Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_015818340.1 TERTU_RS17800 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000023025.1:WP_015818340.1 Length = 415 Score = 182 bits (461), Expect = 2e-50 Identities = 126/418 (30%), Positives = 213/418 (50%), Gaps = 18/418 (4%) Query: 7 SLLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAA 66 S+ ++R++A+ R +++PV A N+ D +GREYIDF G VLN GH +P + A Sbjct: 2 SIFEQRESAI-RAYSRVYPVTFASAANARQTDTDGREYIDFFAGAGVLNFGHNNPLMKNA 60 Query: 67 VQEQLGKLSHTCFQVLAYEPYIELAEEIAKRV--PGDFPKKTLLV-TSGSEAVENAVKIA 123 V + L + + + E E +K + P D P + +G+ AVE A+K+A Sbjct: 61 VIDYLQRDGVVHSLDMQTQAKAEFIETFSKTILAPRDMPHRLQFTGPTGTNAVEAAMKLA 120 Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDD 183 R TGR ++AF A+HG T+ L T PY +P P + + Sbjct: 121 RRVTGRNTIVAFQQAFHGMTLGALAATAN--PYFRNAAGVPLAHV-CHEPFCVDAAEAEQ 177 Query: 184 SIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQ 243 +I+++ + A+ AA ++E +Q EGG + +KS++++L L + G L I D++Q Sbjct: 178 NISALRDRYSRSAERAP-AAFMVETIQAEGGVNIAAKSWLEQLAKLAAELGALFIVDDIQ 236 Query: 244 TGAGRTGTFFATEQLGIVPDLTTFAKSVGG-GFPISGVAGKAEIMDAIAPGGLGGTYAGS 302 G GRTG++F+ + + I PD+ AK VGG G P++ + E + +PG GT+ G Sbjct: 237 VGCGRTGSYFSFDDIDIAPDIICLAKGVGGMGTPLAFNLVRPECDERWSPGEHTGTFRGQ 296 Query: 303 PIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFE 362 ++ A L+ F + +L++ ++ L + A+ + +RG G ++ ++ + Sbjct: 297 NLSFIAGKVGLEYFADNELMQAVADKTRLMQEMLEPLLAEDSSL-SLRGKGMIMGLDFGD 355 Query: 363 GGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAE 420 G +V + EKGLI+ SCG +VI+ + P+TIP+ L GL IL E Sbjct: 356 G--------TRAGSVVKQCFEKGLIVASCGIGGSVIKLIPPLTIPNEDLIAGLNILCE 405 Lambda K H 0.319 0.137 0.393 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: 372 Number of extensions: 19 Number of successful extensions: 5 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: 426 Length of database: 415 Length adjustment: 32 Effective length of query: 394 Effective length of database: 383 Effective search space: 150902 Effective search space used: 150902 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 Sep 24 2021. The underlying query database was built on Sep 17 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