Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate Pf1N1B4_4705 Delta 1-piperideine-2-carboxylate reductase (EC 1.5.1.21) / Delta 1-pyrroline-2-carboxylate reductase (EC 1.5.1.1)
Query= curated2:Q07251 (349 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4705 Length = 280 Score = 129 bits (323), Expect = 1e-34 Identities = 89/249 (35%), Positives = 119/249 (47%), Gaps = 8/249 (3%) Query: 3 ISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVN 62 +S + L I AD+A +A + ++R G SHG+ +P Y + L VN Sbjct: 16 LSFEALTALLEQIFLRHGTSADVAKTLALNCAGAERDGAHSHGVFRIPGYVSTLQSGWVN 75 Query: 63 PQGRAKCVLDQGTLMV-FDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMG 121 Q V D + V D GF Q + +E+ R G ++ +R SHH + Sbjct: 76 GQA-VPVVEDVASGFVRVDAGNGFAQPALAAARSLLVEKARSAGIAVLAIRNSHHFAALW 134 Query: 122 HYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIAT 181 E A G V LS V+N V P G TNP+ FA P NG P +V D+AT Sbjct: 135 PDVEPFADEGLVALS---VVNSMTCVVPHGADRPLFGTNPIAFAAPRANGAP-IVFDLAT 190 Query: 182 SAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVVA 241 SAIA ++ A KGE P G + + G PT D + GALLPFGGHKG AL ++ Sbjct: 191 SAIAHGDVQIAARKGERLPAGMGVDSLGQPTQDPKAVL--EGGALLPFGGHKGSALSMMV 248 Query: 242 ELLAGVLSG 250 ELLA L+G Sbjct: 249 ELLAAALTG 257 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: 287 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: 280 Length adjustment: 27 Effective length of query: 322 Effective length of database: 253 Effective search space: 81466 Effective search space used: 81466 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: 48 (23.1 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