Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011317102.1 AVA_RS01075 acetyl ornithine aminotransferase family protein
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000204075.1:WP_011317102.1 Length = 431 Score = 290 bits (743), Expect = 4e-83 Identities = 172/395 (43%), Positives = 239/395 (60%), Gaps = 24/395 (6%) Query: 14 TYSR-FPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCS 72 +Y+R +P+ + GEG V D +GN ++D+ AGIAV GH HP VV A++EQ RLIH S Sbjct: 39 SYTRDYPLVVNRGEGCMVEDVDGNVFLDMTAGIAVTATGHAHPEVVRAIQEQSARLIHMS 98 Query: 73 NL-YYNEPQAEAARLLAEAAP-KDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGG 130 +Y EP E A LA AP KVFF NSG ES E AIKLAR +T + IAF G Sbjct: 99 GTDFYYEPMVELAENLASQAPFVHDTKVFFTNSGAESNEGAIKLARYYTKRSLIIAFLGA 158 Query: 131 FHGRTMGALSATW-KPEFREPFEPLVPEFEHVPYGDVNAVEKAIDD---------DTAAV 180 FHGRT GA+S T K R F PLVP H+PYG +++ ++ + AA+ Sbjct: 159 FHGRTYGAMSLTGSKTVQRANFGPLVPGVTHIPYGTHASLDYLENNLLTTIIPAHEVAAI 218 Query: 181 IVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDI 240 +VEP+QGE G +P +GFL+ +R +CD +G+L++VDEVQSGMGRTG+ FA EH +V PDI Sbjct: 219 VVEPIQGEGGYIVPEDGFLQRIRNICDRYGILMVVDEVQSGMGRTGRLFAIEHWNVTPDI 278 Query: 241 VCLAKGLGGGVPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAAVSTVLEENLPEA 300 + AKG+ G+P+GA +AR E+ + PG H +TFGGNP+ACAA + +LE L + Sbjct: 279 ITTAKGIASGMPLGAILARAELM-TWPPGSHATTFGGNPVACAAGIVTLK-LLESGLMDN 336 Query: 301 AERKGKLAMRILSEAEDVVEEV---RGRGLMMGVEVGD-----DERAKD-VAREMLDRGA 351 A + G+L L++ + RG+GLM+ V++ D D + +D + +E G Sbjct: 337 ATQMGELLQTGLTQLHQQFPRMSLPRGKGLMVAVDLLDEDGNFDSKLRDRIIQEAFYHGL 396 Query: 352 LVNVTSGDVIRLVPPLVIGEDELEKALAELADALR 386 L+ IR PPLVI ++++ L LA+ LR Sbjct: 397 LLLGCGKAAIRFCPPLVINREQIQTTLDILAEILR 431 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: 421 Number of extensions: 27 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: 389 Length of database: 431 Length adjustment: 31 Effective length of query: 358 Effective length of database: 400 Effective search space: 143200 Effective search space used: 143200 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: 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