Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= curated2:Q05174 (450 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 123 bits (308), Expect = 1e-32 Identities = 125/410 (30%), Positives = 178/410 (43%), Gaps = 51/410 (12%) Query: 43 GPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPY 102 G WL D G RYLD +A LG + ++D A V + + + PS P Y P Sbjct: 27 GSWLTDH-NGKRYLDFVQGWAVNCLGHSNQAMID--ALVDQ--SKKLFNPS-PAFYNEPM 80 Query: 103 AKFVTTFARVLGDP-LLPHLFFVDGGALAVENALKAAFDW-KAQKLGLDDRAVNRLQVLH 160 + AR L D +FF + GA A E A+K A W + K G +++ Sbjct: 81 LRL----ARQLTDASCFDKVFFANSGAEANEGAIKLARKWGRKHKNGA-------FEIIT 129 Query: 161 LERSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEA 220 ++ SFHGR+ TMS + K W I AP + +A+ L + Sbjct: 130 MDHSFHGRTLATMSASG----------KAGWDTIFAPQVP--------GFPKADLNDLAS 171 Query: 221 AEEAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLT 280 E+ D +A L EP+QGEGG S EF+Q ++ L +H LF++DEVQ+GCG Sbjct: 172 VEKLIN--DKTVAIML-EPVQGEGGVIPASREFMQGLRKLADQHKLLFIVDEVQTGCGRC 228 Query: 281 GTAWAYQQLGLRPDLVAFGKKTQVCGVMGGGRIGEVESNVFAVSSRI---SSTWGGNLAD 337 GT +AY+ G+ PD++ GK G+ GG + + S T+ GN Sbjct: 229 GTMFAYELSGVEPDIMTLGK-----GIGGGVPLAALLCKAEVASFEAGDQGGTYNGNPVM 283 Query: 338 MVRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTE 397 + V+ + L SV +G YLR+ L AL + RG GL+ A+ L Sbjct: 284 TAVGSAVISQLTAPGFLQSVQDKGAYLREQLLALTSEFG--LGGERGEGLLRALVLNKDI 341 Query: 398 QRDAVLRRMYTGHQVIALPCGTRG-LRFRPPLTVTESELDQGLEALAASL 446 V Q + L LRF P L VT E+DQ + L L Sbjct: 342 GPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNVTIEEIDQMISMLRTLL 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: 323 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: 395 Length adjustment: 32 Effective length of query: 418 Effective length of database: 363 Effective search space: 151734 Effective search space used: 151734 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