Differences between Mtu strains
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| + | (never mind, I found out that the good people at http://www.tbdb.org have already done this) | ||
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There are several ways to look at pairwise differences between | There are several ways to look at pairwise differences between | ||
Mtu strains: | Mtu strains: | ||
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|2:1 | |2:1 | ||
|{{UniProt2|A5U119|MRA_0985}}, {{UniProt2|A5U122|MRA_0987}} | |{{UniProt2|A5U119|MRA_0985}}, {{UniProt2|A5U122|MRA_0987}} | ||
| - | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX12868.1 | + | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX12868.1 TBFG_00986] |
| (Rv00980c, Rv00986c) PE-PGRS family proteins | | (Rv00980c, Rv00986c) PE-PGRS family proteins | ||
|- | |- | ||
| Line 50: | Line 52: | ||
| [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX15309.1 TBFG_03453] | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX15309.1 TBFG_03453] | ||
| (Rv1587c) REP13E12 repeat protein; (Rv3467) unchar. | | (Rv1587c) REP13E12 repeat protein; (Rv3467) unchar. | ||
| + | |- | ||
| + | |2:1 | ||
| + | |{{UniProt2|A5U5B9|MRA_2450}}, {{UniProt2|A5U4K4|MRA_2192}} | ||
| + | | {{UniProt2|A5WQ40|TBFG_02411}} | ||
| + | | (Rv2424c) (transposase IS116/IS110/IS902 family protein) | ||
| + | |- | ||
| + | |2:1 | ||
| + | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=ABQ75300.1 MRA_3515], {{UniProt2|A5U601|MRA_2672}} | ||
| + | | {{UniProt2|A5WQ40|TBFG_02411}} | ||
| + | | (Rv3475) (transposase IS6110); (Rv1764) (transposase IS1558) | ||
| + | |- | ||
| + | |2:1 | ||
| + | |{{UniProt2|A5U618|MRA_2694}}, {{UniProt2|A5U192|MRA_3147}} | ||
| + | | {{UniProt2|A5WQR9|TBFG_02644}} | ||
| + | | Truncated IS1081 transposase; (Rv2512c) transposase IS1081 | ||
| + | |- | ||
| + | |2:1 | ||
| + | |{{UniProt2|A5U440|MRA_2031}}, {{UniProt2|A5U3D3|MRA_1780}} | ||
| + | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX13633.1 TBFG_01760] | ||
| + | | (Rv1765c) (HNH endonuclease) | ||
| + | |- | ||
| + | |2:1 | ||
| + | |{{UniProt2|A5U544|MRA_2375}}, {{UniProt2|A5U8U4|MRA_3656}} | ||
| + | | {{UniProt2|A5WTI7|TBFG_03607}} | ||
| + | | (Rv3620c) (ESAT-6-like protein) | ||
| + | |- | ||
| + | |n:m | ||
| + | |{{UniProt2|A5TZ63|MRA_0345}}, {{UniProt2|A5TZP5|MRA_0522}} | ||
| + | | [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EAX12222.1 TBFG_00333], {{UniProt2|A5WJN0|TBFG_00515}} | ||
| + | | (Rv0336, Rv0515) Conserved 13E12 repeat family protein (HNH endonuclease) | ||
| + | |- | ||
| + | |n:m | ||
| + | |{{UniProt2|A5U182|MRA_1086}}, {{UniProt2|A5U1P5|MRA_1206}}, {{UniProt2|A5U536|MRA_2367}}, {{UniProt2|A5U544|MRA_2375}}, {{UniProt2|A5U8U4|MRA_3656}} | ||
| + | | {{UniProt2|A5WL60|TBFG_01043}}, {{UniProt2|A5WLM5|TBFG_01203}}, {{UniProt2|A5WPW1|TBFG_02331}}, {{UniProt2|A5WTI7|TBFG_03607}} | ||
| + | | (Rv1038) ESAT-6-like protein '''esxJ'''; (Rv1197) '''esxK'''; (Rv2347c) '''esxP'''; (Rv3620c) (ESAT-6-like protein) | ||
