Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate GFF2766 HP15_2710 L-lactate/malate dehydrogenase
Query= SwissProt::P16115 (319 letters) >FitnessBrowser__Marino:GFF2766 Length = 307 Score = 227 bits (578), Expect = 3e-64 Identities = 119/316 (37%), Positives = 189/316 (59%), Gaps = 11/316 (3%) Query: 1 MKIGIVGLGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDLIHGTPFTRR-ANIYA 59 MK+ ++G G VGS+ AF L +K E+VL+ K+ GD LDL HG F A + A Sbjct: 1 MKVSVIGTGNVGSTLAFVLTLKNIIDELVLVGRSKQSVLGDVLDLRHGQLFVNTPAQVTA 60 Query: 60 GDYADLKGSDVVIVAAGVPQ-KPGETRLQLLGRNARVMKEIARNVSKYAPDSIVIVVTNP 118 G +D GSDV+ V A VP K +RL+L N ++MKE+ +++ +PD +++V+NP Sbjct: 61 GTISDTAGSDVIAVCASVPTPKNMSSRLELAQGNVQLMKELMPELARMSPDCKIVMVSNP 120 Query: 119 VDVLTYFFLKESGMDPRKVFGSGTVLDTARLRTLIAQHCGFSPRSVHVYVIGEHGDSEVP 178 VDVL ++ L+ G P +V G+GT++D++R R L+A+ + Y++GEHGDS+ P Sbjct: 121 VDVLVHYALEFGGFRPNQVIGTGTLVDSSRFRQLLAEELRIHSEDIRAYILGEHGDSQFP 180 Query: 179 VWSGAMIGGIPLQNMCQICQKCDSKILENFAEKTKRAAYEIIERKGATHYAIALAVADIV 238 S A +GG L + E+ RA +E+++ KG T+YA+ALA A+I+ Sbjct: 181 AMSCADVGGETLDA---------TPGRYALFERASRAGFEVLKHKGCTNYAVALAAAEII 231 Query: 239 ESIFFDEKRVLTLSVYLEDYLGVKDLCISVPVTLGKHGVERILELNLNEEELEAFRKSAS 298 E I D K L +S+ ++ +LGV D+C+S+P +G++G+ER+L L+E+E AF SA+ Sbjct: 232 ECIANDSKHTLPVSLRVDGFLGVDDVCLSLPAVVGRNGIERVLHPRLDEKEQAAFLHSAN 291 Query: 299 ILKNAINEITAEENKH 314 +++ I E+ H Sbjct: 292 VVREVIASSAPEKEDH 307 Lambda K H 0.320 0.137 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: 247 Number of extensions: 19 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: 319 Length of database: 307 Length adjustment: 27 Effective length of query: 292 Effective length of database: 280 Effective search space: 81760 Effective search space used: 81760 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 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