Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= curated2:Q05174 (450 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 130 bits (327), Expect = 8e-35 Identities = 105/404 (25%), Positives = 165/404 (40%), Gaps = 49/404 (12%) Query: 52 GTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKPSNPDVYTVPYAKFVTTFAR 111 G RYLD + A LG P F +A A ++Y P + + R Sbjct: 30 GERYLDFAAGIAVNALGHG------HPQFTKAIAEQAATLMHVSNLYGSPQGEALAQ--R 81 Query: 112 VLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLERSFHGRSGY 171 ++ + +FF + G A+E A+K A++ + R +++ + +FHGRS Sbjct: 82 IVDNSFADTVFFTNSGVEAIECAIKT-----ARRYHYVNGNPQRHKLITFKNAFHGRSIG 136 Query: 172 TMSLTNTDPSKTA---RYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAEEAFRAA 228 +S T+ + P FD+ + E A Sbjct: 137 AISATDQPKMRDGFEPLLPGFDYVK------------------------FNDLEGAIAKI 172 Query: 229 DGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGTAWAYQQ 288 D A FL E +QGEGG + EF+Q ++ C H L +LDE+Q G G TG WAY+ Sbjct: 173 DDETAGFLVETVQGEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEH 232 Query: 289 LGLRPDLVAFGKKTQVCGVMGGGRIGEVESNVFAVSSRI----SSTWGGNLADMVRATRV 344 G+ PD++ K G+ G +G + A ST+GGN M V Sbjct: 233 YGITPDILTAAK-----GIGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAV 287 Query: 345 LETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTEQRDAVLR 404 L+ + + V + G+ LR G E L H + RG+GLM + L + + Sbjct: 288 LDVMLEPGFFEHVEKMGERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVA 347 Query: 405 RMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAASLAS 448 + H ++ + G R PPL + ES + + +E L+A S Sbjct: 348 HLRENHGLLTVAAGENVFRVLPPLVIEESHIAECIEKLSAGARS 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: 421 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 450 Length of database: 398 Length adjustment: 32 Effective length of query: 418 Effective length of database: 366 Effective search space: 152988 Effective search space used: 152988 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