D-I-TASSER Q5TAA0-D4

D-I-TASSER results for Q5TAA0-D4

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

Input Sequence in FASTA format

>Q5TAA0 (260 residues)
KQDMAIGTCNMALDVLRDPELNWQAYCTRAKIHIRAYLHDLKRAKMGLGGMPDRNHLACA
KADLEEVVRVCPGFKAYLDIGQVYYYMGVDAVQELLAVDEAALNQALVFLAKAGESELGA
TLPELQLLRGKCLRIKGEDANAAACFKRAVELDDAGSSHTDGFGCLLEALLAQWSQAQLS
DGELGREVDAWLRRAQDKYPAARLRQELQRVWRGHTDEVLGLARALVAQGRPALVRLLFE
TMEREGEGASAPRDRRAVSF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| KQDMAIGTCNMALDVLRDPELNWQAYCTRAKIHIRAYLHDLKRAKMGLGGMPDRNHLACAKADLEEVVRVCPGFKAYLDIGQVYYYMGVDAVQELLAVDEAALNQALVFLAKAGESELGATLPELQLLRGKCLRIKGEDANAAACFKRAVELDDAGSSHTDGFGCLLEALLAQWSQAQLSDGELGREVDAWLRRAQDKYPAARLRQELQRVWRGHTDEVLGLARALVAQGRPALVRLLFETMEREGEGASAPRDRRAVSF
Prediction	CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Confidence	74889999999998587467889999999999999999999986620357972889999999999999708528999999999999720378888873288999999999998725877665899987334999836569999999999960878724677898999999999824678889999999999999988522355789999998745699999999999808679999999998750466665421012469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| KQDMAIGTCNMALDVLRDPELNWQAYCTRAKIHIRAYLHDLKRAKMGLGGMPDRNHLACAKADLEEVVRVCPGFKAYLDIGQVYYYMGVDAVQELLAVDEAALNQALVFLAKAGESELGATLPELQLLRGKCLRIKGEDANAAACFKRAVELDDAGSSHTDGFGCLLEALLAQWSQAQLSDGELGREVDAWLRRAQDKYPAARLRQELQRVWRGHTDEVLGLARALVAQGRPALVRLLFETMEREGEGASAPRDRRAVSF
Prediction	83630251042015124534331301123030203302531550554464244462055035214401522520411230030013012422442342345303400420340161545422340131313014444536501500440152357434214101000100011124642534200310140055047414465035202301242242014004301653314003200400355565554435433256
	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

CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
KQDMAIGTCNMALDVLRDPELNWQAYCTRAKIHIRAYLHDLKRAKMGLGGMPDRNHLACAKADLEEVVRVCPGFKAYLDIGQVYYYMGVDAVQELLAVDEAALNQALVFLAKAGESELGATLPELQLLRGKCLRIKGEDANAAACFKRAVELDDAGSSHTDGFGCLLEALLAQWSQAQLSDGELGREVDAWLRRAQDKYPAARLRQELQRVWRGHTDEVLGLARALVAQGRPALVRLLFETMEREGEGASAPRDRRAVSF

4a1sA

0.09

0.08

3.07

1.33

DEthreader

DYNKAMQYHKHDLTLANDRLGEAKSSGNLGNTLKVMG------------------RFDEAAICCERHLTLAREGRALYNLGNVYHAKGLGQRNPKFGDVKEALTRAVEFYQENLKLMDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIARDAERRANSNLGNSHIFLGQFEDAAEHYKRTLAAEQSCYSLGNTYTLLHEFNTAIEYHRAIADIGEARACWSLGNASALKYAEQHLQL-A----------GGGGGGG

2vq2A

0.15

0.11

3.78

1.29

SPARKS-K

DYRQATASIEDALKSDPKN---ELAWLVRAEIYQYL------------------KVNDKAQESFRQALSIKPSAEINNNYGWFLCG------------RLNRPAESMAYFDKALA-DPTYTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQP-QFPPAFKELARTKMLAGQLGDADYYFKKYQSRVE-----------------------VLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYSE--ELQTVLT-

6af0A

0.11

3.90

0.71

MapAlign

-IDFAIEMLLRGANVLGNQREKLGIITCICWLYLWKSREAPRVAVPASEAKTKEYYLQLATQSLNDASRINPAFPLFLARGVLILLKASLQPSSKADNKAEQLRNALKSFEEAIRV-SQGRNMLAVMGKARALFSLGRYPESLAAYQDVVAKMPDMVDPPRIGIGCCFWQLGFKDDAKIAWERCLEANILLGLYYLDASGHRLYKKAMTYTDKNLPLTCATFAGYFLSRKQFGNVDALAHKAIQYTNAIASDGWYLLARK

