Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_4483 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= reanno::Cup4G11:RR42_RS17300 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4483 Length = 504 Score = 715 bits (1845), Expect = 0.0 Identities = 357/484 (73%), Positives = 404/484 (83%) Query: 14 ARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPDNEDQVCAILRLC 73 AR++ ++ L + +P ALLW EDT PYECDGL AYRQ P+ V LP+ D+V A+LR C Sbjct: 21 ARQAEVVQALGQAVPAHALLWHSEDTTPYECDGLTAYRQRPLVVCLPETYDEVQAVLRAC 80 Query: 74 HSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAVVQPGVRNLAISE 133 H LQVPVV RGAGT LSGGAMP A G+ LSLAKF RI+++ SRTAVVQ GVRNLAISE Sbjct: 81 HRLQVPVVARGAGTGLSGGAMPHAMGVTLSLAKFNRILNLSPESRTAVVQSGVRNLAISE 140 Query: 134 AAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVRAVTMEGDVVEFG 193 AAA +NLYYAPDPSSQIACTIGGNV+ENSGGVHCLKYGLTVHNVL+V+ T+EG+ VEFG Sbjct: 141 AAAPHNLYYAPDPSSQIACTIGGNVAENSGGVHCLKYGLTVHNVLKVKGFTVEGEPVEFG 200 Query: 194 SEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFDDVAKGGNAVADVI 253 SEA D+PG DLLAAVIGSEGMLAV+TEV+V+LIPKPQLA+ IMASFDDV K G+AVA VI Sbjct: 201 SEALDSPGYDLLAAVIGSEGMLAVITEVTVRLIPKPQLARCIMASFDDVRKAGDAVAAVI 260 Query: 254 GAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEVAEEVERMSEVLRA 313 AGIIPAGLEMMDKP TAAVE+FV AGYDL A AILLCESDGTPEEV EE+ RMSEVLRA Sbjct: 261 AAGIIPAGLEMMDKPMTAAVEDFVHAGYDLTAEAILLCESDGTPEEVEEEIGRMSEVLRA 320 Query: 314 SGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKHIGTLLKRIEEMER 373 +GA+ I VS+ E ERLRFWSGRKNAFPA+GRISPDY CMD TIPRK + +L I+EME+ Sbjct: 321 AGATAISVSRDEAERLRFWSGRKNAFPASGRISPDYMCMDSTIPRKRLADILLAIQEMEK 380 Query: 374 KYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVELGGTVTGEHGVGV 433 KY LRC NVFHAGDGN+HPLILFD D D+ HR ELFG+DILE+ V +GGTVTGEHGVGV Sbjct: 381 KYQLRCANVFHAGDGNLHPLILFDANDADQLHRCELFGADILETSVAMGGTVTGEHGVGV 440 Query: 434 EKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYGRMHVKRGLLPHPD 493 EKLNSMCVQF+A+E FG+K AFDPA LLNP K IPTL RCAEYG+M V+ G + HP Sbjct: 441 EKLNSMCVQFTAEENAQMFGLKHAFDPAGLLNPGKVIPTLNRCAEYGKMLVRGGQIRHPA 500 Query: 494 LPRF 497 LPRF Sbjct: 501 LPRF 504 Lambda K H 0.319 0.136 0.402 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: 749 Number of extensions: 14 Number of successful extensions: 1 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: 497 Length of database: 504 Length adjustment: 34 Effective length of query: 463 Effective length of database: 470 Effective search space: 217610 Effective search space used: 217610 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: 52 (24.6 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