D-I-TASSER P52926-D1

D-I-TASSER results for P52926-D1

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

Input Sequence in FASTA format

>P52926 (109 residues)
MSARGEGAGQPSTSAQGQPAAPAPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSP
SKAAQKKAEATGEKRPRGRPRKWPQQVVQKKPAQEETEETSSQESAEED

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSARGEGAGQPSTSAQGQPAAPAPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSPSKAAQKKAEATGEKRPRGRPRKWPQQVVQKKPAQEETEETSSQESAEED
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC
Confidence	9878878898888888899988888889999999998999898899999999987788877666677788888888899887777666678775501057766544479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSARGEGAGQPSTSAQGQPAAPAPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSPSKAAQKKAEATGEKRPRGRPRKWPQQVVQKKPAQEETEETSSQESAEED
Prediction	7456476475456466755766557657554475456778754447446543575657445655556664575546444155444745565546646655465656678
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC
MSARGEGAGQPSTSAQGQPAAPAPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSPSKAAQKKAEATGEKRPRGRPRKWPQQVVQKKPAQEETEETSSQESAEED

6y9cA

0.06

2.73

0.49

CEthreader

NDYITRKNIVIIRGKDSVLRAFYNVCPHRGHELLSGSGKAKNVITCPYHAWTFKLDGSLALARNCDHVESFDKENSSMVPLKVEEYAGFVFINMDENATCVEDQLPGFA

6e2jA

0.11

3.94

0.57

EigenThreader

LEPYFELFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTNAENEFVTIKKDVDGAYMTKVDLQ--AKLDNLQQEIDFLTALYQAELSQMQTQIS--

6mb3E

0.16

0.12

3.98

0.47

FFAS-3D

---NANPNVDPNANPNVDPNANPPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNA-----------------------

