Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate GFF3081 HP15_3024 FAD linked oxidase domain protein
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__Marino:GFF3081 Length = 490 Score = 208 bits (530), Expect = 3e-58 Identities = 137/424 (32%), Positives = 227/424 (53%), Gaps = 24/424 (5%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTEL-EVDA 96 +VV P E+V +++ NE ++PV RG GTGLS GA+P +EG+VLS K + E+D Sbjct: 49 LVVLPETVEQVQRVMRICNENAVPVVARGAGTGLSAGAMPNKEGVVLSLAKFNRIVEIDP 108 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 R A GV + + A ++GL + P P ++ A T+GG +A N+GGV LKYG + Sbjct: 109 LARTARLQPGVRNLAISEEAAQYGLYYGPDPSSQIACTIGGNVAENSGGVHCLKYGLTVH 168 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 +LS+E V A+G ++ VG + + G LL L+ GSEG L V+T+ ++L P+ V Sbjct: 169 NILSVEMVTAEGDVVTVGSDGL-DGCGMDLLALMTGSEGLLGVVTEVKVKLLPKPEVAQV 227 Query: 216 LAIPFPTME---DAMNCVVEVARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLM 272 + F ++ DA+ + ++ ++P LE M+ A+ I + R+ +A LL Sbjct: 228 VMAGFDDVQKGGDAVGGI--ISHGIIPGGLEMMDGHAI-IAADDFAQAGYPRDAKALLLC 284 Query: 273 VFESFDE-----AEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIE--V 325 + +E +A ++ + LGA V + +++++ L K R + + + + Sbjct: 285 EVDGTEEEVHEHIAQAEEVFRKLGATSVRTSQSEEERALLWKGRKSAFPAVGRISPDYYC 344 Query: 326 LDACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFE---- 380 +D +P +IA +++EE+G+ + HAGDGN+ HPL+ ++ FE Sbjct: 345 MDGTIPRREIAYVLTEMEKMSEEFGLRVANVFHAGDGNL--HPLILFDANVPGEFERTEA 402 Query: 381 FRKSLLSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGKV 439 F +L + V +GG I+GEHG+G K+ ++ F E+ + +K FDP ILNPGK Sbjct: 403 FGSRILEMCVEVGGCITGEHGVGVEKIRQMAVQFNDEELQQFHDVKAAFDPAGILNPGKG 462 Query: 440 VRKL 443 V L Sbjct: 463 VPAL 466 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: 518 Number of extensions: 28 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: 490 Length adjustment: 33 Effective length of query: 410 Effective length of database: 457 Effective search space: 187370 Effective search space used: 187370 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