Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme
Query= curated2:Q05174 (450 letters) >FitnessBrowser__Burk376:H281DRAFT_04057 Length = 394 Score = 122 bits (307), Expect = 2e-32 Identities = 121/409 (29%), Positives = 175/409 (42%), Gaps = 49/409 (11%) Query: 43 GPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPY 102 G WL D G RYLD +A LG +++ + + A N +P Y P Sbjct: 27 GSWLYDN-NGKRYLDFIQGWAVNCLGHCDEGMIEA---LNQQAKLLFNP--SPAFYNEPM 80 Query: 103 AKFVTTFARVLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLE 162 AK + +FF + GA A E A+K A W + D A +++ + Sbjct: 81 AKLAALLTQ---HSCFDKVFFANSGAEANEGAIKLARKWGKK---FKDGA---FEIITFD 131 Query: 163 RSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAE 222 SFHGR+ TMS + K W I AP + P A+ N A L A+ Sbjct: 132 HSFHGRTLATMSASG----------KPGWDTIYAPQV--PGFPKADLNDIASVEKLINAK 179 Query: 223 EAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGT 282 + EPIQGEGG + EF+Q +++L +H+ L ++DEVQSGCG GT Sbjct: 180 TV---------AVMLEPIQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGT 230 Query: 283 AWAYQQLGLRPDLVAFGKKTQVCGVMGG----GRIGEVESNVFAVSSRISSTWGGNLADM 338 +AY+ G+ PD++ GK G+ GG + + E VF + T+ GN Sbjct: 231 LFAYELSGVEPDIMTLGK-----GIGGGVPLAALLAKAEVAVFEAGDQ-GGTYNGNPLMT 284 Query: 339 VRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDL-PDTE 397 V+ + L+ V RG+YLR L L+E RG GL+ A+ L D Sbjct: 285 AVGYSVISQLTAPGFLEGVRARGEYLRAKLLELSEERG--FKGERGEGLLRALLLGKDIG 342 Query: 398 QRDAVLRRMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAASL 446 + R ++ LRF P L VT E+DQ + L + L Sbjct: 343 NQIVEKARDMQPDGLLLNAARPNLLRFMPALNVTNEEIDQMMAMLRSIL 391 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: 345 Number of extensions: 13 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: 450 Length of database: 394 Length adjustment: 32 Effective length of query: 418 Effective length of database: 362 Effective search space: 151316 Effective search space used: 151316 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