Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 214 bits (545), Expect = 4e-60 Identities = 140/418 (33%), Positives = 220/418 (52%), Gaps = 41/418 (9%) Query: 35 IAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHISNLYYIPEQG 94 ++ +G LWD G+ YLD +G +C LGH + +A+ AQ+ ++ + Sbjct: 17 VSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENAPA 76 Query: 95 -ALAQWIV--EHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVILSAKSSFHG 151 ALA+ +V +KVFF +SG+EA E+A+KL R+Y + ++ +S + S+HG Sbjct: 77 VALAKALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGE-PQRRRFVSLRPSYHG 135 Query: 152 RTLATITATGQPKYQKHFDPL---------PDGFAYVPYNDIRALEEAITDIDE-----G 197 TL + TG + F + PD + + +D R + + D G Sbjct: 136 STLGALGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHVARVLADTRAAIEAAG 195 Query: 198 NRRVAAIMLEALQGEG-GVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYE 256 +AA +LE + G G R D Y +R +CDE G LL+LDEV G+GRTG ++ Y+ Sbjct: 196 PDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWFAYQ 255 Query: 257 NLGIEPDIFTSAKGL-AGGIPIGAMMCK----DSCAVFNPGEHASTFGGNPFSCAAALAV 311 + G+ PD+ ++AKGL AG P+GA++ + ++ +H T+ GNP +CA LAV Sbjct: 256 HYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATGLAV 315 Query: 312 VETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTS---- 367 VE +E+E +L+NV ARG QL AGL+ L ++P+ DVRG GL+ G+E+ AD + Sbjct: 316 VEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVADAASKAPFPA 375 Query: 368 -----IEVVKAAMEKGLLLAP-------AGPKVLRFVPPLIVSAAEINEAIALLDQTL 413 + A E+GLL+ P AG L PPL + AA+ E + L++ + Sbjct: 376 EQNRFARITALAREEGLLIYPRRTLDGIAGDHFL-ITPPLTIDAADTAELLTRLERAM 432 Lambda K H 0.319 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: 448 Number of extensions: 28 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: 418 Length of database: 450 Length adjustment: 32 Effective length of query: 386 Effective length of database: 418 Effective search space: 161348 Effective search space used: 161348 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