Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate Pf1N1B4_5979 Ureidoglycolate/malate/sulfolactate dehydrogenase family (EC 1.1.1.-)
Query= curated2:Q07251 (349 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5979 Length = 335 Score = 116 bits (291), Expect = 7e-31 Identities = 82/250 (32%), Positives = 119/250 (47%), Gaps = 6/250 (2%) Query: 1 MKISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHS 60 ++++L AR+LA IL A VA ++ +R G SHGL + +L Sbjct: 2 IRLTLIQARELAESILLHNGFNLAHAQAVAATVIAGERDGCASHGLYRILGCVNSLRAGK 61 Query: 61 VNPQGRAKCVLDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRM 120 V+ + + +++ D GGF Q ++ + E+ R +G + + R H + Sbjct: 62 VSADAEPQVIDQAPSIVRVDAGGGFSQLAFQAGLGLLAEKTRANGIAALAINRCVHFSAL 121 Query: 121 GHYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIA 180 E A G V L+ VAP GGRV TNP+ F P G+ P V D A Sbjct: 122 WVEIEQLTAVGLVALACN---PSHAWVAPAGGRVPVFGTNPIAFGWPRA-GQDPFVFDFA 177 Query: 181 TSAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVV 240 TSAIA + G+ PEG + A+G P+TDA+ + GA+L FGGHKG AL + Sbjct: 178 TSAIARGDIELHRRAGKAIPEGWGVDAEGRPSTDANVVLDS--GAMLTFGGHKGSALAAM 235 Query: 241 AELLAGVLSG 250 EL+AG L G Sbjct: 236 VELIAGPLIG 245 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: 275 Number of extensions: 18 Number of successful extensions: 5 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: 335 Length adjustment: 29 Effective length of query: 320 Effective length of database: 306 Effective search space: 97920 Effective search space used: 97920 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 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