| + | |- | ||
| + | |''continued'' | ||
|- | |- | ||
|} | |} | ||
| + | |||
| + | == References == | ||
| + | * Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, and Gaston H. Gonnet: ''OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements.'' In: A. McLysaght et al. (Eds): ''RECOMB 2005 Workshop on Comparative Genomics'', LNBI 3687, pp. 61-72 | ||
| + | * Altenhoff, Adrian M. & Dessimoz, Christophe: ''Phylogenetic and Functional Assessment of Orthologs Inference.'' In: PLoS Comput Biol , Vol. 5 , Nr. 1 Public Library of Science , 01 (2009) , S. e1000262 . | ||
Current revision
(never mind, I found out that the good people at http://www.tbdb.org have already done this)
There are several ways to look at pairwise differences between Mtu strains:
- pairwise differences in the nucleotids of the genomes
- pairwise differences in the amino acid sequences
- pairwise proteomic differences (orthologs, missing genes, gene doubling, additions like prophages)
- pairwise functional differences where known
Since we now have complete genomes of several strains of Mtu, and we have pairs of orthologs for both from a highly accurate algorithm (OMA), and the highly correct phylogenetic trees from OMA show us which strains are nearest, we can most easily give orthologs and paralogs between nearest pairs of strains.
| name | H37Ra | F11 | (H37Rv) function |
|---|---|---|---|
| number of genes | 3990 | 3855 | |
| 1:1 orthologs | 3725 | see this file | |
| 1:n orthologs | 0 | ||
| n:1 orthologs | 12 | ||
| n:m orthologs | 40 | ||
| 2:1 | MRA_0985, MRA_0987 | TBFG_00986 | (Rv00980c, Rv00986c) PE-PGRS family proteins |
| 2:1 | MRA_1598, MRA_3507 | TBFG_03453 | (Rv1587c) REP13E12 repeat protein; (Rv3467) unchar. |
| 2:1 | MRA_2450, MRA_2192 | TBFG_02411 | (Rv2424c) (transposase IS116/IS110/IS902 family protein) |
| 2:1 | MRA_3515, MRA_2672 | TBFG_02411 | (Rv3475) (transposase IS6110); (Rv1764) (transposase IS1558) |
| 2:1 | MRA_2694, MRA_3147 | TBFG_02644 | Truncated IS1081 transposase; (Rv2512c) transposase IS1081 |
| 2:1 | MRA_2031, MRA_1780 | TBFG_01760 | (Rv1765c) (HNH endonuclease) |
| 2:1 | MRA_2375, MRA_3656 | TBFG_03607 | (Rv3620c) (ESAT-6-like protein) |
| n:m | MRA_0345, MRA_0522 | TBFG_00333, TBFG_00515 | (Rv0336, Rv0515) Conserved 13E12 repeat family protein (HNH endonuclease) |
| n:m | MRA_1086, MRA_1206, MRA_2367, MRA_2375, MRA_3656 | TBFG_01043, TBFG_01203, TBFG_02331, TBFG_03607 | (Rv1038) ESAT-6-like protein esxJ; (Rv1197) esxK; (Rv2347c) esxP; (Rv3620c) (ESAT-6-like protein) |
| continued | |||
[edit] References
- Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, and Gaston H. Gonnet: OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. In: A. McLysaght et al. (Eds): RECOMB 2005 Workshop on Comparative Genomics, LNBI 3687, pp. 61-72
- Altenhoff, Adrian M. & Dessimoz, Christophe: Phylogenetic and Functional Assessment of Orthologs Inference. In: PLoS Comput Biol , Vol. 5 , Nr. 1 Public Library of Science , 01 (2009) , S. e1000262 .
