Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase
Query= curated2:Q05174 (450 letters) >NCBI__GCF_021560695.1:WP_027489558.1 Length = 408 Score = 128 bits (322), Expect = 3e-34 Identities = 130/422 (30%), Positives = 183/422 (43%), Gaps = 49/422 (11%) Query: 33 DLVLDLEASAGPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKP 92 +LVLD A W + G Y+D + A LG DP + LAA A Sbjct: 24 ELVLDHGKGARVWDTE---GRDYVDFGAGIAVNALGHQ------DPDLLAALAAQAHKLW 74 Query: 93 SNPDV-YTVPYAKFVTTFARVLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDR 151 + +V YT P + G +F + GA A E A+K W A + R Sbjct: 75 HSSNVFYTEPPLRLAEELVHASG--FAERVFLCNSGAEANEAAIKLVRKWAAAQ----GR 128 Query: 152 AVNRLQVLHLERSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANR 211 A R ++ SFHGR+ T++ T K+ P P E R Sbjct: 129 APERRVIVTFNGSFHGRTLATVTAT--------AQAKYQQGYEPLP----------EGFR 170 Query: 212 EAERRALEAAEEAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLD 271 + EA E F A D +A + EP+QGEGG + FL+ +++LC +HDAL VLD Sbjct: 171 YLDFNDAEALEATFAAGD--VAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLD 228 Query: 272 EVQSGCGLTGTAWAYQQLGLRPDLV----AFGKKTQVCGVMGGGRIGEVESNVFAVSSRI 327 E+Q G G TGT +A+ + PD+V A G + ++ G ++ EV Sbjct: 229 EIQCGMGRTGTLFAHVHDHVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQ-----YGAH 283 Query: 328 SSTWGGNLADMVRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGL 387 +T+GGN A L + +L +V ++ LR GL A + RGRGL Sbjct: 284 GTTFGGNPMAAAVARVALAKLSSPAVLMNVERQANDLRAGL-ARINHELQLFAEVRGRGL 342 Query: 388 MCAVDLPDT--EQRDAVLRRMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAAS 445 M L D + AVL T ++ L G LRF PPLT+T+ EL GL L A+ Sbjct: 343 MIGAVLADAYKGKAGAVLDHAAT-RGLLLLQAGPDVLRFVPPLTITDEELADGLARLHAA 401 Query: 446 LA 447 L+ Sbjct: 402 LS 403 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: 403 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: 408 Length adjustment: 32 Effective length of query: 418 Effective length of database: 376 Effective search space: 157168 Effective search space used: 157168 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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