Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_000009985.1:WP_011384093.1 Length = 459 Score = 197 bits (500), Expect = 7e-55 Identities = 144/408 (35%), Positives = 206/408 (50%), Gaps = 55/408 (13%) Query: 22 PIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRL--IHSSNIYY 79 P+V++ G+G V+D G YI+ AG+ S+G ++ A Q ++L H + Sbjct: 33 PLVITRGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAARQMRQLPFYHLFSHKT 92 Query: 80 TREQVELAKLLTAISP--HDRVFFANSGAEANEGAIKL------ARKFTGKSEIIAAENS 131 VEL L A++P +VF A SG+EAN+ AIKL A K +IIA E + Sbjct: 93 HDVGVELCARLLAMAPVPMSKVFLAGSGSEANDTAIKLIHYRANALGTPDKKKIIAREKA 152 Query: 132 FHGRTLATVTATGQKKYSEPFR-PLP--------------------EGFKHVPYGDIGAM 170 +HG T+AT + TG F P+P E F G++ AM Sbjct: 153 YHGVTVATASLTGLVNNQRSFDLPIPGVLRAACPHHYRFAKDGESEEDFSTRLAGELEAM 212 Query: 171 ADAVGDET-AAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAM 229 A G +T AA EPV G GGVI+PP GY +Q + + DVLL++DEV GFGRTG M Sbjct: 213 ILAEGPDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVLLVVDEVICGFGRTGKM 272 Query: 230 FASQLFGVEPDITTVAKAMGGGY-PIGAVLANERV--AMAFEPG-----DHGSTFGGNPW 281 F ++ FG+ PD+ T+AK + GY PI A++ NERV +A E G HG T+GG+P Sbjct: 273 FGTETFGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESGRIGVFGHGYTYGGHPV 332 Query: 282 GCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGEC 341 A A+ T+ + + + + A++G LR L G V + RGVGL+ +E+ + Sbjct: 333 SAAVALETLNIYAERDILAQVAEVGPVLQDGLR-ALRGHPLVGEARGVGLIGAVELVADK 391 Query: 342 AG-------------VVDAAREMGVLINCTAGKVIRIVPPLVIKKEEI 376 A VV A+ GV++ G + PPLVI K +I Sbjct: 392 ANRAPFPPELAVGARVVAKAQAKGVILR-AMGDAVAFAPPLVISKADI 438 Lambda K H 0.320 0.138 0.404 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: 476 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: 390 Length of database: 459 Length adjustment: 32 Effective length of query: 358 Effective length of database: 427 Effective search space: 152866 Effective search space used: 152866 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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