D-I-TASSER O76024-D3

D-I-TASSER results for O76024-D3

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

Input Sequence in FASTA format

>O76024 (265 residues)
FLFLFALPILVAGLALVGVLQFARWFTSLELTKIAVTVAVCSVPLLLRWWTKASFSVVGM
VKSLTRSSMVKLILVWLTAIVLFCWFYVYRSEGMKVYNSTLTWQQYGALCGPRAWKETNM
ARTQILCSHLEGHRVTWTGRFKYVRVTYKFEITVGMPFSSGADGSRSREEDDVTKDIVLR
ASSEFKSVLLSLRQGSLIEFSTILEGRLGSKWPVFELKAISCLNCMAQLSPTRRHVKIEH
DWRSTVHGAVKFAFDFFFFPFLSAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| FLFLFALPILVAGLALVGVLQFARWFTSLELTKIAVTVAVCSVPLLLRWWTKASFSVVGMVKSLTRSSMVKLILVWLTAIVLFCWFYVYRSEGMKVYNSTLTWQQYGALCGPRAWKETNMARTQILCSHLEGHRVTWTGRFKYVRVTYKFEITVGMPFSSGADGSRSREEDDVTKDIVLRASSEFKSVLLSLRQGSLIEFSTILEGRLGSKWPVFELKAISCLNCMAQLSPTRRHVKIEHDWRSTVHGAVKFAFDFFFFPFLSAA
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCSSSSSSSSSSSSSSSSSSHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCHHHHHHHHCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	3157888999999999999999999999888773130122121223345566655566677766645689999999999999876640125788777787898999866199666663157887851114891799999999999976220100688778888887543468742399996230667775179995899999981567998727999983041257754555431677323789999999999999872220489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| FLFLFALPILVAGLALVGVLQFARWFTSLELTKIAVTVAVCSVPLLLRWWTKASFSVVGMVKSLTRSSMVKLILVWLTAIVLFCWFYVYRSEGMKVYNSTLTWQQYGALCGPRAWKETNMARTQILCSHLEGHRVTWTGRFKYVRVTYKFEITVGMPFSSGADGSRSREEDDVTKDIVLRASSEFKSVLLSLRQGSLIEFSTILEGRLGSKWPVFELKAISCLNCMAQLSPTRRHVKIEHDWRSTVHGAVKFAFDFFFFPFLSAA
Prediction	3230333333331211102110031023231230000000031000011223322021310220344220101112212010101110243562623644031630372044432656330412130340643403040304403023303010201224446555456475343402020343024013303452302030203441436303030420312414254353454242444035202400210011303032448
	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                 200                 220                 240                 260

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

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCSSSSSSSSSSSSSSSSSSHHHCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCHHHHHHHHCCCCCSSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHCCCC
FLFLFALPILVAGLALVGVLQFARWFTSLELTKIAVTVAVCSVPLLLRWWTKASFSVVGMVKSLTRSSMVKLILVWLTAIVLFCWFYVYRSEGMKVYNSTLTWQQYGALCGPRAWKETNMARTQILCSHLEGHRVTWTGRFKYVRVTYKFEITVGMPFSSGADGSRSREEDDVTKDIVLRASSEFKSVLLSLRQGSLIEFSTILEGRLGSKWPVFELKAISCLNCMAQLSPTRRHVKIEHDWRSTVHGAVKFAFDFFFFPFLSAA

4damA

0.09

0.03

1.30

0.44

CEthreader

--------------------------------------------------------------------------------------------------------------------------------SMNEIMICAVGNVATPVFRDLVRFRLAVTARYWDREKNAWTDGHTNFFTVWANRQLATNASGSLAVGDPVVVQGRLKVRTSRTSADIDAVAIGHDLARGTA------------------------------------

6od8A

0.08

0.05

1.92

0.62

EigenThreader

---------------------------------------------AALVEKYKAVFGAAPMVQSTT------------------------YKSRTHIP-------------VSELSRPELV----------DKTVLIRARVSTTRKKGKAFMVLRDGS---------------DS-VQAMAAVEMIDFMGQIATESIVVEATVCKVTSTSHSDIELKVKKIHTVTESLRTLPFTLEDASRIFRLQSRVCQYFRQFLIDKDFCEIH

