Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate GFF2781 PGA1_c28240 putative D-lactate dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__Phaeo:GFF2781 Length = 467 Score = 207 bits (527), Expect = 6e-58 Identities = 134/426 (31%), Positives = 212/426 (49%), Gaps = 17/426 (3%) Query: 56 PLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLDI 115 P AVV P +T+ VA +++ C+ YG+P++P G GTSL G I V + +M + L + Sbjct: 51 PDAVVFPTSTDEVADIVRTCADYGVPVIPYGTGTSLEGHVNAPAGGICVDMMRMDKILAV 110 Query: 116 DLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVT 175 + VQ GVT ++ + G F+ DP + ++GG + G + ++YG Sbjct: 111 HAEDLDVVVQPGVTREQLNTYLRDQGLFFPIDPGAN--ASLGGMAATRASGTNAVRYGTM 168 Query: 176 TNNLLGVKMVLFDGTVIELGGKA-LDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGA 234 +N+L ++ V+ DG VI +A + GYD+ L+ GSEG LG++TE T+RL PE Sbjct: 169 KDNVLALEAVMADGGVIRTAQRAKKSSAGYDMTRLLVGSEGTLGLITELTLRLQGIPEAI 228 Query: 235 RPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLIVE 294 R F S + A V I GI IE +D ++ A+ +G L LL++E Sbjct: 229 RSARCAFRSVDDACRAVMMTIQYGIPVSRIELLDEMSVRAANAY--SGLDLPEMPLLLLE 286 Query: 295 VEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRI---ADYI 351 GS+A + +IA G I + +A E + +W+ R + A+ ++ A I Sbjct: 287 FHGSDAGVVEQADTFAQIAEEFGGFDIAATSTAEERSKLWQARHDMYWASLQLRPGAKGI 346 Query: 352 CMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAEAA 411 D VP+S+L+ + L V H GDGN H L+L N++ EE A+A Sbjct: 347 STDVCVPISKLAECVSAARSKAEEMNLLAPMVGHVGDGNFHALLLINMDSAEEREAADAY 406 Query: 412 GNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQ----QMAARAAFDPQWLMNP 467 + +L + G TGEHG+G KR Y + +LG+ A +AA DP+ ++NP Sbjct: 407 VGWLNELAISIEGTCTGEHGIGQGKR-----PYLQQELGETTRYMAAIKAALDPENILNP 461 Query: 468 SKVFPL 473 K+ + Sbjct: 462 GKILEI 467 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: 552 Number of extensions: 21 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: 479 Length of database: 467 Length adjustment: 33 Effective length of query: 446 Effective length of database: 434 Effective search space: 193564 Effective search space used: 193564 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