Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate GFF3081 HP15_3024 FAD linked oxidase domain protein
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__Marino:GFF3081 Length = 490 Score = 627 bits (1617), Expect = 0.0 Identities = 303/468 (64%), Positives = 372/468 (79%) Query: 14 PKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLK 73 PKV KA L + +A + ++ E +KPYECDG+S Y PLLVVLPE +EQV+ +++ Sbjct: 5 PKVSKAELAEQFRAFIDPDYVITDDETMKPYECDGMSMYCEMPLLVVLPETVEQVQRVMR 64 Query: 74 LCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAI 133 +C++ VPVVARGAGTGLS GA+P ++G++L +A+FN+I+E+DP R AR+QPGVRNLAI Sbjct: 65 ICNENAVPVVARGAGTGLSAGAMPNKEGVVLSLAKFNRIVEIDPLARTARLQPGVRNLAI 124 Query: 134 SQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMT 193 S+ AA Y LYY PDPSSQIAC+IGGNVAEN+GGVHCLKYGLTVHN+L V+++T EG+ +T Sbjct: 125 SEEAAQYGLYYGPDPSSQIACTIGGNVAENSGGVHCLKYGLTVHNILSVEMVTAEGDVVT 184 Query: 194 LGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGRAVGD 253 +GSD LD G DLLAL TGSEG+LG+VTEV VKLLPKP+VA+V++A FD V+K G AVG Sbjct: 185 VGSDGLDGCGMDLLALMTGSEGLLGVVTEVKVKLLPKPEVAQVVMAGFDDVQKGGDAVGG 244 Query: 254 IIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHDDCARVSEVL 313 II+ GIIPGGLEMMD +I AA+DF AGYP DA+A+LLCE+DG E +VH+ A+ EV Sbjct: 245 IISHGIIPGGLEMMDGHAIIAADDFAQAGYPRDAKALLLCEVDGTEEEVHEHIAQAEEVF 304 Query: 314 KLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKGISDL 373 + GAT VR ++ E ER W GRK+AFPAVGRISPDYYCMDGTIPRRE+ VL + + Sbjct: 305 RKLGATSVRTSQSEEERALLWKGRKSAFPAVGRISPDYYCMDGTIPRREIAYVLTEMEKM 364 Query: 374 SEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELCVKVGGSITGEHGV 433 SE+FGLRVANVFHAGDGN+HPLILFDAN PGE ER E G +ILE+CV+VGG ITGEHGV Sbjct: 365 SEEFGLRVANVFHAGDGNLHPLILFDANVPGEFERTEAFGSRILEMCVEVGGCITGEHGV 424 Query: 434 GREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAEF 481 G EKI QM QFN +EL FH VKAAFDP+G+LNPGK +P L C E+ Sbjct: 425 GVEKIRQMAVQFNDEELQQFHDVKAAFDPAGILNPGKGVPALRFCQEY 472 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: 763 Number of extensions: 22 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: 490 Length adjustment: 34 Effective length of query: 465 Effective length of database: 456 Effective search space: 212040 Effective search space used: 212040 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