D-I-TASSER O76024-D2

D-I-TASSER results for O76024-D2

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

Input Sequence in FASTA format

>O76024 (227 residues)
TIDFFAFFIPLVIFYLSFISMVICTLKVFQDSKAWENFRTLTDLLLRFEPNLDVEQAEVN
FGWNHLEPYAHFLLSVFFVIFSFPIASKDCIPCSELAVITGFFTVTSYLSLSTHAEPYTR
RALATEVTAGLLSLLPSMPLNWPYLKVLGQTFITVPVGHLVVLNVSVPCLLYVYLLYLFF
RMAQLRNFKGTYCYLVPYLVCFMWCELSVVILLESTGLGLLRASIGY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| TIDFFAFFIPLVIFYLSFISMVICTLKVFQDSKAWENFRTLTDLLLRFEPNLDVEQAEVNFGWNHLEPYAHFLLSVFFVIFSFPIASKDCIPCSELAVITGFFTVTSYLSLSTHAEPYTRRALATEVTAGLLSLLPSMPLNWPYLKVLGQTFITVPVGHLVVLNVSVPCLLYVYLLYLFFRMAQLRNFKGTYCYLVPYLVCFMWCELSVVILLESTGLGLLRASIGY
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSCCCCSSSSSCCSSSSSSCCHHHHHHHHHHHHHHHHHHHCCCCSSSSSHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCC
Confidence	94489999999999999999999999997437999988999999997168999578888875502128999999999999842678888887458999999999999986313454033346899999999971865568851466651564389827818998553689999999999999997376855765034999999999999999731389999987229
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| TIDFFAFFIPLVIFYLSFISMVICTLKVFQDSKAWENFRTLTDLLLRFEPNLDVEQAEVNFGWNHLEPYAHFLLSVFFVIFSFPIASKDCIPCSELAVITGFFTVTSYLSLSTHAEPYTRRALATEVTAGLLSLLPSMPLNWPYLKVLGQTFITVPVGHLVVLNVSVPCLLYVYLLYLFFRMAQLRNFKGTYCYLVPYLVCFMWCELSVVILLESTGLGLLRASIGY
Prediction	63422212213321331131023000100254641541320030034245614474044423353030001033123221011110473121101000001111300110012424300200000100220033233125403203032432212301320201000201121322320020132550420000000100033012000100341213002112356
	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

CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSCCCCSSSSSCCSSSSSSCCHHHHHHHHHHHHHHHHHHHCCCCSSSSSHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCC
TIDFFAFFIPLVIFYLSFISMVICTLKVFQDSKAWENFRTLTDLLLRFEPNLDVEQAEVNFGWNHLEPYAHFLLSVFFVIFSFPIASKDCIPCSELAVITGFFTVTSYLSLSTHAEPYTRRALATEVTAGLLSLLPSMPLNWPYLKVLGQTFITVPVGHLVVLNVSVPCLLYVYLLYLFFRMAQLRNFKGTYCYLVPYLVCFMWCELSVVILLESTGLGLLRASIGY

4phuA1

0.08

0.07

2.79

0.46

CEthreader

LPPQLSFGLYVAAFALGFPLNVLAIRGATAHARLRLT-------------------------PSAVYALNLGCSDLLLTVSLPLKAVEALAPLYAGGGFLAALSAARYLGAAFPPCYSWGVCAAIWALVLCHLGLVFGLEAPGGWLDHSNTSLGINTPVNGSPVCLLPLAITAFCFVGCLRALARGGSLTHRRKLRAAWVAGGALLTLLLCVGPYNASNVASFLYPN

4f4cA

0.08

3.11

0.78

EigenThreader

TLEKLLLFIGTLVAVITGAGLPLMSILQGKVSQAF-----INEQIVINNQNYTKTDFEHDVMNVVWSYAAMTVGMWAAGQITVTCYLEGTGDKIGMAFQYLSQFITGFIVAFTHSWQLTLVMLAVTPIQALCGFAIAKSMSTFAIAKKAGVLKGLFL--GISFGAMQASNFISFALAFYIGVGWVHDGSLNFGDMLTTFSSVMMGSMALGLAGPQLAVLGTAQGAAS

