Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate N515DRAFT_1250 N515DRAFT_1250 L-lactate dehydrogenase (cytochrome)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Dyella79:N515DRAFT_1250 Length = 379 Score = 279 bits (713), Expect = 1e-79 Identities = 164/382 (42%), Positives = 228/382 (59%), Gaps = 27/382 (7%) Query: 4 ISSPI-NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQI 62 +++PI N+ + +LA+ + + F+Y GA DE+TL+ NRA E IK R R++++V Q Sbjct: 1 MATPITNVLDLRELARRRVPRAFFEYADRGAYDEVTLRGNRAALESIKFRQRVMMNVDQR 60 Query: 63 NLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAE 122 +L TSV+GQP+ +PL IAP L H GE+ A AA AG LST+S S+E+V + Sbjct: 61 SLATSVVGQPISMPLAIAPTGLTGLQHGAGEILGARAATKAGIPFCLSTVSICSIEQVRD 120 Query: 123 -VGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFV 181 V + F WFQLY+ +DRG R L+ RA AG AL LT D V GQR R+ +N Sbjct: 121 AVQAPF-----WFQLYVMRDRGFARDLIRRASDAGCSALMLTADLTVQGQRHREIKNGLS 175 Query: 182 LPPGLHLANLTTISGL-----NIPHAPGES---------------GLFTYFAQQLNPALT 221 +PP + L NL + ++ AP S L + A Q +P L Sbjct: 176 VPPKITLRNLFDVMSKPRWAWSMLRAPSRSFGNLAGRIQGTDSLTTLAQWIANQFDPTLN 235 Query: 222 WDDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEI 281 W DLEW++ L P L+LKGI+ +DA A +G AIVVSNHGGRQLDGA AS++ LP I Sbjct: 236 WQDLEWIRELWPGKLILKGIMDEEDARLAAAHGVDAIVVSNHGGRQLDGAPASIEVLPRI 295 Query: 282 VAAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQK 341 AV K +VL DGGI G D++KALA+GA+A LIG+ L+GL G+ GV+ I ++++ Sbjct: 296 ADAVGDKLDVLFDGGILSGQDVLKALALGARAGLIGKAFLYGLGALGEDGVARTIEIIRR 355 Query: 342 ELNVAMALIGCSQLQDIDTSFL 363 EL+V+MAL G + ++ I L Sbjct: 356 ELSVSMALTGQTDVRRIGRDVL 377 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: 324 Number of extensions: 9 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 365 Length of database: 379 Length adjustment: 30 Effective length of query: 335 Effective length of database: 349 Effective search space: 116915 Effective search space used: 116915 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: 49 (23.5 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