Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate PP_4736 PP_4736 L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Putida:PP_4736 Length = 381 Score = 243 bits (620), Expect = 6e-69 Identities = 145/367 (39%), Positives = 203/367 (55%), Gaps = 24/367 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 +Y A+ L F Y GA E TL+ N + I LR R+L ++S+++L T + + Sbjct: 8 DYRAAAQRKLPPFLFHYADGGAYAEHTLRHNVSDLAGIALRQRVLNNMSELSLETKLFDE 67 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 L +P+ +AP+ + GE+ A AAA+ G +ST+S +EEVA ++ Sbjct: 68 TLSMPVALAPVGLTGMYARRGEVQAARAAAAHGIPFTMSTVSVCPIEEVAPAINR----P 123 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEF---------VL 182 WFQLY+ KDRG R +ERA AAG K L TVD PV G R RD + VL Sbjct: 124 MWFQLYVLKDRGFMRNALERAKAAGVKTLVFTVDMPVPGARYRDAHSGMSGKNGPLRRVL 183 Query: 183 PPGLHLANLTTISGLNIPHAPGE--------SGLFTYFA---QQLNPALTWDDLEWLQSL 231 H + + PH G +GL Y +P+++W DLEW++ Sbjct: 184 QAMTHPEWAWDVGVMGRPHDLGNISKYRGNPTGLADYIGWLGNNFDPSISWKDLEWIREF 243 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 P+++KGIL DDA AV++GA IVVSNHGGRQLDG ++S ALP I AV G ++ Sbjct: 244 WDGPMIIKGILDADDARDAVKFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGDLKI 303 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 L D GIR G D+++ +A+GA VLIGR L+ LAV GQAGV +++ L +KE+ VAM L G Sbjct: 304 LADSGIRSGLDVVRMIALGADTVLIGRAFLYALAVHGQAGVKNLLELFEKEMRVAMVLTG 363 Query: 352 CSQLQDI 358 + +I Sbjct: 364 AKSISEI 370 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: 291 Number of extensions: 19 Number of successful extensions: 3 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: 381 Length adjustment: 30 Effective length of query: 335 Effective length of database: 351 Effective search space: 117585 Effective search space used: 117585 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