Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate CCNA_01209 CCNA_01209 L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Caulo:CCNA_01209 Length = 383 Score = 231 bits (588), Expect = 3e-65 Identities = 142/372 (38%), Positives = 201/372 (54%), Gaps = 24/372 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 ++ + A+ L + FDY GA E T+ N I LR R+L+DVS ++ +T++ G Sbjct: 8 DFREAARRRLPRFLFDYIDGGAYAERTMARNIDDLADIALRQRVLMDVSVVDPSTTLFGV 67 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 LP+ +AP+ + GE A AAA+ G LST+S ++EV S + Sbjct: 68 RQALPVALAPVGLTGMYARRGECQAARAAAAKGVPFCLSTVSVCDVDEVRAA----SATP 123 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP-------- 183 WFQLY+ +DRG R L+ RA AAG L TVD PV G R RD + P Sbjct: 124 FWFQLYVLRDRGFMRDLLARASAAGATTLVFTVDMPVPGARYRDAHSGMSGPNAAARRLV 183 Query: 184 -PGLHLANLTTISGLNIPHAPGE--------SGL---FTYFAQQLNPALTWDDLEWLQSL 231 L A + + PH G SGL + A +P++ W DL+W++ Sbjct: 184 QAALKPAWAWDVGVMGHPHRLGNVAPALGKASGLQDFMGWLAANFDPSIQWSDLKWIRDA 243 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 PLV+KG+L +DA A + GA +VVSNHGGRQLDG ++S ALP I AV + V Sbjct: 244 WKGPLVIKGVLDPEDAKAAADIGADGVVVSNHGGRQLDGVLSSARALPAIADAVGDRLTV 303 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 L DGG+R G D+++ LA+GA+ VLIGR + LA G+AGV+ ++ L+ KE+ VAMAL G Sbjct: 304 LADGGVRSGLDVVRMLALGARGVLIGRAYAYALAARGEAGVTQLLDLIDKEMRVAMALTG 363 Query: 352 CSQLQDIDTSFL 363 + I+ + L Sbjct: 364 VRDVASINETIL 375 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: 286 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 335 Effective length of database: 353 Effective search space: 118255 Effective search space used: 118255 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