Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_004513148.1 GMET_RS06850 malate dehydrogenase
Query= BRENDA::Q27797 (326 letters) >NCBI__GCF_000012925.1:WP_004513148.1 Length = 317 Score = 300 bits (769), Expect = 2e-86 Identities = 154/319 (48%), Positives = 215/319 (67%), Gaps = 9/319 (2%) Query: 8 RKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTS 67 RKKI++IG G IGG + LC LREL DVV+FD+V G+P+GK LD ++ + +V + Sbjct: 3 RKKISLIGGGQIGGVLAQLCALRELGDVVMFDIVEGLPQGKMLDIAEVGPVDGFDVCLKG 62 Query: 68 ANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVI 127 N Y IAGSDVVI+TAGL + PG S R+DL+ N+KI+ +VA+G+K+Y P +FVI Sbjct: 63 TNSYADIAGSDVVIVTAGLPRKPGMS-----RDDLIEVNSKIMTQVAEGIKQYAPNSFVI 117 Query: 128 VVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHG 187 V++NPLD MV + +G P N V G A VLDS+RF FIA +L +S +D+ A +G HG Sbjct: 118 VISNPLDAMVTLCQKITGFPYNRVIGQAGVLDSSRFAAFIAWELGVSVKDVVAVTLGGHG 177 Query: 188 DHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVE----RTKKAGGEIVRLLGQGSAYY 243 D M+PL RY +V G P+ E +++ +AK E++E RT+ AGGE+V LL GSA+Y Sbjct: 178 DDMVPLVRYTSVCGIPVMELLERKYKDKAKAKEVMEAMVKRTRGAGGEVVALLKTGSAFY 237 Query: 244 APALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHE 303 +PA +AI M ++ LKD+KRVLP + QGE+G++ ++G+PAV+G G+EQ+I+ L E Sbjct: 238 SPASAAIAMTESILKDQKRVLPTCCFLQGEFGVNGYYVGVPAVLGENGVEQIIQFNLDAE 297 Query: 304 EQECFRKSVDDVVELNKSL 322 EQ KSV V L SL Sbjct: 298 EQAMMDKSVAAVKSLVDSL 316 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: 263 Number of extensions: 11 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: 317 Length adjustment: 28 Effective length of query: 298 Effective length of database: 289 Effective search space: 86122 Effective search space used: 86122 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