Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 197 bits (500), Expect = 7e-55 Identities = 134/407 (32%), Positives = 207/407 (50%), Gaps = 38/407 (9%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PI+L G+ A +WD DG+ Y+DF+ G+ V +LGHC+P VV+A+Q QA L H + N Sbjct: 22 PISLVKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQQQAATLLHVS-NLYWI 80 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGG 128 P + L + L V S+ NSGAEA E A+K+AR + K II + Sbjct: 81 EPQVQLAQVL---VENSFADKVFFCNSGAEANEGAIKLARKYAKKTWGSDKYEIITMEKS 137 Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188 FHGRTLAT+ + Y++ LP ++P+ LKA++R S Sbjct: 138 FHGRTLATVTATAQ-PKYQKDYEPLPQGFRYVPFGD----------LKALERAISPH--- 183 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 A + EPVQGEGG +P+F Q L + +L+I DE+Q G GRTG+ FA Sbjct: 184 --TCAILVEPVQGEGGVNLAEPSFWQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHY 241 Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 G+ P ++ LAK++AGG P+GA++ ++ A G T+ GNP+ AAA+A + + + Sbjct: 242 GVTPHIMTLAKALAGGAPMGALLATDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLN 301 Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368 + L + R + P+I + G+G M E P +A + Sbjct: 302 DGLMDNCREMAAYFMGHLRRLQEK--YPFITEVRGLGLMVACEL----DRPGADIVANCL 355 Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 E +GL++ + A +++R L PL I ++E + +LE+ LA + Sbjct: 356 E----KGLII--NCTAGNVLRFLPPLIINKADVDEAVAVLEEVLASV 396 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: 405 Number of extensions: 17 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: 432 Length adjustment: 32 Effective length of query: 384 Effective length of database: 400 Effective search space: 153600 Effective search space used: 153600 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: 51 (24.3 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