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 RR42_RS02275 RR42_RS02275 aspartate aminotransferase
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__Cup4G11:RR42_RS02275 Length = 397 Score = 163 bits (412), Expect = 1e-44 Identities = 118/373 (31%), Positives = 184/373 (49%), Gaps = 23/373 (6%) Query: 102 GVP-VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAISHKLKEENGLS 160 G+P V+ GE D TPA I +A A+ G T YT N G LRSA++ + +G + Sbjct: 36 GLPDVLPFWFGESDQVTPAFIRDAASRALAGGATFYTHNLGIAPLRSALADYVSALHGAT 95 Query: 161 YTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSI-S 219 D ++V++ +++ A V PGD + P W + E+ ++ A + + Sbjct: 96 AL-DNVVVTSAGVNALMLAAQLVAGPGDRAVAVTPLWPNLVEIPKILGAEVETVSLDYGA 154 Query: 220 EDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVARHPRLLVISDEIY 279 + LD L + LT +RLL++ SP+NPTG V R + + RH + +I+DE+Y Sbjct: 155 HGWTLDLDKLLAALTPDTRLLMINSPNNPTGWVMSRADQQAVLAHCRRHG-IWIIADEVY 213 Query: 280 EHIIYAP---ATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACNKIQ 336 E + Y A SF + +R + VN FSKA+ MTGWRLG++ P K+ Sbjct: 214 ERLYYGKGDGAIAPSFLDIASRDERVICVNSFSKAWLMTGWRLGWMVLPAALTDDLGKLV 273 Query: 337 SQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISEPRG 396 TS A S Q+A + A+ G A +V R RD+LV + + GV + P G Sbjct: 274 EYNTSCAPSFVQEAGIVAVREGEA---FTRELVGRLRAARDHLVSALAVVPGVDVHAPEG 330 Query: 397 AFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAFGD--DTCIRISYAA 454 A Y+F L+ ++S +LC+ L+ +A++ L PG AFGD + +R YA Sbjct: 331 AMYVFFRLA-----------GASDSLALCKQLVREARLGLAPGSAFGDEGEGFVRWCYAC 379 Query: 455 SLSTLQAAVERIK 467 + L V R++ Sbjct: 380 DPARLDEGVRRLR 392 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: 388 Number of extensions: 22 Number of successful extensions: 8 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