Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate HSERO_RS12985 HSERO_RS12985 L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS12985 Length = 380 Score = 254 bits (648), Expect = 3e-72 Identities = 147/374 (39%), Positives = 215/374 (57%), Gaps = 26/374 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 ++ LAK + + +DY SG+ E T + N +KLR R+ ++V + + T+++G Sbjct: 9 DFRLLAKKRVPKAFYDYADSGSYTESTYRANSKDLAALKLRQRVAINVDERSTRTTMIGH 68 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + +P+ IAP + GE+ A+AA G LST+S S+E+VA V +K Sbjct: 69 DVTMPVAIAPTGLTGMQWANGEMLGAIAAEKFGIPFTLSTMSICSIEDVASVTTKPF--- 125 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 WFQLY+ +DRG ++L+ERA AA AL LT+D +LGQR +D +N +PP L L L Sbjct: 126 -WFQLYVMRDRGFVKSLIERAKAAKCSALVLTLDLQILGQRHKDLKNGMSVPPKLTLETL 184 Query: 192 TTIS----------------GLNIPHAPGESG------LFTYFAQQLNPALTWDDLEWLQ 229 ++ G H G G L + A Q +P L WDD+ W++ Sbjct: 185 LDLASKPGWALRALGGRKTFGNLAGHIKGGEGAGGVQTLSKWTASQFDPTLNWDDVAWIK 244 Query: 230 SLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKA 289 L+LKGIL +DA AV+ GA AIVVSNHGGRQLDGA++S++ALP I AV + Sbjct: 245 QQWGGKLILKGILDVEDAKLAVQSGADAIVVSNHGGRQLDGAMSSIEALPAIAQAVGDQI 304 Query: 290 EVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMAL 349 EV DGGIR G D++KA+A+GA+ +IGR L+ L G GVS ++ +++KEL+V+MAL Sbjct: 305 EVWFDGGIRSGQDVLKAVALGARGTMIGRAFLYSLGAMGGEGVSQMLEIMRKELDVSMAL 364 Query: 350 IGCSQLQDIDTSFL 363 G ++D+ L Sbjct: 365 TGTKDIKDVGPQIL 378 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: 300 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: 380 Length adjustment: 30 Effective length of query: 335 Effective length of database: 350 Effective search space: 117250 Effective search space used: 117250 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