Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_106718625.1 CU100_RS18385 aspartate aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_003010935.1:WP_106718625.1 Length = 481 Score = 206 bits (524), Expect = 1e-57 Identities = 143/406 (35%), Positives = 217/406 (53%), Gaps = 41/406 (10%) Query: 20 VTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKE-QVERLIHCSNLYYNE 78 V + EG +D G +D G GH HP +VEA K+ Q E + + ++ Sbjct: 60 VKIERAEGMHYYDQNGRPILDFFGGFGSLAFGHNHPRIVEARKKFQDEGRQEIAIAFMSQ 119 Query: 79 PQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTK-FIAF-EGGFHGRTM 136 A LA +P DL+ VF +SG+E++E AIK+A + G K IA+ E FHG+T Sbjct: 120 YATALAHNLAACSPGDLDMVFLGSSGSEAMEAAIKVAERAAGPKKPKIAYAENSFHGKTK 179 Query: 137 GALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAI--DDDTAAVIVEPVQGEAGVRIP 194 G LS T +R F+ LV VP+GD++AVE A D + +++E +QG G+ Sbjct: 180 GVLSITDGQLYRGEFK-LVDNTVRVPFGDIDAVESAFRSDPEIGVIVLETIQGGGGIIQA 238 Query: 195 PEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPV 253 P + + LR LCD++G+L + DEVQ G GR+G+F+AFEH V+PD+ LAK LGGG V Sbjct: 239 PSEYWQRLRVLCDQYGVLWVADEVQCGFGRSGKFYAFEHAGVIPDVTALAKSLGGGKAAV 298 Query: 254 GATIAREEV-AEAFEPGDHG-----STFGGNPLACAAVCAAVSTVLEENLPEAAERKGKL 307 GA IAR EV +A+ +TFGG AC A++ + +E+L + A G+ Sbjct: 299 GAMIARREVYMKAYGTPKTAMIHAMATFGGIGEACVTSIEAINILYDEHLIDNAAATGEY 358 Query: 308 AMRILSEAE----DVVEEVRGRGLMMGVEVGD----------------DERAKD-----V 342 ++ L E + ++++VRG+GLM+G+E D D++ K + Sbjct: 359 LLQKLDELKVKYPTMIKDVRGKGLMIGLEFHDFSKTVPMVLRPVLAVLDDKLKGSLPGFI 418 Query: 343 AREML-DRGALVNVT--SGDVIRLVPPLVIGEDELEKALAELADAL 385 +L D G LV T + +VIRL PPL+ G + +++ + L + L Sbjct: 419 GSHLLRDHGVLVAFTEYNRNVIRLEPPLICGREHVDEFIKALDEVL 464 Lambda K H 0.318 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: 433 Number of extensions: 25 Number of successful extensions: 8 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: 389 Length of database: 481 Length adjustment: 32 Effective length of query: 357 Effective length of database: 449 Effective search space: 160293 Effective search space used: 160293 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 26 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