Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 122 bits (306), Expect = 2e-32 Identities = 129/412 (31%), Positives = 181/412 (43%), Gaps = 57/412 (13%) Query: 30 DGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLSQFVP 89 DG+ ID + G+ +P + AI+ Q L H F H P L ++L+ +P Sbjct: 40 DGRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGLVHEPAARLAQRLAALLP 99 Query: 90 VSYPLAGMLTNSGAEAAENALKVA------RGATGKRAIIAFDGGFHGRTLATLNL-NGK 142 T SG+ A E ALK+A +G K+ I+ F G+HG T AT+ L + + Sbjct: 100 GDLERV-FFTESGSVAVEVALKMAIQYWRNKGQAEKQRIVYFRHGYHGDTFATMALCDPE 158 Query: 143 VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV--EDVAAFIFEP-V 199 + G +P + PS +T M R F + L E +AA I EP V Sbjct: 159 EGMHSLFAGAMPDQIM-AELPSDET----------MRRAFELLLETHGERLAAVIIEPLV 207 Query: 200 QGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR----LGIEPDLL 255 QG GG D A + C +L+I DEI +GFGRTG+ FA PD++ Sbjct: 208 QGAGGMQMHDAATLAFIAAACARHKLLLIADEIMTGFGRTGRMFACEEADELTSTIPDIV 267 Query: 256 LLAKSIAGG-MPLGAVVGRKELMAAL----PKGGL--GGTYSGNPISCAAALASLAQMTD 308 L+K++ GG +PL A V R+ + A P L G TY N ++CAAA ASL Sbjct: 268 CLSKALTGGTLPLAATVARRHVFEAFLADDPAAALMHGPTYMANALACAAANASLDLFES 327 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 E A V+ E A+ L P L GV +R G+ +LA + Sbjct: 328 E--------PRLAQVAAIEAQLAAELGP-CRDLAGVAEVR------VKGAIGAVELAGRI 372 Query: 369 E--AARAR----GLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 E A R R G+ + P GK ++ L+ P I AE L + Q L E Sbjct: 373 ELDALRRRFAELGVWVRPFGK---VVYLMPPFVIAAEDLTTLTAAVRQVLTE 421 Lambda K H 0.320 0.137 0.402 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: 426 Number of extensions: 27 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: 416 Length of database: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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