Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate GFF3053 PS417_15625 lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__WCS417:GFF3053 Length = 386 Score = 271 bits (693), Expect = 2e-77 Identities = 152/373 (40%), Positives = 225/373 (60%), Gaps = 26/373 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 + +LA+ + +M +DY SG+ E T + N + F IK R R+ ++ + ++ +++GQ Sbjct: 9 DLRKLAQKRVPRMFYDYADSGSWTESTYRANESDFASIKFRQRVARNIDERSIRATMIGQ 68 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAE-VGSKFSPS 130 + +P+ +AP + H +GE+ TA AAA+ G LST+S SLE++AE VG F Sbjct: 69 EMAMPVALAPTGLAGMQHADGEILTARAAAAFGLRYTLSTMSICSLEDIAEHVGQPF--- 125 Query: 131 LQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLAN 190 WFQLY+ +DR L+ERA AAG AL LT+D +LGQR +D N PP L L N Sbjct: 126 --WFQLYVMRDRAFIEQLIERAKAAGVDALVLTLDLQILGQRHKDLINGLSAPPKLTLPN 183 Query: 191 LTTIS-----------------GLNIPHAPGE---SGLFTYFAQQLNPALTWDDLEWLQS 230 + ++ G + H G S L ++ AQQ +P L+WDD+EW++ Sbjct: 184 ILNMATKPRWVMGMLGTQRRGFGNIVGHVKGVADMSSLSSWTAQQFDPRLSWDDVEWIKK 243 Query: 231 LSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAE 290 L++KGIL +DA A GA A+VVSNHGGRQLDGA +S+ LP IV AV + E Sbjct: 244 CWGGKLIIKGILDVEDAHLAANAGADALVVSNHGGRQLDGAPSSISQLPAIVEAVGERIE 303 Query: 291 VLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALI 350 V LDGGIR G D++KA+A+GA+ +IGRP L+GL G+AGV+ + ++ +EL+V+MAL Sbjct: 304 VWLDGGIRSGQDVLKAMALGAKGTMIGRPHLYGLGAMGEAGVTKALEIIARELDVSMALC 363 Query: 351 GCSQLQDIDTSFL 363 G + ++D++ L Sbjct: 364 GYNDIRDVNREIL 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: 335 Number of extensions: 11 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: 386 Length adjustment: 30 Effective length of query: 335 Effective length of database: 356 Effective search space: 119260 Effective search space used: 119260 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