Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate BPHYT_RS29280 BPHYT_RS29280 4-aminobutyrate aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS29280 Length = 442 Score = 273 bits (698), Expect = 9e-78 Identities = 167/443 (37%), Positives = 243/443 (54%), Gaps = 15/443 (3%) Query: 48 PFNYSPPPYD--GPSTAEIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDA 105 P + P D T IA+R LSP+ FY P+ IV + Y++D+ G YLDA Sbjct: 6 PNGFDPASLDHLDAGTQRHIARRLRLLSPSYRLFYAEPVKIVRGEKVYLYDDQGNDYLDA 65 Query: 106 FGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNHTISDFAEALVSTLPGDLKV--VF 163 + + V GH +P +V++V +QL + T Y+ I D+AE L+ST ++ + Sbjct: 66 YNNVVCV--GHANPRIVDAVTRQLSTLCTHT-RYMQEPILDYAEDLLSTFNTSIRAGQMM 122 Query: 164 FTNSGTEANELAMMMARLYTGCNDIVSLRNSYHGNAAATMGATAQSNWKFNVVQSGVHHA 223 FT +G+EAN+LA +A Y G ++ +YHGN+ T + + S + ++ V Sbjct: 123 FTCTGSEANDLATRIAMQYAGKTGVIVTSEAYHGNSHLT-SSFSPSLGRRALLGPYVRTV 181 Query: 224 INPDPYRGIFGSDGEKYASDV----HDLIQFGTSGQVAGFIGESIQGVGGIVELAPGYLP 279 PD YR G++ A+ V D+ + G G +A FI +S G+ L Sbjct: 182 PAPDSYRMTPSEIGQRMAAQVALQIEDIRRHG--GGLAAFIADSFFSSDGVFAHPTDVLA 239 Query: 280 AAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTT 339 ++VR+AGG+ IADEVQSGF R+GTH WG + HGV+PDIVT+ K +GNG P+ +V Sbjct: 240 PVAEVVRRAGGLFIADEVQSGFGRSGTHMWGHERHGVVPDIVTLGKPMGNGYPVAGLVVR 299 Query: 340 PEI-AGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNK 398 PE+ AG YFNTFGGN + AA A L VL +E + +NA VG+ L L L K Sbjct: 300 PEVVAGFGQDMRYFNTFGGNSVAIAAAQATLDVLRDEHVLDNAQRVGAILAEGLNALARK 359 Query: 399 YELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITP 458 YE IGDVRG GL GVE V+DR K A L +++ +++ VL+ G +V +I P Sbjct: 360 YECIGDVRGTGLYFGVEIVRDRAKKDTDIATALKIVNGLRQRRVLISATGPDASVLKIRP 419 Query: 459 PLCFTLSDADFLVDVMDHAMSKM 481 PL F +DAD L+ +D ++ + Sbjct: 420 PLVFGANDADRLLTELDTVLAAL 442 Lambda K H 0.320 0.136 0.406 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: 558 Number of extensions: 32 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: 481 Length of database: 442 Length adjustment: 33 Effective length of query: 448 Effective length of database: 409 Effective search space: 183232 Effective search space used: 183232 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 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