Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_039653375.1 PN53_RS11750 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000816635.1:WP_039653375.1 Length = 424 Score = 248 bits (633), Expect = 2e-70 Identities = 159/407 (39%), Positives = 225/407 (55%), Gaps = 34/407 (8%) Query: 33 VAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHIS-NLYYIP 91 + + KGEG L +GK LDF +G+A C +GH + A+++A + QIQ+L H N+ Y Sbjct: 22 LGVVKGEGSYLITEDGKKVLDFASGVAVCNIGHNNKAVVEAATKQIQQLIHGGHNVVYYE 81 Query: 92 EQGALAQWIVEHSCADK-VFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVILSAKSSFH 150 LA+ +VE + D V+F NSGAEANE AIKL + + ++ I+S K SFH Sbjct: 82 TYVKLAEKLVELTGGDTMVYFSNSGAEANEGAIKLAKYVS-------KRQGIISFKGSFH 134 Query: 151 GRTLATITATGQPK-YQKHFDPLPDGFAYVPYNDI----------RALEEAITDIDEGNR 199 GRTL T + T Y+K+++ L + Y + E + D+ + Sbjct: 135 GRTLGTTSITASNSAYRKNYEGLLPSVYFAEYANCFRCPYKQKKESCSMECVEQFDDIFK 194 Query: 200 R------VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYW 253 R VAAI++E +QGEGG E+ KA+R ICD+ GI L+ DEVQ G GRTGK + Sbjct: 195 RIIDPYSVAAIIMEPIQGEGGYIVPPKEFMKAIREICDKYGIYLIFDEVQTGFGRTGKMF 254 Query: 254 GYENLGIEPDIFTSAKGLAGGIPIGAMMCKDSCAVFNP-GEHASTFGGNPFSCAAALAVV 312 +EN I+PDI T AK +A G P+ A++ K P G H TFGGNP SCAA+LA + Sbjct: 255 AHENFDIKPDIMTCAKAIASGFPLSAVIGKKEIMKNWPAGAHGGTFGGNPVSCAASLATI 314 Query: 313 ETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVK 372 E LE ++N G L+ L L EKYP DVRG GL+ ME + + + VK Sbjct: 315 EQLE-NGAIQNGVESGAYLKKRLFELKEKYPIIGDVRGIGLMLAMEFVGENNVPNGRAVK 373 Query: 373 ----AAMEKGLLLAPAG--PKVLRFVPPLIVSAAEINEAIALLDQTL 413 ++E GL+L G VLRF+ P VS EI+EA+ ++++ + Sbjct: 374 NIINYSVEHGLILLNCGTYKNVLRFIAPTTVSKGEIDEALGIIEEAI 420 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: 487 Number of extensions: 31 Number of successful extensions: 7 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: 424 Length adjustment: 32 Effective length of query: 386 Effective length of database: 392 Effective search space: 151312 Effective search space used: 151312 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 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