Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_029133337.1 A3GO_RS0110380 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000428045.1:WP_029133337.1 Length = 394 Score = 329 bits (843), Expect = 1e-94 Identities = 172/392 (43%), Positives = 249/392 (63%), Gaps = 12/392 (3%) Query: 35 VMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLHH 94 +M TY R P++ RG G LWDTEGK YLD ++GIA C LGHAHPA+ +A+ DQ L H Sbjct: 5 LMATYNRLPVSFERGDGVWLWDTEGKRYLDALSGIAVCGLGHAHPAIQKAICDQAGTLLH 64 Query: 95 VSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVIL 154 SNLY IP Q +L + + + +VFF NSGAEANEAAIK+ R Y + ++ P I+ Sbjct: 65 TSNLYQIPLQEKLGEKLTALAGMQQVFFANSGAEANEAAIKIARFYGNQ--KGIQNPAIV 122 Query: 155 TAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVAA 214 + SFHGRTLAT+TATG K Q F+PLV GF +P+ DI SL+N + E + V A Sbjct: 123 VMEKSFHGRTLATLTATGNRKVQAGFEPLVQGFVRIPFGDIDSLKN----VAENSPNVVA 178 Query: 215 IFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEPD 274 + +EP+QGEGG+ Y ++R+IC++++ L++ DE+Q G+GR+GK + ++H G+ PD Sbjct: 179 VLVEPVQGEGGINIPADDYLPQIRQICNEHEWLMMLDEIQTGIGRSGKFFSHQHQGIVPD 238 Query: 275 IFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLLD 333 + T AK L G+PIGA + + ++ PGNH +TFGG+PLAC GLAV++T+E L Sbjct: 239 VMTLAKALGNGMPIGACLVNGRAANLLGPGNHGTTFGGSPLACRVGLAVVETVEQFNLTA 298 Query: 334 NVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLLL 393 + G +L + A+ + E+RG GL+ G+E+ E+VK A+EQGLL+ Sbjct: 299 RAEVLGAKLLADFADALTDVAGV-EEIRGQGLLIGIELERPCG----ELVKQALEQGLLI 353 Query: 394 APAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 V+R +PPL++++ E A+ V+ L I Sbjct: 354 NVTADTVIRLLPPLIMSDKEAAKLVQTLSTLI 385 Lambda K H 0.320 0.137 0.405 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: 447 Number of extensions: 27 Number of successful extensions: 6 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: 429 Length of database: 394 Length adjustment: 31 Effective length of query: 398 Effective length of database: 363 Effective search space: 144474 Effective search space used: 144474 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 Jul 25 2024. The underlying query database was built on Jul 25 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