Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_3415 Dsui_3415 FAD/FMN-dependent dehydrogenase
Query= reanno::Cup4G11:RR42_RS17300 (497 letters) >FitnessBrowser__PS:Dsui_3415 Length = 486 Score = 650 bits (1677), Expect = 0.0 Identities = 324/464 (69%), Positives = 374/464 (80%) Query: 16 RSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPDNEDQVCAILRLCHS 75 ++ALLA L +ILP + +PED PYECDGL AYR +P+AVALP+ E +V AIL+LCH Sbjct: 15 QAALLAALGRILPPGRVYGEPEDLRPYECDGLTAYRNLPLAVALPETEAEVQAILQLCHR 74 Query: 76 LQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAVVQPGVRNLAISEAA 135 LQVPVVPRGA T LSGGAMP GL+LSLAKFK+I+ VD +RTA+VQPGVRNLA+SEAA Sbjct: 75 LQVPVVPRGAATGLSGGAMPHHQGLLLSLAKFKKILKVDPVARTALVQPGVRNLAVSEAA 134 Query: 136 AQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVRAVTMEGDVVEFGSE 195 A YNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVL+VR TM G+ V FGS Sbjct: 135 APYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLQVRGYTMAGEAVTFGSA 194 Query: 196 APDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFDDVAKGGNAVADVIGA 255 A DAPG DLLA + GSEGMLAV+TEV VKL PKPQ+A+V++A FD V K GNAVA+VI A Sbjct: 195 ALDAPGFDLLALLNGSEGMLAVITEVLVKLTPKPQVAKVVLAYFDSVTKAGNAVAEVIAA 254 Query: 256 GIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEVAEEVERMSEVLRASG 315 GIIPAGLEMMDKPAT AVE +V+AGYDLDA A+LLCESDGTPEEV EE+ M VL SG Sbjct: 255 GIIPAGLEMMDKPATHAVEPYVKAGYDLDAEAVLLCESDGTPEEVEEEIAAMRAVLEKSG 314 Query: 316 ASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKHIGTLLKRIEEMERKY 375 A+ ++VS +E ERLRFW+GRK AFPA GRI+PDY CMDGTIPRK + +L I ME+KY Sbjct: 315 ATSLRVSANEAERLRFWAGRKAAFPAVGRITPDYLCMDGTIPRKRVAEMLTAIAAMEKKY 374 Query: 376 GLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVELGGTVTGEHGVGVEK 435 GLRC NVFHAGDGN+HPLI++D E +A FG++ILE V LGG++TGEHGVGVEK Sbjct: 375 GLRCANVFHAGDGNLHPLIMYDANQPGELEQATAFGAEILELSVALGGSITGEHGVGVEK 434 Query: 436 LNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEY 479 + MC QF+ +E F GVK +FDPA LLNP KAIPT ARC EY Sbjct: 435 ITQMCAQFTPEELARFEGVKQSFDPAGLLNPGKAIPTPARCREY 478 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: 689 Number of extensions: 15 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: 486 Length adjustment: 34 Effective length of query: 463 Effective length of database: 452 Effective search space: 209276 Effective search space used: 209276 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