Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 3609586 Dshi_2970 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__Dino:3609586 Length = 328 Score = 145 bits (367), Expect = 1e-39 Identities = 100/281 (35%), Positives = 148/281 (52%), Gaps = 33/281 (11%) Query: 44 AQVVSLFVSDKADGPVLEALHSYGVG----LLALRSAGYDHIDIETAKRLGIKVVNVPAY 99 A V+ VSD DG +L GVG L+A AG DHID+ TA++ GI V N P Sbjct: 49 ADVLVPTVSDHIDGAMLA-----GVGDRLKLIANYGAGVDHIDVATARQRGIHVSNTPGV 103 Query: 100 SPHAIADHTLAIMLALIRRLHRAHDKVRLG---DFDLDGLMGFDLNGKVAGVIGLGKIGR 156 AD TLA++LA+ RR+ ++ G + LMG + G+ G++G+G+IG+ Sbjct: 104 LTDDTADMTLALILAVTRRIPEGLALMQTGAWTGWSPTALMGGRIAGRRLGILGMGRIGQ 163 Query: 157 LVATRLKAFGCKVLGYDPY-IQPEIVENVD------LDTLITQADIISIHCPLTRENFHM 209 VA R KAFG ++ ++ + I E ++ LD ++++ D+IS++CP T FH+ Sbjct: 164 AVARRAKAFGMQIHYHNRRRLHKGIEEELEATWWESLDQMVSRMDVISVNCPHTPSTFHL 223 Query: 210 FNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQKE 269 N K MKP A++VNT+RG +ID AL L++G + GA LDV+E+ H+ Sbjct: 224 MNARRLKLMKPSAVIVNTSRGEVIDENALTRMLRAGDIAGAGLDVFEH-------GHEVN 276 Query: 270 GIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVENI 310 +L L NVVL H T E + E + NI Sbjct: 277 -------PRLRELPNVVLLPHMGSATEEGRAEMGEKVIINI 310 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: 257 Number of extensions: 14 Number of successful extensions: 3 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: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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