D-I-TASSER Q9Y265-D1

D-I-TASSER results for Q9Y265-D1

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

Input Sequence in FASTA format

>Q9Y265 (260 residues)
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK
MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI
GLRIKEEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKY
IDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITS
PHGIPLDLLDRVMIIRTMLY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKEEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLY
Prediction	CSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSSCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCSSSCCCSSSSSCCHHHHHHHHHHHHHHHCCCCCCSSSSSCCCCSSSSCCCCCCCCCCCCCHHHHHSSSSSSCCCC
Confidence	91432024651102434333211366855665534123457799999999999999756778967998589997489999999996289986266324311001113378999999874665541112238998656601234677742234444311455432304567788999999997097353288289843102236899999998616788489996166314653788755777899756412689965689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKEEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLY
Prediction	75155247454542333343232332366543433052002044025103100410454641120000102431011100200032244713023030343343415413302420440243434540203030320212214454243134323432446445345523540352055027552251141001013011000300210130144610000000022332414437414102102342031002032458
	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                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCSSSSSSSSSCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCSSSCCCSSSSSCCHHHHHHHHHHHHHHHCCCCCCSSSSSCCCCSSSSCCCCCCCCCCCCCHHHHHSSSSSSCCCC
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKEEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLY

4wvyA2

0.51

0.37

10.58

1.00

DEthreader

---------D--TA-HT-HIKG-LGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGT-KI----------------------------------------PFCPITGSEIYST-E----------------VKKTEVLMENFRLHRMINKVVQIELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIADDL--KAAHGIPPDFLQRLLIIPTHPY

4wvyA2

0.72

0.70

19.87

1.82

SPARKS-K

--ISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVREI-VQDVTLHDLDVANARPII-----SMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

4wvyA

0.64

0.50

14.18

0.84

MapAlign

----------------AHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKI-----------------------------------------PFCPITGSEILKSARGQKGEVHGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

4wvyA

0.72

0.70

19.87

0.66

CEthreader

--ISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRKEIVQDVTLHDLDVANA-----RPIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

4wvyA2

0.73

0.71

20.08

1.65

MUSTER

--ISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRE-IVQDVTLHDLDVANARP-----IISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

4wvyA

0.72

0.70

19.87

1.73

HHsearch

--ISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRETKVQDVTLHDLDVANARPII-----SMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

6etxB3

0.50

0.47

13.61

2.78

FFAS-3D

-------DVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEE--VVHTVSLHEIDVINSRTQGFLALF-----SGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGT-SYQSPHGIPIDLLDRLLIVSTTPY

2c9oA

0.74

0.60

16.90

0.70

EigenThreader

TTKTQRIAS--------HSHVKGLGLDESGLAK--QAASGLQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSK----------------------------------------VPFCPMVGSEVYSTEIPSIFESLQKEEANSGADVTLHDLDVAINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLY

2xszA

1.00

0.90

25.09

2.09

CNFpred

----EVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRI----IQDVTLHDLDVANAR-------------------TEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLY

4wvyA

0.52

0.38

10.90

1.00

DEthreader

---------D--TA-HT-HIKG-LGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGT-KI----------------------------------------PFCPITGSEIYST-E----------------VKKTEVLMENFRLHRMINKVVQIELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPY

