Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate HSERO_RS19105 HSERO_RS19105 FAD-binding protein
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__HerbieS:HSERO_RS19105 Length = 495 Score = 194 bits (493), Expect = 5e-54 Identities = 132/424 (31%), Positives = 216/424 (50%), Gaps = 24/424 (5%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96 VVV P N +V AI+K + + + RG GTGLSGGA P +G+V+ST K + L++D Sbjct: 54 VVVLPENEAQVVAIMKTCHALQVQIVPRGAGTGLSGGATPIADGVVVSTAKFNQILQMDK 113 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 +R A+ GV + +AA HGL + P P ++ A ++GG +A N+GGV LKYG + Sbjct: 114 YSRTAVVQPGVRNLAISEAAAPHGLYYAPDPSSQIACSIGGNVAENSGGVHCLKYGLTVH 173 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 VL + V +G ++ +G + ++ G LL + +GSEG L V+T+ T++L P+ + V Sbjct: 174 NVLRVRMVTIEGEVVELGSGAL-DAPGLDLLAVFIGSEGMLGVVTEVTVKLVPKPQAARV 232 Query: 216 LAIPFPTMEDAMNCVVEV-ARKMLPMALEFMEKRA-------VEIGEKVSGERWVSREGE 267 + F + N V V A ++P LE M+K + V+ G + E + E + Sbjct: 233 IMASFDDVVKGGNAVANVIAAGIIPAGLEMMDKTSSRMVEPFVKAGYDIDAEAILLCESD 292 Query: 268 AHLLMVFESFDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIY--EGLRKEVIEV 325 V E +E + + GA + + ++ ++ R R + G Sbjct: 293 G---TVEEVEEEIGRMTDVLNASGATAIACSQSEAERLRFWSGRKNAFPAAGRISPDYYC 349 Query: 326 LDACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFE---- 380 +D +P K+A+ E+ ++YG+ HAGDGN+ HPL+ ++ F Sbjct: 350 MDGTIPRKKLAQVLLGIAEMEKKYGLRCANVFHAGDGNL--HPLILFDANIADEFHRAEL 407 Query: 381 FRKSLLSLAVSLGGVISGEHGIGAVKLSEL-EELFPEQFELMRQIKLLFDPKNILNPGKV 439 F +L L V +GG I+GEHG+G K++ + + P + E ++K FDP +LNP K Sbjct: 408 FGAEILELCVEVGGTITGEHGVGIEKINSMCVQFSPAERETFFKLKRAFDPAFLLNPDKA 467 Query: 440 VRKL 443 + L Sbjct: 468 IPTL 471 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: 489 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: 495 Length adjustment: 33 Effective length of query: 410 Effective length of database: 462 Effective search space: 189420 Effective search space used: 189420 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