Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate GFF2454 PS417_12515 lactate dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__WCS417:GFF2454 Length = 345 Score = 138 bits (347), Expect = 2e-37 Identities = 108/346 (31%), Positives = 166/346 (47%), Gaps = 24/346 (6%) Query: 3 ISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVN 62 +S + L + I Q +A +AE+ ++R G SHG+ +P Y + L+ V+ Sbjct: 15 LSYEALTLLLQRIFIRQGTSESVAQVLAENCASAERDGAHSHGVFRVPGYVSTLNSGWVD 74 Query: 63 PQGRAKCVLDQ---GTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGR 119 G+A +++ G + V D GF Q + +++ R G ++ + SHH Sbjct: 75 --GKAVPIVEDVASGFVRV-DAVNGFAQPALAAARSLLVDKARSAGIALLAIHNSHHFAA 131 Query: 120 MGHYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDI 179 + E A G V LS V+N V P G TNP+ FA P +G PP+V D+ Sbjct: 132 LWPDVEPFAEEGLVALS---VVNSMTCVVPHGADRPLFGTNPIAFAAPRADG-PPIVFDL 187 Query: 180 ATSAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGV 239 ATSAIA ++ A KGE P G + + G PT D + GALLPFGGHKG AL + Sbjct: 188 ATSAIAHGDVQIAARKGERLPPGMGVDSLGQPTQDPKAIL--EGGALLPFGGHKGSALSM 245 Query: 240 VAELLAGVLSGGGTI----QPDNPRGGVATNNLFAVLLNPALDLGLDWQSAEVEAFVRYL 295 + ELLA L+GG D+P +L++P+ G ++ E VR + Sbjct: 246 MVELLAAALTGGNFSFEFNWSDHPGARTPWTGQLVILIDPSKTTGQNFAERSQE-LVRQM 304 Query: 296 HDTPPAPGVDRVQYPGEYEAANRAQASDT-LNINPAIWRNLERLAQ 340 H A G+ R+ PG+ +RA++ + + IN + L+ LA+ Sbjct: 305 H----AAGLRRL--PGDRRHRSRAKSQEIGIEINAQDLKQLQELAE 344 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: 327 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: 345 Length adjustment: 29 Effective length of query: 320 Effective length of database: 316 Effective search space: 101120 Effective search space used: 101120 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