Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate PP_3745 PP_3745 glycolate oxidase, putative FAD-linked subunit
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__Putida:PP_3745 Length = 499 Score = 892 bits (2304), Expect = 0.0 Identities = 441/499 (88%), Positives = 468/499 (93%) Query: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 MNILYDERVDGALP VD AALL L+ LPDL+ILHR EDLKPYECDGLSAYRT PLLV Sbjct: 1 MNILYDERVDGALPNVDLAALLQALRDALPDLEILHRDEDLKPYECDGLSAYRTVPLLVA 60 Query: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 LPER+EQV+TLLKLCHQRGVPVVARGAGTGLSGGALPL +GILLVMARFN+ILEV+P GR Sbjct: 61 LPERLEQVQTLLKLCHQRGVPVVARGAGTGLSGGALPLAKGILLVMARFNRILEVNPQGR 120 Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 +ARVQPGVRNLAISQAAAP+ +YYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHN+L Sbjct: 121 YARVQPGVRNLAISQAAAPHGMYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNVL 180 Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 KVDILTVEGER++LGSDALDSPGFDLLALF GSEGMLGIVTEVTVKLLPKPQVA+V+LA+ Sbjct: 181 KVDILTVEGERLSLGSDALDSPGFDLLALFIGSEGMLGIVTEVTVKLLPKPQVARVILAS 240 Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 FDSVE AGRAV DIIAAGIIPGGLEMMDNL+IRAAEDFIHAGYPVDA AILLCELDGVEA Sbjct: 241 FDSVEDAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGYPVDAAAILLCELDGVEA 300 Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 DV+DDC RV+ VL AGA EV LA DEAER RFWAGRKNAFPAVGRISPDYYCMDGTIPR Sbjct: 301 DVYDDCERVAAVLTQAGAREVHLACDEAERARFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 RELP VLKGISDLS ++GLRVANVFHAGDGNMHPLILFDAN PGELERAE +GGKILELC Sbjct: 361 RELPRVLKGISDLSAEYGLRVANVFHAGDGNMHPLILFDANLPGELERAEAIGGKILELC 420 Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 VKVGGSITGEHGVGREKINQMC+QFN+DE+TLFHAVKAAFDP GLLNPGKNIPTLHRCAE Sbjct: 421 VKVGGSITGEHGVGREKINQMCAQFNSDEITLFHAVKAAFDPQGLLNPGKNIPTLHRCAE 480 Query: 481 FGRMHIHNGQLPFPELERF 499 FG +H+H GQLPFPELERF Sbjct: 481 FGALHVHQGQLPFPELERF 499 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: 979 Number of extensions: 28 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: 499 Length adjustment: 34 Effective length of query: 465 Effective length of database: 465 Effective search space: 216225 Effective search space used: 216225 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