Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate BPHYT_RS31645 BPHYT_RS31645 FAD-binding protein
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__BFirm:BPHYT_RS31645 Length = 499 Score = 206 bits (523), Expect = 2e-57 Identities = 137/431 (31%), Positives = 218/431 (50%), Gaps = 20/431 (4%) Query: 29 VAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEK 88 +A A +V P E+V A+LKFAN + IPV RG GTGLSGGA+P ++GI+L + Sbjct: 49 LAAYRATPMLVALPDKVEQVEALLKFANAQKIPVVARGAGTGLSGGALPLDKGILLVMAR 108 Query: 89 MTE-LEVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVR 146 LEVD + +A GV + A HGL + P P ++ A ++GG +A NAGGV Sbjct: 109 FNRILEVDPEAGIARVQPGVRNLAISQAVAPHGLYYAPDPSSQIACSIGGNVAENAGGVH 168 Query: 147 ALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRL 206 LKYG N +L LE + DG I +G + + ++ G+ L L GSEG L ++T+ T++L Sbjct: 169 CLKYGLTVNNILKLEILTIDGERITLGSEAL-DAPGFDFLALFTGSEGMLGIVTEVTVKL 227 Query: 207 FPQMRDMTVLAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGERWVSRE 265 + + VL F +E A V + ++P LE M+ A+ E + + Sbjct: 228 LTKPQSAKVLLASFDDIEKAGAAVARIIGAGVIPGGLEMMDNLAIRAAEDFIHAGY-PVD 286 Query: 266 GEAHLLMVFESF-----DEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRK 320 EA LL + ++ E + + GA D+ A + ++ R R + + + Sbjct: 287 AEAILLCEVDGVESDVQEDVERVEALLSAAGATDIRLAKDEAERQRFWAGRKNAFPAVGR 346 Query: 321 EVIE--VLDACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLVY-----EG 373 + +D +P ++ + +L+ EYG+ + HAGDGN+ HPL+ G Sbjct: 347 ISPDYYCMDGTIPRRELPRVLKGIEDLSNEYGLRVANVFHAGDGNM--HPLILFDANAPG 404 Query: 374 WEKSYFEFRKSLLSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKN 432 + +L L V++GG I+GEHG+G K++++ F ++ + +K FDP Sbjct: 405 ETERAEMLGAKILELCVAVGGSITGEHGVGREKINQMCAQFNHDELDFFHALKAAFDPAG 464 Query: 433 ILNPGKVVRKL 443 +LNPGK V L Sbjct: 465 LLNPGKNVPTL 475 Lambda K H 0.317 0.136 0.388 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: 496 Number of extensions: 25 Number of successful extensions: 6 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: 443 Length of database: 499 Length adjustment: 33 Effective length of query: 410 Effective length of database: 466 Effective search space: 191060 Effective search space used: 191060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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