Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 181 bits (459), Expect = 3e-50 Identities = 134/406 (33%), Positives = 203/406 (50%), Gaps = 37/406 (9%) Query: 14 HPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAP 73 +PI+++ G+ + +WD DG+ Y+D + GI V +LGHC+ + E AQA +L H + N Sbjct: 23 YPISVARGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVS-NLFY 81 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG----ATGKRA--IIAFDG 127 L L E+L + S+ NSGAEA E A+K+AR G+ A II G Sbjct: 82 QEEQLDLAERL---LSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTG 138 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGRTLAT+ G+ K + G P P PS D +AL+A Sbjct: 139 AFHGRTLATVAATGQA---KFQDGFYPMPEGFRQVPSGDI-----EALRAA--------I 182 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 A + E VQGEGG LDP +A+A++ C E+G+L + DEIQ+G RTG+ ++F Sbjct: 183 GPQTAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQN 242 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307 G+EPD++ AK++A G+P+GA++ E+ G T+ + A A ++ M Sbjct: 243 YGLEPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEIML 302 Query: 308 DENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367 ++LA + I+ R+ R L I + G+G M G+ A P + +V Sbjct: 303 RDDLAGRAATEGARIMDRF-RAMGQKLPGTIDHVRGLGLMIGVVLA------FPGK--EV 353 Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLA 413 +A RG + + ++RLL LTI L+ D LE L+ Sbjct: 354 WQALIDRGFICNLTQDC--VLRLLPALTIPRADLDAFADALEDILS 397 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: 399 Number of extensions: 19 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: 402 Length adjustment: 31 Effective length of query: 385 Effective length of database: 371 Effective search space: 142835 Effective search space used: 142835 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