.21

6.47

1.17

DEthreader

--------------------RNLTLALLLLHTLHLCLQ-----ALQYLYLQDNALQALPTFRLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLG-RLMTLYLFANNLSALPTEALAPLALQLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPCSL--PQRLAGRDLKRLAAN-DLQGC

4xsqA

0.34

0.27

8.21

2.23

SPARKS-K

---------------------------------CPSACKCTVLYGEVVACGG-GLTEIPEDIPHRAVYLVLKDNNITKITSYSFKGLRNLQGIDLSNNKINHISSAALRHLG-HLDDIDLSRNELTSVSEKLFDFPRFFVYLANNPWGCDCR-AWLAQELAGGSKTGDRHECATP--AALAGRGLSEIPQTSFVCTG

3g3bA

0.29

0.23

6.94

0.45

MapAlign

--------------------------------ACPSQCSCS---GTTVDCSGKSLASVPTGIPTTTQVLYLYDNRITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLT-QLTQLSLNDNQLKSIPRGAFDNLSLHIWLLNNPWDCCSDILYLSRWIPWLVFGHDSARCS------GTNTPVRAVT--KASTSP

1p8tA2

0.22

0.21

6.71

0.34

CEthreader

-------RSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLG-RLMTLYLFANNLSALPTEALAPLRQYLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPCSL--PQRLAGRDLKRLAANDLQGCA

3g3bA

0.32

0.25

7.50

1.92

MUSTER

--------------------------------ACPSQCSCS---GTTVDCSGKSLASVPTGIPTTTQVLYLYDNRITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLT-QLTQLSLNDNQLKSIPRGAFDNLRSHIWLLNNPWDCACSDILYLSRWISQHPDHDSARCSGT------NTPVRAVTKASTSCPG

5y31B

0.29

0.23

7.10

1.05

HHsearch

--------------------------------KCPAVCTCTKD---NALCENA--RSIPRTVPPDVILLLFTSNSFDVISDDAFIGLPHLEYLFIENNNIKSISRHTFRGLK-SLIHLSLANNNLQTLPKDIFKGLDTNVDLRGNSFNCDCKLKWLVEWLGHTNATVEDIYCEG--PPEYKKRKINSLSSKDFDCII

4xsqA

0.32

0.26

7.80

1.80

FFAS-3D

---------------------------------CPSACKCTVSLYGEVVACGGGLTEIPEDIPHRAVYLVLKDNNITKITSYSFKGLRNLQGIDLSNNKINHISSAALRHL-GHLDDIDLSRNELTSVSEKLFDFPISSVYLANNPWGCDCRAWLAQELAGGSKTFGDRHECATP--AALAGRGLSEIPQTSFVCT-

1w8aA

0.24

0.20

6.17

0.75

EigenThreader

--------------------------------DCPAMCTVDCLHTTELLLNDNELGRISFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLH-QLKTLNLYDNQISCVMPGSFEHLNSLTSLASNPFNCNCHLAWFAEWLRKKSLNGGAARCGAPSKV--RDVQIKDLPHSEFKCSS

4xsqA

0.34

0.27

8.22

3.15

CNFpred

---------------------------------CPSACKCTVSGEMVVACGGMGLTEIPEDIPHRAVYLVLKDNNITKITSYSFKGLRNLQGIDLSNNKINHISSAALRHLG-HLDDIDLSRNELTSVSEKLFDFPIFFVYLANNPWGCDCRMAWLAQELAGGSFGDRHMECATPA--ALAGRGLSEIPQTSFVCTG

4rcaB

0.22

0.19

5.92

1.17

DEthreader

--------------------PTSQFANFYNASLHMNLH-F-L-LVKRLHINNNKIKSFTFLGLDDLEYLQADFNLLRDIDPGAFQDLNKLEVLILNDNLISTLPANVFQYV--PITHLDLRGNRLKTLPYEVLEQIGIEILLEDNPWDCTCDLLSLKEWLENIPKLIGRVVCEA--PTRLQGKDLNETTE-QDLCP-