(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	0.6883

(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	4wvyA	0.89	2.26	0.690	0.962	model1_4wvyA.pdb.gz
2	6gejT	0.83	2.44	0.736	0.942	model1_6gejT.pdb.gz
3	2c9oA	0.82	1.67	0.991	0.854	model1_2c9oA.pdb.gz
4	6gejU	0.82	2.68	0.517	0.927	model1_6gejU.pdb.gz
5	4wvyB	0.82	1.87	0.552	0.885	model1_4wvyB.pdb.gz
6	7oleB	0.82	1.43	0.549	0.862	model1_7oleB.pdb.gz
7	2xszD	0.79	0.88	0.573	0.811	model1_2xszD.pdb.gz
8	5mrcWW	0.56	5.27	0.100	0.827	model1_5mrcWW.pdb.gz
9	7mhbA	0.55	3.76	0.165	0.673	model1_7mhbA.pdb.gz
10	7nkuA	0.54	2.90	0.234	0.642	model1_7nkuA.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:0016887	0.99	ATPase activity
GO:0042623	0.98	ATPase activity, coupled
GO:0004003	0.82	ATP-dependent DNA helicase activity
GO:0005524	0.79	ATP binding
GO:0043141	0.71	ATP-dependent 5'-3' DNA helicase activity
GO:0008134	0.64	transcription factor binding
GO:0003682	0.61	chromatin binding
GO:0051117	0.60	ATPase binding
GO:0051082	0.60	unfolded protein binding
GO:0043531	0.60	ADP binding
GO:0042803	0.60	protein homodimerization activity
GO:0031490	0.60	chromatin DNA binding
GO:0001094	0.60	TFIID-class transcription factor binding
GO:0000980	0.60	RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000979	0.60	RNA polymerase II core promoter sequence-specific DNA 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:0009987	0.97	cellular process
GO:0044238	0.95	primary metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0016043	0.95	cellular component organization
GO:0019538	0.93	protein metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044260	0.91	cellular macromolecule metabolic process
GO:0065007	0.88	biological regulation
GO:0051716	0.88	cellular response to stimulus
GO:0050789	0.88	regulation of biological process
GO:0043933	0.88	macromolecular complex subunit organization
GO:0006950	0.88	response to stress
GO:0006259	0.88	DNA metabolic process
GO:0006325	0.87	chromatin organization
GO:0006281	0.87	DNA repair
GO:0044267	0.85	cellular protein metabolic process
GO:0006996	0.85	organelle organization
GO:0050794	0.84	regulation of cellular process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0006464	0.83	cellular protein modification process
GO:0060255	0.82	regulation of macromolecule metabolic process
GO:0016573	0.82	histone acetylation
GO:0006357	0.81	regulation of transcription from RNA polymerase II promoter
GO:0032508	0.79	DNA duplex unwinding
GO:0016568	0.79	chromatin modification
GO:0048518	0.75	positive regulation of biological process
GO:1904874	0.71	positive regulation of telomerase RNA localization to Cajal body
GO:0043968	0.71	histone H2A acetylation
GO:0043967	0.71	histone H4 acetylation
GO:0040008	0.71	regulation of growth
GO:0006310	0.71	DNA recombination
GO:0048522	0.66	positive regulation of cellular process
GO:0051130	0.65	positive regulation of cellular component organization
GO:0045944	0.65	positive regulation of transcription from RNA polymerase II promoter
GO:0051234	0.63	establishment of localization
GO:0045184	0.62	establishment of protein localization
GO:1902275	0.61	regulation of chromatin organization
GO:0072594	0.61	establishment of protein localization to organelle
GO:0051246	0.61	regulation of protein metabolic process
GO:0010638	0.61	positive regulation of organelle organization
GO:0009416	0.61	response to light stimulus
GO:0071899	0.60	negative regulation of estrogen receptor binding
GO:0071733	0.60	transcriptional activation by promoter-enhancer looping
GO:0071392	0.60	cellular response to estradiol stimulus
GO:0071169	0.60	establishment of protein localization to chromatin
GO:0035066	0.60	positive regulation of histone acetylation
GO:0034644	0.60	cellular response to UV
GO:0006457	0.60	protein folding
GO:0065003	0.59	macromolecular complex assembly
GO:0034622	0.56	cellular macromolecular complex assembly
GO:0006338	0.56	chromatin remodeling

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044446	0.84	intracellular organelle part
GO:0044428	0.72	nuclear part
GO:0043234	0.71	protein complex
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005634	0.63	nucleus
GO:0044427	0.53	chromosomal part
GO:0005737	0.52	cytoplasm
GO:1902494	0.51	catalytic complex
GO:0097346	0.51	INO80-type complex
GO:0044454	0.51	nuclear chromosome part
GO:0044444	0.51	cytoplasmic part
GO:0035267	0.50	NuA4 histone acetyltransferase complex
GO:0031011	0.50	Ino80 complex
GO:0000812	0.50	Swr1 complex

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	3glfG	0.492	3.15	0.226	0.581	2.7.7.7	NA
2	0.060	2c9oA	0.823	1.67	0.991	0.854	3.6.4.12	239
3	0.060	1t64A	0.386	5.33	0.044	0.600	3.5.1.98	NA
4	0.060	1zyzA	0.485	5.36	0.036	0.742	1.17.4.1	NA
5	0.060	2cvtA	0.478	5.33	0.049	0.739	1.17.4.1	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:

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
	1	0.95	2c9oA	0.823	1.67	0.991	0.854	1.22	ADP	complex1.pdb.gz	17,18,20,38,39,40,72,73,74,75,76,77,78,260
	2	0.07	1ofhC	0.529	3.42	0.167	0.638	1.17	PO4	complex2.pdb.gz	71,72,73,76

	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.