Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Ac3H11_2838 L-lactate dehydrogenase (EC 1.1.2.3)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2838 Length = 381 Score = 331 bits (849), Expect = 2e-95 Identities = 183/357 (51%), Positives = 240/357 (67%), Gaps = 5/357 (1%) Query: 9 NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSV 68 NL ++E A+ L A+ Y+ GAGDEITL+ NR+ ++ + L PR+L ++ + + Sbjct: 16 NLADHELQARQQLDDNAWAYFSGGAGDEITLRANRSAWDALPLWPRVLRPLAGGHTRVQL 75 Query: 69 LGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAE-VGSKF 127 LG+ L P+L+AP+AFQ LAH +GELA A AAA+ G G+VLST ++ SLE +AE V Sbjct: 76 LGRTLAHPILLAPVAFQRLAHADGELAMAYAAAALGAGVVLSTQASVSLEAIAEAVQPDP 135 Query: 128 SPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLH 187 WFQLY+ DRG T+ALV+RA AAGY+AL LTVDAP G R+R+RR F LPPG+ Sbjct: 136 GRGPLWFQLYLQHDRGFTQALVQRAEAAGYEALVLTVDAPTSGVRDRERRAGFRLPPGVG 195 Query: 188 LANLTTISGLNIPHA-PGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVLKGILRGDD 246 NL + P PG+S LF Q A TWDD+ WLQS++ LP++LKG+L D Sbjct: 196 PVNLAGLPPPPPPDLRPGQSALFDGLLHQ---APTWDDVAWLQSITRLPVLLKGVLHPAD 252 Query: 247 AARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRGTDIIKA 306 A +AV GA ++VSNHGGR LD A A+ ALP +V AV G VL+DGGIRRGTD++KA Sbjct: 253 ARQAVAAGAAGLIVSNHGGRTLDTAPATATALPRVVQAVGGAVPVLVDGGIRRGTDVLKA 312 Query: 307 LAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDIDTSFL 363 +A+GA AVL+GRP +WGLA G GV+HV+ LL+ EL VAMAL GC+ L D + L Sbjct: 313 MALGASAVLVGRPAVWGLANAGATGVAHVLRLLRDELEVAMALTGCATLADATPALL 369 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: 387 Number of extensions: 22 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