Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate AO353_23830 AO353_23830 lactate dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23830 Length = 346 Score = 125 bits (314), Expect = 2e-33 Identities = 100/318 (31%), Positives = 151/318 (47%), Gaps = 23/318 (7%) Query: 11 LARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCV 70 L I ++A +A++ ++R G SHG+ +P Y + L+ VN G+A V Sbjct: 24 LLESIFLRHGTSPEVARVLAQNCAGAERDGAHSHGVFRMPGYVSTLNSGWVN--GKAVPV 81 Query: 71 LDQ---GTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMA 127 ++ G + V D GF Q + + + + R G ++ +R SHH + E Sbjct: 82 VEDVASGFVRV-DAGNGFAQPALAAGRELLVAKARSAGIAVMAIRNSHHFAALWPDVEPF 140 Query: 128 AAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAIN 187 A G V LS V+N V P G TNP+ FA P G P+V D+ATSAIA Sbjct: 141 AYEGLVALS---VVNSMTCVVPHGADRPLFGTNPIAFAAPRA-GADPIVFDLATSAIAHG 196 Query: 188 KARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVVAELLAGV 247 ++ A KGE P G + + G PT D + GALLPFGGHKG AL ++ ELLA Sbjct: 197 DVQIAARKGERLPPGMGVDSLGQPTQDPKAIL--EGGALLPFGGHKGSALSMMVELLAAA 254 Query: 248 LSGGGTI----QPDNPRGGVATNNLFAVLLNPALDLGLDWQSAEVEAFVRYLHDTPPAPG 303 L+GG ++P ++++P+ G ++ + E VR +H A G Sbjct: 255 LTGGNFSFEFDWSNHPGAKTPWTGQLLIVIDPSKAAGQNF-AERSEELVRQMH----AVG 309 Query: 304 VDRVQYPGEYEAANRAQA 321 + R+ PG+ RA++ Sbjct: 310 LRRL--PGDRRHRERAKS 325 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: 337 Number of extensions: 15 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: 346 Length adjustment: 29 Effective length of query: 320 Effective length of database: 317 Effective search space: 101440 Effective search space used: 101440 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