D29p05

CDS : 2686-3153, 468 bp,:  gp5 predicted 17.1 kD protein (155 Aa)



By Snapgen software:

 
 By Artemis software:

D29p04

CDS :   2354-2650, 297 bp,  :  gp4 predicted 11.1 kD protein (98 Aa)
misc_feature: 2405-2569, 165 bp,HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085
misc_feature:2486-2569,active site


By Snapgen software:

By Artemis software:

Aa sequence (98Aa):

misc_feature  HNH nucleases, Aa sequence ( 55Aa):

 misc_feature ;active site,Aa sequence :DDHKPNLCRHS


misc-features: start and end:

 HNH nucleases

HNH motifs:

 consensus: e-x-h-H-i-x-p-x(2,4)-g-x(5,6)-N-l-x(3)-t-p-x(2,3)-H-x(3)-h ; capitalized letters are most conserved.


Scientific works: 

My contribution
By mJemboss software 

Statistics on the protein properties:

  
 one signal cleavage site in  the protein sequence:
 

Poor Pest motif:

Virtual 2G-gel:

In the sequence there are two motifs:

-DVDHK ( D/E X)K


-HSRSNLQAICRVCH

consensus:e-x-h-H-i-x-p-x(2,4)-g-x(5,6)-N-l-x(3)-t-p-x(2,3)-H-x(3)-h

D29p03

CDS :   2106-2357, 252 bp,  : predicted 9.0 kD protein (83 Aa)
misc_feature: 2142-2294, 153 bp, SdiA-regulated; Region: SdiA-regulated; cl19046

By Snapgen software:

By Artemis software:

Aa sequence (83 Aa):

 

misc_feature Aa sequence:

Region: SdiA-regulated; cl19046

Statistics on the protein properties:

-No helix-turn-helix nucleic acid binding motifs
 
-No prediction of transmembrane segments in protein 

- No PEST motif as potential proteolytic cleavage site 

- N0 site of cleavage between a signal sequence and the "mature exported protein"



Virtual 2D-gel:

D29p02

CDS :    1327-2106, 780 bp,  : predicted 28.8 kD protein (259 Aa)

misc_feature: 1570-1815, 246 bp, Protein of unknown function (DUF3626); Region: DUF3626; pfam12294    
 
By Snapgen software:
                                                     

By Artemis software:

Protein of unknown function (DUF3626)

"This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length".

 misc_feature Aa sequence:

Aa sequence (259 Aa):

Statistics on the protein properties:

-No helix-turn-helix nucleic acid binding motifs
 
-No prediction of transmembrane segments in protein 

- No PEST motif as potential proteolytic cleavage site 

- N0 site of cleavage between a signal sequence and the "mature exported protein"

Virtual 2D-gel:

Is there a relationship with gp12? :

CDS:            6606-7370,765bp, gp12 :predicted 28.5 kD protein (254 Aa)
misc_feature: 6726-6983,258bp,Cutinase; Region: Cutinase; pfam01083


Statistics on the protein properties:

Cutinase and cutin is the substrate

1- CUTINASE_1, PS00155; Cutinase, serine active site  (PATTERN)

 Consensus pattern:
P-x-[STA]-x-[LIV]-[IVT]-x-[GS]-G-Y-S-[QL]-G
S is an active site residue

2- CUTINASE_2, PS00931; Cutinase, aspartate and histidine active sites  (PATTERN)

 Consensus pattern:
C-x(3)-D-x-[IV]-C-x-G-[GST]-x(2)-[LIVM]-x(2,3)-H
D and H are active site residues


My contribution:

by Artemis software I download the  Fasta sequence of CDS of gp12 and by Jemboss software  I analyse the Aa sequence in search for these consensus patterns:

 

There is  in gp12 only one consensus pattern: PYAX5GYSQG is inside  of the cutinase region and gp12 is the Lysin B of Mycobacteriophage D29.

 In the hypothetical protein from D29p02:
 

There is not consensus for cutinase activity but there is one motif for a nuclease activity:D X5 (DAK)

Deduction
The hypothetical protein from D29p02 is not correlated  to the gp12 protein.

D29p01

CDS:     401-1213, 813 bp, gp1: predicted 30.3 kD protein (270 Aa)

misc_feature: 461-1048,588 bp, Domain of unknown function
(DUF4417);Region: DUF4417; pfam14386

  By Snapgene software:

By Artemis software:

 
 Domain of unknown function (DUF4417) 
"This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 220 and 340 amino acids in length. There is a single completely conserved residue G (glycine) that may be functionally important".

 Pfam 
 Is a database of protein families (a protein family is a group of evolutionarily-related proteins, and is often nearly synonymous with gene family) that includes their annotations and multiple sequence alignments generated using hidden Markov models.


misc_feature Aa sequence:

Aa sequence (270 Aa):

-No helix-turn-helix nucleic acid binding motifs
 
-No prediction of transmembrane segments in protein 

- one PEST motif as potential proteolytic cleavage site 

- one site of cleavage between a signal sequence and the "mature exported protein"

  hypothetical "sequence" after cuttings

Virtual 2D-gel:

Is there a relationship with gp69 ?

CDS: 44,061-44,870, 810 bp, gp69: predicted 30.7 kD protein(269 Aa)

misc_feature: 44,262-44,843,582 bp, PD-(D/E)XK nuclease superfamily;Region:   PDDEXK_1; pfam12705

 statistics on the protein properties:

 
here

"PD-(D/E)XK nucleases comprise a large and extremely diverse group of proteins that are involved in various processes of nucleic acid metabolism. Typically, different PD-(D/E)XK families share little or no recognizable sequence similarity except for the conserved signature of the active site. As it happens, the name of this large group of nucleases derives from the highly conserved ‘PD’ (in many cases only ‘D’) and ‘(D/E)XK’ (‘X’ denotes the non-conserved position) active site motifs".

 here

  
My contribution:
in practice I verify if there is the Catalytic motif (P)D...Xn...(D/E)XK (where X is any aminoacid) in the sequences.

by Artemis software I download the  Fasta sequence of gp1 CDS and by Jemboss software  I analyse the Aa sequence:

!!!!!!!there are two catalytic motifs.

In the same way for gp69

!!!!!!!there are two catalytic motifs.

gp1 and gp69 have two Catalytic motif (P)D...Xn...(D/E)XK. One catalytic motif :   DX12(DXK)   in the sequences is in the same lenght.

Dot plot by Gepard software:

Deduction:
gp1 could be a protein with the same activity of  the protein gp69.