Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013136555.1 ARNIT_RS13880 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000092245.1:WP_013136555.1 Length = 393 Score = 165 bits (418), Expect = 2e-45 Identities = 127/411 (30%), Positives = 208/411 (50%), Gaps = 47/411 (11%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 + G NA ++D YIDF GIGV+++GH N V +AI Q + +TH + N Sbjct: 19 VNFKRGENATLFDDKDNNYIDFTAGIGVVSVGHGNKQVADAIYEQVSNITHIS-NLYAIE 77 Query: 76 PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGF 129 P L ++++Q Y +A NSGAEA E A+K+AR A K +I + F Sbjct: 78 PQALLAQKIAQLS--GYDVATFFANSGAEANEGAIKIARKYGQTKFANKKYKVITLEHSF 135 Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189 HGRT+ T+ G+ + P + PYP G + + + D S++ E Sbjct: 136 HGRTITTVRATGQ--------DKFHSPNFS-PYPE---GFSYNKQIN--DIYNSID---E 178 Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249 + A + E VQGEGG + Q L +F E+ +L IIDE+Q+G R+G+ A Sbjct: 179 ETVAVMIELVQGEGGVQPFEKEEIQKLAKFLKEKEVLFIIDEVQTGIFRSGEFLASNLYE 238 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGR-KELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308 IEPD++ +AK + GG+P+GAV+ + K++ + G G T+ GN + A+L L + + Sbjct: 239 IEPDIITIAKGLGGGVPIGAVLTKHKDIFS---PGDHGSTFGGNYLVTRASLEVLKILDE 295 Query: 309 -ENLATWGER---QEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQL 364 +N E E + + +E++ +S G+G MRG+ + A L Sbjct: 296 YKNKGALDEAIIYFESKLSALFEKYPNIFISK-----VGLGLMRGLR------AKDEATL 344 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A +++ A +G+L++ SG R+ +R L LTI E ++EG L+ ++++ Sbjct: 345 AAIIKNAFEQGVLVLKSG--RNTLRFLPVLTITKEEIDEGFKRLDDAISKI 393 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: 342 Number of extensions: 21 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: 393 Length adjustment: 31 Effective length of query: 385 Effective length of database: 362 Effective search space: 139370 Effective search space used: 139370 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