1gm5A1

0.11

0.09

3.29

0.49

FFAS-3D

FLFLWALPLEEFLNEVEKMLKIHQLLKELDDPLLENKDLEEKLQAFLDYVKEIP--------NLPEARKRYRIQKSLEMIEKLRSWFLIDYLECSGEEVDLS--------TDIQYAKGVGPNRKKKLKKLPGEKVTTQGKIVSVETKNILTAVLSDG----------------LVHVPLKWNQDYLQTYLKQLTGKEVFVTGTVKSNAYTGQYEIHNAEVTPKEGEYVRRILPIYRLTSGISQKQMRKIFEENIPSL--------

6vejA2

0.11

0.10

3.58

0.68

SPARKS-K

QRVSLGALIIALGLLVDDAMITVEMMITRLELSTAFPMLTGTLVTVAGFVPIGLNASSEYTFTLFAVIAVALLLSWIVAVLFAPVIAVHILPKTLKHKSE-------QKKGRIAERFDSLLHLAMRSLFLMK-FVQ-HQFFPSSDRP-ELLVDLNLPQNSSIHEATLKDDEDIDHWSAYVGEGAIRFYLPLDQQLQNGQLVIVTKDLEARESTYVQPLEMG--------PPVGRPIQYRDKVREYAMGLAGVLDGNPNIGDIVYD

4zivA

0.09

0.08

3.15

0.82

CNFpred

NTLTMFGMVLAIGLLVDDAIVVVENVERVSMGQIQGALVGIAMVLSAVFVPMAFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHG-THHYTDSVGGILRSTRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGA-------------TQERTQKVLNEVTHYYLTKEKNNVESVFAVNGAGA--AGAGQNTGIAFVSLKD-------ADRPGEENKVEAITMRATRAFSQI-AMVFAFN

4a01A

0.06

0.05

2.09

0.83

DEthreader

--NVVKCAEIQNAISEGATSFLFTEYKYVGIFMVAFAILIFLFLGSVEGFS------------SPQ--S-KPALATAIFSTVSFLLGGVTSLVSGGMGLEALKKQLVISTVLMT--A-FLCVAVGLWAGLIIGTETSAYSPVDVIFGLALYKSII------------------------------------------AANTAKGIGSALLVVQISSNGGANAYHASLCHAVITGDKDTPSLNILKLMAVESLVFAPFFATHGGLK

2pffB

0.06

2.59

0.58

MapAlign

YQTYHVLVGDLIKFSAETLSELLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRVAIAETDSWESFFVSVRKAITVLFFLYGLNLTLRGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-GGGGGGGGGGGGG-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLI-----

6eznF

0.10

0.09

3.39

0.61

MUSTER

WLFPAGVFLLFLEHVFVIAYSVLCSYFAGVLMLTLTPVICVSAAVALSKIFDIYLDFKIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVVLPSQ-------TKLALIDDFREAYYWLRMNSDDSKVAWWDYGYQ--IGGMADRTTLVDNNTWNNTHIA-----IVGKAMASPEEKSYEILKEHDV-DYVLVIFGGLIGFGGDDINISEGIWPEEIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNG

1asyA1

0.10

0.05

1.67

0.68

HHsearch

------------------------------------------------------------------------------------------EDTAKDNYGKLPLIQSRDSRTG---------QKRVKFVKDSDKEVLFRARVHNTRQQGATLAFLTLRQQ------------ASLIQGLVKANKNMVKWAGSLNLESIVLVRGIVKKVDEVQNLEIHITKIYTISETPEAL-----------------------------------

1x3eB

0.14

0.06

1.92

0.44

CEthreader

---------------------------------------------------------------------------------------------------------------------------------AGDTTITVVGNLTDPELRFTANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFRTVVEVEVDEIGPSLRYATAKVNKA-------------------------------

