Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate SMc01455 SMc01455 D-lactate dehydrogenase (cytochrome) protein
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__Smeli:SMc01455 Length = 468 Score = 185 bits (469), Expect = 3e-51 Identities = 129/423 (30%), Positives = 203/423 (47%), Gaps = 11/423 (2%) Query: 54 RMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTL 113 ++P AVV PE+ V +++ + +P++P G G+SL G I V + +M+R L Sbjct: 51 QLPDAVVFPESAAEVREIVEIACEHRVPLIPFGTGSSLEGHVNAPHGGISVDMMRMNRVL 110 Query: 114 DIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYG 173 ++ + TV+ GVT ++ + G F+ DP + +IGG + G + ++YG Sbjct: 111 AVNAEDLDCTVEPGVTREELNSYLRDTGLFFPIDPGAN--ASIGGMASTRASGTNAVRYG 168 Query: 174 VTTNNLLGVKMVLFDGTVIELGGKAL-DAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPE 232 N+L V V+ G I +A + GYDL L G+EG LGIVT T+RL PE Sbjct: 169 TMKENVLAVTAVVAGGREIRTAHRARKSSAGYDLTRLFVGAEGTLGIVTSITLRLQGIPE 228 Query: 233 GARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLI 292 + F + A + V I SGI IE +D ++ C A++ G L Sbjct: 229 VISGGVCPFPTIADACNAVILTIQSGIPVARIELLDALQMKACNAYS--GLTYQETPTLF 286 Query: 293 VEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIAD--- 349 VE G+ ++ EIA G + + E A +WK R +A+ A + Sbjct: 287 VEFHGNGESVELQSRQFAEIASEFGSTGFIWTTNPEERARLWKARHNAYWAQKSLMPGRA 346 Query: 350 YICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAE 409 + D VP+S+L+ + T E +A +GL V HAGDGN H +L++ D + A+AE Sbjct: 347 ILSTDVCVPISRLADCVAATHEDIAAHGLVAPIVGHAGDGNFHVGLLFDDKDAADVAQAE 406 Query: 410 AAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRA-DLGQQMAARAAFDPQWLMNPS 468 A + + G TGEHG+G K + + A DL +Q+ + + DP + NP Sbjct: 407 AFVERLNARALSMDGTCTGEHGIGQGKMPFLAAELGDALDLMRQI--KRSLDPDNIFNPG 464 Query: 469 KVF 471 K+F Sbjct: 465 KIF 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: 537 Number of extensions: 26 Number of successful extensions: 5 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: 468 Length adjustment: 33 Effective length of query: 446 Effective length of database: 435 Effective search space: 194010 Effective search space used: 194010 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