Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_4909 D-Lactate dehydrogenase, cytochrome c-dependent (EC 1.1.2.4)
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4909 Length = 474 Score = 223 bits (567), Expect = 1e-62 Identities = 136/422 (32%), Positives = 215/422 (50%), Gaps = 8/422 (1%) Query: 56 PLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLDI 115 P AVV E+T+ VA +K S+Y +P++P GAG+SL G + + I + +S+M++ L I Sbjct: 57 PSAVVFAESTQDVADAVKLASQYEVPVIPYGAGSSLEGHLLAVQGGISIDVSRMNQVLSI 116 Query: 116 DLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVT 175 + + T TVQ G+T +++A+ G F+ DP + +IGG + G + ++YG Sbjct: 117 NAEDLTVTVQPGITRKALNEAIKDTGLFFPIDPGAD--ASIGGMCATRASGTNAVRYGTM 174 Query: 176 TNNLLGVKMVLFDGTVIELGGKAL-DAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGA 234 N+L +++V G VI G +A + GYDL L+ GSEG LGI+TE TVRL PE Sbjct: 175 RENVLALEVVTASGEVIHTGTRAKKSSAGYDLTRLMVGSEGTLGIMTEITVRLYPLPEAV 234 Query: 235 RPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLIVE 294 + F S E+A I G+ +E +D + + A ++ L E +L++E Sbjct: 235 SAAICSFPSIEAAVRTTIQTIQIGVPIARVELIDHHTVRMVNAHSKL--TLREEPMLLME 292 Query: 295 VEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIAD---YI 351 GS A + + +IA G + + E +W R +A+ A + I Sbjct: 293 FHGSPASVKEQAEMVQDIASEFGGQAFEWASTPEERTRLWTARHNAYFAAVQSRPGCRAI 352 Query: 352 CMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAEAA 411 D VP+S+L+ L + + V G+ V H GDGN H L + N EE +AEA Sbjct: 353 STDTCVPISRLADCLLESVDEVEASGIPYFLVGHVGDGNFHFGYLIDPNSAEERTKAEAM 412 Query: 412 GNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKVF 471 + ++ + GG TGEHGVG+ K +L + + A + A DP+ ++NP K+F Sbjct: 413 NHTLVARALSMGGTCTGEHGVGVHKMGFLLDETGTGAVDMMRAIKRALDPKNILNPGKIF 472 Query: 472 PL 473 L Sbjct: 473 AL 474 Lambda K H 0.320 0.138 0.404 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: 526 Number of extensions: 17 Number of successful extensions: 4 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: 479 Length of database: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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