Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate PP_3745 PP_3745 glycolate oxidase, putative FAD-linked subunit
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__Putida:PP_3745 Length = 499 Score = 205 bits (521), Expect = 3e-57 Identities = 131/422 (31%), Positives = 221/422 (52%), Gaps = 20/422 (4%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96 +V P E+V +LK +++ +PV RG GTGLSGGA+P +GI+L + LEV+ Sbjct: 58 LVALPERLEQVQTLLKLCHQRGVPVVARGAGTGLSGGALPLAKGILLVMARFNRILEVNP 117 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 R A GV + AA HG+ + P P ++ A ++GG +A NAGGV LKYG + Sbjct: 118 QGRYARVQPGVRNLAISQAAAPHGMYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVH 177 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 VL ++ + +G +++G + +S G+ LL L +GSEG L ++T+ T++L P+ + V Sbjct: 178 NVLKVDILTVEGERLSLGSDAL-DSPGFDLLALFIGSEGMLGIVTEVTVKLLPKPQVARV 236 Query: 216 LAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274 + F ++EDA V + +A ++P LE M+ A+ E + + A LL Sbjct: 237 ILASFDSVEDAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGY-PVDAAAILLCEL 295 Query: 275 ES-----FDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIE--VLD 327 + +D+ E A + GA +V+ A + ++ R R + + + + +D Sbjct: 296 DGVEADVYDDCERVAAVLTQAGAREVHLACDEAERARFWAGRKNAFPAVGRISPDYYCMD 355 Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-----YEGWEKSYFEFR 382 +P ++ + ++L+ EYG+ + HAGDGN+ HPL+ G + Sbjct: 356 GTIPRRELPRVLKGISDLSAEYGLRVANVFHAGDGNM--HPLILFDANLPGELERAEAIG 413 Query: 383 KSLLSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGKVVR 441 +L L V +GG I+GEHG+G K++++ F ++ L +K FDP+ +LNPGK + Sbjct: 414 GKILELCVKVGGSITGEHGVGREKINQMCAQFNSDEITLFHAVKAAFDPQGLLNPGKNIP 473 Query: 442 KL 443 L Sbjct: 474 TL 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: 508 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: 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