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 GFF973 Psest_1004 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__psRCH2:GFF973 Length = 390 Score = 197 bits (500), Expect = 7e-55 Identities = 131/399 (32%), Positives = 200/399 (50%), Gaps = 20/399 (5%) Query: 75 SLSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHT 134 S S R +++P +A+ ++A L G VI L GEPDF T APIV AG A+ GHT Sbjct: 4 SYSARSRAIEPFHVMALLERANQLQVQGHDVIHLEIGEPDFTTAAPIVAAGQAALAAGHT 63 Query: 135 RYTPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPA 194 RYTP G +LR AI+ + GLS P +IL++ G +++ A + PG L+ Sbjct: 64 RYTPARGLPQLREAIAAFYAQRYGLSIDPGRILITPGGSGALLLAASLLVDPGKHWLLAD 123 Query: 195 PYWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYP 254 P + RL + ++P + L P+L+E S ++ SP+NPTG++ Sbjct: 124 PGYPCNRHFLRLVEGAAQLVPVGPDVRYQLTPELVERYWDRDSVGALVASPANPTGTLLE 183 Query: 255 RKLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAM 314 R L +++ + LV+ DEIY + Y AS+ + D +N FSK F M Sbjct: 184 RDELARLSAALKERGGHLVV-DEIYHGLTYG----VDAASVLEVDDDAFVLNSFSKYFGM 238 Query: 315 TGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRE 374 TGWRLG++ P + K+ A S++Q AA+A A E++ F Sbjct: 239 TGWRLGWLVAPPTAVPELEKLAQNLYISAPSMAQHAALAC--FEPATLEILEARRAEFAR 296 Query: 375 RRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQV 434 RRD+L+ + E+ EP+GAFYL+ D+S++ G ++ + C+++L+ V Sbjct: 297 RRDFLLPALRELGFGIAVEPQGAFYLYADISAFGG----------DAYAFCQHMLETEFV 346 Query: 435 ALVPGDAFGDDTC---IRISYAASLSTLQAAVERIKKAL 470 A+ PG FG +R +Y L LQ AVERI + L Sbjct: 347 AITPGLDFGRFQAGHHVRFAYTQDLPRLQQAVERIARGL 385 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: 440 Number of extensions: 19 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: 479 Length of database: 390 Length adjustment: 32 Effective length of query: 447 Effective length of database: 358 Effective search space: 160026 Effective search space used: 160026 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: 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