4jq6A

0.09

0.07

2.81

0.80

FFAS-3D

--DYVG-----ISFWLAAAIMLASTVFFFDVPVKWKTSLTVAGLVTG------VAFWHYLYMRGVWIRYIDWLITVPLQIIEFYLIIAV---FWKLLIASLVMLIGGFIGEAGLGDVVVWWIVGMIAWLYIIYEIFLFNT-----------------------IKWIVTVGWAIYPIGYA-WGYFGDGLNEDALNIVYNLADLINKAAFGLA----IWAAAMKD---

5y78A

0.10

3.57

0.78

SPARKS-K

LVHTLKVGFYFFLWYFFNFIFNIANKRTLNMWKYTIQLGVGALYCTFLWTKPNVSK---KLIKALIWPSLGHTLGHAATCMSFSLV-----AISFTHVVKSAEPVFGAVGSALTFTWTGFITAMISNVAFVTRNITSKFKNEKTLIAQNTYALITIISAKLFGSIMFCSLFYHLYNEVSYLCLDNVS--PVSFSIGNTIKRVIIIFGSILVFRTPNFIGSTIAIIGT

3rkoB

0.07

2.73

1.09

CNFpred

--EGYSRFFAYTNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIGFYYDPKNGAAAMKAFVVTRVGDVFLAFALFILYNELTLNFREMV-MLMWATLMLLGGAVGKSAQLPLQTWLADAMAGPTPVSALIHAA---------TMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMFLALGVQAWDAAIFHLMTHA

4pl0A1

0.08

0.07

2.78

1.00

DEthreader

---SLMDVRGKFLFFSMLFITSLSSIIIS-IS--PL-ILAKITDLLSGSLSSYYLVLLACLYMFCVSNKASVFLFMILQSSLRINMQMKSIYILVRNVSNILSPVIQLISTIVLAGVFFLYILVFVIFNTRLTGSLASL----------R-HSMITLSYS-EAQYWLSSKVLLLNSLLAVIFG-FIFITSYIILLSTPVENIGALLSEIQSMSSLAGFI--------

5b5ec

0.07

2.76

0.76

MapAlign

-KNKMTTILGFHLIVLGIGALLLVAKAMFVITNPTPRVIFGYLLKS-PFGGEGWIVSV---NNLEDVVGGHIWIGLICIAGGIWHIAYLSYSLGALSMMGFIATCFVWFVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPGLGKYLMRSPTGEIIFGGQERRAAEYMTHAPLGVGGVATEINSVNFVSRSWLATSHFVLAFFFLVGH-LWHAGRARAAA

5ezmA

0.11

0.10

3.70

0.55

MUSTER

DWGLWRRLHLALGVVVMLVITVPWFYLVSVRNPEFPNFFFIHEHWQRRSGSVFYFLPLVIGGFL-FRPALMAGIWAIAIFVFFSISRSKLPGYIVPVIPALGILAGVALDRLSPRSWGKQLIGMAIVAACGLLASPVVAT-------LNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMGMYLGFTVALLGHETVGRPSGADIAPQIAQK

5tj5A

0.15

0.14

4.74

0.90

HHsearch

GLPTIVTF-P-FMFAIMFFLMTLAALSLVLNEKKINKMEIFDMVFSMYTGALLFSNSHMNDIIGNFIPGLLFMQGIFGYLSVYKVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKF-DIMIHQ-----VIHTIEF--CLNCVSHTQLSSVLWTMTIQIAFGGFVGVFMTVALFAMWFALTCAVLV------LMEGTSAW

7bpuA

0.08

3.13

0.44

CEthreader

IGYLISSNFEIDILKSLLVFFVVFFVCAYGNVINDIFDIEIDRINKPSRPLPSGKIKLNEAKKFSAILLILGLVLSLFINIYALIIAVINAPIGNFIIGYLTGSVFLFGGVAGKNVMPVVILFLCSLLSIWGREIVKDFEDMEGDKKEGVISLPIKYG---KKSLYFATFLVVLAVILSPLPYILKIFGIWYLILIAICDILFIYAMALLLKEPNKETASKVSKFLK

