Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_010441713.1 G7G_RS0112215 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000192475.1:WP_010441713.1 Length = 395 Score = 478 bits (1229), Expect = e-139 Identities = 236/388 (60%), Positives = 292/388 (75%) Query: 1 VIPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAH 60 +IP V+PTY RA + F +GEG +L DGRRFLD AG+AVN LGHA+P LV ALT QAH Sbjct: 1 MIPSVLPTYNRAPLTFVKGEGAWLTEADGRRFLDLGAGIAVNALGHAHPALVAALTEQAH 60 Query: 61 KLWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120 LWH SNL+ + Q++LA +L E TFADTVFFTNSG E+ E K+ RKY Y+KG + Sbjct: 61 ALWHVSNLYNIPQQQALADKLVEHTFADTVFFTNSGTESCELAVKMARKYFYDKGQAEKV 120 Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICL 180 IITF+ +FHGR+ A ++AA EK+ KGFGPLL GF + FGDL+ V NA+ + TA I + Sbjct: 121 EIITFDGSFHGRSSAGIAAAGSEKMTKGFGPLLPGFVHLTFGDLDGVTNAINENTAAIMI 180 Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240 EP+QGEGGIR L+ LR+ICD++GLLL LDE+QCG+GRTGKLFAHEWAGITPD+M Sbjct: 181 EPVQGEGGIRPVPDAELKALRQICDDNGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMM 240 Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300 VAKGIGGGFPLGA LATE+AASGMTAGTHGSTYGGNPL AVG AV+D+V P FL+ V Sbjct: 241 VAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVIDQVATPAFLEGVN 300 Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360 R GLL+ +L GL+A++P VF+ VRG GLMLGL C P DVV A N +++VPA DNV Sbjct: 301 RKAGLLRQKLEGLIADHPEVFEEVRGSGLMLGLKCKPTNIDVVNAGYDNEVITVPAADNV 360 Query: 361 VRLLPPLNIGEAEVEEAVAILAKTAKEL 388 +RLLPPL + E ++ +A+ L K A ++ Sbjct: 361 IRLLPPLTLTEDDIAQAMIRLDKAAAQV 388 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: 504 Number of extensions: 24 Number of successful extensions: 1 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 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