Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate PP_0654 PP_0654 putative malate dehydrogenase
Query= BRENDA::Q9GT92 (321 letters) >FitnessBrowser__Putida:PP_0654 Length = 310 Score = 207 bits (527), Expect = 3e-58 Identities = 114/302 (37%), Positives = 174/302 (57%), Gaps = 6/302 (1%) Query: 6 KIAVIGSGQIGGNIAYIVGKDNLA-DVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGT 64 K+ ++G+G +G A I+ +D L ++VL D+ + QGKALD+ + V GS + V G Sbjct: 4 KLTIVGAGLVGEAAAQIIARDELCRELVLMDVQGELAQGKALDVWQAAVDSGSDTHVHGG 63 Query: 65 NDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPL 124 + GS++V+ITA +P +P R ++L N ILDS+ +K + P A V+ ++NP+ Sbjct: 64 AKAEMLEGSELVVITAGVPRKPGQSRQDVLSTNLPILDSIMADIKHHAPTATVLVVSNPV 123 Query: 125 DVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPV 184 DV+ VSG +KV G AGVLD++R + FIA+ G +A D++A V+GGHGD MVP+ Sbjct: 124 DVLTYRAWSVSGQGRDKVFGQAGVLDTARMKCFIAEQTGFSARDITALVLGGHGDSMVPL 183 Query: 185 TSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMA 244 +G VPLS F ++ EQI++IV TR E+ KTG+A AP A +M Sbjct: 184 MRYCQIGSVPLSHF-----LSSEQIEQIVERTRKGGGEILGLKKTGSACDAPGVAIAQMV 238 Query: 245 EAYLKDRKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLKQKLLGESIN 304 +A R ++P A YG I MGVP ++ + G+ I+EL L +Q + S + Sbjct: 239 DAIANGRNRILPAVAILEGEYGRTDIAMGVPCVLAEKGLARIIELPLDAQEQAMFDHSAD 298 Query: 305 EV 306 +V Sbjct: 299 QV 300 Lambda K H 0.319 0.136 0.394 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: 246 Number of extensions: 13 Number of successful extensions: 2 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: 321 Length of database: 310 Length adjustment: 27 Effective length of query: 294 Effective length of database: 283 Effective search space: 83202 Effective search space used: 83202 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