Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate AZOBR_RS29980 AZOBR_RS29980 saccharopine dehydrogenase
Query= BRENDA::Q5LX24 (368 letters) >FitnessBrowser__azobra:AZOBR_RS29980 Length = 375 Score = 379 bits (972), Expect = e-110 Identities = 194/365 (53%), Positives = 255/365 (69%), Gaps = 1/365 (0%) Query: 4 NICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVL-NRMGVATKQVDAKDEAGLAK 62 +I ++G GKIG+ I LK + +Y VTVAD AL L + T+ VDA D A LA+ Sbjct: 3 DILLMGGGKIGETIGDFLKATGDYRVTVADRSAEALERLPTHPRMETRVVDAADPAELAE 62 Query: 63 ALGGFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQTAFMPQCG 122 A+ G AV+SA P+ LT +A+AA+ AG HY DLTEDVA+T V+ LA+ + AF+PQCG Sbjct: 63 AMRGKFAVLSALPYHLTVGVAEAARDAGTHYLDLTEDVASTRRVKELADGAPCAFIPQCG 122 Query: 123 LAPGFVGIAGAALAAEFDEIDSLHMRVGALPLYPTNALKYNLTWSTDGLINEYCNPCDAI 182 LAPGF+ I +A+ FD +D++ MRVGALP YP+NAL YNLTWST+G+INEY PC+AI Sbjct: 123 LAPGFISIVANDVASRFDTLDTVRMRVGALPKYPSNALNYNLTWSTEGVINEYLEPCEAI 182 Query: 183 VNGERVKTAPLEDYEILGHDGVEYECFNTSGGLGTLPETLDGKARSVSYRSIRYPGHRDI 242 V G V PLE+ E DGV YE FNTSGGLGTL ETL GK R+++YRS+RYPGHRD+ Sbjct: 183 VEGRLVSVPPLEEREEFSLDGVLYEAFNTSGGLGTLCETLAGKVRTLNYRSVRYPGHRDL 242 Query: 243 LRLLLNDLGLERRRDLLKDIFETALPRTDQDVVLVYCTAKGRIGGQLREKSLINKSYSRV 302 ++ LL+DL L RR+LLKDI E ++P T QDVVL++ T G G+L +++ NK Y R Sbjct: 243 MKALLHDLRLGSRRELLKDILEHSIPATLQDVVLIFVTVTGTKRGRLLQETYANKIYGRE 302 Query: 303 IDGQVWSAIQVTTAAGVLGVVDLMRAGTLPAKGFVRQEQVKFADFLETEFGRLYRAGDLT 362 I G ++ IQ+TTA+G+ V+DL+ GTLP +GFV+QE+V++ADF+ FGR Y D Sbjct: 303 IGGTFYNGIQITTASGMCAVLDLLADGTLPQRGFVKQEEVRYADFIANRFGRNYAMTDAA 362 Query: 363 AQNKA 367 Q A Sbjct: 363 PQQGA 367 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: 351 Number of extensions: 13 Number of successful extensions: 2 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: 375 Length adjustment: 30 Effective length of query: 338 Effective length of database: 345 Effective search space: 116610 Effective search space used: 116610 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