Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_001046645.1:WP_066608605.1 Length = 436 Score = 182 bits (463), Expect = 1e-50 Identities = 132/425 (31%), Positives = 215/425 (50%), Gaps = 19/425 (4%) Query: 6 DSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKA 65 D+ + RR + + P +A+ + D +G Y+DF G + LN GH HP +K Sbjct: 15 DTAIYERRESAVRSYARAMPRQFNQAQGVWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKN 74 Query: 66 AVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLV--PGDFAKKSALFT--SGSEAVENAIK 121 A+ + + T + L ++ L ++ P D + A+FT +G+ AVE AIK Sbjct: 75 ALVDYIVNDGITHGLDLHTDAKADFLAALEDVILTPRDLDYR-AMFTGPTGTNAVEAAIK 133 Query: 122 VARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSE 181 +AR T R VIAFT+G+HG T+ ALA TG A G G+ +V + HG Sbjct: 134 LARKITGRELVIAFTNGFHGMTLGALACTGNAAKRG-GAGVPLNHVSHEPYD-GYHGPGV 191 Query: 182 DDAMASIERIFKNDAEPSDI-AAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240 D A +ER + + D AAI++E VQGEGG AA+P +++++ ++ R G ++I D Sbjct: 192 DTA-EQLERRLSDPSSGLDAPAAILVETVQGEGGLNAASPRWLRQIADIAKRHGALMIID 250 Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAG-GFPLSGITGRAEVMDAIGPGGLGGTY 299 ++Q G GRTG FF+ E MG DI T AKS++G G P + R E +D PG GT+ Sbjct: 251 DIQAGCGRTGNFFSFEGMGFTPDIVTMAKSLSGMGLPFALTLFRPE-LDQWSPGEHNGTF 309 Query: 300 GGSPLACAAALAVIEVFEEEKLLERSNA-IGQTIKSAIGELASRYPQIAEVRGLGSMIAI 358 G+ A A A + F + ++ A G ++ + +A+ + +RG G M I Sbjct: 310 RGNNHAFVTATATLRHFWSDGNFQQDIARRGALLERRLAAMATEHG--LSIRGRGMMRGI 367 Query: 359 ELMENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAEC 418 ++ + E + +GLI+ + G + ++++L P+ D + GL+I+ + Sbjct: 368 DV-----GSGEIAQTITAACFAQGLIIETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQS 422 Query: 419 FEAVL 423 + L Sbjct: 423 VRSAL 427 Lambda K H 0.319 0.136 0.391 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: 441 Number of extensions: 28 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: 425 Length of database: 436 Length adjustment: 32 Effective length of query: 393 Effective length of database: 404 Effective search space: 158772 Effective search space used: 158772 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: 51 (24.3 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