5o9zH

0.11

3.96

1.42

SPARKS-K

FDKWQEPPPVKQVKPLPAPLDGQRKKRGGRRYRKMKERL-GLTEIRKQANRMSFGEIEEDAYQEDLGFSLGKSGSGRVRQTQVNEATKARISKTLQRTLQKQSVVYGGK

1a02F

0.11

0.04

1.31

0.59

CNFpred

--------------------------------------------------------------------------AAKSRNRRRELTDTLQAETDQLEDEKSALQTEIAN

4l79A

0.02

1.31

0.83

DEthreader

-KTVNDNSSRRQPRG--SYNYGYRDADLLYSQEPAK------V-NLKRP-QASVATLM-------RY-GLLE-VRRANPRFQLEDLRKQRLEDLATLIQKIYRGWKCRT

1s5lv

0.05

2.24

0.79

MapAlign

LTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIA

1r5sA

0.11

3.96

0.98

MUSTER

LGSPSKDCGSPKYAYFNGCSSPTAPLSPMSPPGYKLVTGDRNNSSCRNYNK-QASEQNWANYSAEQNRMGQAGSTISNSHAQPFDFPDDNQNAKKVAAGHELQPLAIVD

1ub1A

0.26

0.19

5.95

0.51

HHsearch

VPEAASPKQRRSIIRDRGPDPTLLKQRKSGRSGKYDVYPQGDTSFTTGRGSPSRREQRPPKK--AKSPKSPGSGRGRGRPKGSG-------------------------

3au2A

0.06

2.73

0.49

CEthreader

KEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPK

(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	0.4289

(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	2p10C	0.51	4.46	0.039	0.881	model1_2p10C.pdb.gz
2	6z1sA	0.51	4.63	0.029	0.872	model1_6z1sA.pdb.gz
3	6m9rA	0.50	4.17	0.030	0.798	model1_6m9rA.pdb.gz
4	5ey0B1	0.50	3.73	0.067	0.761	model1_5ey0B1.pdb.gz
5	7k18A	0.49	3.95	0.020	0.752	model1_7k18A.pdb.gz
6	4f1nA3	0.49	4.55	0.047	0.844	model1_4f1nA3.pdb.gz
7	3lfvA1	0.49	3.66	0.031	0.734	model1_3lfvA1.pdb.gz
8	2yhaA2	0.42	5.02	0.052	0.752	model1_2yhaA2.pdb.gz
9	1ykdA1	0.40	4.62	0.000	0.706	model1_1ykdA1.pdb.gz
10	4ei1A	0.39	4.60	0.041	0.679	model1_4ei1A.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:0003824	0.89	catalytic activity
GO:0016787	0.88	hydrolase activity
GO:0016788	0.86	hydrolase activity, acting on ester bonds
GO:0003700	0.86	transcription factor activity, sequence-specific DNA binding
GO:0003906	0.85	DNA-(apurinic or apyrimidinic site) lyase activity
GO:0097159	0.64	organic cyclic compound binding
GO:1901363	0.63	heterocyclic compound binding
GO:0003676	0.60	nucleic acid binding
GO:0003677	0.56	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:0065007	0.99	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0010468	0.95	regulation of gene expression
GO:0009987	0.94	cellular process
GO:0080090	0.92	regulation of primary metabolic process
GO:0031323	0.92	regulation of cellular metabolic process
GO:0051252	0.91	regulation of RNA metabolic process
GO:2000112	0.88	regulation of cellular macromolecule biosynthetic process
GO:0008152	0.87	metabolic process
GO:0006355	0.87	regulation of transcription, DNA-templated
GO:0071704	0.86	organic substance metabolic process
GO:0044238	0.86	primary metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0033554	0.86	cellular response to stress
GO:0044260	0.85	cellular macromolecule metabolic process
GO:0034641	0.85	cellular nitrogen compound metabolic process
GO:0090304	0.84	nucleic acid metabolic process
GO:0006259	0.83	DNA metabolic process
GO:0006284	0.80	base-excision repair
GO:0044699	0.64	single-organism process
GO:0048518	0.62	positive regulation of biological process
GO:0044763	0.57	single-organism cellular process
GO:0009893	0.57	positive regulation of metabolic process
GO:0048519	0.56	negative regulation of biological process
GO:0010604	0.56	positive regulation of macromolecule metabolic process
GO:0048523	0.55	negative regulation of cellular process
GO:0048522	0.55	positive regulation of cellular process
GO:0044767	0.55	single-organism developmental process
GO:0016043	0.55	cellular component organization
GO:0010628	0.55	positive regulation of gene expression
GO:0050793	0.53	regulation of developmental process
GO:0048869	0.53	cellular developmental process
GO:0048583	0.53	regulation of response to stimulus
GO:0031325	0.53	positive regulation of cellular metabolic process
GO:0009892	0.53	negative regulation of metabolic process
GO:0031324	0.52	negative regulation of cellular metabolic process
GO:0010605	0.52	negative regulation of macromolecule metabolic process
GO:0045893	0.51	positive regulation of transcription, DNA-templated
GO:0045892	0.51	negative regulation of transcription, DNA-templated
GO:0006325	0.51	chromatin organization
GO:0080135	0.50	regulation of cellular response to stress
GO:0051094	0.50	positive regulation of developmental process
GO:0048584	0.50	positive regulation of response to stimulus
GO:0042127	0.50	regulation of cell proliferation
GO:0022607	0.50	cellular component assembly

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:0043229	0.92	intracellular organelle
GO:0005634	0.90	nucleus
GO:0044446	0.71	intracellular organelle part
GO:0044428	0.61	nuclear part
GO:0032991	0.60	macromolecular complex
GO:0044427	0.52	chromosomal part
GO:0000785	0.51	chromatin
GO:0043234	0.50	protein 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	3fa3B	0.449	4.38	0.038	0.789	4.1.3.32	NA
2	0.060	1v8zB	0.453	4.87	0.052	0.817	4.2.1.20	NA
3	0.060	1s2mA	0.452	4.99	0.049	0.881	3.6.4.13	NA
4	0.060	2fiqC	0.478	4.16	0.069	0.789	2.7.1.144	79
5	0.060	1ukwA	0.448	4.33	0.032	0.798	1.3.99.3	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	3nq1A	0.471	4.56	0.078	0.817	0.56	KOJ	complex1.pdb.gz	51,75,78

	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.