Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 196 bits (498), Expect = 1e-54 Identities = 130/390 (33%), Positives = 195/390 (50%), Gaps = 15/390 (3%) Query: 83 PLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNH 142 P+ A+ V+D GR ++D GGIA ++ GH HP+V +V QL+ +H+ + L + Sbjct: 25 PIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGY 84 Query: 143 -TISDFAEALVSTLPGDL--KVVFFTNSGTEANELAMMMARLYTGCNDIVSLRNSYHGNA 199 + E L +PGD K FT SG+EA E A+ +AR YT +++ + YHG Sbjct: 85 ESYIQVCEKLNQLVPGDFAKKTALFT-SGSEAVENAVKVARAYTKRAGVIAFTSGYHGRT 143 Query: 200 AATM---GATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQFGTSGQV 256 A + G A + ++ + V A P G+ SD + AS + Sbjct: 144 MAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGV--SDDDAMASIERIFKNDAEPSDI 201 Query: 257 AGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGV 316 A I E +QG GG ++P ++ + + G + IADEVQ+G RTGT F+ + GV Sbjct: 202 AAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGT-FFAMEQMGV 260 Query: 317 IPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEK 376 DI T AK I G PL + ++ + T+GGNP+ AA AVL V EEK Sbjct: 261 SADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEK 320 Query: 377 LQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQ 436 L E AN +G +K L ++ ++ I DVRG G M +E ++D PA ++ + Sbjct: 321 LLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMED---GKPAPQYCAQILAE 377 Query: 437 MKEMGVLVGKGGFYGNVFRITPPLCFTLSD 466 + G+++ G YGNV RI PL T+SD Sbjct: 378 ARNRGLILLSCGTYGNVLRILVPL--TVSD 405 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: 467 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 481 Length of database: 425 Length adjustment: 33 Effective length of query: 448 Effective length of database: 392 Effective search space: 175616 Effective search space used: 175616 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