(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	0.6349

(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	4a01A	0.46	6.13	0.042	0.770	model1_4a01A.pdb.gz
2	4iggA	0.43	5.26	0.056	0.660	model1_4iggA.pdb.gz
3	4av3A	0.43	6.01	0.011	0.713	model1_4av3A.pdb.gz
4	6r9tA	0.43	4.88	0.051	0.608	model1_6r9tA.pdb.gz
5	6jfkA	0.42	5.47	0.048	0.660	model1_6jfkA.pdb.gz
6	2w6dA	0.42	5.34	0.049	0.660	model1_2w6dA.pdb.gz
7	5ganA	0.42	5.50	0.057	0.653	model1_5ganA.pdb.gz
8	6jbjA1	0.42	4.78	0.055	0.581	model1_6jbjA1.pdb.gz
9	3amtA1	0.42	4.26	0.028	0.558	model1_3amtA1.pdb.gz
10	4aurA1	0.36	5.80	0.040	0.581	model1_4aurA1.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:0019899	1.00	enzyme binding
GO:0051117	0.80	ATPase binding
GO:0031625	0.61	ubiquitin protein ligase 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:0080090	1.00	regulation of primary metabolic process
GO:0060255	1.00	regulation of macromolecule metabolic process
GO:0050821	1.00	protein stabilization
GO:0048523	1.00	negative regulation of cellular process
GO:0048513	1.00	animal organ development
GO:0044767	1.00	single-organism developmental process
GO:0031323	1.00	regulation of cellular metabolic process
GO:0009987	0.87	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0008152	0.84	metabolic process
GO:0044238	0.83	primary metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0043170	0.83	macromolecule metabolic process
GO:0048522	0.82	positive regulation of cellular process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0050877	0.81	neurological system process
GO:0032879	0.81	regulation of localization
GO:0032268	0.81	regulation of cellular protein metabolic process
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0010604	0.81	positive regulation of macromolecule metabolic process
GO:0006508	0.81	proteolysis
GO:0051928	0.80	positive regulation of calcium ion transport
GO:0045927	0.80	positive regulation of growth
GO:0043524	0.80	negative regulation of neuron apoptotic process
GO:0042593	0.80	glucose homeostasis
GO:0032469	0.80	endoplasmic reticulum calcium ion homeostasis
GO:0031398	0.80	positive regulation of protein ubiquitination
GO:0030433	0.80	ER-associated ubiquitin-dependent protein catabolic process
GO:0007605	0.80	sensory perception of sound
GO:0007601	0.80	visual perception
GO:0003091	0.80	renal water homeostasis
GO:0001822	0.80	kidney development
GO:0048583	0.63	regulation of response to stimulus
GO:0023051	0.63	regulation of signaling
GO:0080134	0.62	regulation of response to stress
GO:0065009	0.62	regulation of molecular function
GO:0048585	0.62	negative regulation of response to stimulus
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0023057	0.62	negative regulation of signaling
GO:0010648	0.62	negative regulation of cell communication
GO:0010605	0.62	negative regulation of macromolecule metabolic process
GO:0009966	0.62	regulation of signal transduction
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:1903892	0.61	negative regulation of ATF6-mediated unfolded protein response
GO:0043433	0.61	negative regulation of sequence-specific DNA binding transcription factor activity
GO:0000122	0.61	negative regulation of transcription from RNA polymerase II promoter

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:0043226	0.87	organelle
GO:0044444	0.86	cytoplasmic part
GO:0043229	0.86	intracellular organelle
GO:0043227	0.86	membrane-bounded organelle
GO:0044425	0.85	membrane part
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0044446	0.84	intracellular organelle part
GO:0016021	0.82	integral component of membrane
GO:0044432	0.81	endoplasmic reticulum part
GO:0005783	0.81	endoplasmic reticulum
GO:0030176	0.80	integral component of endoplasmic reticulum membrane
GO:0042995	0.64	cell projection
GO:0097458	0.63	neuron part
GO:0043005	0.62	neuron projection
GO:0030425	0.61	dendrite
GO:0016020	0.52	membrane

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	2ckjA	0.292	6.71	0.032	0.536	1.17.1.4 1.17.3.2	NA
2	0.060	1ygeA	0.327	6.73	0.068	0.623	1.13.11.12	NA
3	0.060	1no3A	0.372	6.21	0.034	0.641	1.13.11.12	NA
4	0.060	2vf4X	0.275	5.90	0.020	0.434	2.6.1.16	NA
5	0.060	2zkmX	0.371	6.64	0.035	0.694	3.1.4.11	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:

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	0.01	2voyK	0.119	0.79	0.000	0.121	0.79	III	complex1.pdb.gz	122,125,126
	2	0.01	2w6dB	0.411	5.60	0.044	0.653	0.78	CPL	complex2.pdb.gz	128,129,131

	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.