Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Ac3H11_1623 L-lactate dehydrogenase (EC 1.1.2.3)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1623 Length = 390 Score = 256 bits (654), Expect = 7e-73 Identities = 148/371 (39%), Positives = 219/371 (59%), Gaps = 26/371 (7%) Query: 16 LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75 +A+ + +M +DY SG+ E T + N + F+RIKLR R+ V++ + T+++GQ + + Sbjct: 16 IAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRTTMVGQDVAM 75 Query: 76 PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSLQWFQ 135 P+ IAP + H +GE+ A AA + G LST+S S+E++AE + WFQ Sbjct: 76 PVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGRHP---FWFQ 132 Query: 136 LYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTIS 195 +Y+ +DR L++RA AA AL LT+D +LGQR +D +N PP +ANL ++ Sbjct: 133 VYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIANLINLA 192 Query: 196 -----------------GLNIPHAPGE---SGLFTYFAQQLNPALTWDDLEWLQSLSPLP 235 G + HA G S L ++ A+Q +P L W D+EW++ Sbjct: 193 TKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIKKRWGGK 252 Query: 236 LVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEI---VAAVNGKAEVL 292 L+LKGI+ +DA AV GA A++VSNHGGRQLDGA +S+ ALP I VA + G EV Sbjct: 253 LILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMGGGIEVW 312 Query: 293 LDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGC 352 +DGGIR G D++KA A+GAQ LIGR L+GL G+AGV+ + ++QKEL++ MA G Sbjct: 313 MDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDITMAFCGH 372 Query: 353 SQLQDIDTSFL 363 + + +D S L Sbjct: 373 TNINTVDRSIL 383 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: 321 Number of extensions: 19 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: 390 Length adjustment: 30 Effective length of query: 335 Effective length of database: 360 Effective search space: 120600 Effective search space used: 120600 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