D-I-TASSER Q86YS7-D1

D-I-TASSER results for Q86YS7-D1

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

Input Sequence in FASTA format

>Q86YS7 (231 residues)
MPGKLKVKIVAGRHLPVMDRASDLTDAFVEVKFGNTTFKTDVYLKSLNPQWNSEWFKFEV
DDEDLQDEPLQITVLDHDTYSANDAIGKVELCSDSLPSHPFPPAKAMTVEKASPVGDGNF
RNRSAPPCANSTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLREEGGVSGFLHAF
IAEVFAMVRAHVAALGGNAVVSYIMKQCVFMENPNKNQAQCLINVSGDAVV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPGKLKVKIVAGRHLPVMDRASDLTDAFVEVKFGNTTFKTDVYLKSLNPQWNSEWFKFEVDDEDLQDEPLQITVLDHDTYSANDAIGKVELCSDSLPSHPFPPAKAMTVEKASPVGDGNFRNRSAPPCANSTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLREEGGVSGFLHAFIAEVFAMVRAHVAALGGNAVVSYIMKQCVFMENPNKNQAQCLINVSGDAVV
Prediction	CCSSSSSSSSSSSCCCCCCCCCCCCCCSSSSSSCCSSSSSCCSCCCCCCCSCCCSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCCCCCHHHHHCCCCCSCCCSSSSSCCCCCCCCCCCCSSSCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCSSSSSSSSSSSSCCCCCCCSSSSSSSSSCCSSC
Confidence	974899999981189865578998485699998998887330138997942640899985402237977999998157899885236999743115656553100011013531575018614667654333212220236679995124563430456541335443358862578888998788888888560774366778754552389884327999875142419
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPGKLKVKIVAGRHLPVMDRASDLTDAFVEVKFGNTTFKTDVYLKSLNPQWNSEWFKFEVDDEDLQDEPLQITVLDHDTYSANDAIGKVELCSDSLPSHPFPPAKAMTVEKASPVGDGNFRNRSAPPCANSTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLREEGGVSGFLHAFIAEVFAMVRAHVAALGGNAVVSYIMKQCVFMENPNKNQAQCLINVSGDAVV
Prediction	764343020130564333234613000101020475534043255202041444203040437615733330301031434431200202020430344434223323255434235130324333343323333342342431462404412320423124424504754524220230034043202320342312001113133114235432110000010213026
	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                 100                 120                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCSSSSSSSSSSSCCCCCCCCCCCCCCSSSSSSCCSSSSSCCSCCCCCCCSCCCSSSSSSCCCCCCCCSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCCCCCHHHHHCCCCCSCCCSSSSSCCCCCCCCCCCCSSSCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCSSSSSSSSSSSSCCCCCCCSSSSSSSSSCCSSC
MPGKLKVKIVAGRHLPVMDRASDLTDAFVEVKFGNTTFKTDVYLKSLNPQWNSEWFKFEVDDEDLQDEPLQITVLDHDTYSANDAIGKVELCSDSLPSHPFPPAKAMTVEKASPVGDGNFRNRSAPPCANSTVGVVKMTPLSFIPGAKITKYLGIINMFFIRETTSLREEGGVSGFLHAFIAEVFAMVRAHVAALGGNAVVSYIMKQCVFMENPNKNQAQCLINVSGDAVV

5ue8A

0.15

0.10

3.19

0.83

DEthreader

WSAKISITVVCAQGLQ-A-G---SSDPYVTVQVGKTKKRTKTIYGNLNPVWEEN-FHFECH--N-SSDRIKVRVWDE----SDDFLGQTIIEVRTLS---------GEMDVWYNLD--KS---------G--AI-RL-HISVE--------K-APHVQTIYQAM---------------STLLANINFAASN-------GKERVKLLLDL---------------------

3hn8A

0.22

0.19

5.88

1.72

SPARKS-K

GSDQLVVRILQALDLPAKDS-NGFSDPYVKIYLLPKKFQTKVHRKTLNPIFNETFQFS-VPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDLELAEQPPDR-------PLWRDILEGGS---------EKADLGELNFSLCYLPTA------GLLTVT-IIKASNLKAMDLTG--------FSDPYVKASLISEG-RRLKKRKTSIKKNTLNPTYNEALVFDVAPESVEN

