Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 185 bits (469), Expect = 3e-51 Identities = 142/435 (32%), Positives = 215/435 (49%), Gaps = 27/435 (6%) Query: 67 LGPSLFHYYQKPL--NIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQS 124 + PS Y P + K YL+DE+GR+YLD +G ++ + GH DI A+ Q Sbjct: 1 MDPSHLFYQAGPALPEVSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQL 60 Query: 125 KLLQHATTIYLHHAIG-DFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGSL-- 181 + +A A+AL L+ V+FV+SGSEA E A+ +AR Y + Sbjct: 61 DRVAFTYRTQFENAPAVALAKALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGE 120 Query: 182 ----EMISLRNAYHGGSSNTIGLTALNTWKYPLPQGEIHH--VVNPDPYRGVFGSDGSLY 235 +SLR +YHG + +G+T + P I V PD YR DG Sbjct: 121 PQRRRFVSLRPSYHGSTLGALGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHV 180 Query: 236 AK---DVHDHIEYGTSGKVAGFIAETIQGVG-GAVELAPGYLKSVYEIVRNAGGVCIADE 291 A+ D IE +A F+ E + G GA +L YL + + G + I DE Sbjct: 181 ARVLADTRAAIEAAGPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDE 240 Query: 292 VQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGL-PLGAVVTTPEIASVLASKILF--- 347 V TG GRTG+ ++ +Q V PD+++ AKG+G G P+GAV++ +I + + F Sbjct: 241 VLTGIGRTGT-WFAYQHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHG 299 Query: 348 NTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMV 407 +T+ GNP+ A GLAV+ I++EK ++ A G L L+ ++ R +GDVRG GL+ Sbjct: 300 HTYAGNPLACATGLAVVEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLW 359 Query: 408 GIELVSDRKDKTPAKAET---SVLFEQLRELGILV----GKGGLHGNVFRIKPPMCFTKD 460 G+ELV+D K P AE + + RE G+L+ G+ G+ F I PP+ Sbjct: 360 GVELVADAASKAPFPAEQNRFARITALAREEGLLIYPRRTLDGIAGDHFLITPPLTIDAA 419 Query: 461 DADFLVDALDYSISR 475 D L+ L+ ++ R Sbjct: 420 DTAELLTRLERAMQR 434 Lambda K H 0.320 0.138 0.412 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: 535 Number of extensions: 31 Number of successful extensions: 6 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: 476 Length of database: 450 Length adjustment: 33 Effective length of query: 443 Effective length of database: 417 Effective search space: 184731 Effective search space used: 184731 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 10 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