D-I-TASSER O43353-D2

D-I-TASSER results for O43353-D2

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

Input Sequence in FASTA format

>O43353 (240 residues)
TFLEAVIQLKKTKLQSVSSAIHLCDKKKMELSLNIPVNHGPQEESCGSSQLHENSGSPET
SRSLPAPQDNDFLSRKAQDCYFMKLHHCPGNHSWDSTISGSQRAAFCDHKTTPCSSAIIN
PLSTAGNSERLQPGIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTK
PTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKSM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| TFLEAVIQLKKTKLQSVSSAIHLCDKKKMELSLNIPVNHGPQEESCGSSQLHENSGSPETSRSLPAPQDNDFLSRKAQDCYFMKLHHCPGNHSWDSTISGSQRAAFCDHKTTPCSSAIINPLSTAGNSERLQPGIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKSM
Prediction	CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	913567788776512688753335431012566787778886777776557644468875433578755542358999864234556887631343125566644467776521010357542235755457751899999999999999863015799999997287528889999835884899999999998744899999999998625431344765233677988665234569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| TFLEAVIQLKKTKLQSVSSAIHLCDKKKMELSLNIPVNHGPQEESCGSSQLHENSGSPETSRSLPAPQDNDFLSRKAQDCYFMKLHHCPGNHSWDSTISGSQRAAFCDHKTTPCSSAIINPLSTAGNSERLQPGIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKSM
Prediction	741412231453515354533433555336141614264535663334442455444462443251444442163654443334146253452155324434524336443342443344234453447435544045104541530053046330331022026451034311420364434363033004104541440041013103522512152323145144324363444455
	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

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

SS
Seq

CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
TFLEAVIQLKKTKLQSVSSAIHLCDKKKMELSLNIPVNHGPQEESCGSSQLHENSGSPETSRSLPAPQDNDFLSRKAQDCYFMKLHHCPGNHSWDSTISGSQRAAFCDHKTTPCSSAIINPLSTAGNSERLQPGIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKSM

2n7zA

1.00

0.44

12.37

1.62

SPARKS-K

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

2n7zA

1.00

0.44

12.37

1.28

CNFpred

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

2n7zA

1.00

0.44

12.37

1.25

MUSTER

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

2n7zA

1.00

0.44

12.37

4.05

HHsearch

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

2n7zA

1.00

0.44

12.37

0.39

CEthreader

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

4g1tA

0.05

2.35

0.55

EigenThreader

EFNLLAYLKHLKEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNQYLKVLLALKLHKMKLVEEALEKAPVLRSAAKFYRRKDEPDKAIELLKKANAYLHCQIGCCYRAKVFQVMNLGLLELIGHAVAHLKKADEANDNLF

2n7zA

1.00

0.44

12.37

0.95

FFAS-3D

-------------------------------------------------------------------------------------------------------------------------------------GIAQQWIQSKREDIVNQMTEACLNQSLDALLSRDLIMKEDYELVSTKPTRTSKVRQLLDTTDIQGEEFAKVIVQKLKDNKQMGLQPYPEILVVSRSPSLNLLQNKS-

4btgA

0.13

0.12

4.35

0.97

SPARKS-K

ALFIAYQDMVKQRGRAEVISSTIIPWFIEAMSEVSPFKLRPINETTSYIGQTSAIDHMGQPSHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEGISDRMSATLAPIGNTFAVSAVYEAVSQRGTVNSGFPSVPMVAIAALRTGIASNDLKRSMFNYYAAVMHYAVAHQGSLYLVWNVRT-ELRI--PVGYNAIEGSIRTPEPLEAIAYNKPIQ----PSEVLQAKVLDLPWHEASTE

2dbdA

0.32

0.10

3.01

0.76

CNFpred

----------------------------------------------------------------------------------------------------------------------------------------IQLLKSNRELLVTHIR--NTQCLVDNLLKNDYFSAEDAEIVCACPTQPDKVRKILDLVQSKGEEVSEFFLYLLQQLA---------------------------

5wtjA

0.04

0.03

1.69

0.83

DEthreader

----NPKNEPFFSDFKNQEIKKQIKDIND-----------RITVKTSDD--QLTLRNECTEKKNLIKADAKFLFNIDGNKNKISEIDAKLNKKYIKKLKENDNYKSFEKDYVSEYKKIR-------------EF---L-NKIESYLIDINWKLAIQ-ARFERDHYICFGIDSEISIRNYIYSIAEQIDRVSNLLS-YSTRYNNSTYASVFE-VFK--DVNLDYDELKK------------

(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	0.4709

(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	6jtdA	0.50	5.85	0.054	0.850	model1_6jtdA.pdb.gz
2	2c1zA	0.50	5.87	0.054	0.854	model1_2c1zA.pdb.gz
3	6vrbA2	0.49	5.82	0.048	0.825	model1_6vrbA2.pdb.gz
4	3hbjA	0.49	6.09	0.065	0.858	model1_3hbjA.pdb.gz
5	5tmbA	0.49	5.73	0.048	0.825	model1_5tmbA.pdb.gz
6	2pq6A	0.49	6.16	0.067	0.863	model1_2pq6A.pdb.gz
7	3wc4A	0.49	5.98	0.036	0.850	model1_3wc4A.pdb.gz
8	6lf6A	0.48	5.76	0.042	0.812	model1_6lf6A.pdb.gz
9	6lg1A	0.48	5.82	0.065	0.825	model1_6lg1A.pdb.gz
10	6lfnA	0.48	5.88	0.074	0.821	model1_6lfnA.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:0050700	0.96	CARD domain binding
GO:0046983	0.58	protein dimerization activity
GO:0042802	0.58	identical protein binding
GO:0042803	0.57	protein homodimerization activity
GO:0005102	0.54	receptor binding
GO:0030274	0.53	LIM domain 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:0065007	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0010604	0.96	positive regulation of macromolecule metabolic process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.93	cellular process
GO:0010468	0.92	regulation of gene expression
GO:0080090	0.89	regulation of primary metabolic process
GO:0048522	0.89	positive regulation of cellular process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0048584	0.88	positive regulation of response to stimulus
GO:0044093	0.88	positive regulation of molecular function
GO:0001934	0.88	positive regulation of protein phosphorylation
GO:0007165	0.85	signal transduction
GO:0051239	0.84	regulation of multicellular organismal process
GO:0042221	0.84	response to chemical
GO:0035556	0.84	intracellular signal transduction
GO:0006950	0.84	response to stress
GO:0006355	0.84	regulation of transcription, DNA-templated
GO:0002682	0.84	regulation of immune system process
GO:0002376	0.84	immune system process
GO:0071225	0.83	cellular response to muramyl dipeptide
GO:0070423	0.83	nucleotide-binding oligomerization domain containing signaling pathway
GO:0051092	0.83	positive regulation of NF-kappaB transcription factor activity
GO:0006952	0.83	defense response
GO:0051240	0.80	positive regulation of multicellular organismal process
GO:0001817	0.80	regulation of cytokine production
GO:0070431	0.79	nucleotide-binding oligomerization domain containing 2 signaling pathway
GO:0050852	0.79	T cell receptor signaling pathway
GO:0050731	0.79	positive regulation of peptidyl-tyrosine phosphorylation
GO:0045087	0.79	innate immune response
GO:0033138	0.79	positive regulation of peptidyl-serine phosphorylation
GO:0010800	0.79	positive regulation of peptidyl-threonine phosphorylation
GO:0007249	0.79	I-kappaB kinase/NF-kappaB signaling
GO:0002250	0.79	adaptive immune response
GO:0001819	0.79	positive regulation of cytokine production
GO:0044699	0.70	single-organism process
GO:0044763	0.66	single-organism cellular process
GO:0009966	0.64	regulation of signal transduction
GO:0050790	0.63	regulation of catalytic activity
GO:0043410	0.63	positive regulation of MAPK cascade
GO:0008152	0.60	metabolic process
GO:0043123	0.59	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0042981	0.59	regulation of apoptotic process
GO:0071704	0.58	organic substance metabolic process
GO:0044238	0.57	primary metabolic process
GO:0044237	0.57	cellular metabolic process
GO:0043170	0.56	macromolecule metabolic process
GO:0044260	0.55	cellular macromolecule metabolic process
GO:0002224	0.55	toll-like receptor signaling pathway
GO:0034134	0.54	toll-like receptor 2 signaling pathway
GO:0031398	0.54	positive regulation of protein ubiquitination

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:0043226	0.95	organelle
GO:0005737	0.95	cytoplasm
GO:0043229	0.94	intracellular organelle
GO:0043227	0.94	membrane-bounded organelle
GO:0043234	0.91	protein complex
GO:0043232	0.91	intracellular non-membrane-bounded organelle
GO:0031982	0.90	vesicle
GO:0005856	0.90	cytoskeleton
GO:0044444	0.77	cytoplasmic part
GO:0005829	0.72	cytosol

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	3dzcB	0.426	6.08	0.079	0.758	5.1.3.14	NA
2	0.060	2c1zA	0.499	5.87	0.054	0.854	2.4.1.115	NA
3	0.060	1y8zA	0.419	6.10	0.072	0.733	2.4.1.26	NA
4	0.060	3c4qA	0.435	6.36	0.051	0.804	2.4.1.14	NA
5	0.060	2gejA	0.431	5.96	0.044	0.754	2.4.1.57	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	2z4tA	0.440	5.93	0.036	0.758	0.22	C5P	complex1.pdb.gz	194,197,198,199
2	0.01	3iaaB	0.464	5.52	0.031	0.762	0.16	TYD	complex2.pdb.gz	169,170,195,199
3	0.01	1sqfA	0.436	5.19	0.068	0.679	0.25	SAM	complex3.pdb.gz	160,161,162,194,195,198
4	0.01	1rrvA	0.456	5.74	0.042	0.762	0.23	III	complex4.pdb.gz	188,191,192,197,198,199,201,206,209
5	0.01	3c4qA	0.435	6.36	0.051	0.804	0.15	UDP	complex5.pdb.gz	137,195,201,209
6	0.01	2iyfB	0.446	5.77	0.049	0.750	0.16	UDP	complex6.pdb.gz	152,213,214,215
7	0.01	1pn3B	0.440	6.04	0.048	0.783	0.20	III	complex7.pdb.gz	201,204,205,208,209
8	0.01	3hbfA	0.485	5.99	0.043	0.838	0.21	UDP	complex8.pdb.gz	173,196,198,199,200,201
9	0.01	2c1zA	0.499	5.87	0.054	0.854	0.10	U2F	complex9.pdb.gz	3,149,214,217
10	0.01	3s27G	0.341	6.43	0.040	0.625	0.11	UDP	complex10.pdb.gz	167,188,192,193,194,197

	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.