Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate GFF481 PGA1_c04920 l-lactate dehydrogenase IldD
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Phaeo:GFF481 Length = 388 Score = 243 bits (621), Expect = 5e-69 Identities = 145/370 (39%), Positives = 214/370 (57%), Gaps = 24/370 (6%) Query: 9 NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSV 68 N+ + +++ + + +M +DY SG+ E T ++N FE+I+LR R+ VD++ + + + Sbjct: 6 NINDLKRIYERRVPRMFYDYAESGSWTEQTFRDNTNDFEKIRLRQRVAVDMAGRSTASQM 65 Query: 69 LGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFS 128 +GQ + +P+ +AP+ + H +GE+ A AA + G LST+S S+EEVAE +K Sbjct: 66 IGQDVSMPVALAPVGLTGMQHADGEIKAARAAETFGVPFTLSTMSINSIEEVAEATTKPF 125 Query: 129 PSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLH- 187 WFQLY KD R L++RA A AL +T+D +LGQR +D +N PP L Sbjct: 126 ----WFQLYTMKDDDYVRRLIQRAKDARCSALVITLDLQILGQRHKDLKNGLSAPPKLTP 181 Query: 188 --LANLTTI--------------SGLNIPHAPG---ESGLFTYFAQQLNPALTWDDLEWL 228 +ANL T G + H G S L + A+Q +P+L W + L Sbjct: 182 KTIANLMTKWSWGLQMLSAKRRNFGNIVGHVEGISDASSLGAWTAEQFDPSLDWSKIAKL 241 Query: 229 QSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGK 288 L ++LKGIL +DA A + GA AIVVSNHGGRQLDGA++S+ LP I+ AV + Sbjct: 242 IELWDGKVILKGILDVEDAKMAAKLGADAIVVSNHGGRQLDGALSSIQMLPAIMDAVGDQ 301 Query: 289 AEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMA 348 EV LD GIR G D++KALA+GA+ +IGR ++GL GQ GV+ + +L KEL+ MA Sbjct: 302 IEVHLDSGIRSGQDVLKALALGAKGTMIGRAFVYGLGAMGQHGVTRALEVLHKELDTTMA 361 Query: 349 LIGCSQLQDI 358 L G + D+ Sbjct: 362 LCGEKSVADL 371 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: 293 Number of extensions: 13 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: 388 Length adjustment: 30 Effective length of query: 335 Effective length of database: 358 Effective search space: 119930 Effective search space used: 119930 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