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 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 391 bits (1004), Expect = e-113 Identities = 205/400 (51%), Positives = 277/400 (69%), Gaps = 7/400 (1%) Query: 76 LSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTR 135 LS R+NS+ PS T+A++ ++ L G+ VI L+ GEPDF+TP I EA AI + +R Sbjct: 4 LSDRLNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFSR 63 Query: 136 YTPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAP 195 Y+P G LR+AI KLK+ENGL YT QI +NGAKQS+ A+L + +PGDEV++PAP Sbjct: 64 YSPVPGYPALRNAIVEKLKKENGLEYTAAQISCANGAKQSVCNAILVLVNPGDEVIVPAP 123 Query: 196 YWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPR 255 YWVSYPEM ++A+ TPVI+ I +DF + PK LE+ +T K++ LILCSPSNPTGSVY + Sbjct: 124 YWVSYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSK 183 Query: 256 KLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMT 315 + L +A ++A++P+++VI+DEIYEHI Y A H S A P M +RT+ VNG SKA+AMT Sbjct: 184 EELAGLAAVLAKYPQVVVIADEIYEHINYIGA-HQSIAQFPEMKERTVIVNGVSKAYAMT 242 Query: 316 GWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAG-GELVATMVKSFRE 374 GWR+G+IAGP+ + ACNK+Q Q+TSG S+SQKAA AA Y G E V M K+F Sbjct: 243 GWRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAA----YVGTQEPVKEMQKAFER 298 Query: 375 RRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQV 434 RRD +VK E+ G +++ P+GAFYLF S ++G + +G I NS+ L YLL+ A V Sbjct: 299 RRDLIVKLAKEVPGFEVNVPQGAFYLFPKCSYFFG-KSNGERKIENSDDLAMYLLEDAHV 357 Query: 435 ALVPGDAFGDDTCIRISYAASLSTLQAAVERIKKALVTIK 474 A V G +FG CIR+SYA S + A+ RIK+AL +K Sbjct: 358 ACVGGTSFGAPECIRMSYATSDENIVEAIRRIKEALAKLK 397 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: 464 Number of extensions: 18 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: 397 Length adjustment: 32 Effective length of query: 447 Effective length of database: 365 Effective search space: 163155 Effective search space used: 163155 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 Aug 03 2021. The underlying query database was built on Aug 03 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