4p42A

0.14

0.12

3.97

0.92

MapAlign

PKGVLRIHFIEAQDLQGKDTYLKKSDPYGIIRVGNQIFQSRVIKENLSPKWNE-VYEALVYE--HPGQELEIELFDED-PDKDDFLGSLMIDLIEVEKERLL-------DEWFTLDEV-------------PKGKLHLRLEWLTLLTDIGLSSALLILYL-DSARNLPS-----------SSNPNPVVQMSVG------HKAQESKIRYKTNEPVWEENFTFFIHNPKRQ-

3hn8A

0.21

0.18

5.77

0.51

CEthreader

GSDQLVVRILQALDLPAKD-SNGFSDPYVKIYLLKKKFQTKVHRKTLNPIFN-ETFQFSVPLAELAQRKLHFSVYDFDRFSRHDLIGQVVLDNLLELA-----EQPPDRPLWRDILEG----------------GSEKADLGELNFSLCYLPTAGLLTVTIIKASNLKAMDL--------TGFSDPYVKASLI-SEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVEN

4v29A

0.25

0.17

5.38

1.27

MUSTER

LLGLLRIRIKRGVNLAVRD--ISSSDPYVVVKMGKQKLKTRVINKDVNPEWN-EDLTLSVTDSN---LTVLLTVYDHDMFSKDDKMGDAEFEIKPYIEALRMQLDGLPSGTIVTTVKPSRRNCLAEESRVTWVDGKLVQDLVLRLRHVEC---GEVEAQLQWI-----DLPGSKGL-------------------------------------------------------

4p42A

0.14

0.11

3.85

2.00

HHsearch

PKGVLRIHFIEAQDLQGKDTYKGKSDPYGIIRVGNQIFQSRVIKENLSPKWNEV-YEALVY--EHPGQELEIELFDEDP-DKDDFLGSLMIDLIEVEKER-------LLDEWFTLDEV--------------PKGKLHLRLEWLTLMPNGLSSALLILY-LDSARNLPS-SSNPN----------PVVQMSV------GHKAQESKIRYKTNEPVWEENFTFFIHNPKQDL

2dmhA

0.22

0.12

3.83

1.53

FFAS-3D

-SGMLRVIVESASNIPKTK--FGKPDPIVSVIFKDEKKKTKKVDNELNPVWNEILEFDLRGIPLDFSSSLGIIVKDFETIGQNKLIGTATVALKDLTGDQSRSLPYKLISLLNEKGQIDLVIGYDPPSGPSS---------------------------------------------------------------------------------------------------

4npjA

0.09

0.07

2.79

0.82

EigenThreader

KGVLRIHFIEAQDLQTYLKGLVKGKSDPYGIRVGNQIFQSRVIKENLSPKWN--EVYEALEH----PGQELEIELFDEDPDKDDFLGSLMIDLIEVEKERDEVPK--GLMPNASNLDKVLTDIKADKDQANDGLSS--------------ALLILYLDSARNLPSGN------------------PNPVVQMS---VGHKAQESKIR---YKTNEPVWEENFTFFIHNPKR

2r83A

0.21

0.18

5.76

2.76

CNFpred

QNNQLLVGIIQAAELPALDM-GGTSDPYVKVFLL-KKFETKVHRKTLNPVFNE-QFTFKVPYSELAGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFG-------HVTEEWRDLQSAEKEEQE--------KLGDICFSLRYVPT------AGKLTVV-ILEAKNLKKMDVGG--------LSDPYVKIHLMQN-GKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQK

6ewgA

0.11

0.06

2.35

0.83

DEthreader

DMFVLSVTVAFATKLELVSTMKSASEFFFYYSLLGNDITSEPFHNLLPDFEPERASVRISLKAFLSQQSLQIHLCCG-----NHSLGSTDVSLSALGISDLDNKAATVEGAF-ILQ-PPKRVKQTATDLQP-TL-GV-AVTLR-EVA-LQ---------------------------------------------------------------------------------

