Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= curated2:Q05174 (450 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 129 bits (325), Expect = 1e-34 Identities = 105/332 (31%), Positives = 162/332 (48%), Gaps = 37/332 (11%) Query: 122 FFVDGGALAVENALKAAFDWKAQKLGLDDRAVNRLQVLHLERSFHGRSGYTMSLTNTDPS 181 FF + GA A E ALK A +++ D ++ +++ +SFHGR+ +T+S+ Sbjct: 101 FFANSGAEANEAALKLA-----RRVAFDRHGADKYEIISFTQSFHGRTFFTVSVGGQ--- 152 Query: 182 KTARYPKFDWPRIPAPALEHPLTTHAEANREAERRALEAAEEAFRAADGMIACFLAEPIQ 241 PK+ P PA TH N +EA ++A A + EPIQ Sbjct: 153 -----PKYSEGFGPVPAG----ITHLPYND------IEAVKKAIGA---QTCAVIVEPIQ 194 Query: 242 GEGGDNHFSAEFLQAMQDLCHRHDALFVLDEVQSGCGLTGTAWAYQQLGLRPDLVAFGKK 301 GEGG FL+A+++ C +H AL + DEVQ+G G +G +AYQ+ G+ PD++ K Sbjct: 195 GEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAK- 253 Query: 302 TQVCGVMGGGRIGE-VESNVFAVSSRI---SSTWGGNLADMVRATRVLETIERTDLLDSV 357 + G IG + +N A ++ +T+GGN A +V+E + LL+ V Sbjct: 254 ----ALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKLLEGV 309 Query: 358 VQRGKYLRDGLEALAERHPGVVTNARGRGLMCAVDLPDTEQRDAVLRRMYTG-HQVIALP 416 R + L+ L L ER G+ T RGRGL+ +L + + A G H VI L Sbjct: 310 RSRSEALKGHLAKLNERF-GLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVIMLM 368 Query: 417 CGTRGLRFRPPLTVTESELDQGLEALAASLAS 448 G LRF P L + ++++G E LA ++ S Sbjct: 369 AGPDVLRFVPSLIMPLDDMNEGFERLAKAIES 400 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: 390 Number of extensions: 21 Number of successful extensions: 4 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: 411 Length adjustment: 32 Effective length of query: 418 Effective length of database: 379 Effective search space: 158422 Effective search space used: 158422 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 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