(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	0.637

(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	4pl0A	0.62	4.13	0.084	0.850	model1_4pl0A.pdb.gz
2	4ry2A	0.58	4.66	0.056	0.863	model1_4ry2A.pdb.gz
3	4mycA	0.56	4.87	0.051	0.850	model1_4mycA.pdb.gz
4	3qf4B	0.56	4.49	0.068	0.833	model1_3qf4B.pdb.gz
5	3wmeA	0.53	5.05	0.072	0.833	model1_3wmeA.pdb.gz
6	3b5xA	0.52	5.07	0.058	0.824	model1_3b5xA.pdb.gz
7	2onjA1	0.48	5.77	0.046	0.819	model1_2onjA1.pdb.gz
8	3b5wA	0.45	4.78	0.041	0.652	model1_3b5wA.pdb.gz
9	2yl4A1	0.45	3.83	0.066	0.612	model1_2yl4A1.pdb.gz
10	3efzB	0.38	4.92	0.079	0.568	model1_3efzB.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	0.81	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	0.88	cellular process
GO:0008152	0.85	metabolic process
GO:0071704	0.84	organic substance metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0048518	0.83	positive regulation of biological 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:0032501	0.82	multicellular organismal process
GO:0019538	0.82	protein metabolic process
GO:0051928	0.81	positive regulation of calcium ion transport
GO:0045927	0.81	positive regulation of growth
GO:0043524	0.81	negative regulation of neuron apoptotic process
GO:0042593	0.81	glucose homeostasis
GO:0032469	0.81	endoplasmic reticulum calcium ion homeostasis
GO:0031398	0.81	positive regulation of protein ubiquitination
GO:0030433	0.81	ER-associated ubiquitin-dependent protein catabolic process
GO:0007605	0.81	sensory perception of sound
GO:0007601	0.81	visual perception
GO:0003091	0.81	renal water homeostasis
GO:0001822	0.81	kidney development
GO:0048583	0.63	regulation of response to stimulus
GO:0023051	0.63	regulation of signaling
GO:0010646	0.63	regulation of cell communication
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:0044444	0.86	cytoplasmic part
GO:0043226	0.86	organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0044446	0.84	intracellular organelle part
GO:0044425	0.84	membrane part
GO:0016021	0.82	integral component of membrane
GO:0030176	0.81	integral component of endoplasmic reticulum membrane
GO:0005783	0.81	endoplasmic reticulum
GO:0097458	0.62	neuron part
GO:0042995	0.62	cell projection
GO:0030425	0.61	dendrite

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	3iayA	0.460	5.66	0.071	0.775	2.7.7.7	NA
2	0.060	1occA	0.440	5.53	0.085	0.714	1.9.3.1	NA
3	0.060	3g61A	0.526	5.26	0.065	0.837	3.6.3.44	NA
4	0.060	2r72A	0.459	6.10	0.047	0.819	2.7.7.48	NA
5	0.060	3btaA	0.438	5.55	0.041	0.700	3.4.24.69	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	1d0zA	0.508	4.86	0.047	0.793	0.16	PNQ	complex1.pdb.gz	91,92,93,94,95
2	0.01	1s5gA	0.516	4.88	0.061	0.802	0.10	ADP	complex2.pdb.gz	34,35,36,38,39
3	0.01	2v26A	0.506	5.22	0.068	0.815	0.13	UUU	complex3.pdb.gz	189,190,191,195
4	0.01	1br2A	0.499	4.98	0.047	0.788	0.11	UUU	complex4.pdb.gz	34,35,36
5	0.01	1d0xA	0.506	4.84	0.047	0.784	0.20	MNQ	complex5.pdb.gz	38,39,40,41
6	0.01	1l2oA	0.513	4.90	0.056	0.797	0.30	PDM	complex6.pdb.gz	29,192,193
7	0.01	1kwoA	0.514	4.87	0.062	0.802	0.18	AGS	complex7.pdb.gz	33,35,36,37,38,39
8	0.01	1br10	0.516	5.04	0.048	0.811	0.15	III	complex8.pdb.gz	190,194,198,199,200,201,202,204,205,206,208,209,212

	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.