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 Ac3H11_256 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_256 Length = 390 Score = 149 bits (377), Expect = 1e-40 Identities = 111/352 (31%), Positives = 168/352 (47%), Gaps = 28/352 (7%) Query: 105 VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAIS---HKLKEENGLSY 161 V++ GE D TP I +A I ++++G T Y N G ELR AI+ H L + Sbjct: 26 VLQFWFGESDEVTPDFIRDAAIASLQKGETFYAHNLGLPELRHAIAGYMHGLHPQQHTDA 85 Query: 162 TPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSISED 221 D+I V++G ++ AV A+ GDEV++ P W + R+ A +P D Sbjct: 86 WFDRIAVTSGGVNGLMVAVQALVDAGDEVVLVTPVWPNLVAQPRILGAQVRTVPLVADAD 145 Query: 222 --FLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVA--RHPRLLVISDE 277 + LD L + +T +RLL++ +P+NPTG R E+ A I+A R +++DE Sbjct: 146 GAWQLDMDALLAAITPGTRLLVVNAPNNPTGWTLTR---EEQATILAHCRRTGTWIVADE 202 Query: 278 IYEHIIYAPATHT----SFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACN 333 +YE + YA T SF + DR + + FSK+F MTGWRLG++ P A Sbjct: 203 VYERLYYAGDTANGAAPSFLDVAEPEDRLVVTHSFSKSFLMTGWRLGWLVLPPSMTPAVG 262 Query: 334 KIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISE 393 K+ TS A Q+ A AL E+ +V R RD LV ++ GV ++ Sbjct: 263 KLIEFNTSCAPVFVQRGATVAL---QRTDEVTPALVNHLRNCRDTLVPLLADVPGVSVAT 319 Query: 394 PRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAFGDD 445 PRG Y F + + + L + L+ +A + L PG AFG + Sbjct: 320 PRGGMYAFFHIDGH-----------DECLPLAKRLVREAGLGLAPGSAFGGE 360 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: 437 Number of extensions: 19 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: 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 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