Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_073036145.1 BUB04_RS00940 malate dehydrogenase
Query= BRENDA::Q27797 (326 letters) >NCBI__GCF_900129305.1:WP_073036145.1 Length = 309 Score = 303 bits (775), Expect = 5e-87 Identities = 154/316 (48%), Positives = 210/316 (66%), Gaps = 10/316 (3%) Query: 7 RRKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVT 66 +RKKI ++G+G +G T + +EL DV L D+V GMP+GKALD +A+ + + + Sbjct: 2 KRKKITVVGAGFVGATAAHWAAAKELGDVCLIDIVEGMPQGKALDLMEASPVEGFDAHII 61 Query: 67 SANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFV 126 N Y A SD+VIITAGL + PG S R+DLL N +I++ V + V KY P AF+ Sbjct: 62 GTNDYADTADSDIVIITAGLPRKPGMS-----RDDLLAKNTEIVKSVTEQVAKYSPDAFL 116 Query: 127 IVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTH 186 I+V+NPLD MV H+ SG P N V GMA VLD+ARFR FIA +L +S D+ A V+G H Sbjct: 117 IIVSNPLDAMVYVAHKVSGFPTNRVMGMAGVLDAARFRTFIAMELNVSVEDVTAFVLGGH 176 Query: 187 GDHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPA 246 GD M+PL RY TV+G PL + + K+ +VERT+ G EIV LL GSA++AP+ Sbjct: 177 GDTMVPLPRYSTVAGIPLPDL-----LPPEKIEALVERTRNGGAEIVNLLKTGSAFFAPS 231 Query: 247 LSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQE 306 SA+ MA++ LKD+KR+LPC+ YC EYG+ F+G+P +G GG+EQVIE++L EE+E Sbjct: 232 ASAVQMAESILKDKKRILPCAAYCDKEYGVGGYFVGVPVKLGAGGVEQVIEIKLLPEEKE 291 Query: 307 CFRKSVDDVVELNKSL 322 F+KSVD V L K + Sbjct: 292 AFQKSVDAVKNLVKKI 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: 246 Number of extensions: 10 Number of successful extensions: 3 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: 309 Length adjustment: 27 Effective length of query: 299 Effective length of database: 282 Effective search space: 84318 Effective search space used: 84318 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 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