Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_011952251.1 SWIT_RS07135 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000016765.1:WP_011952251.1 Length = 396 Score = 182 bits (461), Expect = 2e-50 Identities = 139/389 (35%), Positives = 194/389 (49%), Gaps = 44/389 (11%) Query: 31 GKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAPHGPYLALMEQLSQFVP 89 G+RY+DF GI V LGH +P +V+AI QA L H + +P G A + V Sbjct: 30 GERYLDFASGIAVNILGHGHPDLVKAIADQAATLMHTSNLYGSPQGEAFA-----QKLVD 84 Query: 90 VSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTLATLNLNGKV 143 ++ TNSGAEA E A+K AR G+ + II+F FHGRTL T++ + Sbjct: 85 KTFADTVFFTNSGAEAVECAIKTARRYHYVNGSPERTKIISFSNAFHGRTLGTISATSQP 144 Query: 144 APYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGEG 203 K R G P P D E A A+D A F+ EPVQGEG Sbjct: 145 ---KMRDGFEPLLPGFQVVPFNDL----EAARAAVDAT---------TAGFLVEPVQGEG 188 Query: 204 GFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAG 263 G P F + LR+ CDE+G+L+I+DE+Q G+ RTG FA + GI PD++ +AK IAG Sbjct: 189 GMTPSKPEFLKGLRQICDEQGLLLILDEVQCGYCRTGTFFAHEQYGITPDIMAVAKGIAG 248 Query: 264 GMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL-AQMTDE---NLATWGERQE 319 G PLGA + +E + G G TY GNP++ AA A + DE N+ G+R Sbjct: 249 GFPLGACLATEEAAKGMVFGTHGSTYGGNPLAMAAGEAVFKVAVNDEFLANVRATGDRLR 308 Query: 320 QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLM 379 QAI + G+G M GI+ D A A +A + + GLL + Sbjct: 309 QAIEQLIPNHDG-----VFDSVRGLGLMIGIKL--KDAVEARAFVAHLRD---HHGLLTV 358 Query: 380 PSGKARHIIRLLAPLTIEAEVLEEGLDIL 408 +G+ +++R+L PL IE + E ++ L Sbjct: 359 AAGE--NVVRILPPLVIEESHIAECIEKL 385 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: 409 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 385 Effective length of database: 365 Effective search space: 140525 Effective search space used: 140525 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 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