Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 332 bits (851), Expect = 1e-95 Identities = 176/412 (42%), Positives = 247/412 (59%), Gaps = 11/412 (2%) Query: 8 QSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY 67 + + ++ NAE+WD +G+R+IDF GI V N GH +P ++ AI+ Q TH Sbjct: 16 RGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHT 75 Query: 68 AFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDG 127 A+ P+ Y+ L E+L++ P +P +GAEA ENA+K+AR ATG+ +IAF G Sbjct: 76 AYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTG 135 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 GFHGRTL + L GKVAPYK G P V+H P+P+ GVT +LKA++ LF ++ Sbjct: 136 GFHGRTLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTADSLKAIEFLFKADID 195 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 + VAA IFEPVQGEGGF F +ALR+ C+E GIL+I DE+Q+GF RTG+ FA Sbjct: 196 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 255 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307 + PDL+ +AKS+AGGMPL V+GR ++M A GGLGGTY+GNP++ AAA A L + Sbjct: 256 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIID 315 Query: 308 DENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363 +E L G+R + +++ P I + G G M +EF A G+ A+ Sbjct: 316 EEKLCERATLLGDRVKAKLIA------LQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAE 369 Query: 364 LAK-VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 K V A RGLLL+ G +++R L PLTI+ V +E + ILE + + Sbjct: 370 FTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIKD 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: 551 Number of extensions: 24 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 384 Effective length of database: 395 Effective search space: 151680 Effective search space used: 151680 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 09 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