Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate PP_3591 PP_3591 Delta 1-piperideine-2-carboxylate reductase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__Putida:PP_3591 Length = 332 Score = 130 bits (327), Expect = 5e-35 Identities = 84/251 (33%), Positives = 119/251 (47%), Gaps = 6/251 (2%) Query: 1 MKISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHS 60 M++ T + L + I +A +A + + R G SHG+ +P Y + L Sbjct: 1 MRVPFTELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLASGW 60 Query: 61 VNPQGRAKCVLDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRM 120 V+ Q + + D GGF Q + + + + R G ++ + SHH + Sbjct: 61 VDGQATPQVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFAAL 120 Query: 121 GHYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIA 180 E A G V LS V+N V P G R TNP+ FA P P+V D+A Sbjct: 121 WPDVEPFAEEGLVALS---VVNSMTCVVPHGARKPLFGTNPIAFAAPCAE-HDPIVFDMA 176 Query: 181 TSAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVV 240 TSA+A ++ A G+ PEG + ADG PTTD + GALLPFGGHKG AL ++ Sbjct: 177 TSAMAHGDVQIAARAGQQLPEGMGVDADGQPTTDPKAIL--EGGALLPFGGHKGSALSMM 234 Query: 241 AELLAGVLSGG 251 ELLA L+GG Sbjct: 235 VELLAAALTGG 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: 339 Number of extensions: 19 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: 332 Length adjustment: 28 Effective length of query: 321 Effective length of database: 304 Effective search space: 97584 Effective search space used: 97584 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