(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	0.6299

(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	5ue8A	0.52	3.83	0.154	0.645	model1_5ue8A.pdb.gz
2	4npjA	0.50	3.39	0.129	0.597	model1_4npjA.pdb.gz
3	4rj9A	0.49	2.38	0.267	0.550	model1_4rj9A.pdb.gz
4	6ewgA	0.49	2.86	0.138	0.580	model1_6ewgA.pdb.gz
5	4v29A	0.49	2.43	0.265	0.550	model1_4v29A.pdb.gz
6	3l4cB	0.49	3.21	0.126	0.584	model1_3l4cB.pdb.gz
7	2dmhA	0.48	2.92	0.194	0.563	model1_2dmhA.pdb.gz
8	1cjyA	0.47	2.28	0.108	0.524	model1_1cjyA.pdb.gz
9	2ep6A	0.47	2.50	0.268	0.532	model1_2ep6A.pdb.gz
10	1djiB4	0.47	2.31	0.256	0.524	model1_1djiB4.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:0005543	0.89	phospholipid binding
GO:0005509	0.87	calcium ion binding
GO:0005544	0.86	calcium-dependent phospholipid binding
GO:0000149	0.61	SNARE binding
GO:0030276	0.52	clathrin binding
GO:0019905	0.52	syntaxin 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	0.95	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0009987	0.90	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0006810	0.82	transport
GO:1902578	0.80	single-organism localization
GO:0051649	0.80	establishment of localization in cell
GO:0051641	0.79	cellular localization
GO:0032940	0.79	secretion by cell
GO:0032879	0.79	regulation of localization
GO:0060627	0.78	regulation of vesicle-mediated transport
GO:0016192	0.78	vesicle-mediated transport
GO:0016043	0.78	cellular component organization
GO:1902580	0.77	single-organism cellular localization
GO:0099643	0.77	signal release from synapse
GO:0099531	0.77	presynaptic process involved in chemical synaptic transmission
GO:0099003	0.76	vesicle mediated transport in synapse
GO:0048489	0.76	synaptic vesicle transport
GO:0044802	0.75	single-organism membrane organization
GO:0017158	0.75	regulation of calcium ion-dependent exocytosis
GO:0045055	0.72	regulated exocytosis
GO:0016079	0.71	synaptic vesicle exocytosis
GO:0006996	0.70	organelle organization
GO:1902589	0.69	single-organism organelle organization
GO:0048791	0.68	calcium ion-regulated exocytosis of neurotransmitter
GO:0006906	0.68	vesicle fusion

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:0044424	1.00	intracellular part
GO:0016020	0.93	membrane
GO:0005886	0.84	plasma membrane
GO:0043227	0.81	membrane-bounded organelle
GO:0044444	0.76	cytoplasmic part
GO:0043229	0.68	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044446	0.50	intracellular organelle part

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	2x38A	0.443	3.22	0.057	0.541	2.7.1.153	116
2	0.060	1ffuB	0.431	5.89	0.075	0.753	1.2.99.2	NA
3	0.060	3hi7A	0.436	5.20	0.026	0.701	1.4.3.22	NA
4	0.060	3b9jI	0.239	5.37	0.023	0.390	1.17.1.4 1.17.3.2	12,15,44
5	0.060	1jrpB	0.437	5.47	0.058	0.732	1.17.1.4	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	0.12	1tjxA	0.451	2.12	0.300	0.498	0.44	CA	complex1.pdb.gz	115,116,117
2	0.03	1a250	0.445	2.06	0.265	0.489	0.71	III	complex2.pdb.gz	14,15,16,17,18,19,78
3	0.01	2x38A	0.443	3.22	0.057	0.541	0.47	IC8	complex3.pdb.gz	74,75,88,115,133,134,135
4	0.01	3pfqA	0.305	6.68	0.039	0.602	0.66	ANP	complex4.pdb.gz	87,89,116,117,118

	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.