Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate AZOBR_RS20195 AZOBR_RS20195 aminotransferase
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__azobra:AZOBR_RS20195 Length = 369 Score = 163 bits (413), Expect = 8e-45 Identities = 111/367 (30%), Positives = 174/367 (47%), Gaps = 19/367 (5%) Query: 106 IRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAISHKLKEENGLSYT-PD 164 I L G PD PA +++ AI EG +Y P GT +LR A++ + GL Sbjct: 11 INLGQGFPDERGPADVLDVAAKAILEGWNQYPPMMGTPDLRQALAAHGRRFYGLDIDWKT 70 Query: 165 QILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSISEDFLL 224 ++LV++GA +++ ++L + PGDEV++ P + SY + RLA P + + D+ Sbjct: 71 EVLVTSGATEALTASLLGLIEPGDEVVLFQPMYDSYLPIVRLAGGVPRFVSLK-APDWSF 129 Query: 225 DPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVARHPRLLVISDEIYEHIIY 284 LE+ + K++L+++ P NP V+ R LE +AE V R V DE+YEHI++ Sbjct: 130 TRADLEAAFSPKTKLVLINDPLNPAAKVFSRAELELLAEFVQRFDAFAVC-DEVYEHIVF 188 Query: 285 APATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACNKIQSQFTSGAS 344 H +LPGM DR L + K F++TGW++GY+ G H + K T Sbjct: 189 DGRQHIPLMTLPGMRDRCLKIGSAGKTFSLTGWKVGYVTGAPHLLQPVAKAHQYITFTTP 248 Query: 345 SISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISEPRGAFYLFIDL 404 Q A LG A A + + +RD L + G ++ G +++ D+ Sbjct: 249 PNLQTAVAYGLGKDDA---YFAGLSSGLQAKRDRLADGLRAV-GFEVLPSAGTYFVVADV 304 Query: 405 SSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAF----GDDTCIRISYAASLSTLQ 460 S FG N E+ CR L +A V +P AF + IR ++ L Sbjct: 305 SP--------FGFDGNDEAFCRRLTAEAGVTAIPVGAFFVQDAPRSFIRFCFSKRDEILD 356 Query: 461 AAVERIK 467 AVER++ Sbjct: 357 GAVERLR 363 Lambda K H 0.317 0.132 0.375 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: 376 Number of extensions: 21 Number of successful extensions: 6 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: 479 Length of database: 369 Length adjustment: 32 Effective length of query: 447 Effective length of database: 337 Effective search space: 150639 Effective search space used: 150639 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 (21.7 bits) S2: 50 (23.9 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