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 WP_012466715.1 CLIM_RS09085 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::E9L7A5 (479 letters) >NCBI__GCF_000020465.1:WP_012466715.1 Length = 416 Score = 164 bits (416), Expect = 4e-45 Identities = 116/364 (31%), Positives = 184/364 (50%), Gaps = 29/364 (7%) Query: 90 AITDQATALVQAGVPVIRLAAGEPD---FDTPAPIVEAGINAIREGHTRYTPNAGTMELR 146 A+ +++ A AG PV L G+P F P + EA I A+REG YT + G R Sbjct: 28 ALAEESAA---AGKPVTSLNIGDPTLYGFHPPPALTEACITALREGCNSYTSSCGIATAR 84 Query: 147 SAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARL 206 AISH+ E ++ + ++I++++GA ++ A+ +PGDEVL P+P + Y + Sbjct: 85 EAISHEASERR-IATSAEEIIITSGATEAADLLCTAILNPGDEVLCPSPGYPLYTALVAR 143 Query: 207 ADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVA 266 +A V ++L DP+ +E +T +++LLI+ +P+NPTG++YP +LL IAE A Sbjct: 144 QEAVSVPYRLDPGNNWLPDPEEIERLITPRTKLLIVINPNNPTGALYPPELLASIAE-TA 202 Query: 267 RHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPK 326 R L+ ++DE+Y ++Y+ +H FAS G T+ SK F + GWR G++ Sbjct: 203 RRNNLVCLADEVYRKLLYS-GSHHPFASFAGNDLPVCTLESLSKNFMVPGWRTGWMTMTN 261 Query: 327 HFI-----AACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVK 381 + A K+ A + Q A AL L G + + +++ R RRD V+ Sbjct: 262 SRLIPDIRRALRKLADARVC-APAAPQFAIPEALSL---GNDYLLPVLEKLRVRRDLTVR 317 Query: 382 SFGEIEGVKISEPRGAFYLF--IDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPG 439 IEG+ S P GAFY+ +D+S Y + E LL K ++ V G Sbjct: 318 MINGIEGLSCSNPEGAFYVMAKLDMSLY---------PFASDEEFIVELLRKKRILFVHG 368 Query: 440 DAFG 443 FG Sbjct: 369 SGFG 372 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: 468 Number of extensions: 23 Number of successful extensions: 5 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: 416 Length adjustment: 33 Effective length of query: 446 Effective length of database: 383 Effective search space: 170818 Effective search space used: 170818 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 10 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