Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 474 bits (1219), Expect = e-138 Identities = 238/385 (61%), Positives = 288/385 (74%) Query: 1 VIPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAH 60 +IP V+PTY RA + F +GEG +L DGRRFLD AAG+AVN LGHA+P LV+ALT QA Sbjct: 1 MIPSVLPTYNRAPLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAE 60 Query: 61 KLWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120 LWH SNL+ + Q++LA RL E +FADTVFFTNSG E+ E K+ RKY ++KG R Sbjct: 61 TLWHVSNLYHIPQQQALADRLVEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERV 120 Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICL 180 I+TF +FHGR+ A +SAA EK+ GFGP+L GF + FGDL+ V +A+TD+TA I + Sbjct: 121 EILTFSGSFHGRSSAGISAAGSEKMTAGFGPMLPGFKHLMFGDLDGVTDAITDQTAAILI 180 Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240 EP+QGEGGIR L+ LR+ICDEHGLLL LDE+QCG+GRTGKLFAHEWAGITPD+M Sbjct: 181 EPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMM 240 Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300 VAKGIGGGFPLGA LATE+AASGMTAGTHGSTYGGNPL AVG AV+D V +P FL V Sbjct: 241 VAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVS 300 Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360 R GLL+ +L GLVA +P VF+ VRG GLMLGL C A DVV A +++VPA DNV Sbjct: 301 RKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANTDVVAAGYEAEVVTVPAADNV 360 Query: 361 VRLLPPLNIGEAEVEEAVAILAKTA 385 VRLLPPL + + ++ EA A L + A Sbjct: 361 VRLLPPLTLTDEDIAEAFARLDQAA 385 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: 496 Number of extensions: 20 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: 394 Length adjustment: 31 Effective length of query: 358 Effective length of database: 363 Effective search space: 129954 Effective search space used: 129954 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