Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 167 bits (424), Expect = 4e-46 Identities = 123/389 (31%), Positives = 186/389 (47%), Gaps = 46/389 (11%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIADFSEALAS 150 ++D + ++YLD + G AV++ GH +P V + +Q+ ++ Y N LA Sbjct: 22 VWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVG----FYSNSVKIPLQVQLAE 77 Query: 151 KLPGDLK-----VVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ 205 KL G++ +F NSG EANE AL +A Y G + ++A +HG + + T Sbjct: 78 KL-GEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHGRTSLAVAVTDN 136 Query: 206 S--MWKFNVVQNSVHHALNPD-PYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQ 262 + N +N + N + F + G + I+ I E IQ Sbjct: 137 PKIVAPVNQTENVIFLPFNNEIALEETFKAQGNE----------------ISAVIIEGIQ 180 Query: 263 GVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKG 322 GVGGI E + +L + ++IAD VQ G+ RTG+F+ + V D+ TMAKG Sbjct: 181 GVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKG 240 Query: 323 IGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGS 382 +GNGFP+ + + TFGGN ++ A LAVL V+EK+ L +NA VG+ Sbjct: 241 MGNGFPVAGISIASKFKP--WHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGN 298 Query: 383 YLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGK 442 YL +L +K E + +VRGRGLM+G+EL AE H+ ++ I Sbjct: 299 YLIAEL----KKFEQVVEVRGRGLMIGIEL----------PAELAHVKKELL-FTHHIFT 343 Query: 443 GGYFGNVFRITPPLCFTKDDADFLVEAMD 471 G NV R+ P L TK AD + A + Sbjct: 344 GEAKPNVIRLLPALNLTKAHADEFLAAFE 372 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: 429 Number of extensions: 25 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: 382 Length adjustment: 32 Effective length of query: 445 Effective length of database: 350 Effective search space: 155750 Effective search space used: 155750 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