Difference between revisions of "Claudia's Assignment"

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(Introduction)
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==Cation Pumps==
 
==Cation Pumps==
 +
 
The following is a list of the cation pumps and cation-influenced structures encoded in our organism's genome:
 
The following is a list of the cation pumps and cation-influenced structures encoded in our organism's genome:
  
Line 9: Line 10:
 
A BLAST (megablast) of the gene encoding this ion pump produced the following results:<br>
 
A BLAST (megablast) of the gene encoding this ion pump produced the following results:<br>
 
[[Image:Picture 5.png]]
 
[[Image:Picture 5.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032129 Kef-type K+ ransport system, predicted NAD-binding component 644032129]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032129 Kef-type K+ ransport system, predicted NAD-binding component 644032129]<br>
Line 14: Line 16:
 
A BLAST (blastn) of the gene encoding this ion pump produced the following results:<br>
 
A BLAST (blastn) of the gene encoding this ion pump produced the following results:<br>
 
[[Image:Picture 6.png]]
 
[[Image:Picture 6.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032240 Ca2+/Na+ antiporter 644032240]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032240 Ca2+/Na+ antiporter 644032240]<br>
Line 19: Line 22:
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 7.png]]
 
[[Image:Picture 7.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032307 Mn2+/Fe2_ transporter, NRAMP family 644032307]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032307 Mn2+/Fe2_ transporter, NRAMP family 644032307]<br>
 
A BLAST using megablast produced the following results:<br>
 
A BLAST using megablast produced the following results:<br>
 
[[Image:Picture 8.png]]
 
[[Image:Picture 8.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032373 H(+)-transporting ATP synthase, vacuolar type, subunit D ( EC:3.6.3.14 ) 644032373]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032373 H(+)-transporting ATP synthase, vacuolar type, subunit D ( EC:3.6.3.14 ) 644032373]<br>
 
A BLAST using megablast produced the following results:<br>
 
A BLAST using megablast produced the following results:<br>
 
[[Image:Picture 10.png]]<br>
 
[[Image:Picture 10.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 11.png]]
 
[[Image:Picture 11.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032378 archaeal/vacuolar-type H+-ATPase subunit B ( EC:3.6.3.14 ) 644032378]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032378 archaeal/vacuolar-type H+-ATPase subunit B ( EC:3.6.3.14 ) 644032378]<br>
 
A BLAST using megablast produced the following results:<br>
 
A BLAST using megablast produced the following results:<br>
 
[[Image:Picture 12.png]]<br>
 
[[Image:Picture 12.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 13.png]]
 
[[Image:Picture 13.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032380 archaeal/vacuolar-type H+-ATPase subunit F ( EC:3.6.3.14 ) 644032380]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032380 archaeal/vacuolar-type H+-ATPase subunit F ( EC:3.6.3.14 ) 644032380]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 14.png]]
 
[[Image:Picture 14.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032382 archaeal/vacuolar-type H+-ATPase subunit E ( EC:3.6.3.14 ) 644032382]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032382 archaeal/vacuolar-type H+-ATPase subunit E ( EC:3.6.3.14 ) 644032382]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 15.png]]
 
[[Image:Picture 15.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032384 archaeal/vacuolar-type H+-ATPase subunit I ( EC:3.6.3.14 ) 644032384]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032384 archaeal/vacuolar-type H+-ATPase subunit I ( EC:3.6.3.14 ) 644032384]<br>
 
A BLAST using megablast produced the following results:<br>
 
A BLAST using megablast produced the following results:<br>
 
[[Image:Picture 16.png]]<br>
 
[[Image:Picture 16.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 17.png]]
 
[[Image:Picture 17.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032472 K+ transport system, NAD-binding component 644032472]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032472 K+ transport system, NAD-binding component 644032472]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blast n produced the following results:<br>
 
A BLAST using blast n produced the following results:<br>
 
[[Image:Picture 18.png]]
 
[[Image:Picture 18.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032488 NAD+ synthetase ( EC:6.3.5.1 ) 644032488]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032488 NAD+ synthetase ( EC:6.3.5.1 ) 644032488]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 19.png]]
 
[[Image:Picture 19.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032494 NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) (IMGterm) 644032494]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032494 NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) (IMGterm) 644032494]<br>
Line 67: Line 86:
 
[[Image:Picture 22.png]]<br>
 
[[Image:Picture 22.png]]<br>
 
[[Image:Picture 21.png]]<br>
 
[[Image:Picture 21.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 24.png]]
 
[[Image:Picture 24.png]]
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032648 ABC-type Mn2+/Zn2+ transport system, permease component 644032648]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032648 ABC-type Mn2+/Zn2+ transport system, permease component 644032648]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blast n produced the following results:<br>
 
A BLAST using blast n produced the following results:<br>
 
[[Image:Picture 27.png]]<br>
 
[[Image:Picture 27.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component 644032689]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component 644032689]<br>
Line 81: Line 104:
 
Trk active potassium channel<br>
 
Trk active potassium channel<br>
 
Potassium channel protein<br>
 
Potassium channel protein<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Picture 30.png]]<br>
 
[[Image:Picture 30.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032725 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit ( EC:1.6.5.3 ) 644032725]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032725 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit ( EC:1.6.5.3 ) 644032725]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic3.png]]<br>
 
[[Image:Pic3.png]]<br>
 
[[Image:Pic1.png]]<br>
 
[[Image:Pic1.png]]<br>
 
[[Image:Pic2.png]]<br>
 
[[Image:Pic2.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032854Kef-type K+ transport system, membrane component 644032854]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032854Kef-type K+ transport system, membrane component 644032854]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic4.png]]<br>
 
[[Image:Pic4.png]]<br>
 
[[Image:Pic5.png]]<br>
 
[[Image:Pic5.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032916 NhaP-type Na+(K+)/H+ antiporter 644032916]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032916 NhaP-type Na+(K+)/H+ antiporter 644032916]<br>
Line 101: Line 130:
 
[[Image:Pic6.png]]<br>
 
[[Image:Pic6.png]]<br>
 
[[Image:Pic7.png]]<br>
 
[[Image:Pic7.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic8.png]]<br>
 
[[Image:Pic8.png]]<br>
 
[[Image:Pic9.png]]<br>
 
[[Image:Pic9.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032920 AAA+ family ATPase 644032920]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032920 AAA+ family ATPase 644032920]<br>
Line 109: Line 140:
 
[[Image:Pic10.png]]<br>
 
[[Image:Pic10.png]]<br>
 
[[Image:Pic11.png]]<br>
 
[[Image:Pic11.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic12.png]]<br>
 
[[Image:Pic12.png]]<br>
 
[[Image:Pic13.png]]<br>
 
[[Image:Pic13.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033032 ABC-type Fe3+ transport system, periplasmic component 644033032]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033032 ABC-type Fe3+ transport system, periplasmic component 644033032]<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 
A BLAST using megablast produced no results other than our own species.<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic14.png]]<br>
 
[[Image:Pic14.png]]<br>
 
[[Image:Pic15.png]]<br>
 
[[Image:Pic15.png]]<br>
 +
  
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033110 ABC-type Mn2+/Zn2+ transport system, permease component 644033110]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033110 ABC-type Mn2+/Zn2+ transport system, permease component 644033110]<br>
Line 123: Line 158:
 
[[Image:Pic16.png]]<br>
 
[[Image:Pic16.png]]<br>
 
[[Image:Pic17.png]]<br>
 
[[Image:Pic17.png]]<br>
 +
 
A BLAST using blastn produced the following results:<br>
 
A BLAST using blastn produced the following results:<br>
 
[[Image:Pic18.png]]<br>
 
[[Image:Pic18.png]]<br>
 
[[Image:Pic19.png]]<br>
 
[[Image:Pic19.png]]<br>

Revision as of 04:15, 1 October 2009

Introduction

From the background information on our species, Halomicrobium mukohataei, we know that our organism is not only a halophile, or salt-loving, but also that the organism in fact requires a high salinity environment to survive. This trait is unique and compelling because of the harsh environment and the many pumps and mechanisms that must be present for an living organism to survive. However, our organism is not the only one to have such adaptations. There are a number of halophile species as well as a number of salt-tolerant organisms, including a number of bacteria and a few yeasts.
Originally, I wanted to look into the genes that encoded adaptations to the high-salinity environment, specifically ion (cation) pumps. Of the proteins with known functions, our organism appears to encode 21 different proteins functioning as ion or ion-dependent pumps. I wanted to investigate these pumps, and their roles within the organism's metabolic pathways.

