Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= curated2:Q05174 (450 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 102 bits (253), Expect = 3e-26 Identities = 115/399 (28%), Positives = 164/399 (41%), Gaps = 54/399 (13%) Query: 52 GTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPYAKFVTTFAR 111 G YLDL+ A +G + P + + N + +P K + T Sbjct: 27 GNEYLDLYGGHAVISIGHS------HPHYTKRIKEQLDNIAFYSNSVQIPIQKELATKLG 80 Query: 112 VLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLERSFHGRSGY 171 L LF + GA A ENALK A ++ K G + + FHGR+ Sbjct: 81 QLSGYPDYDLFLCNSGAEANENALKLA-SFETGKKGF----------IAFTKGFHGRTSG 129 Query: 172 TMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAEEAFRAADGM 231 ++LT D P+I AP H E LEA E+ + A G Sbjct: 130 AVALT-------------DNPKIIAPFNAH------EGVHILPFNDLEAVEK--QLATGT 168 Query: 232 IACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGTAWAYQQL-G 290 IA + E IQG GG FL + L ++ A +LDEVQSG +G +A+Q + G Sbjct: 169 IAGVIVEGIQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEG 228 Query: 291 LRPDLVAFGKKTQVCGVMGGGRIGEV--ESNVFAVSSRISSTWGGNLADMVRATRVLETI 348 L+PDL+ K G+ G IG V A + +T+GGN A VLE I Sbjct: 229 LKPDLITVAK-----GMGNGFPIGGVLISPEFKASHGLLGTTFGGNHLACAAALAVLEVI 283 Query: 349 ERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTEQRDAVLRRMYT 408 + +L+ + + GK + LE +A VT RG+GLM DL + V + Sbjct: 284 DEENLITAAAENGKAIMAALEKVAG-----VTEVRGKGLMIGFDL--ATEAGPVRAALIH 336 Query: 409 GHQVIALPCGTR-GLRFRPPLTVTESELDQGLEALAASL 446 H++ G + +R PPL + L LE L L Sbjct: 337 EHKIFTGSAGGKHTIRLLPPLNIEPKALTLFLEKLETVL 375 Lambda K H 0.321 0.136 0.411 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: 348 Number of extensions: 20 Number of successful extensions: 3 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: 450 Length of database: 381 Length adjustment: 31 Effective length of query: 419 Effective length of database: 350 Effective search space: 146650 Effective search space used: 146650 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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