Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate Pf6N2E2_137 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_137 Length = 511 Score = 203 bits (517), Expect = 9e-57 Identities = 137/422 (32%), Positives = 219/422 (51%), Gaps = 20/422 (4%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96 +V P E+V A+LK + +PV RG GTGLSGGA+P E G++L + + L +D Sbjct: 70 LVALPRRVEQVQALLKLCHGLDVPVVARGAGTGLSGGALPLESGVLLVMARFNQILHIDP 129 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 D R A GV + AA GL + P P ++ A ++GG +A NAGGV LKYG + Sbjct: 130 DARTARLQPGVRNLAISQAAAPFGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVH 189 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 +L LE + +G + +G + + +S G LL L GSEG L VIT+ T++L P+ + V Sbjct: 190 NLLKLEILTIEGERLTLGSEAL-DSPGLDLLALFTGSEGLLGVITEVTVKLLPRPQVAKV 248 Query: 216 LAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274 L F +++ A V + +A ++P LE M+ A+ E + E EA LL Sbjct: 249 LLASFDSVDKAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGY-PVEAEAILLCEL 307 Query: 275 ES-----FDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIE--VLD 327 + D+ E ++ + GA +V A + ++ R R + + + + +D Sbjct: 308 DGVEADVHDDCERVRQVLEQAGATEVRQARDEAERLRFWAGRKNAFPAVGRLAPDYYCMD 367 Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFEFRKSL- 385 +P + E +R L E+G+ + HAGDGN+ HPL+ ++ + E ++L Sbjct: 368 GTIPRRALPEVLQRIASLGAEHGLRVANVFHAGDGNM--HPLILFDANQPGELERAETLG 425 Query: 386 ---LSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGKVVR 441 L L V +GG I+GEHG+G K++++ F ++ L +K FDP+ +LNPGK + Sbjct: 426 GKILELCVQVGGSITGEHGVGREKINQMCTQFNSDELNLFHAVKAAFDPQGLLNPGKNIP 485 Query: 442 KL 443 L Sbjct: 486 TL 487 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: 498 Number of extensions: 25 Number of successful extensions: 7 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: 511 Length adjustment: 33 Effective length of query: 410 Effective length of database: 478 Effective search space: 195980 Effective search space used: 195980 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