Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate 206254 DVU0827 glycolate oxidase, subunit GlcD, putative
Query= reanno::Cup4G11:RR42_RS17300 (497 letters) >MicrobesOnline__882:206254 Length = 471 Score = 257 bits (657), Expect = 5e-73 Identities = 162/471 (34%), Positives = 247/471 (52%), Gaps = 9/471 (1%) Query: 5 HEVSLVADDARRSALLAG---LAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALPD 61 H ++ A++A A L +LP+ L+ E+T+ + D + P+AV P Sbjct: 3 HTANVTAEEAVHGLSAAQRRFLEGLLPEGDRLFSAEETLVFGTDA-SRKCGTPLAVVRPT 61 Query: 62 NEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTAV 121 E QV +LR + ++PV PR T++ GG +P G+VLS + RI+ +D AV Sbjct: 62 TEAQVVELLRWADAERLPVYPRARATNVVGGCVPQRPGIVLSTLRMARIIDIDEHDFVAV 121 Query: 122 VQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRVR 181 VQPGV + A L+Y PDP+SQ +IGGNV+ +GG+ ++YG+T VL +R Sbjct: 122 VQPGVITADLQRAVEARGLFYPPDPASQNISSIGGNVATCAGGMRAVRYGVTRDYVLGLR 181 Query: 182 AVTMEGDVVEFGSEA-PDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD 240 AV G+V+ GS + GLDL+ ++GSEG L +TEV++KL+P P+ ++A F Sbjct: 182 AVLPGGEVLATGSRCHKNVVGLDLVRLLVGSEGTLGCLTEVTLKLLPLPEATASLLAGFS 241 Query: 241 DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV 300 D+ +AV +V AGI+P LE M + A LL DG+ + Sbjct: 242 DLGAAMDAVRNVFAAGILPVALEFMGPEVLDCAALLNDVPWPKTVRAALLFRLDGSRAAL 301 Query: 301 AEEVERMSEVLRASGA--SRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPR 358 EV+R++ +R + S + V + E E L W+ R++ PA+ + PD D T+PR Sbjct: 302 PLEVDRLAAAVRDAAPVWSAVGVGRDEEEPL--WTIRRSINPASFLVKPDKMSDDVTVPR 359 Query: 359 KHIGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESC 418 + L+ I + L + H GDGN+H I+ D + +E A ++ + Sbjct: 360 GRLREALEGIRAIAEARSLTILTFGHVGDGNIHVNIMHDASVTEEREHALAAKGEVTDLI 419 Query: 419 VELGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKA 469 + LGGT++GEHGVG+ K + Q S ER L VKAAFDP ++NP KA Sbjct: 420 LSLGGTLSGEHGVGLTKAPYVHRQLSKLERGLMAQVKAAFDPHGIMNPGKA 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: 529 Number of extensions: 24 Number of successful extensions: 3 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: 471 Length adjustment: 34 Effective length of query: 463 Effective length of database: 437 Effective search space: 202331 Effective search space used: 202331 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