D-I-TASSER Q9Y2H2-D3

D-I-TASSER results for Q9Y2H2-D3

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

Input Sequence in FASTA format

>Q9Y2H2 (148 residues)
SQERNQMTNQVSNETQSESTEQTPSRPSQLDVSLSATGPQFLSVEPAHSVASQKTPTSAS
SMLELETGLHVTPSPSESSSSRAVSPFAKIRSSMVQVASITQAGLTHGINFAVSKVQKSP
PEPEIINQVQQNELKKMFIQCQTRIIQI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| SQERNQMTNQVSNETQSESTEQTPSRPSQLDVSLSATGPQFLSVEPAHSVASQKTPTSASSMLELETGLHVTPSPSESSSSRAVSPFAKIRSSMVQVASITQAGLTHGINFAVSKVQKSPPEPEIINQVQQNELKKMFIQCQTRIIQI
Prediction	CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHSHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHSSCC
Confidence	9763211112031111355678999952145667888996242268753446888887555545566766799987788864337246654567766655443211342001000115888854323245789999999875421219
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| SQERNQMTNQVSNETQSESTEQTPSRPSQLDVSLSATGPQFLSVEPAHSVASQKTPTSASSMLELETGLHVTPSPSESSSSRAVSPFAKIRSSMVQVASITQAGLTHGINFAVSKVQKSPPEPEIINQVQQNELKKMFIQCQTRIIQI
Prediction	8754543355246645456477445444515152645434214144344344654454444334344434444444555444223213503431241241343323331421134146445547336525654145114404433376
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHSHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHSSCC
SQERNQMTNQVSNETQSESTEQTPSRPSQLDVSLSATGPQFLSVEPAHSVASQKTPTSASSMLELETGLHVTPSPSESSSSRAVSPFAKIRSSMVQVASITQAGLTHGINFAVSKVQKSPPEPEIINQVQQNELKKMFIQCQTRIIQI

2wv0D2

0.08

0.07

2.64

0.43

CEthreader

----------------------------PKMEQALQGLTSFTEDMKSRGMTPGDSTEELAAILGCGHPITRVRLANDIPMAIESSGELNESHFQSSIYDHIERYNSIPISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQN

4u6uB

0.09

3.36

0.57

EigenThreader

HQTTTLLRSSLIYVHMISQLQMMPLENIAANPNLATLQLIKSCENNVVSPNRQELLRYLSTNLTRDCLNLIKALYTLSPVDLFDTIDKVLSSKIQTTAQVLSKTSLDDAMENRNSILTLQNLMAACN--TLRNYLSQFWSKVTNSFKR

5zeyC

0.08

0.07

2.92

0.31

FFAS-3D

----------TKKSASSNNKVVATNRKARHNYTILDTYEAGIVLMGTEVKSLREGQASLADAFATVRNVHIAEYHHGTWTNHAPRRNRKLLLHRKQIDNLIGKIRDGNVELALARGKQAHDKRQDLRDAQREVIRELGRRAKGKI---

4k17A1

0.09

0.08

3.05

0.87

SPARKS-K

-----PRELESIKDVIGRKIKISVKKKVKLEVKGDRVENKVLVLTSCRFLLSARIPSKLELTVICHKPAQVVETEKCNSKVSP--------EDVSEVLAHIGTCLRRIFPLSPLRIKKVSEPSERLASLQALWDSQTLAEP-------

3j4qA

0.14

0.07

2.30

0.50

CNFpred

---------------------------------------YFLSIPITNKKITA--------------------------------GIKVLQNSILRQDNLTKAMVGGSFHITLLVMQ-------LLNEDEVNIGTDALLELKPFVEEI

1g8xA

0.06

0.05

2.03

0.83

DEthreader

-------------------RQVKANQRNPKFDGV------KRYYLLAPN--VPKATDAVLKIDPEQYFRAQL----------ARIEEAREQRLGSEQTKSDYLKRANELVQWINDKQALESRDFGVSFNAHKEYKTEKPPKGQEVSEE

1vt4I

0.03

1.73

1.21

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

5oacA1

0.09

0.08

3.13

0.56

MUSTER

PFMTSYSIRANQATDLVNLGNDVTR--LSMTNDVSNIPNAFTDVTLSSDRLDKNFNSNQLILEHSKCIEDSVRSHANEVDSYLIHEDIEIDSAKVHL-KMNPAKIRENTIYLVRSHF------QTSLEILQKAVAMEEKHQSADIAKV

2pffB

0.21

6.66

0.59

HHsearch

SLENNPMSNLTQEQVQVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLRKAKAPSGLDQALTFEDLKSKGLIPADAAALASLADVMSIESLVEVVFYRTQVAVPGRSNFSQEALQYVVERVEIVNYNVEGDLRALDTVTNLQKIDI

4eacA

0.04

2.09

0.39

CEthreader

LDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVDPPRPILGLPRIVSTITGSYGVRADRSTMREDNPKTFHEAAHLNGDVYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTNPGYIGRLKGLAEVRGV

