Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= curated2:Q05174 (450 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 117 bits (293), Expect = 6e-31 Identities = 105/321 (32%), Positives = 155/321 (48%), Gaps = 41/321 (12%) Query: 122 FFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLERSFHGRSGYTMSLTNTDPS 181 FF + GA A E ALK A +L + R V + QVL +E SFHGR+ T++ T Sbjct: 94 FFCNSGAEANEAALKLA------RLHANARHVAQPQVLVMENSFHGRTLATLAATGNPAV 147 Query: 182 KTARYPKFD-WPRIPAPALEHPLTTHAEANREAERRALEAAEEAFRAADGMIACFLAEPI 240 + P + R+P +E E + A ++ D I L EP+ Sbjct: 148 QRGFEPLMPGFLRVPYDNIE------------------EIRKVAAQSPD--IVAVLVEPV 187 Query: 241 QGEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGTAWAYQQLGLRPDLV---- 296 QGEGG + SA +LQA++ LC HD L ++DEVQ+G G TG + YQ G+ PD++ Sbjct: 188 QGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITLAK 247 Query: 297 AFGKKTQVCGVMGGGRIGEVESNVFAVSSRISSTWGGN-LADMVRATRVLETIERTDLLD 355 A G + + G+ E+ S +ST+GGN LA V T VL+ +ER + Sbjct: 248 ALGNGFPIGACLARGKAAELFS-----PGHHASTFGGNPLACRVGCT-VLDIMERDHIPQ 301 Query: 356 SVVQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTEQRDAVLRRMYTGHQVIAL 415 G+ L L+ H VV + RG GLM ++L + + + V R + +I + Sbjct: 302 RAATSGRRLLAALQEALGNHSEVV-SIRGLGLMVGIEL-NRQCAELVGRALDEQRLLITV 359 Query: 416 PCGTRGLRFRPPLTVTESELD 436 GT LR PPL +S++D Sbjct: 360 TRGTT-LRLLPPLICEDSQID 379 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: 368 Number of extensions: 19 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: 390 Length adjustment: 32 Effective length of query: 418 Effective length of database: 358 Effective search space: 149644 Effective search space used: 149644 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