Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate SMc01712 SMc01712 L-lactate dehydrogenase (cytochrome) protein
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Smeli:SMc01712 Length = 403 Score = 256 bits (653), Expect = 1e-72 Identities = 145/370 (39%), Positives = 214/370 (57%), Gaps = 24/370 (6%) Query: 9 NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSV 68 N ++ ++AK L F+Y A DE+T + N A FE L P +L V ++++ +V Sbjct: 30 NFHDFRRMAKRRLPSPIFNYIDGAADDEVTYRRNTAAFEGCDLVPNVLRGVGDVDMSVTV 89 Query: 69 LGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFS 128 +GQ L +P+ +P A Q L H +GE A A AAA GT +S+L T SLEE + Sbjct: 90 MGQRLAMPVYCSPTALQRLFHHQGERAVAAAAAKFGTMFGVSSLGTVSLEEARRI----C 145 Query: 129 PSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHL 188 Q +Q Y HKDRGL R ++ RA AG + + LTVD+ G RERD+R F +P L+L Sbjct: 146 DGPQVYQFYFHKDRGLNREMMARAKQAGIEVMMLTVDSITGGNRERDKRTGFAIPFKLNL 205 Query: 189 ANLTTIS-----GLN-IPHAP--------------GESGLFTYFAQQLNPALTWDDLEWL 228 A +T + +N + H P G + YF + L+P+++WDD+ + Sbjct: 206 AGITQFAIKPSWAVNYVRHEPFRLPQLENHVDMGRGAMSISRYFTEMLDPSMSWDDVAEM 265 Query: 229 QSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGK 288 LKG++ +DA RAVE G IV+SNHGGRQLDG+ + D L EIV AV + Sbjct: 266 VQHWGGQFCLKGVISVEDAKRAVEIGCTGIVLSNHGGRQLDGSRTAFDQLDEIVQAVGDR 325 Query: 289 AEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMA 348 +V++DGG++RGT ++KAL++GA+AV +GR L+ LA GQAGV + L++ E+ M Sbjct: 326 IDVMMDGGVQRGTHVLKALSLGAKAVGLGRYYLFPLAAAGQAGVERALELMRVEIERGMK 385 Query: 349 LIGCSQLQDI 358 L+GCS + ++ Sbjct: 386 LMGCSSVDEL 395 Lambda K H 0.320 0.136 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: 299 Number of extensions: 12 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: 365 Length of database: 403 Length adjustment: 30 Effective length of query: 335 Effective length of database: 373 Effective search space: 124955 Effective search space used: 124955 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: 50 (23.9 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