Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 281 bits (718), Expect = 3e-80 Identities = 158/382 (41%), Positives = 228/382 (59%), Gaps = 8/382 (2%) Query: 11 RADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFR 70 R ++VF G+G +L +G+R+LDF G AVN LGH+N +++AL Q+ KL++ S F Sbjct: 17 RPELVFTEGKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFY 76 Query: 71 VAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAFH 130 LA++LT+A+ D VFF NSGAEA E KL RK+ K IIT + +FH Sbjct: 77 NEPMLRLARQLTDASCFDKVFFANSGAEANEGAIKLARKWG-RKHKNGAFEIITMDHSFH 135 Query: 131 GRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEGGIR 190 GRTLA +SA+ + F P + GF DL +V + D+T I LEP+QGEGG+ Sbjct: 136 GRTLATMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLINDKTVAIMLEPVQGEGGVI 195 Query: 191 AGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGGGFP 250 S EF++GLR++ D+H LL +DE+Q G GR G +FA+E +G+ PD+M + KGIGGG P Sbjct: 196 PASREFMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGGVP 255 Query: 251 LGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRL 310 L A L + AS AG G TY GNP+ TAVG+AV+ ++ PGFL VQ G L+++L Sbjct: 256 LAALLCKAEVAS-FEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLREQL 314 Query: 311 AGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVA----LRANGLLSVPAGDNVVRLLPP 366 L +E G RG+GL+ L +G +V ++ GLL N++R +P Sbjct: 315 LALTSE--FGLGGERGEGLLRALVLNKDIGPQLVEEARDMQPQGLLLNSPRPNLLRFMPA 372 Query: 367 LNIGEAEVEEAVAILAKTAKEL 388 LN+ E+++ +++L K+L Sbjct: 373 LNVTIEEIDQMISMLRTLLKKL 394 Lambda K H 0.321 0.139 0.414 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: 382 Number of extensions: 19 Number of successful extensions: 4 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: 395 Length adjustment: 31 Effective length of query: 358 Effective length of database: 364 Effective search space: 130312 Effective search space used: 130312 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 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