Cation Pumps

The following is a list of the cation pumps and cation-influenced structures encoded in our organism's genome:

Na+/proline symporter 644032116
A BLAST (megablast) of the gene encoding this ion pump produced the following results:
Picture 5.png


Kef-type K+ ransport system, predicted NAD-binding component 644032129
A BLAST using megablast produced no results other than our own species.
A BLAST (blastn) of the gene encoding this ion pump produced the following results:
Picture 6.png


Ca2+/Na+ antiporter 644032240
A BLAST using megablast produced no results other than our own species.
A BLAST using blastn produced the following results:
Picture 7.png


Mn2+/Fe2_ transporter, NRAMP family 644032307
A BLAST using megablast produced the following results:
Picture 8.png


H(+)-transporting ATP synthase, vacuolar type, subunit D ( EC:3.6.3.14 ) 644032373
A BLAST using megablast produced the following results:
Picture 10.png

A BLAST using blastn produced the following results:
Picture 11.png


archaeal/vacuolar-type H+-ATPase subunit B ( EC:3.6.3.14 ) 644032378
A BLAST using megablast produced the following results:
Picture 12.png

A BLAST using blastn produced the following results:
Picture 13.png


archaeal/vacuolar-type H+-ATPase subunit F ( EC:3.6.3.14 ) 644032380
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Picture 14.png


archaeal/vacuolar-type H+-ATPase subunit E ( EC:3.6.3.14 ) 644032382
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Picture 15.png


archaeal/vacuolar-type H+-ATPase subunit I ( EC:3.6.3.14 ) 644032384
A BLAST using megablast produced the following results:
Picture 16.png

A BLAST using blastn produced the following results:
Picture 17.png


K+ transport system, NAD-binding component 644032472
A BLAST using megablast produced no results other than our own species.

A BLAST using blast n produced the following results:
Picture 18.png


NAD+ synthetase ( EC:6.3.5.1 ) 644032488
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Picture 19.png


NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) (IMGterm) 644032494
A BLAST using megablast produced the following results:
Picture 20.png
Picture 22.png
Picture 21.png

A BLAST using blastn produced the following results:
Picture 24.png


ABC-type Mn2+/Zn2+ transport system, permease component 644032648
A BLAST using megablast produced no results other than our own species.

A BLAST using blast n produced the following results:
File:Picture 27.png


K+ transport system, NAD-binding component 644032689
A BLAST using megablast produced the following results:
Picture 28.png
Picture 29.png
Trk active potassium channel
Potassium channel protein

A BLAST using blastn produced the following results:
Picture 30.png


NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit ( EC:1.6.5.3 ) 644032725
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Pic3.png
Pic1.png
Pic2.png


K+ transport system, membrane component 644032854
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Pic4.png
Pic5.png


NhaP-type Na+(K+)/H+ antiporter 644032916
A BLAST using megablast produced the following results:
Pic6.png
Pic7.png

A BLAST using blastn produced the following results:
Pic8.png
Pic9.png


AAA+ family ATPase 644032920
A BLAST using megablast produced the following results:
Pic10.png
Pic11.png

A BLAST using blastn produced the following results:
Pic12.png
Pic13.png


ABC-type Fe3+ transport system, periplasmic component 644033032
A BLAST using megablast produced no results other than our own species.

A BLAST using blastn produced the following results:
Pic14.png
Pic15.png


ABC-type Mn2+/Zn2+ transport system, permease component 644033110
A BLAST using megablast produced the following results:
Pic16.png
Pic17.png

A BLAST using blastn produced the following results:
Pic18.png
Pic19.png