Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_013682998.1 ARCVE_RS01415 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000194625.1:WP_013682998.1 Length = 371 Score = 219 bits (557), Expect = 1e-61 Identities = 141/390 (36%), Positives = 213/390 (54%), Gaps = 26/390 (6%) Query: 6 ASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDT-PDFIKEACIRALREGKTK 64 A R+S + S + +E R KG+DV+ GEPDFDT P+ +++AC A+R+ T Sbjct: 3 ARRLSQISTSMIRRMFEVVQEARKKGIDVVNLSIGEPDFDTHPEIVEKAC-EAMRKSFTH 61 Query: 65 YAPSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSP 124 Y + GI ELR AIAE+ E P ++V+AGA L +A ++EG +V++PSP Sbjct: 62 YTSNFGIDELRAAIAERYGVE------PKNVMVTAGASEALMNAALAFIEEGSKVVIPSP 115 Query: 125 YWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEE 184 +++Y + GG V+ LK F++ ++ + E + + + IN PNNPTG V +E Sbjct: 116 NFLSYFTYAKVCGGKIVQ--LKTHPTFEIDVDALNELMDKDVSLVFINYPNNPTGVVADE 173 Query: 185 EELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMT 244 + LK + E + ++SDE Y+ +Y D K S A + V VN FSKS +MT Sbjct: 174 KTLKAVVEIASDCNAIVVSDEIYD-AIYYDKKPTSLAGMENVV-----VVNGFSKSLAMT 227 Query: 245 GWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRR 304 GWRIG+V E + ++ + FAQ + L + K+ + NEM F +RR Sbjct: 228 GWRIGFVIASETLLDSMLKVHQVNGVCAPAFAQKAVADVLLSGKADEIANEMVGEFRKRR 287 Query: 305 DTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFG 364 D +EL K+ G++VVKPEGAFY+FP ++ +E L+EK VAV PG FG Sbjct: 288 DYVYDELKKM-GLEVVKPEGAFYLFPRVPINC------IEFAEKLVEKG-VAVTPGLPFG 339 Query: 365 --APGFLRLSYALSEERLVEGIRRIKKALE 392 ++R+SYA S E L + R+K+ +E Sbjct: 340 DWNENYVRISYATSMENLRIAMERMKEFVE 369 Lambda K H 0.317 0.135 0.383 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: 404 Number of extensions: 23 Number of successful extensions: 6 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: 394 Length of database: 371 Length adjustment: 30 Effective length of query: 364 Effective length of database: 341 Effective search space: 124124 Effective search space used: 124124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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