Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 188 bits (477), Expect = 3e-52 Identities = 120/382 (31%), Positives = 187/382 (48%), Gaps = 38/382 (9%) Query: 90 YLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVL--YLNHAIADFSEA 147 Y++ G +Y+D +GI V N GH HP V++ + +Q+ + H V Y+ ++A Sbjct: 30 YMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGEYVQSPQTQLAKA 89 Query: 148 LASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSM 207 L LP L V+ NSG+EA E AL +AK YTG ++I++ N YHG++ + G + Sbjct: 90 LTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYTGRREILSCVNAYHGSSHGALSVGGNEI 149 Query: 208 WK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQGVG 265 +K + + + H +P D D I T A + E +QG Sbjct: 150 FKRAYRPLLPGIRHLDFNEP--------------DQLDQI----TEETAAIMVETVQGEA 191 Query: 266 GIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIGN 325 GI Y A + G L I DE+Q+GF RTG FW F+ +++VPDIV AKG+G Sbjct: 192 GIRVGTKEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGG 251 Query: 326 GFPLGAVVTTPEIAGVLTRR---SYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGS 382 G P+GA + I V + TFGG+ VS A LA ++++ EKL ++ + Sbjct: 252 GMPIGAFIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVERKAN 311 Query: 383 YLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGK 442 K+ L H I ++R +GLM+ V+ + LK I+D+ ELG++ Sbjct: 312 LFKKHL-----NHPKIQEIRNKGLMMAVKFEAFEVLKP--------IIDRAIELGIITDW 358 Query: 443 GGYFGNVFRITPPLCFTKDDAD 464 + + RI PPL T ++ + Sbjct: 359 FLFCEDSMRIAPPLTITDEEIE 380 Lambda K H 0.320 0.136 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 427 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 477 Length of database: 393 Length adjustment: 32 Effective length of query: 445 Effective length of database: 361 Effective search space: 160645 Effective search space used: 160645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory