Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate Dsui_3415 Dsui_3415 FAD/FMN-dependent dehydrogenase
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__PS:Dsui_3415 Length = 486 Score = 194 bits (493), Expect = 5e-54 Identities = 143/458 (31%), Positives = 227/458 (49%), Gaps = 31/458 (6%) Query: 7 LSKIVEVFPPSDAY------RFDETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSI 60 L+ + + PP Y R E L A R V P EV AIL+ + + Sbjct: 19 LAALGRILPPGRVYGEPEDLRPYECDGLTAYRNLP-LAVALPETEAEVQAILQLCHRLQV 77 Query: 61 PVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDADNRVAICGAGVTLKQLDDAAFRH 119 PV RG TGLSGGA+P +G++LS K + L+VD R A+ GV + +AA + Sbjct: 78 PVVPRGAATGLSGGAMPHHQGLLLSLAKFKKILKVDPVARTALVQPGVRNLAVSEAAAPY 137 Query: 120 GLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIK 178 L + P P ++ A T+GG ++ N+GGV LKYG + VL + G + G + Sbjct: 138 NLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLQVRGYTMAGEAVTFGSAAL- 196 Query: 179 NSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTVLAIPFPTMEDAMNCVVEV-ARKM 237 ++ G+ LL LL GSEG LAVIT+ ++L P+ + V+ F ++ A N V EV A + Sbjct: 197 DAPGFDLLALLNGSEGMLAVITEVLVKLTPKPQVAKVVLAYFDSVTKAGNAVAEVIAAGI 256 Query: 238 LPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVFESFDEAEEAAK-------IAQSL 290 +P LE M+K A E + + +A +++ ES EE + + + Sbjct: 257 IPAGLEMMDKPATHAVEPYVKAGY---DLDAEAVLLCESDGTPEEVEEEIAAMRAVLEKS 313 Query: 291 GAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIEVL--DACVPPAKIAEYWRRSNELAEE 348 GA + + + ++ R R + + + + L D +P ++AE + ++ Sbjct: 314 GATSLRVSANEAERLRFWAGRKAAFPAVGRITPDYLCMDGTIPRKRVAEMLTAIAAMEKK 373 Query: 349 YGIELITYGHAGDGNVHQHPLV-YEGWEKSYFE----FRKSLLSLAVSLGGVISGEHGIG 403 YG+ HAGDGN+ HPL+ Y+ + E F +L L+V+LGG I+GEHG+G Sbjct: 374 YGLRCANVFHAGDGNL--HPLIMYDANQPGELEQATAFGAEILELSVALGGSITGEHGVG 431 Query: 404 AVKLSEL-EELFPEQFELMRQIKLLFDPKNILNPGKVV 440 K++++ + PE+ +K FDP +LNPGK + Sbjct: 432 VEKITQMCAQFTPEELARFEGVKQSFDPAGLLNPGKAI 469 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: 464 Number of extensions: 22 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: 486 Length adjustment: 33 Effective length of query: 410 Effective length of database: 453 Effective search space: 185730 Effective search space used: 185730 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