Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate WP_011461131.1 DHAF_RS09770 hypothetical protein
Query= curated2:Q07251 (349 letters) >NCBI__GCF_000021925.1:WP_011461131.1 Length = 349 Score = 147 bits (371), Expect = 4e-40 Identities = 105/322 (32%), Positives = 151/322 (46%), Gaps = 14/322 (4%) Query: 29 VAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCVLDQGTLMVFDGDGGFGQH 88 V ++L+ ++ G SHG+S P Y + +VNPQ + L+ DGD G G Sbjct: 33 VVDNLLYAELRGIKSHGVSRFPVYLRRIQMGAVNPQPQISMEQRTPVLLKVDGDNGLGSV 92 Query: 89 VGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAAGFVLLSFTNVINRAPVVA 148 V + +E Q G C V ++ S+H G G+Y E+AA G V + T + P Sbjct: 93 VMVHALNRGMELAEQLGICAVGIKGSNHCGASGYYCELAAEQGLVSIVLT---DGPPATP 149 Query: 149 PFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAINKARVLAEKGEPAPEGSIIGAD 208 P+GGR A TNP+ F P +P ++VD+ATS A K A +GE PEG + + Sbjct: 150 PWGGRKAYFGTNPMAFGLPRAQ-KPHIIVDLATSLAARGKVIRAAAQGEKIPEGWALDRE 208 Query: 209 GNPTTDASTMFGEHPGALLPFGGHKGYALGVVAELLAGVLSGGG---TIQPDNPRGGVAT 265 G PTTD G LLP G KGYAL +V E LAGVL G G + G Sbjct: 209 GLPTTDPQAALA---GVLLPMAGAKGYALSLVVEHLAGVLVGAGFGKDVAWQYSEGNKPA 265 Query: 266 N-NLFAVLLNPALDLGLDWQSAEVEAFVRYLHDTPPAPGVDRVQYPGE--YEAANRAQAS 322 N F +L+ + + E FV + P APG ++ PGE +E +A Sbjct: 266 NVGHFIILVKADAFMEMADYHKRTEQFVEEIKKIPLAPGTKEIKLPGERSWEQQQNTEAQ 325 Query: 323 DTLNINPAIWRNLERLAQSLNV 344 + ++ + L+ +AQ L + Sbjct: 326 GII-LDADLQAALQTIAQELTI 346 Lambda K H 0.319 0.136 0.409 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: 305 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: 349 Length of database: 349 Length adjustment: 29 Effective length of query: 320 Effective length of database: 320 Effective search space: 102400 Effective search space used: 102400 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: 49 (23.5 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