Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_011386481.1 AMB_RS20900 FAD-binding oxidoreductase
Query= reanno::psRCH2:GFF3772 (499 letters) >NCBI__GCF_000009985.1:WP_011386481.1 Length = 936 Score = 140 bits (353), Expect = 2e-37 Identities = 139/520 (26%), Positives = 209/520 (40%), Gaps = 76/520 (14%) Query: 17 DKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCH 76 D +ALL +L +P ++ Y D S YR P +V +V+ +L C Sbjct: 7 DYSALLQDLTGVMPVSRLITDPLRRLAYGTDA-SFYRLVPQVVAEVRDEAEVKGVLAACR 65 Query: 77 QRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAISQA 136 + G PV R AGT LSG A+ +L+++ V+ G+ R+QPGV ++ Sbjct: 66 RHGAPVTFRAAGTSLSGQAV--SDSVLMILGTGWTQAVVEDEGKRIRLQPGVIGAEANRR 123 Query: 137 AAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMTLGS 196 A + PDP+S +C IGG A NA G+ C + ++ + ++ +G + G+ Sbjct: 124 LAAFARKIGPDPASIDSCKIGGIAANNASGMCCGTSDNSYQTVMSMRLVLADGTLVDTGN 183 Query: 197 ---------------DALDSPG------------------------------------FD 205 LD G D Sbjct: 184 PESVAAFRASHAELLSRLDDMGRRVRDDETLAGRIRHKFAIKNTTGYSLNALVDFTDPLD 243 Query: 206 LLA-LFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGRAVGDIIAAGIIPGGL 264 +L L GSEG LG + E+T + +P+ L F + +A RAV + A + + Sbjct: 244 ILTHLMIGSEGTLGFIAEITYRTVPEHAHKASALLLFPDIAEACRAVVALKQAPV--SAV 301 Query: 265 EMMDNLSIRAAEDFIHAGYPV------DAEAILLCELDGVEADVHDDCARVSEVLK-LAG 317 E+MD S+R ED G P D LL E G A+ A ++E+ + L+G Sbjct: 302 ELMDRASLRCVED--KPGMPAQIRGLADGVTSLLVEARGETAEAL--AANLAEIGRVLSG 357 Query: 318 ATEV---RLAKDEAERVRFWAGRKNAFPAVG---RISPDYYCMDGTIPRRELPGVLKGIS 371 T + D E W RK FPA+G ++ D P L + Sbjct: 358 VTTLFPPAFTDDPYEYGTLWKIRKGLFPALGAVRKVGTTVIIEDVAFPIESLAAATTDLE 417 Query: 372 DLSEQFGLRVANVF-HAGDGNMHPLILFDANQPGELERAEDLGGKILELCV-KVGGSITG 429 L + G A +F HA DGN+H D E++R ++ EL V K GS+ Sbjct: 418 HLCRKHGYDEAIIFGHALDGNLHFTFTQDFGIKEEVDRYARFMDEVAELVVNKYDGSLKA 477 Query: 430 EHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPG 469 EHG GR + ++ + L +K DP GLLNPG Sbjct: 478 EHGTGRNMAPFVEMEWGTEATALMWDIKGLLDPLGLLNPG 517 Lambda K H 0.320 0.140 0.412 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: 999 Number of extensions: 47 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 936 Length adjustment: 39 Effective length of query: 460 Effective length of database: 897 Effective search space: 412620 Effective search space used: 412620 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: 54 (25.4 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