3sf4A

0.11

0.10

3.73

0.43

CEthreader

DYAKALEYHHHDLTLAGDQLGEAKASGNLGNTLKVL------------------GNFDEAIVCCQRHLDISREARALYNLGNVYHAKGKSFGGEFPEEVRDALQAAVDFYEENLSLVTALAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGRRAYSNLGNAYIFLGEFETASEYLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARL

2q7fA

0.16

0.12

3.85

1.09

MUSTER

----AAEAFTKAIEENKED---AIPYINFANLLSSV------------------NELERALAFYDKALELDSSATAYYGAGNVYVVKE-------------MYKEAKDMFEKALRAGMEN--GDLFYMLGTVLVKLEQPKLALPYLQRAVELNEND-TEARFQFGMCLANEGMLDEALSQFAAVTEQ-------------------------PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL--

6af0A

0.13

4.41

0.77

HHsearch

KIDFAIEMLLRGANVLQGNQRELGIITCICWLYLWKSRATSRINPAFPPLFARAEQLRNALKSFEEAIRSQGRNLAVMGKARALFSLGRYPGIGCCFWQLGFKDDAKIAWERCLEINPDS--KHANILLGLYYLDASLYKKAMTYTQKSFKLDK-NLPLTCATFAGYFLSRKQFGNVDALAHKAIVNADGWYLLARKEHYDGNLERASDYYRGGYLPAKFGAAQLSVLKNDLGEAKLRLEKMIQ-HSKNYEAMILLGTLY

3iegA

0.13

0.12

4.14

2.10

FFAS-3D

QLADALSQFHAAVDGDPDNY---IAYYRRATVFQGKLDEAEDDFKKVLKSNPSGADYTAAITFLDKILEVCVWAELRELRAECFIKEG-------------EPRKAISDLKAASKLKSDN--TEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYK-QVKKLNKLIESAEELIRDATSKYRSKERICHCFSKDEKPVEAIRICSEDNVNALKDRAEAYLI-EEYDEAIQDYEAAQEHNENDQQIREGLEKAQ

4a1sA

0.16

0.14

4.60

0.73

EigenThreader

RFDEAAICCERHLTLARDRLSEGRALYNLGNVYHAKGKHLGQRNP-GKFGDDVKEALTRAVEFYQENLKLMAQGRACGNLGNTYYLLGD-------------FQAAIEHHQERLRIAREFGDRRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELG---------------------DEARACWSLGNAHSAIGGHERALKYAEQHLQLAGGGGGGGGGGGGGG

6eouA

0.15

0.14

4.82

1.35

CNFpred

RLDRSAHFSTLAIKQN---PLLAEAYSNLGNVAIEHYRHAFIDGYINLAAALAAGDMEGAVQAYVSALQYNPLYCVRSDLGNLLKALGRL-NLGCVFNAQGEIWLAIHHFEKAVTLDPN--FLDAYINLGNVLKEARIFDRAVAAYLRALSFSP-NHAVVHGNLACVYYEQGLIDLAIDTYRRAIHFPDAYCNLANALKEKGSVAEAEDCYNTAHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVL

3sf4A

0.10

0.08

3.16

1.17

DEthreader

DYAKALEYHHHDLTLAGDQLGEAKASGNLGNTLKVLG------------------NFDEAIVCCQRHLDISREARALYNLGNVYHAKGKSF-GGEFPEVRDALQAAVDFYEENLSLVDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKDAERRAYSNLGNAYIFLGEFETASEYYKKTLLAEQSCYSLGNTYTLQYEAIDYHLKHAIALDIGEGRACWSLGNTAFAEKHLEISRE-V-----------G-DKSG

