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_012283547.1 HM1_RS11430 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::E9L7A5 (479 letters) >NCBI__GCF_000019165.1:WP_012283547.1 Length = 395 Score = 248 bits (632), Expect = 3e-70 Identities = 148/367 (40%), Positives = 216/367 (58%), Gaps = 21/367 (5%) Query: 105 VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAISHKLKEENGLSYTP- 163 VI L GEPDF TP + E+ A+ G+T YT N GT ELR I+ ++ G+ Y P Sbjct: 34 VISLGVGEPDFVTPWHVRESCFYALERGYTMYTSNFGTPELRKEITRFIQRSYGVDYDPL 93 Query: 164 DQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSISEDFL 223 ++LV+ GA +++ A+ + PGDEVL+P P +VSY +A V +PT + +DF Sbjct: 94 SEVLVTVGASEAVDLAMRMLLCPGDEVLVPEPSYVSYSPTVTMAGGVAVAVPTYVKDDFQ 153 Query: 224 LDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVARHPRLLVISDEIYEHII 283 L + LE K++ ++++L+LC P+NPTG++ R LE IA A L+V++DEIY + Sbjct: 154 LTVEALEKKVSPRTKMLVLCYPNNPTGAIMTRPELEAIARF-AEERDLIVLADEIYAELT 212 Query: 284 YAPATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACNKIQSQFTSGA 343 Y H FA LPGM DRT+ +NG SK+ AMTGWR+GY+ G K FIA KI A Sbjct: 213 Y-EEQHVCFAGLPGMRDRTVLINGLSKSHAMTGWRIGYVCGNKDFIAQMTKIHQYTILCA 271 Query: 344 SSISQKAAVAALGLGYAGGEL-VATMVKSFRERRDYLVKSFGEIEGVKISEPRGAFYLFI 402 + Q AA+ AL G+L + MV + +RR ++V F ++ G+ PRGAFY F Sbjct: 272 PIMGQMAALEAL----RNGDLEKSRMVNQYDQRRRFVVARFNQM-GLTCFNPRGAFYAFP 326 Query: 403 DLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAFG--DDTCIRISYAASLSTLQ 460 +++ G+ D F C LL + +VA+VPG AFG + IR+SYA+S++ L Sbjct: 327 SITA-TGLSSDDF---------CEQLLAEEKVAVVPGTAFGASGEGFIRVSYASSMANLT 376 Query: 461 AAVERIK 467 A++RI+ Sbjct: 377 TALDRIE 383 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: 403 Number of extensions: 19 Number of successful extensions: 6 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: 395 Length adjustment: 32 Effective length of query: 447 Effective length of database: 363 Effective search space: 162261 Effective search space used: 162261 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