Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 194 bits (494), Expect = 3e-54 Identities = 130/403 (32%), Positives = 199/403 (49%), Gaps = 38/403 (9%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + VWDT G+ YIDF GGI V LGH +P ++ + Q +L H N + P L L Sbjct: 29 GLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIG-NGYTNEPVLRL 87 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGAT------GKRAIIAFDGGFHGRTL 134 ++L +++ NSGAEA E ALK+AR K II+F FHGRT Sbjct: 88 AKRLED---LTFADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFHGRTF 144 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194 T+++ G+ Y + G +P + HLPY + ++A+ A A Sbjct: 145 FTVSVGGQ-PKYSEGFGPVPAGITHLPYNDIEA---VKKAIGAQ------------TCAV 188 Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254 I EP+QGEGG + DPAF +ALR CD+ G L+I DE+Q+G GR+G +A+ G+ PD+ Sbjct: 189 IVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVTPDI 248 Query: 255 LLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATW 314 L AK++ G P+GA++ EL A G G TY GNP+ A A + ++D L Sbjct: 249 LTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKLL-- 306 Query: 315 GERQEQAIVSRYERWKA--SGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAAR 372 + + SR E K + L+ G T V RG+ + + AA Sbjct: 307 -----EGVRSRSEALKGHLAKLNERFGLFTEVRG-RGLLIGAELNEAFKGRAKDFVTAAG 360 Query: 373 ARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 G++++ +G ++R + L + + + EG + L + + + Sbjct: 361 QHGVIMLMAGP--DVLRFVPSLIMPLDDMNEGFERLAKAIESI 401 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: 463 Number of extensions: 23 Number of successful extensions: 4 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: 411 Length adjustment: 31 Effective length of query: 385 Effective length of database: 380 Effective search space: 146300 Effective search space used: 146300 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