Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_011372678.1 SUDEN_RS05500 malate dehydrogenase
Query= BRENDA::Q27797 (326 letters) >NCBI__GCF_000012965.1:WP_011372678.1 Length = 319 Score = 233 bits (594), Expect = 5e-66 Identities = 130/319 (40%), Positives = 195/319 (61%), Gaps = 11/319 (3%) Query: 5 VSRRKKIAMIGSGMIGGTMGY-LCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNV 63 +++ K++ +IG+G +G T+ Y L +L +++L D + +GKALD SQA + ++ Sbjct: 1 MNQGKRVGIIGAGNVGATVAYSLAMLGSCHEIILRDNKIDVAKGKALDMSQAAAAVRSHT 60 Query: 64 SVTSANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPL 123 V+ A + + DVV++TAG ++PG S R+DLL NA I ++V GV KY P Sbjct: 61 IVSVAEEMADLTNCDVVVVTAGSPRLPGMS-----RDDLLMINANITKDVIAGVAKYSPD 115 Query: 124 AFVIVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVI 183 A +I+V+NPLD M + SG ++ V GMA +LDSAR FI ++L I+A+V+ Sbjct: 116 AIIIMVSNPLDAMTYVALKESGFDRSRVIGMAGILDSARMASFIQEKLGYGGGQIRASVM 175 Query: 184 GTHGDHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYY 243 G HGD M+PLARY TV+G PL + M+ +++ EIV RT+ G EIV L GSAYY Sbjct: 176 GGHGDDMVPLARYSTVAGVPLTDL-----MSTSEINEIVIRTRNGGAEIVGHLKTGSAYY 230 Query: 244 APALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHE 303 APA + M +A LKD K++ PC+V+ +GEYG D+ G+P ++G G E++IE+ L Sbjct: 231 APAKATALMVEAILKDTKQIHPCAVFLEGEYGHSDVVSGVPVMLGANGAEKIIEISLDES 290 Query: 304 EQECFRKSVDDVVELNKSL 322 E+ F S + V L +L Sbjct: 291 EKIMFEGSCNSVRTLIDTL 309 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: 233 Number of extensions: 7 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: 319 Length adjustment: 28 Effective length of query: 298 Effective length of database: 291 Effective search space: 86718 Effective search space used: 86718 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