Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_015798369.1 AFER_RS04845 aspartate aminotransferase family protein
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000023265.1:WP_015798369.1 Length = 431 Score = 273 bits (698), Expect = 8e-78 Identities = 155/421 (36%), Positives = 229/421 (54%), Gaps = 18/421 (4%) Query: 63 EIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVV 122 ++I + R L L +Y+ P+ + + +V+D +G RYLD FGGI T S GH PE+V Sbjct: 2 DLIERHRRVLPSWLSLYYDEPIELDRGEGCWVWDAHGERYLDCFGGILTTSVGHNVPEIV 61 Query: 123 NSVVKQLKLINHSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLY 182 +++ Q + HS+ LYLN + + AE L VFFT SGTEAN+ A+++A Sbjct: 62 SAISDQAARVIHSSTLYLNRPMIELAERLAKASGIPDAKVFFTTSGTEANDAALLLATAA 121 Query: 183 TGCNDIVSLRNSYHGNAAATMGATAQSNWK--------FNVVQSGVHHAINPDPYRGIFG 234 G N + +LRNSYHG + + T W + +Q G P G+ Sbjct: 122 LGSNQVFALRNSYHGRSFTEIAVTGNRTWSPTSYSPLSVSWLQGGSRLR---GPLAGL-- 176 Query: 235 SDGEKYA---SDVHDLIQFGTSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGV 291 SD E A +D+ D + T+G+VA I E IQGVGG GY + + ++ G + Sbjct: 177 SDAEYVARGVADLEDALLTTTAGRVAALIAEPIQGVGGFCLPPDGYFGELWRVTQREGIL 236 Query: 292 CIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSY 351 I+DEVQ+GF RTG HFWG+++HG+ PD++T AKG+GNG+ L V+ E+ L S Sbjct: 237 WISDEVQTGFGRTGEHFWGYEAHGITPDLITFAKGVGNGMSLAGVIGRAEVMDALGTNS- 295 Query: 352 FNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLM 411 +TFGG+P+ AAG A + + L NA G+ L+ L + IG+VRG+GLM Sbjct: 296 ISTFGGSPITAAAGVATFDYIIDHDLMANARARGAELREGLDAIARSTPAIGEVRGKGLM 355 Query: 412 LGVEFVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLV 471 GVE V ++ PA ++ + GVL+GKGG +GNV RI PP+ + + + Sbjct: 356 QGVELVWPGTVE-PAPELATRALEAARREGVLIGKGGLHGNVLRIAPPMTISAEQIEHAL 414 Query: 472 D 472 + Sbjct: 415 E 415 Lambda K H 0.320 0.136 0.406 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: 557 Number of extensions: 19 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: 481 Length of database: 431 Length adjustment: 33 Effective length of query: 448 Effective length of database: 398 Effective search space: 178304 Effective search space used: 178304 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