Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 186 bits (473), Expect = 1e-51 Identities = 133/429 (31%), Positives = 202/429 (47%), Gaps = 49/429 (11%) Query: 63 EIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVV 122 E + R E L + Y P+++ + ++D +GR Y+D GIA S GHCH E+ Sbjct: 6 EALKAREESLLCRTYGRY--PISVARGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELA 63 Query: 123 NSVVKQLKLINHSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLY 182 Q + + H + L+ D AE L+ST FF NSG EANE A+ +AR Y Sbjct: 64 EVAAAQARKLVHVSNLFYQEEQLDLAERLLST--SHCTKAFFCNSGAEANEAAIKLARRY 121 Query: 183 TG------CNDIVSLRNSYHGNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGSD 236 +I++L ++HG AT+ AT Q+ + Q G + P+ +R + D Sbjct: 122 MQRVQGREAYEIITLTGAFHGRTLATVAATGQAKF-----QDGFYPM--PEGFRQVPSGD 174 Query: 237 GEKYASDVHDLIQFGTSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADE 296 E + + Q AG + E +QG GG+ L P Y A + R+ G + + DE Sbjct: 175 IEALRAAI--------GPQTAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDE 226 Query: 297 VQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFG 356 +Q+G RTG FW FQ++G+ PDIV+ AK + NG+P+GA++TT E+A S+ TFG Sbjct: 227 IQAGMCRTG-RFWSFQNYGLEPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFG 285 Query: 357 GNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYE-LIGDVRGRGLMLGVE 415 + +A + ++ + L A G+ + R + K I VRG GLM+GV Sbjct: 286 AGALVSAVASRTVEIMLRDDLAGRAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVV 345 Query: 416 FVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGN-----VFRITPPLCFTLSDADFL 470 L P K L+D+ GF N V R+ P L +D D Sbjct: 346 ------LAFPGKEVWQALIDR-----------GFICNLTQDCVLRLLPALTIPRADLDAF 388 Query: 471 VDVMDHAMS 479 D ++ +S Sbjct: 389 ADALEDILS 397 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: 403 Number of extensions: 15 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: 402 Length adjustment: 32 Effective length of query: 449 Effective length of database: 370 Effective search space: 166130 Effective search space used: 166130 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