Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_089322763.1 CHB58_RS03685 malate dehydrogenase
Query= BRENDA::Q27797 (326 letters) >NCBI__GCF_900188395.1:WP_089322763.1 Length = 313 Score = 269 bits (688), Expect = 6e-77 Identities = 147/315 (46%), Positives = 207/315 (65%), Gaps = 14/315 (4%) Query: 8 RKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTS 67 RKKI ++G+G IG T+ L RE+ADV L D+ G+ +GKALD +A+ I N V Sbjct: 3 RKKITIVGAGNIGATLALLLARREVADVYLIDIDEGIAKGKALDIMEASPILGFNSRVYG 62 Query: 68 ANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVI 127 YE A SD+V+ITAG + PG S R+DLL N +I++ V + VKKY P AF+I Sbjct: 63 TGNYEDTANSDLVVITAGFPRKPGMS-----RDDLLFKNFEIVKSVTEQVKKYSPEAFII 117 Query: 128 VVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHG 187 VVTNPLD M + SG P N V GMA LD+ARF F++++ IS +I+A VIG+HG Sbjct: 118 VVTNPLDAMTYTALKVSGFPTNRVMGMAGALDAARFAYFLSEKTGISVENIRAFVIGSHG 177 Query: 188 DHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPAL 247 D M+PL Y T+SG P+R F +++ +L +++ERT+ AGGEIV LL GSA+YAPA Sbjct: 178 DDMVPLKNYTTISGIPVRYF-----LSDEELEKLIERTRFAGGEIVSLLKHGSAFYAPAA 232 Query: 248 SAITMAQAFLKDEKRVLPCSVYCQGE----YGLHDMFIGLPAVIGGGGIEQVIELELTHE 303 S + MA + L ++++++ CSVY +GE YG + +G+P V+G GIE+VI+LEL+ + Sbjct: 233 SILDMAVSILWNKRKIISCSVYLEGEAGEYYGAEGLCVGVPVVLGKDGIEKVIKLELSDD 292 Query: 304 EQECFRKSVDDVVEL 318 E +RKSV+ V +L Sbjct: 293 EWTQWRKSVESVKKL 307 Lambda K H 0.320 0.137 0.395 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: 256 Number of extensions: 13 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: 326 Length of database: 313 Length adjustment: 28 Effective length of query: 298 Effective length of database: 285 Effective search space: 84930 Effective search space used: 84930 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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