D-I-TASSER P43354-D1

D-I-TASSER results for P43354-D1

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

Input Sequence in FASTA format

>P43354 (79 residues)
MPCVQAQYGSSPQGASPASQSYSYHSSGEYSSDFLTPEFVKFSMDLTNTEITATTSLPSF
STFMDNYSTGYDVKPPCLY

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MPCVQAQYGSSPQGASPASQSYSYHSSGEYSSDFLTPEFVKFSMDLTNTEITATTSLPSFSTFMDNYSTGYDVKPPCLY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCC
Confidence	9730132478999998665565556777666444685444010136887534566787235543356665456887679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MPCVQAQYGSSPQGASPASQSYSYHSSGEYSSDFLTPEFVKFSMDLTNTEITATTSLPSFSTFMDNYSTGYDVKPPCLY
Prediction	6523445344445344334443444455524443144733423241545634444434313322543446243535147
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCC
MPCVQAQYGSSPQGASPASQSYSYHSSGEYSSDFLTPEFVKFSMDLTNTEITATTSLPSFSTFMDNYSTGYDVKPPCLY

4i0oA2

0.10

3.73

0.61

CEthreader

YCEERYTLDLAGTSNTKLLGCQSIERPDTSVSVFTKPSVYLGLFDINRWYHAQPDSLRSGESLHNCSYFALWSLDSVVS

6ly9N2

0.04

2.03

0.58

EigenThreader

LLILLSVAFGVVLVFFGLALRAYLGLKHRHMAHFWEGVGYLGGLVGVLALAASYLGNLQAGWLQGLMYLGFGVFLLAVL

7abiK

0.11

0.10

3.62

0.32

FFAS-3D

----NGKVITNKAVKGKYKFLQKYYHRGAFFMDEDEEVYKRDFSAPTLEDHFNKTILPKV-----MQVKNFGRSGRTKY

6f1tg2

0.05

2.37

1.04

SPARKS-K

ASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPL

4z4hA

0.15

0.05

1.71

0.47

CNFpred

---------------------------------------IFLGADVTHPPA-GDGKKPSIAAVVGSM------------

3rkoM1

0.04

1.99

1.00

DEthreader

LGLMWIMLVFQASGLVLIALALVHYATNTPMEYLLMLGFFIAFAVKMPHLAHSQAPTAGVDLAGILLKAYGLLRFL---

1ekmA

0.07

0.06

2.63

0.66

MapAlign

----LVVSQIFTAANYEYCLYWVFMQDGAIRLDIRGDGNSAAACDAKSSPYPLGSPENMYGNAFYSEGRSWDIFNPN--

1m0fB

0.17

0.14

4.57

0.67

MUSTER

EQLTKNQRDEIEAGKSYCSRRFGGATCDDKSAQIY-ARF-----DKNDWRIQPA----EFYRFHDAEVNTFGYF-----

2vpsA

0.08

0.04

1.48

0.47

HHsearch

-----------------------------------------SSLQRASVSFN-KPGHIPFGAVQGYAPGGVPA-YSNKH

5mdnA1

0.10

3.73

0.54

CEthreader

MRFWPLDATYSVVGGVPEVRVFGVDGEGRRVVLVDRRFRPYFYAKCDKCDASLAKEVVERRFFGRPTIFLKVVAKVPED

(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	0.5089

(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	7lgpA1	0.44	4.04	0.014	0.810	model1_7lgpA1.pdb.gz
2	3bujA	0.44	4.04	0.065	0.848	model1_3bujA.pdb.gz
3	1s31A	0.44	3.63	0.042	0.797	model1_1s31A.pdb.gz
4	6ro8A	0.44	4.15	0.026	0.861	model1_6ro8A.pdb.gz
5	5jnqA	0.44	4.28	0.080	0.886	model1_5jnqA.pdb.gz
6	6g71A	0.44	4.36	0.065	0.873	model1_6g71A.pdb.gz
7	3bpmA	0.44	4.78	0.038	0.924	model1_3bpmA.pdb.gz
8	4j72A	0.44	4.12	0.013	0.835	model1_4j72A.pdb.gz
9	1yvbA	0.44	4.70	0.038	0.899	model1_1yvbA.pdb.gz
10	5gweA	0.44	3.90	0.079	0.823	model1_5gweA.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:0003700	0.91	transcription factor activity, sequence-specific DNA binding
GO:0046983	0.90	protein dimerization activity
GO:0001077	0.90	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0046982	0.73	protein heterodimerization activity
GO:1901363	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound binding
GO:0003676	0.61	nucleic acid binding
GO:0003677	0.60	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:0030154	1.00	cell differentiation
GO:0065007	0.80	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0080090	0.72	regulation of primary metabolic process
GO:0071542	0.72	dopaminergic neuron differentiation
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0048518	0.72	positive regulation of biological process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0048522	0.71	positive regulation of cellular process
GO:0050896	0.70	response to stimulus
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0006355	0.70	regulation of transcription, DNA-templated
GO:0045893	0.69	positive regulation of transcription, DNA-templated
GO:0010033	0.69	response to organic substance
GO:1901700	0.68	response to oxygen-containing compound
GO:0045944	0.68	positive regulation of transcription from RNA polymerase II promoter
GO:0009719	0.68	response to endogenous stimulus
GO:0071376	0.67	cellular response to corticotropin-releasing hormone stimulus
GO:0045444	0.67	fat cell differentiation
GO:0008152	0.66	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0044238	0.58	primary metabolic process
GO:0032502	0.58	developmental process
GO:0044767	0.57	single-organism developmental process
GO:0043170	0.55	macromolecule metabolic process
GO:1901360	0.54	organic cyclic compound metabolic process
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0009058	0.54	biosynthetic process
GO:1901362	0.53	organic cyclic compound biosynthetic process
GO:0048856	0.53	anatomical structure development
GO:0034641	0.53	cellular nitrogen compound metabolic process
GO:0032774	0.52	RNA biosynthetic 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:0044424	1.00	intracellular part
GO:0043229	0.79	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0005634	0.77	nucleus
GO:0044446	0.72	intracellular organelle part
GO:0044428	0.69	nuclear part
GO:0005654	0.54	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	2q3uA	0.337	3.90	0.058	0.646	3.5.3.12	NA
2	0.060	1i8dA	0.421	4.66	0.052	0.911	2.5.1.9	NA
3	0.060	1deuA	0.411	4.68	0.013	0.937	3.4.18.1	9
4	0.060	3b46B	0.425	4.33	0.065	0.873	2.6.1.7	NA
5	0.060	1kfyA	0.409	3.77	0.092	0.772	1.3.99.1	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	1d4cA	0.429	3.39	0.032	0.734	0.21	HEM	complex1.pdb.gz	9,15,37,41
2	0.01	1d4dA	0.412	3.34	0.034	0.696	0.13	HEM	complex2.pdb.gz	3,8,9
3	0.01	1theA	0.321	4.98	0.076	0.797	0.13	0E6	complex3.pdb.gz	13,61,65

	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.