Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate WP_090438616.1 BLS63_RS01140 saccharopine dehydrogenase
Query= BRENDA::Q5LX24 (368 letters) >NCBI__GCF_900100495.1:WP_090438616.1 Length = 365 Score = 378 bits (971), Expect = e-109 Identities = 186/353 (52%), Positives = 245/353 (69%) Query: 4 NICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKA 63 N+ ++GAG IG IA LL + +Y V VAD D +L + +G+AT+Q+D+ D + L Sbjct: 2 NVLLLGAGHIGYTIAQLLHNTGDYQVLVADRDANSLKAIAALGIATRQLDSADRSALEAV 61 Query: 64 LGGFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQTAFMPQCGL 123 + G DAV++A P+ + +A+AAK G HYFDLTEDV AT + LA+D++TAFMPQCGL Sbjct: 62 MQGQDAVLNALPYHMAITVAQAAKNTGTHYFDLTEDVHATKTIMELAKDAKTAFMPQCGL 121 Query: 124 APGFVGIAGAALAAEFDEIDSLHMRVGALPLYPTNALKYNLTWSTDGLINEYCNPCDAIV 183 APGF+GIA +LA +FD + + MRVGALP +PTNALKYNLTWS DGL+NEYC+PC+AI Sbjct: 122 APGFIGIAAHSLARDFDSVREVKMRVGALPEFPTNALKYNLTWSVDGLVNEYCHPCEAIR 181 Query: 184 NGERVKTAPLEDYEILGHDGVEYECFNTSGGLGTLPETLDGKARSVSYRSIRYPGHRDIL 243 NG+ PLE E DGVEYE FNTSGGLGTL ETL+GK + Y+++RYPGHRD++ Sbjct: 182 NGKLQMVQPLEGLEHFSLDGVEYEAFNTSGGLGTLCETLEGKVEVLDYKTVRYPGHRDLM 241 Query: 244 RLLLNDLGLERRRDLLKDIFETALPRTDQDVVLVYCTAKGRIGGQLREKSLINKSYSRVI 303 + LL DL L +++ LKDI A+P T QDVVLV+ T G GG+L ++ K ++ Sbjct: 242 KFLLEDLRLSGQQEKLKDILRGAVPSTMQDVVLVFVTVNGMKGGKLVQQVFSRKIFAAEQ 301 Query: 304 DGQVWSAIQVTTAAGVLGVVDLMRAGTLPAKGFVRQEQVKFADFLETEFGRLY 356 +G++ SAIQ+TTAAG+ +DL RA LP GF+ QEQV DFL FG Y Sbjct: 302 NGRLTSAIQITTAAGICAALDLFRAKRLPQSGFISQEQVSLDDFLANRFGLAY 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: 336 Number of extensions: 10 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 24 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