Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate PP_0762 PP_0762 Glycerate dehydrogenase
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__Putida:PP_0762 Length = 321 Score = 135 bits (341), Expect = 1e-36 Identities = 93/281 (33%), Positives = 143/281 (50%), Gaps = 20/281 (7%) Query: 35 ETTVEKAKGAQVVSLFVSDKADGPVLEALHSYGVGLLALRSAGYDHIDIETAKRLGIKVV 94 E E+ +GA V VS+K + + L+ + + G +++D+ A+ GI V Sbjct: 41 EQVAERLQGAVAV---VSNKVMLDAATLAANPQLKLILVAATGTNNVDLAAARAQGITVC 97 Query: 95 NVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLGDFDLDG---LMGF---DLNGKVAGV 148 N Y ++A HTLA++LAL RL + V G + L+ F +L GK G+ Sbjct: 98 NCQGYGTPSVAQHTLALLLALATRLCDYNQAVADGQWAKASQFCLLDFPIVELEGKTLGL 157 Query: 149 IGLGKIGRLVATRLKAFGCKVLGYDPYIQPEIVENVDLDTLITQADIISIHCPLTRENFH 208 +G G++G VA +AFG +VL +PE + + LD L+ Q D +++HCPL H Sbjct: 158 LGHGELGGAVARLAEAFGMRVLSGQIPGRPERADRLPLDELLPQVDALTLHCPLNEHTRH 217 Query: 209 MFNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQK 268 M +KP A++VNTARGGLID +AL +AL+ G LGGAA DV E + Sbjct: 218 MLGARELALLKPNALVVNTARGGLIDEQALADALRGGHLGGAATDVLSVEPPV-----NG 272 Query: 269 EGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVEN 309 + +P G+ +++T H A+ E+ + I EN Sbjct: 273 NPLLEP------GIPRLIITPHSAWGAVESRQRIVGQLSEN 307 Lambda K H 0.321 0.140 0.407 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: 209 Number of extensions: 8 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: 325 Length of database: 321 Length adjustment: 28 Effective length of query: 297 Effective length of database: 293 Effective search space: 87021 Effective search space used: 87021 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 (21.8 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