Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate 3607536 Dshi_0948 L-lactate dehydrogenase (cytochrome) (RefSeq)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Dino:3607536 Length = 390 Score = 238 bits (608), Expect = 2e-67 Identities = 140/372 (37%), Positives = 217/372 (58%), Gaps = 24/372 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 + +++ K + +M +DY SG+ E T +EN + F+ +KLR R+ +D+ + T+++GQ Sbjct: 9 DLKRIYKRRVPKMFYDYAESGSWTEQTFRENSSDFDLLKLRQRIAMDMDNRSTKTTMVGQ 68 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + +P+ +AP+ + H +GE+ A AA G LST+S S+E+VA + + Sbjct: 69 EVAMPVALAPVGLTGMQHADGEIKAARAAEKFGVPFTLSTMSICSIEDVAA----HTETP 124 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGL---HL 188 WFQ+Y KD + L +RA A AL +TVD +LGQR RD +N PP L + Sbjct: 125 FWFQVYTLKDDDFMKRLFDRAKEAKCSALVITVDLQLLGQRHRDLKNGLSAPPKLTPASI 184 Query: 189 ANLTT--------------ISGLNIPHAPG---ESGLFTYFAQQLNPALTWDDLEWLQSL 231 AN+ T G + HA G S L ++ A+ + +L W+ ++ +S Sbjct: 185 ANMMTKVQWGLGMLGTKRRFFGNIVGHAKGVTDPSSLSSWTAEAFDQSLDWERIKQFRSW 244 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 P++LKGIL +DA A+ GA AIV SNHGGRQLDGA++S+ LP+I+ AV K EV Sbjct: 245 WDGPVILKGILDPEDAKMALNVGADAIVCSNHGGRQLDGALSSIRMLPQIMDAVGDKIEV 304 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 LD GIR G D++KA+A+GA+ +IGR +GL G+AGV+ + ++ KEL+++M L G Sbjct: 305 HLDSGIRSGQDVLKAVALGARGTMIGRAWTYGLGAMGEAGVTRALEVIHKELDLSMGLCG 364 Query: 352 CSQLQDIDTSFL 363 ++D+D S L Sbjct: 365 RRSVEDLDASNL 376 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: 309 Number of extensions: 15 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