Align L-lactate dehydrogenase; EC 1.1.1.27 (characterized)
to candidate 353437 BT3911 malate dehydrogenase (NCBI ptt file)
Query= CharProtDB::CH_024078 (330 letters) >FitnessBrowser__Btheta:353437 Length = 313 Score = 236 bits (601), Expect = 7e-67 Identities = 124/315 (39%), Positives = 194/315 (61%), Gaps = 14/315 (4%) Query: 16 NKISLIGSGNIGGVMAYLAQLKELGD-VVLFDIAPKLGAAKALDIMHANAIYDTSQNVIG 74 +K++++G+GN+G A + E+ D VV+ D+ + KA+D+M + V+G Sbjct: 2 SKVTVVGAGNVGATCANVLAFNEVADEVVMLDVKEGVSEGKAMDMMQTAQLLGFDTTVVG 61 Query: 75 TTS-YEDIAGSDVCIITAGLAKLPNKSDDEWSRDDLVAPNSKIMFTIGENIKKYAPNAFV 133 T+ Y A SDV +IT+G+ + P + R++L+ N+ I+ ++ ENI KY+PNA + Sbjct: 62 CTNDYAQTANSDVVVITSGIPRKPGMT-----REELIGVNAGIVKSVAENILKYSPNAIL 116 Query: 134 ICITNPLDVMVKMLLKSTGFPKNKVVGMGGLLDSSRMCHYIADKLRVNPRYVHGSCIGGH 193 + I+NP+D M + LK+ G PKN+++GMGG LDSSR ++++ L N V G IGGH Sbjct: 117 VVISNPMDTMTYLSLKALGLPKNRIIGMGGALDSSRFKYFLSQALGCNANEVEGMVIGGH 176 Query: 194 GD-SMIPLTNHVTVNGIPIQRFIERGEITQAELDKIAERTIGSGMELVQLYGNGSAFFAP 252 GD +MIPLT T G+P+ F I++ +L+++A T+ G L +L G SA++AP Sbjct: 177 GDTTMIPLTRFATYKGMPVTNF-----ISEEKLNEVAAATMVGGATLTKLLGT-SAWYAP 230 Query: 253 ATAAIEMASAYLSDKRSVIVCSCYLEGEYGHNDVYLGTPAIIGANGIEKIITLKLSAEEQ 312 A + + L D++ +I CS YLEGEYG +D+ +G P I+G NGIEKI+ L L+A+E+ Sbjct: 231 GAAGAFVVESILHDQKKMIPCSVYLEGEYGESDICIGVPVILGKNGIEKIVELDLNADEK 290 Query: 313 AKLDASVKEIRRLEA 327 AK AS K + A Sbjct: 291 AKFAASAKAVHGTNA 305 Lambda K H 0.319 0.136 0.390 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: 306 Number of extensions: 14 Number of successful extensions: 6 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: 330 Length of database: 313 Length adjustment: 28 Effective length of query: 302 Effective length of database: 285 Effective search space: 86070 Effective search space used: 86070 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 (21.7 bits) S2: 48 (23.1 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