Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate 8500826 DvMF_1567 D-lactate dehydrogenase (cytochrome) (RefSeq)
Query= reanno::Cup4G11:RR42_RS17300 (497 letters) >FitnessBrowser__Miya:8500826 Length = 474 Score = 262 bits (669), Expect = 2e-74 Identities = 157/463 (33%), Positives = 247/463 (53%), Gaps = 16/463 (3%) Query: 10 VADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPDNEDQVCAI 69 V DA R+A++A + +AA+L P + PY+ D + R V LP+ +QV A+ Sbjct: 20 VLTDAHRAAIVAAVG----EAAVLHSPGE--PYDRDA-SELRAPADLVVLPETVEQVQAL 72 Query: 70 LRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAVVQPGVRNL 129 LR + +PV+PRG GT L+GG + + G+VLSL + RI ++D R+ A V+ GV + Sbjct: 73 LRCASAHAIPVIPRGGGTGLAGGCLAVRGGVVLSLERMNRIRAIDTRNLVAEVEAGVISQ 132 Query: 130 AISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVRAVTMEGDV 189 + +AAA+ LYY PDP+ TIGGNV+ N+GG C+KYG+T VL V AV +G++ Sbjct: 133 RVRDAAAEQGLYYPPDPAGMDRSTIGGNVATNAGGPACVKYGVTRDYVLGVEAVLPDGEL 192 Query: 190 VEFGSEA-PDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFDDVAKGGNA 248 + G G D+ + GSEG L V+T +++KL+P P + +F D+A Sbjct: 193 LRAGVRTRKGVVGYDMAHLLCGSEGTLGVITALTLKLVPLPPATVSMAVAFPDMAAAMRG 252 Query: 249 VADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEVAEEVERMS 308 VA V+G G +P+ +E +D + E + D ++L+ E DG E++ E++ ++ Sbjct: 253 VAAVLGGGHLPSAIEFLDHRCIRLLGELLPIPVPGDKPSLLIIELDGAREQIVPELDLVA 312 Query: 309 EVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKHIGTLLKRI 368 + R GA+ + + E R+R W R+ + Y D +P I L+ + Sbjct: 313 AICRQQGATHVLPAADEETRVRVWGARRQVSLRIHDYAALYMSEDVAVPLGAIAELVAAL 372 Query: 369 EEMERKYGLRCMNVFHAGDGNMHPLILF---DGADQDEWHRAELFGSDILESCVELGGTV 425 E E++YG+ HAGDGN+H + D D E EL G +ELGGT+ Sbjct: 373 PEFEQRYGMEIFAFGHAGDGNIHLNVTAPTRDTRDVVEQGIVELVG-----KVLELGGTI 427 Query: 426 TGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDK 468 +GEHG+G K + + ++ S L G++ FDP ++NP K Sbjct: 428 SGEHGIGEAKKHLLPLELSPASIRLQRGIRQVFDPRGIMNPGK 470 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: 633 Number of extensions: 45 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: 497 Length of database: 474 Length adjustment: 34 Effective length of query: 463 Effective length of database: 440 Effective search space: 203720 Effective search space used: 203720 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