Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate BPHYT_RS11250 BPHYT_RS11250 saccharopine dehydrogenase
Query= BRENDA::Q5LX24 (368 letters) >FitnessBrowser__BFirm:BPHYT_RS11250 Length = 365 Score = 375 bits (963), Expect = e-108 Identities = 191/352 (54%), Positives = 237/352 (67%) Query: 5 ICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKAL 64 + +VGAG IG IA +L+ + +Y V D D AL L G+ T +VD+ D A L A+ Sbjct: 3 VAIVGAGLIGHTIAHMLRETGDYDVVAFDRDQHALDKLAAQGIPTHRVDSADAAALRAAV 62 Query: 65 GGFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQTAFMPQCGLA 124 GFDA+I+A P++L +A AAK AG HYFDLTEDV AT+A+RA+A+D+ AFMPQCGLA Sbjct: 63 QGFDALINALPYYLAVNVASAAKGAGVHYFDLTEDVRATHAIRAIADDADHAFMPQCGLA 122 Query: 125 PGFVGIAGAALAAEFDEIDSLHMRVGALPLYPTNALKYNLTWSTDGLINEYCNPCDAIVN 184 PGF+GIA LA F EI + MRVGALP +PTNALKYNLTWS DGLINEYC PC+AI + Sbjct: 123 PGFIGIAAHELANRFTEIRDVKMRVGALPEFPTNALKYNLTWSVDGLINEYCQPCEAIRD 182 Query: 185 GERVKTAPLEDYEILGHDGVEYECFNTSGGLGTLPETLDGKARSVSYRSIRYPGHRDILR 244 PLE E DG EYE FNTSGGLGTL ETL G+ S+ Y+S+RYPGHR++++ Sbjct: 183 SRTQWVQPLEGLEHFSLDGTEYEAFNTSGGLGTLCETLSGRVESLDYKSVRYPGHRNLMQ 242 Query: 245 LLLNDLGLERRRDLLKDIFETALPRTDQDVVLVYCTAKGRIGGQLREKSLINKSYSRVID 304 LL DL L RD LK I ++P T QDVVLV+ T G GQL ++ K +++ + Sbjct: 243 FLLEDLRLASDRDTLKTIMRRSVPSTAQDVVLVFITVSGMRDGQLVQEVFTRKIFAKTVC 302 Query: 305 GQVWSAIQVTTAAGVLGVVDLMRAGTLPAKGFVRQEQVKFADFLETEFGRLY 356 G SAIQ+TTA + V+DL R LP KGFVRQEQV DFL FG+LY Sbjct: 303 GVPMSAIQITTAGAMCAVLDLFREQKLPQKGFVRQEQVSLRDFLANRFGQLY 354 Lambda K H 0.320 0.136 0.397 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: 339 Number of extensions: 8 Number of successful extensions: 1 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: 368 Length of database: 365 Length adjustment: 30 Effective length of query: 338 Effective length of database: 335 Effective search space: 113230 Effective search space used: 113230 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: 49 (23.5 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