(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	0.7239

(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	1p8tA	0.79	3.01	0.217	0.909	model1_1p8tA.pdb.gz
2	2v70A	0.77	2.86	0.191	0.893	model1_2v70A.pdb.gz
3	4p8sA	0.77	3.38	0.181	0.914	model1_4p8sA.pdb.gz
4	4rcaB	0.77	3.15	0.176	0.898	model1_4rcaB.pdb.gz
5	2v9tB	0.77	2.83	0.212	0.873	model1_2v9tB.pdb.gz
6	4u7lA	0.76	3.37	0.196	0.924	model1_4u7lA.pdb.gz
7	2o6qA	0.76	3.16	0.189	0.893	model1_2o6qA.pdb.gz
8	5a5cA	0.76	3.02	0.214	0.888	model1_5a5cA.pdb.gz
9	4rcwA	0.76	3.21	0.160	0.898	model1_4rcwA.pdb.gz
10	4y61B	0.76	3.11	0.171	0.888	model1_4y61B.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:0098772	0.69	molecular function regulator
GO:0030234	0.68	enzyme regulator activity
GO:0097367	0.67	carbohydrate derivative binding
GO:0004857	0.67	enzyme inhibitor activity
GO:0019887	0.66	protein kinase regulator activity
GO:0019210	0.66	kinase inhibitor activity
GO:0005102	0.55	receptor binding
GO:1901681	0.51	sulfur compound binding
GO:0005539	0.51	glycosaminoglycan 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:0065007	0.89	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0009987	0.85	cellular process
GO:0044699	0.81	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0032502	0.74	developmental process
GO:0044767	0.73	single-organism developmental process
GO:0048583	0.67	regulation of response to stimulus
GO:0048519	0.66	negative regulation of biological process
GO:0048523	0.65	negative regulation of cellular process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0016043	0.65	cellular component organization
GO:0007165	0.65	signal transduction
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0023051	0.64	regulation of signaling
GO:0010646	0.64	regulation of cell communication
GO:0051246	0.63	regulation of protein metabolic process
GO:0009966	0.63	regulation of signal transduction
GO:0009653	0.63	anatomical structure morphogenesis
GO:0032268	0.62	regulation of cellular protein metabolic process
GO:1902531	0.61	regulation of intracellular signal transduction
GO:0050790	0.61	regulation of catalytic activity
GO:0009968	0.61	negative regulation of signal transduction
GO:0001932	0.61	regulation of protein phosphorylation
GO:0045936	0.60	negative regulation of phosphate metabolic process
GO:0045859	0.60	regulation of protein kinase activity
GO:0043086	0.60	negative regulation of catalytic activity
GO:0031400	0.60	negative regulation of protein modification process
GO:1904893	0.59	negative regulation of STAT cascade
GO:0046425	0.59	regulation of JAK-STAT cascade
GO:0033673	0.59	negative regulation of kinase activity
GO:0001933	0.59	negative regulation of protein phosphorylation
GO:0051239	0.54	regulation of multicellular organismal process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0051128	0.53	regulation of cellular component organization
GO:0048518	0.53	positive regulation of biological process
GO:0051960	0.51	regulation of nervous system development
GO:0045595	0.51	regulation of cell differentiation
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0050770	0.50	regulation of axonogenesis
GO:0007166	0.50	cell surface receptor signaling pathway

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:0016020	1.00	membrane
GO:0044464	0.97	cell part
GO:0044424	0.88	intracellular part
GO:0044425	0.76	membrane part
GO:0031224	0.75	intrinsic component of membrane
GO:0016021	0.74	integral component of membrane
GO:0005737	0.63	cytoplasm
GO:0005886	0.54	plasma membrane
GO:0043226	0.51	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	2o1dA	0.556	4.85	0.065	0.843	4.2.2.2	101,148
2	0.060	1czfA	0.521	5.04	0.056	0.838	3.2.1.15	NA
3	0.060	1airA	0.576	4.65	0.059	0.863	4.2.2.2	NA
4	0.060	1ogoX	0.550	4.97	0.054	0.868	3.2.1.11	99
5	0.060	1xg2A	0.516	5.09	0.040	0.812	3.1.1.11	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	0.09	3a79B	0.710	3.27	0.173	0.853	0.89	UUU	complex1.pdb.gz	119,121,141,143
2	0.08	3cigA	0.665	4.06	0.146	0.878	1.04	UUU	complex2.pdb.gz	94,96,97,119
3	0.04	2z81A	0.694	3.16	0.171	0.827	0.50	PCJ	complex3.pdb.gz	63,70,72,96,100,101,102,103,104,107
4	0.03	3a7cA	0.695	3.16	0.166	0.827	0.53	PDK	complex4.pdb.gz	78,99,124
5	0.03	1xec0	0.657	3.62	0.155	0.827	0.57	III	complex5.pdb.gz	36,37,39,50,52,53,54,72,73,97,122,141,143,167

	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.