Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011425253.1 RHE_RS10125 aspartate aminotransferase family protein
Query= curated2:Q7NN66 (400 letters) >NCBI__GCF_000092045.1:WP_011425253.1 Length = 444 Score = 191 bits (485), Expect = 4e-53 Identities = 134/414 (32%), Positives = 196/414 (47%), Gaps = 23/414 (5%) Query: 3 VQQAFEQHVMHTYARFSVVFERGEGCYLEDSEGRRYLDFVAGIATCVLGHAHPVLSAAVA 62 + + F +F V+ R G + D G +LD+ +G+ LGH + AA+ Sbjct: 32 LSEIFRNEPPSVLTQFPTVWTRASGSQIFDPYGNIWLDWTSGVIAANLGHGSEAVGAAII 91 Query: 63 EQA-RTLIHVSNLYYTPQQACLAEWLTAHSAADQVFFCNSGAEANEGAIKLARKYGRTVL 121 E A R L+H S +Y T ++A + ++ +G+EA E AIK+A + G + Sbjct: 92 EVASRPLLH-SYVYPTLERAAYLNMVKEVLGYEKALLLTTGSEAVEAAIKIALRNGASR- 149 Query: 122 GIAEPQIICAHQSFHGRTMATVTATGQPKYQKHFHPLVPGFVHVPY-------NDFEALR 174 + +I+ +FHGRTM +A G Q F +P+ + F+ + Sbjct: 150 --GKEKIVSFDYAFHGRTMGAQSAGGIAAQQTWLPQNSRTFTRIPFPARDSVADGFDPVE 207 Query: 175 A-----QVTDATAAVLIEPIQGEGGVVPGDVEFFQKLRRFCSERRILLMLDEVQTGMGRT 229 + AAVLIEP QG V D + ++C LL+ DEVQ G GRT Sbjct: 208 PLSKLEEEGGGVAAVLIEPYQGSSLKV-ADKAAVANIEKWCRAHNALLICDEVQAGFGRT 266 Query: 230 GRLFGYEHLGIEPDVFTLAKALGGGVPIG-ALCAKEAFAIFEPGDHASTFGGNPLACAAA 288 GR+FGYE+L IEPD+ K + G P+ LC+ E F G+ +ST GNPL AAA Sbjct: 267 GRMFGYEYLNIEPDLVCCGKGISNGFPMAMVLCSNEVVRNFNLGELSSTHSGNPLGLAAA 326 Query: 289 LAVCQTLEAEQLVDNARERGAQLAAGLGRLVERFKPLVRTARGRGLMQGLVLSEPRAAEI 348 AV ++ N R AQL GL + F P + RG GL GLV +PR + Sbjct: 327 TAVLNAFTNSNILANVTARSAQLLEGLHAISAEFHPHIEDVRGVGLAAGLVFKDPRICAL 386 Query: 349 VRLAMEQGLLLVSA--GPE--VIRFVPPLIVSAIEVDEALAILEGVFARLPVTV 398 V Q LLV A G E +++F PPL +SA ++ + L L G + + T+ Sbjct: 387 VAKRSWQSGLLVFAPIGREKTILKFTPPLSISAEQIADGLLALHGAVSTVVETI 440 Lambda K H 0.323 0.138 0.409 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: 442 Number of extensions: 23 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: 400 Length of database: 444 Length adjustment: 32 Effective length of query: 368 Effective length of database: 412 Effective search space: 151616 Effective search space used: 151616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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