Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 360 bits (925), Expect = e-104 Identities = 192/375 (51%), Positives = 241/375 (64%), Gaps = 3/375 (0%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRR-FLDFAAGVAVNVLGHANPYLVEALTAQAHKLW 63 +M YARA I F+RGEG +LY DG +LD AGVA N LGH +P LV AL AQA KLW Sbjct: 5 LMNVYARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLW 64 Query: 64 HTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123 H SN+F + GQ +LA+RLT A+FADTVFFTNSG EA EC K+ R+YH +G+ R +I Sbjct: 65 HISNMFEMPGQNALAERLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVI 124 Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDE-TAGICLEP 182 F AFHGRT A++AA + GFG L GF + A+ A+ D TA + +EP Sbjct: 125 GFSGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEP 184 Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEW-AGITPDVMAV 241 +QGEGG RA + FL LR C HG+LL DE+Q GMGRTGKLFAH+W TPD+MA+ Sbjct: 185 VQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMAL 244 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AK +G GFP+GACLAT +AASGM G HG+T GGNPLA AV A D++ +P L H + Sbjct: 245 AKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHARE 304 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVV 361 + L+ L L A +P V +RGKGL++G+ P + A R LL GDN V Sbjct: 305 VAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNRAFMAAAREQRLLVAGGGDNCV 364 Query: 362 RLLPPLNIGEAEVEE 376 RLLPPL + AE ++ Sbjct: 365 RLLPPLTLTVAEADQ 379 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: 464 Number of extensions: 16 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: 398 Length adjustment: 31 Effective length of query: 358 Effective length of database: 367 Effective search space: 131386 Effective search space used: 131386 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