Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein
Query= reanno::psRCH2:GFF3772 (499 letters) >NCBI__GCF_900115975.1:WP_092483962.1 Length = 458 Score = 335 bits (859), Expect = 2e-96 Identities = 177/438 (40%), Positives = 264/438 (60%), Gaps = 2/438 (0%) Query: 34 ILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSG 93 +L E+ Y DG +A R P LVVLP +V +++L +++G P+ RGAGTGLSG Sbjct: 18 VLESPEERICYSYDG-TARRGIPALVVLPGNAREVAEIVRLANEKGFPIFPRGAGTGLSG 76 Query: 94 GALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIA 153 G++P EQG+ +V++R N+ILE+ A V+PGV + +A L+Y PDPSS Sbjct: 77 GSVPAEQGLAMVLSRMNRILEISRDDLLAVVEPGVVTGRLHRAVEKEGLFYPPDPSSLQT 136 Query: 154 CSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMTLGSDALDS-PGFDLLALFTG 212 C+IGGNVAENAGG KYG+T +L ++++T GE + G + + G+DL L TG Sbjct: 137 CTIGGNVAENAGGPRAFKYGVTRDYVLGLEVVTPTGEIINTGGRTVKNVTGYDLTGLLTG 196 Query: 213 SEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSI 272 SEG LGI+T +T++L+PKP+ + LA ++ VE A V +I GIIP LE+MD ++I Sbjct: 197 SEGTLGIITRITLRLVPKPRAVQTALAVYNRVEDAASTVTAMIRRGIIPATLELMDRITI 256 Query: 273 RAAEDFIHAGYPVDAEAILLCELDGVEADVHDDCARVSEVLKLAGATEVRLAKDEAERVR 332 R E+++ G P+DA AILL E+DG+ A V ++ V + + ++ A D AER R Sbjct: 257 RCVENYLRLGLPMDAGAILLIEVDGLPAQVAEEMKLVEDACRQNSCRALQTATDAAERER 316 Query: 333 FWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNM 392 W R+ A+ +I P D T+PR ++P +++ + + E++GL + HAGDGN+ Sbjct: 317 LWKARRAVSTAIVQIKPTKISEDATVPRSKIPEMVERLKSIGEKYGLHLPVFGHAGDGNL 376 Query: 393 HPLILFDANQPGELERAEDLGGKILELCVKVGGSITGEHGVGREKINQMCSQFNADELTL 452 HP IL D P E+E+AE +I + +GG+++GEHGVG K + + A + Sbjct: 377 HPNILVDKRDPVEMEKAEKAVQEIFRAALDLGGTLSGEHGVGLLKKPYLEWEAGAGGIEY 436 Query: 453 FHAVKAAFDPSGLLNPGK 470 A+K A DP +LNPGK Sbjct: 437 MKAIKKAVDPRNVLNPGK 454 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: 591 Number of extensions: 23 Number of successful extensions: 2 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: 499 Length of database: 458 Length adjustment: 34 Effective length of query: 465 Effective length of database: 424 Effective search space: 197160 Effective search space used: 197160 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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