(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	0.7792

(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	4a1sA	0.81	2.09	0.103	0.896	model1_4a1sA.pdb.gz
2	3sf4A	0.80	2.47	0.110	0.908	model1_3sf4A.pdb.gz
3	5dseA	0.79	2.35	0.154	0.892	model1_5dseA.pdb.gz
4	6af0A	0.76	3.58	0.109	0.946	model1_6af0A.pdb.gz
5	1w3bA	0.74	2.35	0.132	0.842	model1_1w3bA.pdb.gz
6	4bujB	0.73	3.42	0.102	0.904	model1_4bujB.pdb.gz
7	5c6gA	0.73	3.10	0.073	0.900	model1_5c6gA.pdb.gz
8	3q15A	0.72	3.57	0.050	0.923	model1_3q15A.pdb.gz
9	2fi7A	0.65	3.36	0.126	0.777	model1_2fi7A.pdb.gz
10	3pe3A	0.61	3.22	0.141	0.727	model1_3pe3A.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:0030234	0.74	enzyme regulator activity
GO:0019899	0.70	enzyme binding
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0051787	0.51	misfolded protein binding
GO:0051087	0.51	chaperone binding
GO:0019901	0.51	protein kinase binding
GO:0004860	0.51	protein kinase inhibitor activity
GO:0003824	0.50	catalytic 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:0009987	0.86	cellular process
GO:0071704	0.85	organic substance metabolic process
GO:0044238	0.84	primary metabolic process
GO:0043170	0.84	macromolecule metabolic process
GO:0050794	0.80	regulation of cellular process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0080090	0.76	regulation of primary metabolic process
GO:0060255	0.76	regulation of macromolecule metabolic process
GO:0019538	0.76	protein metabolic process
GO:2000112	0.75	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.75	regulation of nitrogen compound metabolic process
GO:0050896	0.75	response to stimulus
GO:0048523	0.75	negative regulation of cellular process
GO:0031325	0.75	positive regulation of cellular metabolic process
GO:0010604	0.75	positive regulation of macromolecule metabolic process
GO:0007165	0.75	signal transduction
GO:0001932	0.75	regulation of protein phosphorylation
GO:0080135	0.74	regulation of cellular response to stress
GO:0060548	0.74	negative regulation of cell death
GO:0051173	0.74	positive regulation of nitrogen compound metabolic process
GO:0045936	0.74	negative regulation of phosphate metabolic process
GO:0032270	0.74	positive regulation of cellular protein metabolic process
GO:0031328	0.74	positive regulation of cellular biosynthetic process
GO:0010557	0.74	positive regulation of macromolecule biosynthetic process
GO:0010468	0.74	regulation of gene expression
GO:0051716	0.73	cellular response to stimulus
GO:0048585	0.73	negative regulation of response to stimulus
GO:0010628	0.73	positive regulation of gene expression
GO:0001933	0.73	negative regulation of protein phosphorylation
GO:0050790	0.72	regulation of catalytic activity
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0051179	0.64	localization
GO:0051641	0.61	cellular localization
GO:0051234	0.59	establishment of localization
GO:0044699	0.57	single-organism process
GO:0051649	0.56	establishment of localization in cell
GO:0009628	0.53	response to abiotic stimulus
GO:0006950	0.53	response to stress
GO:0051338	0.52	regulation of transferase activity
GO:0044763	0.52	single-organism cellular process
GO:0043086	0.52	negative regulation of catalytic activity
GO:0043069	0.52	negative regulation of programmed cell death
GO:1903912	0.51	negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation
GO:0070417	0.51	cellular response to cold
GO:0051603	0.51	proteolysis involved in cellular protein catabolic process
GO:0043066	0.51	negative regulation of apoptotic process
GO:0036494	0.51	positive regulation of translation initiation in response to endoplasmic reticulum stress
GO:0030968	0.51	endoplasmic reticulum unfolded protein response
GO:0006469	0.51	negative regulation of protein kinase activity
GO:0048856	0.50	anatomical structure development
GO:0044767	0.50	single-organism developmental process
GO:0006464	0.50	cellular protein modification process

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:0044444	1.00	cytoplasmic part
GO:0044446	0.97	intracellular organelle part
GO:0043226	0.96	organelle
GO:0043229	0.95	intracellular organelle
GO:0016020	0.93	membrane
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0005737	0.86	cytoplasm
GO:0044425	0.84	membrane part
GO:0043234	0.75	protein complex
GO:0005829	0.75	cytosol
GO:0031988	0.65	membrane-bounded vesicle
GO:0098796	0.55	membrane protein complex
GO:0044428	0.55	nuclear part
GO:0005634	0.55	nucleus
GO:0070062	0.52	extracellular exosome
GO:0044432	0.52	endoplasmic reticulum part
GO:0031205	0.51	endoplasmic reticulum Sec complex
GO:0005788	0.51	endoplasmic reticulum lumen
GO:0005783	0.51	endoplasmic reticulum
GO:0005654	0.50	nucleoplasm

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	1fo2A	0.589	4.63	0.069	0.850	3.2.1.113	127,129,163
2	0.060	1dl2A	0.597	4.51	0.034	0.850	3.2.1.113	NA
3	0.060	2vn7A	0.535	5.05	0.043	0.792	3.2.1.3	NA
4	0.060	2c0lA	0.570	4.18	0.097	0.700	2.3.1.176	144,148,151
5	0.060	1h54B	0.550	5.36	0.063	0.846	2.4.1.8	218

	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	0.14	3fp2A	0.702	3.01	0.078	0.842	1.11	III	complex1.pdb.gz	127,131,134,146,159,163,189,192,193
2	0.09	3hymF	0.680	3.07	0.074	0.835	0.59	III	complex2.pdb.gz	9,24,28,31,32,73,75,78,79,127,128,131,134,135,139,156,158,160,162,166,169,170,192,193,196,200
3	0.04	1dl2A	0.597	4.51	0.034	0.850	0.75	UUU	complex3.pdb.gz	128,131,132,135,159,162,163,166
4	0.02	2qfcB	0.590	4.01	0.061	0.788	0.83	III	complex4.pdb.gz	27,31,32,75,78,79,82,121,124,127

	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.