(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	0.5078

(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	2j8sA3	0.51	4.69	0.015	0.777	model1_2j8sA3.pdb.gz
2	5tj3A1	0.50	4.58	0.059	0.797	model1_5tj3A1.pdb.gz
3	3mzkB	0.50	4.25	0.049	0.730	model1_3mzkB.pdb.gz
4	6ajfA	0.50	4.44	0.038	0.763	model1_6ajfA.pdb.gz
5	7k65A1	0.50	4.29	0.044	0.757	model1_7k65A1.pdb.gz
6	6mcaA	0.50	4.61	0.022	0.804	model1_6mcaA.pdb.gz
7	3jd8A	0.50	4.54	0.070	0.790	model1_3jd8A.pdb.gz
8	1dwfM	0.50	4.48	0.015	0.784	model1_1dwfM.pdb.gz
9	4el8A	0.49	4.71	0.035	0.818	model1_4el8A.pdb.gz
10	1l2aA	0.48	4.96	0.069	0.851	model1_1l2aA.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:0042803	1.00	protein homodimerization activity
GO:0016791	1.00	phosphatase activity
GO:0034596	0.77	phosphatidylinositol phosphate 4-phosphatase activity
GO:0052745	0.58	inositol phosphate phosphatase activity
GO:0052833	0.57	inositol monophosphate 4-phosphatase activity

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:0050794	1.00	regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:1902532	0.83	negative regulation of intracellular signal transduction
GO:0001933	0.83	negative regulation of protein phosphorylation
GO:0006810	0.80	transport
GO:0016192	0.77	vesicle-mediated transport
GO:0051049	0.76	regulation of transport
GO:0009987	0.76	cellular process
GO:2001135	0.75	regulation of endocytic recycling
GO:0072583	0.75	clathrin-mediated endocytosis
GO:0044699	0.74	single-organism process
GO:0008152	0.70	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0044238	0.67	primary metabolic process
GO:0044237	0.67	cellular metabolic process
GO:0044710	0.66	single-organism metabolic process
GO:0044255	0.62	cellular lipid metabolic process
GO:0048518	0.61	positive regulation of biological process
GO:0019637	0.61	organophosphate metabolic process
GO:0007165	0.61	signal transduction
GO:0006796	0.61	phosphate-containing compound metabolic process
GO:0050896	0.60	response to stimulus
GO:0048522	0.60	positive regulation of cellular process
GO:0046488	0.60	phosphatidylinositol metabolic process
GO:0051239	0.59	regulation of multicellular organismal process
GO:0035556	0.59	intracellular signal transduction
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0006950	0.59	response to stress
GO:2000026	0.58	regulation of multicellular organismal development
GO:0080135	0.58	regulation of cellular response to stress
GO:0060284	0.58	regulation of cell development
GO:0051241	0.58	negative regulation of multicellular organismal process
GO:0051129	0.58	negative regulation of cellular component organization
GO:0048015	0.58	phosphatidylinositol-mediated signaling
GO:0046856	0.58	phosphatidylinositol dephosphorylation
GO:0046434	0.58	organophosphate catabolic process
GO:0044242	0.58	cellular lipid catabolic process
GO:0031344	0.58	regulation of cell projection organization
GO:0023056	0.58	positive regulation of signaling
GO:0003008	0.58	system process
GO:2000145	0.57	regulation of cell motility
GO:0048681	0.57	negative regulation of axon regeneration
GO:0042518	0.57	negative regulation of tyrosine phosphorylation of Stat3 protein
GO:0031161	0.57	phosphatidylinositol catabolic process
GO:0014898	0.57	cardiac muscle hypertrophy in response to stress
GO:0001921	0.57	positive regulation of receptor recycling
GO:0051896	0.50	regulation of protein kinase B signaling

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:0055037	1.00	recycling endosome
GO:0045334	1.00	clathrin-coated endocytic vesicle
GO:0005769	1.00	early endosome
GO:0016020	0.84	membrane
GO:0044425	0.80	membrane part
GO:0005905	0.77	clathrin-coated pit
GO:0044446	0.59	intracellular organelle part
GO:0031090	0.51	organelle membrane
GO:0098588	0.50	bounding membrane of 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	2cerA	0.478	4.47	0.032	0.750	3.2.1.23	143
2	0.060	3f9mA	0.484	4.79	0.007	0.838	2.7.1.2	NA
3	0.060	2f6dA	0.481	4.96	0.064	0.784	3.2.1.3	35
4	0.060	1wdpA	0.474	5.04	0.076	0.831	3.2.1.2	NA
5	0.060	2a2zB	0.479	4.46	0.078	0.716	2.7.1.74	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	3goiA	0.481	4.71	0.008	0.824	0.28	GLC	complex1.pdb.gz	40,41,42,104,108,109,141
2	0.01	3a0iX	0.493	5.21	0.051	0.899	0.12	AJI	complex2.pdb.gz	100,101,104,107,108
3	0.01	2f6dA	0.481	4.96	0.064	0.784	0.18	ACR	complex3.pdb.gz	107,109,111
4	0.01	1oya0	0.478	4.26	0.072	0.757	0.14	III	complex4.pdb.gz	37,105,106,109,110,113,116
5	0.01	1v4sA	0.492	5.35	0.058	0.899	0.15	MRK	complex5.pdb.gz	100,101,115
6	0.01	1r3qA	0.491	4.65	0.094	0.824	0.13	1CP	complex6.pdb.gz	39,112,113,114
7	0.01	1r3wA	0.490	4.65	0.094	0.824	0.15	CP3	complex7.pdb.gz	38,40,110,112,116
8	0.01	1j930	0.492	4.84	0.028	0.851	0.11	III	complex8.pdb.gz	70,71,96,99,100,103,104,105,108,111,118
9	0.01	1bwlA	0.477	4.29	0.071	0.757	0.11	FMN	complex9.pdb.gz	108,109,110,139
10	0.01	1r3sA	0.490	4.64	0.094	0.824	0.11	1CP	complex10.pdb.gz	38,39,40,41,46,109,110

	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.