Align D-lactate dehydrogenase (cytochrome) (EC 1.1.2.4) (characterized)
to candidate GFF2925 PGA1_c29720 glycolate oxidase subunit GlcD
Query= BRENDA::W1QLN6 (564 letters) >FitnessBrowser__Phaeo:GFF2925 Length = 482 Score = 199 bits (506), Expect = 2e-55 Identities = 127/426 (29%), Positives = 207/426 (48%), Gaps = 16/426 (3%) Query: 134 PVAVVYPENTEEVSAILKVCHKHKVPVVPFSGGTSLEGQFIPTRKGICIDLGKMNKILEL 193 P+ VV P T+EVS +L++CH VPVVP GTSL G +PT + + + +MN +LE Sbjct: 52 PMLVVLPRTTKEVSDVLRICHAAGVPVVPRGAGTSLAGGALPTADCVILGVARMNAVLET 111 Query: 194 HKDDLDVVVQPAVGWEDLRDYLQDYNLMFGPDPGP--GACIGGMIGTSCSGTNAARYGTM 251 D+ + VQ + +++ + PDP I G I + G + +YG Sbjct: 112 DYDNRIIRVQTGRTNLSVSGAVEEEEFFYAPDPSSQLACAIAGNIAMNSGGAHCLKYGVT 171 Query: 252 KENVVGVTVVLADGTIVKTKKRPKKSSAGYNLTGLFIGSEGTLGIVTEATLKLHVKPRYE 311 N++GVT+V+ DGT+V+ + G +L G+ GSEG LG+VTEATL++ KP Sbjct: 172 TNNLMGVTMVMMDGTVVEI-GGAHLDAGGLDLLGVICGSEGQLGVVTEATLRILRKPEGA 230 Query: 312 NVLVVAFPSLVDAANTVAEMVQRAIPANAIELLDENMMHYVNFSGETSSKYDELPTLMLK 371 +++ + S A V+++++ + AIE +D + + E ++ Sbjct: 231 RPVLIGYDSNEVAGACVSDIIKAGVLPVAIEFMDRPCIEACEAFAKAGYPMCEALLIVEV 290 Query: 372 LGGDSKESTQHVTRAVEQICKQHNRKSFRFAESDEEKFELWNARKVALWSTINYGKQTID 431 G D++ H R + +I + HN R A +E +W RK A +G Sbjct: 291 EGSDAE--IDHQLRLITEIARSHNPVELREARDSDEAARIWLGRKSA------FGAMGQI 342 Query: 432 EDIQVWTTDVAVPISRLCQSLQETKDEISKAGLNASIVGHVGDGNYHAVILF---KKDQY 488 D D +P++ L L+ + + GL+ + V H GDGN H +ILF K Sbjct: 343 NDYM--CLDGTIPVTSLPHVLRRIGEMSKEFGLDVANVFHAGDGNMHPLILFDANKPGDL 400 Query: 489 ELTKKLVQGMIDRALLAEGTVTGEHGVGYGKRDYLIEEAGEDAVDLMRKIKMALDPNRIL 548 E + ++ + G +TGEHGVG KRD ++++ G ++ ++K DP +L Sbjct: 401 ETCEAFGAEILKLCVEVGGCLTGEHGVGIEKRDLMLDQYGVADIEAQLRVKDVFDPKWLL 460 Query: 549 NPDKIF 554 NP K+F Sbjct: 461 NPAKVF 466 Lambda K H 0.316 0.135 0.391 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: 547 Number of extensions: 31 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: 564 Length of database: 482 Length adjustment: 35 Effective length of query: 529 Effective length of database: 447 Effective search space: 236463 Effective search space used: 236463 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 (21.6 bits) S2: 52 (24.6 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