Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05725 AZOBR_RS05725 FAD-binding protein
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__azobra:AZOBR_RS05725 Length = 495 Score = 573 bits (1478), Expect = e-168 Identities = 281/490 (57%), Positives = 362/490 (73%), Gaps = 2/490 (0%) Query: 10 DGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVE 69 DG + + + ++A L+A +P ++ +L+ YECDGL+AYR P++VVLP +EQV Sbjct: 8 DGVIAR--RREIIAALRAIVPGEGVIADESELRAYECDGLTAYRQLPMVVVLPSTVEQVS 65 Query: 70 TLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVR 129 +L+ C + GV VV RGAGT LSGGALPL G+LL M +FN+IL++D A R QPGV Sbjct: 66 RVLRTCKEMGVKVVPRGAGTSLSGGALPLADGVLLGMGKFNRILDIDFANRCVVTQPGVT 125 Query: 130 NLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEG 189 NL IS A A YYAPDPSSQIAC+IGGN+AEN+GGVHCLKYGLT +N+L ++++ ++G Sbjct: 126 NLGISTAVAHEGFYYAPDPSSQIACTIGGNIAENSGGVHCLKYGLTTNNVLGLEMVLMDG 185 Query: 190 ERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGR 249 + LG LD+ G+DL+ + TGSEG+LG+VTEVTV++L KP A+ +L F + E+ G Sbjct: 186 TVLRLGGKHLDAGGYDLMGVVTGSEGLLGVVTEVTVRILKKPATARAVLIGFPTSEQGGD 245 Query: 250 AVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHDDCARV 309 V IIAAGIIPGG+EMMD +I AAEDF+HAGYP+D EA+L+ ELDG A+V +V Sbjct: 246 CVAAIIAAGIIPGGMEMMDKPAIHAAEDFVHAGYPLDVEALLIVELDGPAAEVDHLIDQV 305 Query: 310 SEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKG 369 +E+ + G R++ E ER+ FWAGRK AFPAVGRISPDYYCMDGTIPR+ LP VL Sbjct: 306 AEIARSKGCCYSRVSTSEEERLSFWAGRKAAFPAVGRISPDYYCMDGTIPRKALPLVLHR 365 Query: 370 ISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELCVKVGGSITG 429 + ++S+++ LRVANVFHAGDGN+HPLIL+DAN+PGELERAE G IL LCV+VGG +TG Sbjct: 366 MQEMSDRYALRVANVFHAGDGNLHPLILYDANKPGELERAEAFGNDILRLCVEVGGVLTG 425 Query: 430 EHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAEFGRMHIHNG 489 EHGVG EK + M QF+ +L +K AFDP GLLNPGK P LHRCAE GR+HIH G Sbjct: 426 EHGVGVEKRDLMTDQFDEVDLDQQQRIKCAFDPDGLLNPGKVFPKLHRCAELGRVHIHKG 485 Query: 490 QLPFPELERF 499 +L FP++ RF Sbjct: 486 ELRFPDIPRF 495 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: 802 Number of extensions: 26 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: 499 Length of database: 495 Length adjustment: 34 Effective length of query: 465 Effective length of database: 461 Effective search space: 214365 Effective search space used: 214365 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