Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 321 bits (823), Expect = 2e-92 Identities = 177/410 (43%), Positives = 245/410 (59%), Gaps = 9/410 (2%) Query: 8 QSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY 67 + + ++ NA +WD +G++Y DF GI VLN GH +P V++A+ AQ R TH Sbjct: 16 RGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHT 75 Query: 68 AFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDG 127 A+ P+ Y+AL E+++ VP+ L +GAEA ENA+K+AR TG+ +IAF G Sbjct: 76 AYQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKIARAHTGRPGVIAFSG 135 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 GFHGRTL + L GKVAPYK G P +YH P+P GV+ EQ+++A++ LF ++ Sbjct: 136 GFHGRTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTEQSIQALESLFKTDID 195 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 + VAA I EPVQGEGGF F Q LR CD+ GIL+I DE+Q+GFGRTG+ FA Sbjct: 196 PQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMSH 255 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307 + PDL+ +AKS+AGGMPL AV GR +M A GGLGGTY+GNP++ AAA A + + Sbjct: 256 YPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIETIE 315 Query: 308 DENL---ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFAN-ADGSPAPAQ 363 E L AT +Q +A + +AS P I + G+G+M +EF + A G P+ Sbjct: 316 QERLCERATALGKQLKAALQ-----QASQTCPGIADIRGLGSMVAVEFHDPATGQPSAEL 370 Query: 364 LAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLA 413 +V A GL+L+ G + IR L PLTI + L +L + LA Sbjct: 371 AKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVLA 420 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: 538 Number of extensions: 22 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: 424 Length adjustment: 32 Effective length of query: 384 Effective length of database: 392 Effective search space: 150528 Effective search space used: 150528 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