Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_019865912.1 METMI_RS0108805 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000384075.1:WP_019865912.1 Length = 392 Score = 345 bits (886), Expect = 1e-99 Identities = 183/394 (46%), Positives = 251/394 (63%), Gaps = 11/394 (2%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 ++M TYGR V +GEG LWD +GK YLD ++GIA C LGHAHPA+ QA+ Q KL Sbjct: 4 HIMPTYGRLAVTFERGEGAWLWDDQGKRYLDALSGIAVCNLGHAHPAVHQALCEQSGKLV 63 Query: 83 HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 H SN+Y I Q LA ++E S D VFF NSGAEANEAAIKL RKY H + +E P I Sbjct: 64 HTSNIYRIALQEQLANRLIEKSGMDNVFFSNSGAEANEAAIKLARKYGHGLG--VENPAI 121 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 + + SFHGRTLAT++ATG PK Q+ F PL +GF VPYNDI A+E AI+ G+ + Sbjct: 122 IVMEKSFHGRTLATLSATGNPKVQQGFGPLVEGFIRVPYNDIGAVEAAIS----GHGNIV 177 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 AI+ E +QGEGGV +Y +R +CD++ +LL+LDE+Q G+GRTGK++ Y++ GI P Sbjct: 178 AILAEPIQGEGGVNIPAADYLNQLRSLCDQHNLLLMLDEIQTGIGRTGKFFAYQHNGILP 237 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ T AK L G+PIGA + + A V G H STFGGNP +C+AALAV+ TL+ + LL Sbjct: 238 DVCTVAKALGNGVPIGACLARGKAAEVLTAGTHGSTFGGNPLACSAALAVLATLDADGLL 297 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 ++G + AG + P+ D+R G++ G+E L+ +V A+E GLL+ Sbjct: 298 AAAASKGAAICAGFTGHLQGNPHIVDIRHKGMMIGIE----LDTPCTGLVGQALEAGLLI 353 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTLAA 415 K +R +PPLI+ +I + + L ++A Sbjct: 354 NVTYEKNIRLLPPLIMDELQIQQLVGTLSSLISA 387 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: 425 Number of extensions: 18 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: 392 Length adjustment: 31 Effective length of query: 387 Effective length of database: 361 Effective search space: 139707 Effective search space used: 139707 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: 50 (23.9 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